Basic Organic Chemistry 1774073595, 9781774073599

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BASIC ORGANIC CHEMISTRY

BASIC ORGANIC CHEMISTRY

Ramesh Chandra, Snigdha Singh and Aarushi Singh

ARCLER

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Basic Organic Chemistry Ramesh Chandra, Snigdha Singh and Aarushi Singh

Arcler Press 2010 Winston Park Drive, 2nd Floor Oakville, ON L6H 5R7 Canada www.arclerpress.com Tel: 001-289-291-7705 001-905-616-2116 Fax: 001-289-291-7601 Email: [email protected] e-book Edition 2020 ISBN: 978-1-77407-424-4 (e-book) This book contains information obtained from highly regarded resources. Reprinted material sources are indicated and copyright remains with the original owners. Copyright for images and other graphics remains with the original owners as indicated. A Wide variety of references are listed. Reasonable efforts have been made to publish reliable data. Authors or Editors or Publishers are not responsible for the accuracy of the information in the published chapters or consequences of their use. The publisher assumes no responsibility for any damage or grievance to the persons or property arising out of the use of any materials, instructions, methods or thoughts in the book. The authors or editors and the publisher have attempted to trace the copyright holders of all material reproduced in this publication and apologize to copyright holders if permission has not been obtained. If any copyright holder has not been acknowledged, please write to us so we may rectify. Notice: Registered trademark of products or corporate names are used only for explanation and identification without intent of infringement.

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ABOUT THE AUTHORS

Prof. Ramesh Chandra is an outstanding scientist, revered teacher and an exceptionally successful administrator. He is currently heading Department of Chemistry, University of Delhi, where he is serving as Professor for the last more than 26 years and Founder Director of Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, since March 1991. He has been Vice-Chancellor, Bundelkhand University, Jhansi for six years (1999-2005); Member, Planning Commission, Government of U.P, India as well as the President of the Indian Chemical Society (2004-2006). Professor Chandra started his research career at the University of Delhi, thereafter he went to The New York Hospital-Cornell University Medical Center and the Rockefeller University, New York; State University of New York at Stonybrook, USA as Assistant Research Professor. He conducted advanced research at the Harvard University Medical SchoolMassachusetts General Hospital, jointly at MIT, Cambridge, USA. Over the last 38 years, Professor Chandra has contributed largely in the field of Chemical Sciences and particularly in New Drug Discovery and Development as well as Drug Metabolism. He has to his credit several patents, published more than 300 original Scientific Research Papers/ Review Articles in International journals of repute and six of his internationally acclaimed scientific Books. Prof. Chandra is the recipient of several professional national/ international recognitions; these includes: Millennium Plaques of Honor (Life Time Achievement Award for Contribution in Science & Technology) by the Indian Science Congress Association (ISCA) for 2017-2018, Award of the Highest Honor of Soka University, Tokyo, Japan (2000); J William Fulbright Scholarship (1993); The Rockefeller Foundation USA-Biotechnology Career Award (1993); and several others.

Snigdha Singh completed her M.Tech. degree (Chemical Synthesis and Process Technologies) in 2016 from University of Delhi, India. After that she joined Prof. Ramesh Chandra group at Department of Chemistry, University of Delhi for her doctoral studies. She is involved in miscellaneous projects for development of novel hydroxyethylamine molecules as potent multistage Antimalarial. Her sincere efforts and excellent performance has culminated her into a keen researcher. Currently, she is working at University of Siena under the supervision of Prof. Maurizio Taddei on Synthesis of novel 8-hydroxyquinolines as Gli-1 Hedgehog Inhibitors. She has successfully optimized complex organic syntheses during her doctoral research. Her research efforts are directed towards the synthesis of bioactive heterocyclic molecules. She has already published 9 papers in international and national reputed Journals and also presented her work in many conferences.

Ms. Aarushi Singh completed her Masters degree in chemistry (2013) from University of Delhi, Delhi, India. Thereafter, she joined as senior research fellow at Indian Agricultural Research Institute, Pusa, Delhi, India. Then, she joined Lingaya’s University, Faridabad, India as Assistant Professor in Chemistry.

TABLE OF CONTENTS

List of Figures ........................................................................................................xi List of Tables ........................................................................................................xv List of Abbreviations .......................................................................................... xvii Preface........................................................................ ................................... ....xix Chapter 1

Introduction to Chemistry and Organic Chemistry ................................... 1 1.1. Introduction ........................................................................................ 2 1.2. Branches of Chemistry ........................................................................ 3 1.3. Importance And Scope of Chemistry ................................................... 5 1.4. Organic Chemistry.............................................................................. 9 1.5. Origin of Organic Chemistry............................................................. 10 1.6. Applications o Organic Chemistry .................................................... 13 1.7. Conclusion ....................................................................................... 19 Review Questions .................................................................................... 21 References ............................................................................................... 22

Chapter 2

Organic Molecules and Functional Groups ............................................. 23 2.1. Introduction ...................................................................................... 24 2.2. Functional Groups And Reactivity..................................................... 25 2.3. Role of Functional Groups ................................................................ 27 2.4. Alcohols ........................................................................................... 30 2.5. Ethers................................................................................................ 33 2.6. Aldehydes And Ketones .................................................................... 34 2.7. Carboxylic Acids............................................................................... 36 2.8. Physical Properties and Characterization .......................................... 37 Review Questions .................................................................................... 40 References ............................................................................................... 41

Chapter 3

Nomenclature of Organic Molecules ...................................................... 43 3.1. Introduction ...................................................................................... 44 3.2. History of The Nomenclature of Organic Molecules ......................... 45 3.3. Basic Steps For Nomenclature of The Organic Molecules.................. 49 3.4. How To Name Organic Compounds Using The Iupac Rules .............. 51 3.5. Guidelines For The Nomenclature of Organic Molecules .................. 57 Review Questions .................................................................................... 60 References ............................................................................................... 61

Chapter 4

Acids And Bases ...................................................................................... 63 4.1. Introduction ...................................................................................... 64 4.2. Acids .................................................................................................... 4.3. Bases ................................................................................................ 69 4.4. Neutralization................................................................................... 71 4.5. Arrhenius Theory............................................................................... 74 4.6. Bronsted-Lowry Theory ..................................................................... 77 4.7. Lewis Theory..................................................................................... 81 Review Questions .................................................................................... 84 References ............................................................................................... 85

Chapter 5

Understanding Organic Reactions........................................................... 87 5.1. Introduction ...................................................................................... 88 5.2. Types of Organic Reactions ............................................................... 89 5.3. Principal Methods of Forming The Organic Reactions ....................... 91 5.4. Role of Organic Reactions In The Modern World .............................. 94 5.5. Importance of Catalyst In Organic Reactions .................................... 95 5.6. Organic Chemistry Is All Around Us ................................................. 98 Review Questions .................................................................................. 104 References ............................................................................................. 105

Chapter 6

Stereochemistry .................................................................................... 109 6.1. Introduction .................................................................................... 110 6.2. Historical Perspective of Stereochemistry ........................................ 111 6.3. Fundamentals of Stereochemistry.................................................... 115 6.4. Chirality.......................................................................................... 116

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6.5. Stereoisomers ................................................................................. 117 6.6. Absolute Configuration And The (R) And (S) System ........................ 121 6.7. Fischer Projections .......................................................................... 124 Review Questions .................................................................................. 127 References ............................................................................................. 128 Chapter 7

Amino Acids And Proteins..................................................................... 131 7.1. Introduction .................................................................................... 132 7.2. Proteins .......................................................................................... 135 7.3. The 20 Amino Acids And Their Role In Protein Structures................ 140 7.4. What Is The Difference Between A Protein And An Amino Acid?..... 150 7.5. What Are Essential Amino Acids? .................................................... 151 Review Questions .................................................................................. 153 References ............................................................................................. 154

Chapter 8

Carbohydrates ....................................................................................... 157 8.1. Introduction .................................................................................... 158 8.2. History Of Carbohydrates ............................................................... 160 8.3. Carbohydrates................................................................................. 161 8.4. Classification and Nomenclature .................................................... 162 8.5. Carbohydrates as The Monosaccharides .......................................... 165 8.6. Disaccharides ................................................................................. 167 Review Questions .................................................................................. 173 References ............................................................................................. 174

Chapter 9

Alcohols And Ethers .............................................................................. 175 9.1. Introduction .................................................................................... 176 9.2. Physical Properties of Alcohols And Ethers ...................................... 178 9.3. Chemical Properties of Alcohols And Phenols................................. 186 9.4. Preparation Of Alcohols.................................................................. 188 9.5. Nucleophilic Properties: Ether Formation ........................................ 190 9.6. Some Commercially Important Alcohols ......................................... 192 Review Questions .................................................................................. 194 References ............................................................................................. 195

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Chapter 10 Spectroscopy ......................................................................................... 197 10.1. Introduction .................................................................................. 198 10.2. What Is Spectroscopy.................................................................... 200 10.3. Different Types Of Spectroscopy For Chemical Analysis ................ 200 10.4. What Is Electromagnetic Radiation (EMR)? .................................... 207 10.5. Basic Components Of Spectroscopic Instruments.......................... 208 10.6. Spectroscopy Based On Absorption .............................................. 211 10.7. Conclusion ................................................................................... 212 Review Questions .................................................................................. 214 References ............................................................................................. 215 Index ..................................................................................................... 217

LIST OF FIGURES Figure 1.1. Representation of the branch of chemistry Figure 1.2. Representation of organic chemistry Figure 1.3. Frederich Wöhler provided a breakthrough in the field of organic chemistry Figure 2.1. Glucose structure Figure 2.2. Coffee contains caffeine Figure 2.3. The representation of an alcohol group Figure 2.4. Structure of an alcohol group Figure 2.5. Representation of ether group Figure 3.1. Different methods are being followed for the nomenclature of organic molecules in the modern world Figure 3.2. There is a history for the development of the guidelines of the nomenclature of the organic molecules Figure 3.3. There are certain guidelines that have to be followed in the naming of the organic molecules Figure 3.4. As the saturated hydrocarbons, there is a different set of rules for the nomenclature of the alkanes Figure 3.5. While naming an organic molecule, it is important to recognize the number of branched chains Figure 4.1. pH scale with examples of every pH level Figure 4.2. Blue and red litmus paper Figure 4.3. Titration using burette and beaker Figure 4.4. Swedish chemist Svante Arrhenius who gave Arrhenius theory Figure 4.5. 3D diagram of Bronsted and Lowry theory Figure 4.6. Image shows the reaction between ammonia and boron trifluoride (BF3)

Figure 5.1. According to many researchers, the life and all the life-related functions were started on the planet earth after the initiation of organic reactions xi

Figure 5.2. The direction of arrow plays a very crucial role in displaying the direction of the reaction Figure 5.3. The role of the catalyst is to alter the rate of the reaction and assist in the completion of the reaction Figure 5.4. The understanding of the organic reaction is very necessary in the medicine industry Figure 5.5. Various variable materials comprise majorly of the organic compounds and are formed by the organic reactions Figure 6.1. 1-Bromo-1-chloroethane Figure 6.2. Orientation of D-glucose and L-glucose Figure 6.3. Orientation of D-glucose and D-altrose Figure 6.4. A meso compound and a regular chiral compound Figure 6.5. Relative priority as per the Cahn-Ingold-Prelog (CIP) rules Figure 6.6. The stereocenters are labeled as R or S Figure 6.7. Comparison of glucose and galactose Figure 7.1. General structure of amino acid Figure 7.2. General structure of alpha-amino acid Figure 7.3. Classification of the amino acid and proteins Figure 7.4. Structure of glycine Figure 7.5. Structure of alanine Figure 7.6. Structure of valine Figure 7.7. Structure of leucine Figure 7.8. Structure of isoleucine Figure 7.9. Structure of proline Figure 7.10. Structure of phenylalanine Figure 7.11. Structure of tyrosine Figure 7.12. Structure of tryptophan Figure 7.13. Structure of serine Figure 7.14. Structure of threonine Figure 7.15. Structure of cysteine Figure 7.16. Structure of methionine Figure 7.17. Structure of asparagines xii

Figure 7.18. Structure of glutamine Figure 7.19. Structure of lysine Figure 7.20. Structure of arginine Figure 7.21. Structure of histidine Figure 7.22. Structure of aspartate Figure 7.23. Structure of glutamate Figure 7.24. Chemical structure of amino acid Figure 9.1. Nomenclature of alcohol Figure 9.2. Isomeric representation Figure 9.3. 3-methyl-2-pentanone synthesis Figure 9.4. Synthesis of metronidazole Figure 9.5. Williamson-ether-synthesis Figure 9.6. Ether peroxide formation Figure 9.7. Ether Figure 10.1. Ultraviolet-visible spectroscopy Figure 10.2. Infrared spectroscopy Figure 10.3. Nuclear magnetic resonance spectroscopy Figure 10.4. Electromagnetic wave

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LIST OF TABLES Table 4.1. Some acids and their conjugate bases

LIST OF ABBREVIATIONS

AAS

atomic absorption spectroscopy

AES

atomic emission spectroscopy

AFS

atomic fluorescence spectroscopy

BF3

boron trifluoride

CIP

Cahn-Ingold-Prelog

DNA

deoxyribonucleic acid

EMR

electromagnetic radiation

IACS

International Association of Chemical Societies

IR

infrared

ISO

International Organization for Standardization

IUPAC

International Union of Pure and Applied Chemistry

IUPAP

International Union of Pure and Applied Physics

NMR

nuclear magnetic resonance

SERS

surface-enhanced Raman spectroscopy

SI

International System of Units

UV

ultraviolet

PREFACE

Subject and Content Organic chemistry is a field of chemistry that deals in the study of the compounds containing carbon. It deals with the structural analysis, properties, composition, reactions related to those compounds, and the processes related to their preparation. The organic chemistry also lists all the uses and applications of the compounds that fall under the field of study. Organic chemistry plays a significant role in the preparation of various materials and products in the field of manufactured and processed goods. It explains the various phenomena related to the synthesis of compounds and the manner in which they can be reacted with each other to form new products. The motive of this book is to elaborate on the various aspects of organic chemistry and the related fields. It dwells on the preparation of various organic compounds and discusses the ways in which those compounds may be used further to form new products and goods that can be applied in various sectors. Salient Features of the Book •

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The book introduces the readers to chemistry and explains them the various aspects related to the subject. It discusses the various elements related to the field of chemistry. It explains the several applications of chemistry and its uses in their daily lives. It also explains the various fields that originate from the main chemistry and dwells upon their classification and fundamentals related to those fields. The book goes on to explain organic chemistry to the readers. It explains how the various molecules group themselves together to form certain structures in the organic chemistry. It explains various kinds of shapes and forms that the compounds form and also enlists several functional groups that exist in the organic chemistry. The book dwells upon the classification of the organic compounds based on these functional groups and the structures they form resulting from it. Moving further, the book dwells upon the procedures that are used for the nomenclature of the organic compounds. It lists all the standards that

need to be followed while naming a compound. It also enlists various groups that are referenced when naming a compound and the use of bonds while doing so. • The book goes on to explain the meaning and relevance of acids and bases in the organic chemistry. It elaborates upon the significance of both the types in the compounds and explains how the various properties of the compounds vary according to what group they belong to. • The book dwells upon the subject of understanding how the reactions go through in organic chemistry. In the organic chemistry, there is generally rue to the way reactions happen, and the book explains the methods and rules to the readers in detail. • The book further goes on to define the roles of ethers, alcohols, aldehydes, amino acids, carbohydrates, and other such groups in characterizing several compounds in organic chemistry. It dwells upon the significance of each of these groups in the organic chemistry and establishes ways in which they react with each other and form various compounds and products. This book has been compiled to elaborate on the subject of organic chemistry and its relevance in the modern world. It lists various aspects related to the field of organic chemistry and tries to discover the aspects related to this field of chemistry in detail.

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1 INTRODUCTION TO CHEMISTRY AND ORGANIC CHEMISTRY

LEARNING OBJECTIVES: Chemistry is a branch of science concerned with the study of matter and its reactions. The learning objectives of this chapter are to gain an understanding of the following: • • • • • •

The field of chemistry. The various branches of chemistry. Importance and scope of chemistry. The sub-discipline of organic chemistry. The history of organic chemistry. Applications of organic chemistry.

KEY TERMS: • • • • •

Analytical chemistry Cleansing agents Inorganic chemistry Organic chemistry Quantum mechanics

• • • •

Sterilizing agents Textiles and clothing Thermodynamics Three-dimensional structure of the compound

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Basic Organic Chemistry

1.1. INTRODUCTION Chemistry is defined as a branch of science that studies the matter and the reactions it undergoes. Other branches of science like physics, biology, and geology also deal with the study of matter. But chemistry is the only branch that deals with the reactions that matter undergoes. It includes a study of the composition of the matter, its structure, properties, and its reactions. Chemistry is a complex and fascinating subject. Chemistry provides an answer to most of the questions regarding how or why something is in the natural world. For example, the reason behind the sky appearing blue. The color depends on the chemical composition of the substances and the light they reflect. Example of another simple question related to chemistry is how an insect walks on the surface of the water without drowning. The unique properties of water provide a high surface tension, which does not let small objects sink. Chemistry surrounds us and anything that concerns matter has its answer in chemistry (Figure 1.1).

Figure 1.1: Representation of the branch of chemistry. Source: http://www.picpedia.org/highway-signs/images/chemistry.jpg

Chemists make new compounds by understanding the reactions between elements and compounds. Chemistry finds its applications in

Introduction to Chemistry and Organic Chemistry

the chemical and pharmaceutical industry. It is used in making plastics, ceramics, fillers, alloys, drugs, etc. The target compound is synthesized using chemical reactions under conditions that are determined optimum so that output is produced in a cost-effective manner. The compound is purified after the best conditions are identified and finally identified by chemists. The process of identification is to ensure that the compound contains all elements in the right proportion and also the determination of the three-dimensional structure of the compound.

1.2. BRANCHES OF CHEMISTRY Chemistry is divided into many branches or disciplines since it is a vast subject. Dividing it into manageable topics helps more accurately. The main branches are organic chemistry, inorganic chemistry, analytical chemistry, physical chemistry, and biochemistry.

1.2.1. Organic Chemistry It involves the study of carbon and its compounds that make up living things. It is basically the chemistry of life.

1.2.2. Inorganic Chemistry Inorganic chemistry covers the study of compounds that is not a part of organic chemistry. Its studies compounds that are inorganic, and does not contain a C-H bond. Many inorganic compounds contain metals.

Compound means to combine; a compound is a combination or mixture of two or more things.

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Basic Organic Chemistry

1.2.3. Analytical Chemistry

Analytical chemistry is the science of obtaining, processing, and communicating information about the composition and structure of matter.

Analytical chemistry is the analysis of chemicals, their properties, and reactions. It also includes developing tools and techniques for the purpose of analytical work. Analytical chemistry is used by chemists of all disciplines, but some experts focus on the development of analytical methods.

1.2.4. Physical Chemistry This branch of chemistry comprises of the study of physical principles of atoms and compounds. In other words, it is a branch of chemistry which uses principles of physics and can be called as the physics of chemical compounds. It involves the study of how particles move, how energy is used in reactions, the interaction between light and energy, and the speed of reactions. It includes the applications of thermodynamics and quantum mechanics.

1.2.5. Biochemistry Quantum mechanics is the body of scientific laws that describe the wacky behavior of photons, electrons and the other particles that make up the universe.

It is the study of the chemical process that happens within living organisms. It includes large biological molecules like carbohydrates, DNA, proteins, and lipids. Chemistry can be divided into categories in other ways. These five are the main topics in the study of chemistry. These branches overlap in certain areas. Organic chemistry and biochemistry, for example, share a lot in common. An organic chemist may be required to have knowledge of the rate of reaction of organic compound, which involves physical chemistry. Similarly, an inorganic chemist may

Introduction to Chemistry and Organic Chemistry

use analytical method to understand the crystal structure of inorganic matter. Besides these broad categories, there are many other specializations in this branch. Environmental chemistry is concerned with the chemical processes occurring in nature. A geochemist is concerned with the composition and chemical processes of the earth, soil, rock, etc. Other branches include medicinal chemistry, polymer chemistry, and even chemical engineering.

1.3. IMPORTANCE AND SCOPE OF CHEMISTRY Chemistry is important for the day-to-day life and has a huge scope.

1.3.1. Supply of Food Knowledge about chemistry has led to the manufacture of chemical fertilizers like urea, sodium nitrate, calcium superphosphate, and ammonium sulfate. These fertilizers have played a significant role in increasing the yield of vegetables, fruits, and other crops and address food security issues. Use of fertilizers helps to cater to the ever-growing demand for food. Pesticides and insecticides help to protect the crops from pests and microbes. Another way by which chemistry has addressed the issue of food spoilage is by the discovery of preservatives. These chemicals help increase the shelf life of food items. Moreover,

Organic chemistry is a subdiscipline of chemistry that studies the structure, properties and reactions of organic compounds, which contain carbon in covalent bonding. Study of structure determines their chemical composition and formula.

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Basic Organic Chemistry

chemical tests also help in detecting the presence of adulterants in food and determine the quality of food.

1.3.2. Contribution to Improved Health and Sanitation Facilities Chemistry has contributed immensely to the field of healthcare. It has led to the discovery of many lifesaving medicines. The discovery of penicillin saved millions from death due to pneumonia, and the discovery of sulfa drugs made a cure for dysentery. Other lifesaving drugs include taxol and cisplatin for cancer patients and AZT for AIDS victims. Some common medicines that help to solve the various health issues include: • Analgesics: Helps in control different types of pain. • Antibiotics: Cures infection and diseases. • Tranquillizers: Reduce tension and eases mental diseases by making the patients calm. • Antiseptics: Prevents infection of cuts and wounds. • Disinfectants: Destroys microbes present in toilets, floor, and drains. • Anesthetics: It has revolutionized surgical operations and increased their success rate. • Insecticides: Such as Gammexane and DDT has minimized the risk of diseases caused by mosquitoes, rats, and flies.

Introduction to Chemistry and Organic Chemistry

1.3.3. The Scope of Chemistry in Saving the Environment Chemistry has also contributed immensely to make chemicals environmentally benign. Organic chemicals are environment-friendly and help in protecting nature. For example, the substitution of CFCs as cooling agents in refrigerators.

1.3.4. Comfort in Daily Life Advancement in chemistry has made day-to-day life more comfortable in various ways: • Synthetic Fibers: These materials are comfortable, attractive, and sturdy. Examples of synthetic material are nylon, rayon, etc. They are easy to handle as well, can be washed easily, dried, and used without ironing. The chemicals provide bright and fast colors, which increase the attractiveness of these clothes. • Building Materials: The construction materials have been invented with the help of chemistry. The invention of materials like steel, cement, etc. has made the construction of homes and multistoried buildings possible. These materials are durable and are used for the construction of infrastructure facilities that has led to urbanization. • Supply of Metals: Metals like gold, copper, silver, aluminum, zinc, iron, and the various alloys have been discovered by chemists. These metals have various uses in our daily life like

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Basic Organic Chemistry

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Energy security is the association between national security and the availability of natural resources for energy consumption.

•

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making ornaments, utensils, coins, plants, and equipment for industries, etc. Articles of Domestic Use: Chemistry has vast applications in domestic purposes. It has made life comfortable by providing many articles for domestic uses like oils, detergents, sugar, paper, plastic, glass, cosmetics, cooking gas, etc. The chemicals used in the refrigerators and air conditioners have been developed using principles of chemistry. Entertainment: Even the world of entertainment is dominated by inventions in the field of chemistry. Cinema, cameras, DSLR use films made out of celluloid. They are coated with suitable chemicals to make them fir for the purpose. Fireworks used in festivals and occasions are a product of chemistry. Transport and Communication: The various modes of transport need fuel. All vehicles from airplanes, ships, trains, and automobiles use different chemical products like coal, petrol, diesel, etc. Without chemistry, the modern transport system would not have developed. Nuclear Atomic Energy: This is one of the greatest discoveries in the field of chemistry. This alternative source of energy is environmentally benign and addresses the issue of energy security.

Introduction to Chemistry and Organic Chemistry

1.3.5. The Scope of Chemistry in Industry Chemistry has played a huge role in the growth and development of industries such as textile, paper, glass, chemical, cement, textile, dye paints, pharmaceuticals, etc. Industrialization has provided employment opportunities to billions around the globe. It has also made economic development possible.

1.3.6. The Scope of Chemistry in Defense The defense system owes all its innovations to chemistry. It has led to the discovery of explosives like dynamite, TNT, nitroglycerine, etc. Poisonous gases like Phosgene, mustard gas have been invented due to advancement in chemistry. The modern defense system is entirely a product of discoveries in this field.

1.4. ORGANIC CHEMISTRY Organic chemistry involves the scientific study of the structure, properties, composition, reactions, and synthesis of organic compounds that by definition contain carbon. It is called the study of life. All carbon reaction is not organic. Only those carbon-containing compounds are organic that contains the carbon-hydrogen (CH) bond. Organic chemistry is possibly the most important branch of chemistry since it deals with all chemical reactions that are associated with life. The various experts who make life easier like doctors, dentists, chemical engineers, and veterinary doctors owe their knowledge to chemistry.

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Basic Organic Chemistry

Organic chemistry has various applications in daily life. It is responsible for the development of food, drugs, fuels, construction materials, and other chemicals, which have transformed human life (Figure 1.2).

Figure 1.2: Representation of organic chemistry. Source: https://cdn.pixabay.com/photo/2017/10/23/01/08/adrenaline-2879838_960_720. png

1.5. ORIGIN OF ORGANIC CHEMISTRY Pharmacology is the branch of biology concerned with the study of drug or medication action, where a drug can be broadly defined as any man-made, natural, or endogenous (from within the body) molecule which exerts a biochemical or physiological effect on the cell, tissue, organ, or organism.

The history of organic chemistry has its roots in ancient times when men extracted chemicals from plants and animals to cure their community.Although they did not coin the term organic chemistry, they maintained a record of useful properties. For example, the use of willow barks in helping to ease the pain. It was later established that willow bark contains acetylsalicylic acid the ingredient in aspirin. Chewing the bark extracted the aspirin. Their knowledge laid the foundation of modern pharmacology, which depended on the knowledge of organic chemistry. Organic chemistry was first recognized as a branch of modern science during the 1800s. Jon

Introduction to Chemistry and Organic Chemistry

Jacob Berzelius was the founder of this branch. He classified chemical compounds into organic and inorganic. Organic compounds are those that originated from living matter and inorganic from non-living matter such as minerals. Most of the chemists during that period believed in Vitalism. It basically denoted that action of some vital force alone could extract organic compounds from living organisms. A student of Berzelius discovery led to the abandonment of Vitalism as a scientific theory. In 1828 Frederich Wöhler discovered that inorganic compounds could also produce the organic compound. He made urea by heating ammonium cyanate. Urea is an organic compound while ammonium cyanate is inorganic. Wohler combined ammonium chloride and silver cyanate to produce aqueous ammonium cyanate and solid silver chloride (Figure 1.3).

Figure 1.3: Frederich Wöhler provided a breakthrough in the field of organic chemistry. Source: https://upload.wikimedia.org/wikipedia/ commons/9/93/Friedrich_W%C3%B6hler_Litho2. jpg

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Basic Organic Chemistry

He then separated the filtered the mixture to separate the two compounds. He evaporated the water to purify aqueous ammonium cyanate. Surprisingly, the substance that remained after evaporation had properties of urea and not ammonium cyanate. Wohler’s experiment led to the synthesis of an organic compound from an inorganic one for the first time.

1.5.1. A Breakthrough in Science History

Isomerism is the phenomenon in which more than one compounds have the same chemical formula but different chemical structures.

Wohler’s observation was a breakthrough because of two reasons. First, it led to discarding the theory of Vitalism by generating an organic compound from inorganic matter. Second, it led to the discovery of isomerism, which represents the possibility of two or more structures based on the same chemical formula. In his experiment, ammonium cyanate crystals and urea crystals were based on N2H4CO. Post this experiment, chemists started to experiment to find out the cause of isomerism. This led to the origin of the structure of chemical compounds. By the 1860s, chemists like Kékulé were coming up with explanations about the link between the chemical composition of a compound and the physical distribution of its atom. In the 1900s, chemists were trying to develop models for electron distribution for explaining the nature of chemical bonding. During this period, more organic compounds were being discovered each year. In the 20th century, many subdisciplines started branching out from organic chemistry such as petrochemistry, pharmacology, bioengineering, polymer chemistry, and others.

Introduction to Chemistry and Organic Chemistry

During that century, the innumerable new substance was being identified or synthesized. In the present day, more than 98 percent of the compounds known are organic. A number of organic compounds present, and their reactions is astonishing.

1.6. APPLICATIONS OF ORGANIC CHEMISTRY All substances having the element carbon are called organic compounds, and organic chemistry is concerned with these substances. The subject deals with compounds that have carbon ranging from solids like graphite to solvents and gases. Almost all compounds that surround us have carbon. Most of the substances that are used in daily human life are organic. This includes edibles like bread, milk, sugar, etc. Besides, clothes, belts, shoes, tires, and medicines also come under this category.

1.6.1. Medicine The most important application of organic chemistry is in the field of medicine. Majority of the drugs are organic in nature. Antibiotics, painkillers, anti-cancer drugs, anesthetics, anti-depressants, and cardiac drugs are some examples. There are three broad applications of organic chemistry in the field of medicine. • Drugs to Cure Disease: As mentioned, since most drugs used to cure disease are organic, they are bitter, water-insoluble, and moves

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Basic Organic Chemistry

Uric acid is a chemical created when the body breaks down substances called purines.

easily in the body tissues. In order for the drug to access the innermost part of body tissue, lipid solubility has to be enhanced. Change in organic ration, i.e., carbon content can ensure this. Organic chemistry is concerned with the study of drugs in order to make them more effective and ensure their reach and safety. To make the drugs safe, their toxicity is minimized through metabolism. Sometimes organic compounds have a varying effect on the body despite the same chemical structure due to stereoisomerism. The ‘Cis’ and ‘Trans’ isomers play a different role. The drugs L-DOPA, which is used to treat Parkinson and Levofloxacin, which is an antibiotic, have L-configuration. Both of them are Levoisomers of the same substance. However, Levo is more efficient than Dextro. • Pathophysiology of the Diseases: Knowledge of biochemistry and organic chemistry is indispensable for investigating diseases. Most disease progress the same way before death ensues. For example, in gout, the purine metabolism is hindered, which are important moieties of DNA and RNA molecules. The uric acid generated during purine metabolism does not convert to urea and instead gets stored. The crystals accumulate in the smaller joints, and this leads to gout. Checking the uric acid levels in blood indicates gout.

Introduction to Chemistry and Organic Chemistry

In case of infections like malaria, biochemical components of the body are destroyed. The malaria-causing parasite damages hemoglobin, which causes the hemoglobin levels to drop. This can be detected by variances in the organic functional group when compared to a healthy individual. The variance in organic compound indicates the severity of the disease and helps to study its course. • Diagnosis of Disease: Organic chemistry has its application in diagnosis as well. It helps in detecting the organic part of the disturbed substance. For instance, increased sugar levels indicate diabetes. The disease in severe cases is accompanied by an elevated level of ketone. Sugars comprise aldehyde groups (CHO) and ketones (C=O) groups. These groups are investigated. Higher the level of these groups, higher is the severity of the disease. This way, organic group helps in diagnosis by checking the levels of the disturbed organic functional group. Similarly, for patients with heart disease, cholesterol levels are tested.

1.6.2. Food Food is entirely made up of carbon compounds, namely fat (CH-COO-CH), carbohydrates (CHO) and proteins (NH2-CH-COOH). All vitamins are also organic. The body requirement during specific conditions like pregnancy, disease, or fitness determines the requirement of food and nutrients. For example, folic acid

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is taken during pregnancy to maintain the fetal health. For those desirous of building muscles, a protein-rich diet is recommended. Even beverages like beer, vodka, and wine, which contain ethyl alcohol have organic content. Knowledge of organic chemistry is required to ensure their flavor, quality, and handling.

1.6.3. Textiles and Clothing The cloth is made of various textures like wool, cotton, silk, polyester, etc. These materials contain carbon. Organic chemistry aids in the studies of textile material. This enables with controlling the quality, durability, color, and cleaning methods.

1.6.4. Cleansing Agents Organic solvents are widely used in the industries for cleaning. For example, when a drug is extracted from plants, petroleum is used to remove the fatty matter from the pulp. Even for domestic purpose, organic compounds are used for cleaning. For example, phenol and other agents are used to clean walls and floor. These sanitizing agents are manufactured using principles of organic chemistry to remove dirt and eliminate microorganisms. The organic chemistry principles provide a knowledge of solubility, polarity, and partition factors which helps in putting the solvents to better use.

Introduction to Chemistry and Organic Chemistry

1.6.5. Sterilizing Agents The disinfectants and sterilizing agents are mostly organic compounds, for example, phenol, formaldehyde, and others. They are very potent due to their solubility; pH levels etc. and can destroy microbes and human tissue cells as well. They dissolve the cell wall of the microbes or damage their protein layers, thereby killing them. The efficiency of these agents is increased by making adjustments to the organic composition. Gases like ethylene oxide are also used besides these solvents. They find their application in the sterilization of drugs and manufactured substances.

1.6.6. Analytic Material Chemical compounds like drugs, cosmetics, pesticides undergo a test for their safety and quality check. This testing is enabled by different techniques using principles of organic chemistry like titrations, spectrophotometry, chromatography, etc. The reagents used in the techniques like acids, bases, oxidizing, and reducing agents are organic. Further, the endpoint indicators in the titration are also organic compounds.

1.6.7. Valuables There are many carbon compounds that are precious, durable, and amongst the hardest substances. Graphite and diamond are pure carbon compounds and contain no other elements. They are widely used and very expensive.

Solubility is the property of a solid, liquid or gaseous chemical substance called solute to dissolve in a solid, liquid or gaseous solvent.

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Organic chemistry helps in studying the properties of these compounds. Petroleum is also a very valuable fuel across the world and influences the world economy. There are various petroleum products, which are derived and classified as per their uses.

1.6.8. Other Applications and Uses Organic chemistry is applied to wide areas in the field of medicine, petroleum, pesticide, textile, etc. • Analysis: Since all organic substances are not soluble in water, non-aqueous titration can analyze them. This is done using organic solvents like acetone, pyridine, methanol, etc. Many techniques like spectroscopy, chromatography, etc. also use organic solvents for analysis. This analysis helps to test the quality, quantity, etc. of the compounds to be investigated. • Synthesis: Organic chemistry principles are applied in the synthesis of many compounds, which are employed on a wide scale. For example, a drug molecule that is found in nature can be synthesized using principles of organic chemistry and made available for large-scale use. Many drug manufacturers apply for a patent to synthesize the same drug using their method. The same compound can be synthesized using various steps. Pharma companies stick to organic methods since they cost less and can

Introduction to Chemistry and Organic Chemistry

ensure higher profits. It is the knowledge of organic chemistry, which makes this possible. • Identification: Organic chemistry plays a major role in the identification of compounds. Specific tests enable identification of substances extracted from animals and plants. These tests are conducted using organic compounds and techniques linked to them. • Better Molecules: A molecule that is being used since long can be substituted by similar molecules by altering its chemistry marginally. This alternation is made to ensure more effective performance. The replacement of certain organic functional groups makes this possible.

1.7. CONCLUSION Chemistry is an important branch of science that studies matter as well as its reactions. It provides answers to most questions regarding occurrences in the natural world, and thus has been able to solve many complex issues. Chemistry has five major branches and many sub-branches. The major branches are organic chemistry, inorganic chemistry, analytical chemistry, physical chemistry, and biochemistry. These fields often overlap each other in applications. Chemists have been able to synthesize new compounds by using principles of chemistry. This has led to major inventions in the world. It has addressed food security issues by the

Inorganic chemistry deals with the synthesis and behavior of inorganic and organometallic compounds.

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invention of pesticides, which has minimized the loss of food. A noteworthy contribution has been in the field of health care and medicines. The drugs invented have saved millions of lives by finding a cure to fatal illness. Chemistry is responsible for the majority of the amenities that provide comfort in our daily life like clothing, homes, infrastructure, metals, etc. Its application in the field of defense and industries is also vast. Organic chemistry is a significant branch of chemistry, which deals with compounds containing carbon. It deals with all chemical reactions that are associated with life. The origin of organic chemistry can be traced in ancient times when men used medicines extracted from plants. A significant development in this field has occurred over the years since the 1800s. The two noteworthy contributors in this field are Jon Jacob Berzelius and Frederich Wöhler. Today the application of organic chemistry is seen in every aspect of life. All the requirements for sustaining life are supported by the field of chemistry. Organic chemistry has helped in developing drugs, improving the yield of food and preserving it, killing microbes present in the living space of humans among others. Path-breaking inventions still continue in this field, which transforms every aspect of human life.

Introduction to Chemistry and Organic Chemistry

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REVIEW QUESTIONS 1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

What does the field of chemistry deal with, and what are the various branches of this field? Explain how the branches of chemistry overlap each other. How has chemistry helped in food and energy security? Explain the scope of chemistry in saving lives and from lifethreatening diseases. What does organic chemistry deal with? What was the notable contribution of Frederich Wöhler in the field of organic chemistry? What did the theory of vitalism suggest? Explain five applications of organic chemistry. Why is organic chemistry important? What was the notable contribution of Jon Jacob Berzelius in the field of organic chemistry?

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REFERENCES 1.

2.

3.

4.

5.

6.

7.

A Brief History of Organic Chemistry, (n.d.). [eBook] Available at: http://greenmedicine.ie/school/images/Library/A%20Brief%20 History%20of%20Organic%20Chemistry.pdf (Accessed on 15 June 2019). Marie, H. A., (2019). The 5 Main Branches of Chemistry and What Each Involves. [online] ThoughtCo. Available at: https://www. thoughtco.com/the-5-branches-of-chemistry-603911 (Accessed on 15 June 2019). Marie, H. A., (2019). What You Should Know About Organic Chemistry. [online] ThoughtCo. Available at: https://www. thoughtco.com/organic-chemistry-introduction-608693 (Accessed on 15 June 2019). Study Read, (2019). The Importance of Organic Chemistry Explained with 10 Applications. [online] Available at: https://www. studyread.com/importance-of-organic-chemistry/ (Accessed on 15 June 2019). Study.com. (2018). What is Chemistry? – Definition, History & Topics – Video & Lesson Transcript | Study.com. [online] Available at: https://study.com/academy/lesson/what-is-chemistry-definitionhistory-topics.html (Accessed on 15 June 2019). Toppr-guides, (n.d.). Importance and Scope of Chemistry: Applications, Uses, Videos, Examples. [online] Available at: https://www.toppr.com/guides/chemistry/some-basic-concepts-ofchemistry/importance-and-scope-of-chemistry/ (Accessed on 15 June 2019). Wiredchemist.com. (n.d.). What is Chemistry? [online] Available at: http://www.wiredchemist.com/chemistry/instructional/anintroduction-to-chemistry/what-is-chemistry (Accessed on 15 June 2019).

2 ORGANIC MOLECULES AND FUNCTIONAL GROUPS

LEARNING OBJECTIVES: In this chapter, you will learn about: • Major group of organic molecules. • Types of nucleic acids. • Role of amino groups. • Alcohols are functional groups.

KEY TERMS: • • • • • •

Aldehyde Carbohydrates Cholesterol Hydrophilic Ketones Lipids

• • • • •

Molecules Polar Properties of ethers Similarities of aldehydes and ke tones Structure of ethers

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2.1. INTRODUCTION Organic molecules are found in living systems, including the human body and are generally defined as compounds that contain molecules that have carbon covalent bond, or a carbon-hydrogen covalent bond. Covalent bonds being bonds where electrons are shared between the atoms. There are four major groups of organic molecules such as carbohydrates, lipids or fats, proteins, and nucleic acids. These are often referred to as the molecules of life. All carbohydrates contain carbon, oxygen, and hydrogen, usually in a ratio of 1:2:1. The linear model of a glucose molecule represents that being one of the most important smaller or simpler carbohydrates. Simple carbohydrates can link together in chains or rings to form longer more complex carbohydrates. Lipids are composed mainly of carbon, hydrogen, and Oxygen. However, lipids contain a lower proportion of oxygen atoms than do carbohydrates. It has been observed that some lipids do contain nitrogen and phosphorus. There are several types of lipids, and all proteins contain four elements that are carbon, hydrogen, oxygen, and nitrogen. Proteins are giant macromolecules that are made up of amino acid building blocks. The amino acid molecules bonded together to form a dipeptide molecule. The building block of structural organic chemistry is the tetravalent carbon atom. With few exceptions, carbon compounds can be formulated with four covalent bonds to each carbon, regardless of whether the combination is with carbon or some other element. Amino acids can link together to form long chains; typically, a protein consists of 100 or more amino acids linked together. Some proteins contain phosphorus, sulfur, iron, zinc, magnesium, and other trace metals. There are two main types of nucleic acids that are DNA (Deoxyribonucleic acid) and RNA (Ribonucleic acid). Nucleic acids are large molecules that are made up of smaller molecules called nucleotides. The nucleotides in these molecules are linked together through covalent bands and through hydrogen bonds. DNA is a double standard nucleic acid, and its molecules take on a double helix

Organic Molecules and Functional Groups

formation. Most RNA molecules are singlestranded nucleic acids, and many times they form a folded compacted structure with some hydrogen bonding within the molecule. The two-electron bond, which is illustrated by the carbon-hydrogen bonds in methane or ethane and the carbon-carbon bond in ethane, is called a single bond. In these and many related substances, each carbon is attached to four other atoms. In other words, organic molecules are carbon-based, so carbon is the building block of organic molecules. For example, Fruits are high in carbohydrates, and eggs are high in proteins because proteins are a category of an organic molecule.

2.2. FUNCTIONAL GROUPS AND REACTIVITY Hydrocarbons are interesting especially if the person want to combust things and if they want some fuel and it will become more interesting by adding things to the hydrocarbons, and the things that should be added are called as functional groups. The size and shape of molecules are as much a part of molecular structure as is the order in which the component atoms are bonded. Contrary to the impression you may get from structural formulas, complex molecules are not flat and formless, but have well-defined spatial arrangements that are determined by the lengths and directional character of their chemical bonds.

Dipeptide is an organic compound derived from two amino acids.

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When O-H is attached to the carbon backbone, then it turns the entire molecule into alcohol. The proteins are as amazing as they can play so many roles and carbon is the element of life, and after exploring so many things, the first things that comes in mind is compounds that contain carbon. There is a time when people believe that carbon compounds could only be produced by living things. So, early chemists called them as organic compounds. Scientists back then considered biological molecules to be almost mystical in origin. Biological molecules are just chemicals that could be created and manipulated in the lab. Suddenly, a new branch of chemistry was born that is organic chemistry. It has been observed that carbon is in group 14 on the periodic table and like all of the elements in that group, it has four valence electrons. So, in carbon, those four electrons can bond to other atoms in a really promiscuous number of configurations to form all kinds of structures that is why carbon is to biology, which silicon is to geology just as silicon forms the basis not only for sand but also most of the rocks on earth. Carbon is the foundation of most biological molecules. The simplest organic molecules are pure hydrocarbons containing only carbon and hydrogen, which forms hydro-carbon. When all carbons in a pure hydrocarbon are bound to the maximum number of atoms like four atoms each so that there are no double or triple bonds anywhere. These compounds are considered to be full or saturated which means that all the carbons

Organic Molecules and Functional Groups

have four bonds, either with other carbon atoms or with hydrogen atoms, in which case the hydrogen is bound to one carbon. These are the simplest rules that govern some of the world’s most useful, or at least, used compounds. The hydrocarbons that humans use today for the purpose of diesel fuel, gasoline, methane, propane.

2.3. ROLE OF FUNCTIONAL GROUPS The glucose is the fuel of life, and the O-H is attached to the carbon atoms, which is a functional group that’s called hydroxyl (Figure 2.1).

Figure 2.1: Glucose structure. Source: https://commons.wikimedia.org/wiki/ File:Glucose_structure.svg

Hydroxyl consists of oxygen and hydrogen that represent the rest of the molecule that the functional group is attached. Think of hydroxyl as a water molecule that’s lost its second hydrogen, and the oxygen will have a partial

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Carbonyl group is a functional group composed of a carbon atom double-bonded to an oxygen atom: C=O. It is common to several classes of organic compounds, as part of many larger functional groups.

negative charge whereas the hydrogen will have a partial positive charge that polarity will make any molecular region where hydroxyl is attached hydrophilic, and that’s why the molecules with hydroxyl groups are water soluble. Coffee contains caffeine and caffeine has several functional groups, but now it is important to focus on the carbonyl group. This group is a carbon double bonded to oxygen like hydroxyl it’s polar and hydrophilic. The carbonyl group with the carbon attached to a hydroxyl and when dissolves in water, the hydrogen tends to break off, making a carboxyl group a weak acid and leaving the ionized form of carboxyl behind that is needed to be found in a cell (Figure 2.2).

Figure 2.2: Coffee contains caffeine. Source: https://pixabay.com/photos/coffee-caffeinecup-beverage-2538476/

Amino groups consist of nitrogen attached to two hydrogens. When someone connects an amino group to a molecule that makes it a base because the amino group in water will pick up a proton from the solution increasing the pH. That makes the amino group look something like who have three hydrogens and the positive charge. Amino sounds like the ammonia and

Organic Molecules and Functional Groups

ammonia formula are nh3, and it’s a base just like the amino group. The macromolecules are important for living things, and some molecules look like carbohydrates and lipids, nucleic acids and proteins. For example, carbohydrates are known to be a good energy source, and things such as sugars, glucose, sucrose, fructose, galactose, and maltose. They are all simple sugar monosaccharides, and disaccharides and all of them end in the suffix OSE because any time in biology, a molecule name ends with OSC and it means that it can be sugar whereas other functions of carbohydrates are as energy storage. In organic chemistry, a functional group is a specific group of atoms or bonds within a compound that is responsible for the characteristic chemical reactions of that compound. The same functional group will behave in a similar fashion, by undergoing similar reactions, regardless of the compound of which it is a part.

2.3.1. Carbohydrates and Lipids Plant store their energy in the form of carbohydrate called starch and animals will store energy short term in a carbohydrate called glycogen, which it can found a lot stored in muscles and in the liver. Carbohydrates are also used as a structural material. For example, cellulose, which is the primary component of the plant cell walls its plant fiber and chitin, is a carbohydrate that is found in the exoskeleton of autopods also in the cell walls of

Glycogen is a multibranched polysaccharide of glucose that serves as a form of energy storage in animals, fungi, and bacteria.

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fungal cells. The carbohydrates are more look like a polymer; almost all the biomolecules are polymers. Lipids are very clear as a nonpolar organic molecule. This group of molecules is very diverse meaning, and there are a lot of different types, but it is not as simple as carbohydrates. Lipids should be at a good place to store energy. For example, fats and oils, as their structural material especially phospholipids and cholesterol as they are found plentiful in the cell membranes of all cells. Water barriers are a great example of lipids because of their nonpolar hydrophobic nature, and they make a good water barrier. Oils and waxes are built from lipids, or they are lipids, and finally, another example of a function of lipids is a messenger molecule which acts as hormones, or some of the steroid lipids are the hormones. The buildings blocks of the lipids are one of the building blocks are fatty acids. Functional groups also play an important part in organic compound nomenclature; combining the names of the functional groups with the names of the parent alkanes provides a way to distinguish compounds.

2.4. ALCOHOLS Alcohols may be defined as those kinds of functional groups that are represented by the -OH group in their chemical formula. Alcohols can be described as those compounds in organic chemistry that contain a hydroxyl group (-OH) attached to a carbon atom of that compound. Alcohols represent a very significant class of

Organic Molecules and Functional Groups

functional groups that have several applications in scientific, industrial, and medical fields (Figure 2.3).

Figure 2.3: The representation of an alcohol group. Source: https://upload.wikimedia.org/wikipedia/ commons/9/93/Alcohol-%28general%29-skeletal. png

2.4.1. Structure and Physical Properties of Alcohols The alcoholic compounds are similar to water in their structural appearance. It can be seen from their bent shape. This structural representation represents a case in which the effects of the repulsive forces between the electrons can be seen. Another thing that makes up the structural appearance of these compounds is the increased steric bulk of the element on the atom at the central position. In a manner similar to that of water, the alcohols are polar in nature and constitute of an unsymmetrical spread of charge between the atoms of hydrogen and oxygen. The increased electronegativity exhibited by the oxygen atom as opposed to that of carbon tends to shorten the bond on the -OH group and in turn, make it stronger (Figure 2.4).

Electronegativity is a measure of the tendency of an atom to attract a bonding pair of electrons.

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Figure 2.4: Structure of an alcohol group. Source: https://upload.wikimedia.org/wikipedia/ commons/0/02/Alcohol.png

Protonation is the addition of a proton (H+) to an atom, molecule, or ion, forming the conjugate acid.

The -OH group that is present in the compound forms hydrogen bonds with the other -OH groups that are present in other compounds, or the hydrogen atoms that may be there or other similar molecules. This characteristic of the -OH groups tends to give a property to the compounds in which they have a high boiling point when compared to other compounds having similar parent molecules. Alcohols have a tendency to take part in several chemical reactions. The process of deprotonation is one that they exhibit when they are treated with a strong base. This tendency of these compounds that exhibits their weak behavior as acids tend to form an alkoxide salt and a water molecule. The hydroxyl groups cannot be defined as groups that leave well, on their own. Generally, the instance of them participating in the reactions that exhibit nucleophilic substitution is characterized by the protonation of the oxygen atom, which results in a group known as water moiety that acts as a better group when talked about leaving a compound.

Organic Molecules and Functional Groups

2.5. ETHERS Ethers represent those kinds of organic compounds in which there is an oxygen atom which is bonded with two aryl or alkyl groups.

2.5.1. Structure of Ethers The kinds of organic compounds that consist of an ether group are known as ethers. An ether group can be recognized from the description that in them, one oxygen atom is bonded with two aryl or alkyl groups. There is a typical formula that they follow which is given by R-O-R’ (Figure 2.5)

Figure 2.5: Representation of ether group. Source: https://upload.wikimedia.org/wikipedia/ commons/5/51/Ether-%28general%29.png

The bond represented by C-O-C is defined by angles between them, which is 104.5°, and the distance between them being approximately 140 pm. The oxygen of ether shows more electronegativity as compared to the carbon atoms in the compound. This is the reason that the hydrogens in consideration show increased acidic nature when compared to the typical chains that are formed by various hydrocarbons.

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2.5.2. Properties of Ethers

Alkyl group is a type of functional group that has a carbon and hydrogen atom present in its structure.

The existence of an alkyl group on any side of the central oxygen is the reason behind the nonpolar property of ethers. The oxygen atom is mainly not able to take part in hydrogen bonding due to the existence of heavy alkyl groups. The alcohols of the same molecular weight have a lower boiling point in relation to ethers. The variation in boiling points becomes less due to elongation of the alkyl chain of the ethers. This is due to the effect of increased Van der Waals interactions as the number of carbons increases, and therefore, the number of electrons increases as well. The ethers build hydrogen bonds with water due to the presence of two lone pairs of oxygen on the atoms of oxygen. The alkenes are less polar than ethers, and not as polar like esters, alcohols or amides of similar structures.

2.6. ALDEHYDES AND KETONES The category of organic compounds that contain a carbonyl (C=O) group is defined as Aldehydes and ketones.

2.6.1. Ketones Ketone is defined as the molecule containing the carbonyl functional group. The organic compounds with the shape RC(=O) R,’ where R and R’ can be a type of group containing carbon is defined as ketones. IUPAC nomenclature rules dictate that the ketone molecules should be given the name by altering the suffix of the parent carbon molecule to “-one.”

Organic Molecules and Functional Groups

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As required by rules of IUPAC nomenclature. If the position of the ketone must be specified, then a number is put between the parent chain name and the “-one” prefix, for example, propane-2-one, or in the start of the IUPAC name to specify the ketone place. The ketone working group is defined by the prefixes “oxo-” and “keto-.”

2.6.2. Aldehyde The carbonyl group with the central carbon attached to a hydrogen and R group (R-CHO) is the organic compound also known as Aldehydes differ from ketones in that the carbonyl is placed at the end of the carbon skeleton instead of in between two carbon atoms of the backbone and in this way ketones are different from aldehydes. The aldehydes are sp2-hybridized form, and it can be found in the keto or enol tautomer like ketones. The deletion of the suffix of the parent molecule, and addition of the suffix “-al.” is done to give the name to aldehydes. For example, the three-carbon chain, together with the aldehyde group on a terminal carbon, might be propanal. In order to determine the carbon atom is part of the aldehyde group prefix “oxo-” is used to designate it, if there are higher order working groups on the compound. The number can be placed among the parent chain and suffix, or at the start of the name of the compound to specify the position of aldehyde.

Carbon skeleton is the chain of carbon atoms that forms the “backbone,” or foundation, of any organic molecule.

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2.6.3. Similarities of Aldehydes and Ketones The alkene with a hydroxyl group attached to one of the carbon atoms comprising of the double bond is known as enol form, the aldehydes and ketones remain in balance with their enol forms. In ketones mostly outweighs the balance in keto form. The deprotonated enolate form is a strong nucleophile is the reason of enol form being important for some reactions. In the room temperature, the keto form is given priority the balance is strongly driven by thermodynamic property. The existence of the acid or a base is used as a catalyst in interconversion.

2.7. CARBOXYLIC ACIDS The carbon atom that takes part equally in hydroxyl and a carbonyl functional group are organic acids known as carboxylic acids. The carbonyl group (C=O) together with the hydroxyl group (O-H) fixed with the similar carbon atom are contained in a working group known as the carboxyl group (COOH). The formula -C(=O) OH, normally written as -COOH or CO2H is used to represent the Carboxyl groups. The existence of one carboxyl group indicates the group of molecules known as carboxylic acids. The carboxylic acids are categorized as Brønsted-Lowry acids as donors of the proton. The dicarboxylic, tricarboxylic are known as acids with two or more carboxylic groups. The carboxylates are described as salts and esters of carboxylic acids. The carboxylate ions are made stable to resonance. In comparison to alcohols,

Organic Molecules and Functional Groups

the increased stability is the cause of more acidity. The carboxylic acids have the suffix “-oic acid” though “-ic acid” is the suffix normally in use used as per IUPAC nomenclature.

2.7.1. Esters The reduction of alcohol with carboxylic acid produces the functional groups known as esters, and are named according to the components.

2.7.1.1. Structure and Bonding The 120° C-C-O and O-C-O bond angles due to sp2 hybridization is the reason behind the carbonyl center contained in esters. The rotation near the C-O-C bonds has less energy restrictions is the reason behind esters being structurally flexible functional groups in comparison to amides. The pKa of the alpha-hydrogens, or the hydrogens attached to the carbon adjacent to the carbonyl, on esters is around 25, making them essentially non-acidic except in the presence of very strong bases.

2.8. PHYSICAL PROPERTIES AND CHARACTERIZATION The ethers are less polar than esters, but less in comparison to alcohols. In contrast with parent alcohols and carboxylic acids, it takes part in hydrogen bonds as the hydrogen bond acceptors, yet cannot play the role as hydrogen bond acceptors. It rests on the length of the alkyl chains connected is the reason behind the solubility in water property of bonding of hydrogen. Since they have no hydrogens bonded to oxygens, as

Hybridization is the idea that atomic orbitals fuse to form newly hybridized orbitals, which in turn, influences molecular geometry and bonding properties.

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alcohols and carboxylic acids do, the esters do not attach themselves as hydrogens attach to oxygen and alcohols to carboxylic acids. The esters are more explosive than carboxylic acids of the same molecular weight as a result.

2.8.1. Amines The compounds that are recognized by the existence of a nitrogen atom, a single pair of electrons, and three contents are called amines. The primary nitrogen atom with a single pair of electrons constitutes the amine functional group. The one or more hydrogen atoms have switch places with the carboncontaining element, and this group is extracted from ammonia. The amides are described as compounds with the nitrogen group connected to a carbonyl inside the structure, and they have the shape of R-CO-NR’R.” The aromatic amines are defined as amine groups attached to an aromatic structure. The existence of the amine group reduces in a large amount the reactivity of the ring as the reason is an electron donating effect whereas aromatic structure reduces the alkalinity of the amine importantly. The amine compound, when being named, is given the prefix “amino-” or the suffix “-amine.” An organic compound with multiple amino groups is called the diamine, triamine, tetramine, are defined as the organic compound with multiple amino groups

2.8.2. Classification by Functional Groups The functional groups are defined as a number

Organic Molecules and Functional Groups

of repeating varieties of structural features in organic compounds. The division of compounds as per the functional groups is defined as a traditional method to the subject of organic chemistry. The functional groups of alkenes, alkynes, carbonyl elements, alcohols, amines, and nitriles are C=CC=C, C≡CC≡C, C=OC=O, OHOH, NH2NH2, and C≡NC≡N, respectively. There is the probability in future that systematic names like the methanol, 2-propanone, and ethanoic acid will be exchanged by the commonly used nonsystematic names formaldehyde, acetone, and acetic acid. The organic chemist has the concept of the compounds the names methanal, 2-propanone, and ethanoic acid represent, so the students can display these names and later become familiar with and use the special names. The functional groups also define and separate according to the corresponding chemical behavior, and this is the reason behind the categorization. The physical properties are greatly affected by the behavior of the functional groups exist and the reactions of compounds. There are many organic reactions that contain change of the functional group, and it does not impact the rest of the molecule. For example, without changing the structure of the hydrocarbon group R the alcohols, R−OH, can be altered into a number of other compounds, such as organic halides, R−Cl or R−Br; ethers, R−O−R; and amines, R−NH2. The specific functional group is required to display reactions features of that group and to some limit minimum, of inorganic compounds with same practical groups.

Ethanoic acid is a chemical with a sharp, acrid smell. You may recognize the smell as being similar to vinegar.

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40

REVIEW QUESTIONS 1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

What are the Organic Molecules? Define four major groups of organic molecules? How are proteins useful? Where does the carbon stand in the periodic table? Define the concept of Hydroxyl? Give examples of Carbohydrates and Lipids? Explain the properties of Esters? Define the Structure of Ethers? Describe the physical properties of Amines. What are the similarities of Aldehydes and Ketones?

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REFERENCES 1.

2.

3.

4.

Chemistry LibreTexts, (2017). 2.3: Classification by Functional Groups. [online] Available at: https://chem.libretexts.org/ Bookshelves/Organic_Chemistry/Book%3A_Basic_Principles_of_ Organic_Chemistry_(Roberts_and_Caserio)/02%3A_Structural_ Organic_Chemistry._The_Shapes_of_Molecules_and_Functional_ Group/2.3%3A_Classification_by_Functional_Groups (Accessed on 15 June 2019). Chemistry LibreTexts., (2019). 24.1: Functional Groups and Classes of Organic Compounds. [online] Available at: https://chem.libretexts.org/Bookshelves/General_Chemistry/ Map%3A_Chemistry_(Averill_and_Eldredge)/24%3A_Organic_ Compounds/24.1%3A_Functional_Groups_and_Classes_of_ Organic_Compounds (Accessed on 15 June 2019). Courses.lumenlearning.com. (n.d.). Functional Group Names, Properties, and Reactions | Boundless Chemistry. [online] Available at: https://courses.lumenlearning.com/boundless-chemistry/ chapter/functional-group-names-properties-and-reactions/ (Accessed on 15 June 2019). Structural Organic Chemistry: The Shapes of Molecules. Functional Groups, (n.d.). [eBook] p. 1. Available at: https://authors.library. caltech.edu/25034/3/BPOCchapter2.pdf (Accessed on 15 June 2019).

3 NOMENCLATURE OF ORGANIC MOLECULES LEARNING OBJECTIVES: In this chapter, you will learn about: • To understand the importance of the Nomenclature of the Organic Molecules. • To gain knowledge about the history of the Formation of the International Union of Pure and Applied Chemistry (IUPAC). • To understand the basic concept of the nomenclature of the Organic Molecules. • To gain the knowledge about the different families of the Organic Molecules and how their nomenclature is done. • To understand the difference between the specifications of the different families of Organic Molecules. • To understand the guidelines of the Nomenclature of the Organic Molecules.

KEY TERMS: • • • • • •

Calibration of atomic weights Calibration of physical quantities Expurgation tables of quantities International system of units (SI) Nomenclature scheme Organic molecules

• • • • •

International Standard Organization (ISO) The halogen atom The International Union of Pure and Applied Chemistry (IUPAC) Nomen clature Scheme The tetravalency of carbon Unsaturated organic compounds

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3.1. INTRODUCTION A rational method of nomenclature scheme should perform two things at a minimum. In the initial phase, it should designate how the carbon atoms of a specified compound are fused all together in a distinguishing lattice of chains and rings. In the second phase, it should recognize and place any type of the functional groups that is available in the compound. In the meantime, hydrogen is one of the common components of organic compounds, the quantity and the place of the hydrogen can be presumed from the tetravalency of carbon, and it is not required to be definite in many of the instances (Figure 3.1).

Figure 3.1: Different methods are being followed for the nomenclature of organic molecules in the modern world. Source: http://www.thebluediamondgallery.com/tablet/images/alcohol.jpg

The International Union of Pure and Applied Chemistry (IUPAC) nomenclature scheme of the organic compounds is considered as a series of logical guidelines that is planned and used by organic chemists to avoid the issues that are caused by arbitrary nomenclature.

Nomenclature of Organic Molecules

By the understanding of these set of logical guidelines and given a structural formula, the individual should be able to write down an exclusive name for every single distinct compound. In a similar way, given an IUPAC name, the individual should be able to document a structural formulation of the organic compound. In a general context, an IUPAC name will have three important characteristics: • A root or base that is representing a main chain or ring of carbon atoms that are present in the molecular structure; • A suffix or other element(s) that are labeling the functional groups that are founded in the compound; and • Terms of substituent clusters, other than hydrogen, that complete the entire structure of the molecular compounds. As an overview to the IUPAC nomenclature system, the organic compounds should be considered that have no definite functional groups. Such types of organic compounds are comprised of just carbon atoms and hydrogen atoms that are fused together by the bonds that are known as sigma bonds. In sigma bonds, all carbons are spa hybridized.

3.2. HISTORY OF THE NOMENCLATURE OF ORGANIC MOLECULES The calibration of masses, measures, terms, and signs is important to the continual achievement of the logical enterprise and to the smooth

45

Applied Chemistry is the application of the study of chemical elements and compounds to industry and the arts.

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Chemical nomenclature is a set of rules to generate systematic names for chemical compounds.

growth and evolution of worldwide trade and business. This wish for international collaboration amongst the chemists and simplification of the work of the international, but fragmented, chemistry community, were the initial features of the Union. The creation of I IUPAC (1919) prospered its precursor body, the International Association of Chemical Societies (IACS) that was born in Paris in the year 1911, and created a set of suggestions for the work that the new Union had to pursuit. These comprise of: • nomenclature in chemistry; • calibration of atomic weights; • calibration of physical quantities; • expurgation tables of quantities; • expansion of chemical certification; and • calibration of journals. If 1911 might now appear an initial date for chemists to start speaking regarding the opportunity of and want for international alliance and calibration in the field of Pure Chemistry, earlier conferences were held as the first Congress of chemists, in Karlsruhe in the year 1860 to describe about the atom and the organic molecule, then the initial international one on organic chemical nomenclature in Geneva in the year 1892. Together, the international congresses on Applied Chemistry raised up since the year 1894 to the year 1912 (Figure 3.2).

Nomenclature of Organic Molecules

Figure 3.2: There is a history for the development of the guidelines of the nomenclature of the organic molecules. Source: https://live.staticflickr.com/1040/11603884 24_1743e6f386_b.jpg

In the year 1919, taking over from IACS, IUPAC desired to associate the pure and applied features of chemistry. It envisioned establishing an everlasting collaboration among the chemical relations of the following states, to organize their technical and mechanical resources, to contribute to the growth of chemistry in all facets of its field. Commissions functioned in the direction of these objectives, each one into a specific area. Accordingly, in the interwar time, IUPAC offered a calibration of some of these matters, contributing to the formation of a common language. After the Second World War, IUPAC restructured on a frequent basis, accompanying or inspiring the arrival of the innovative chemical sciences departments, those are known to become complete disciplines. In the meantime, it stretched its act to several numbers of other nations. In the year 1919, five

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countries have begun the Union. These five nations include France, Great Britain, Belgium, the United States of America and Italy. On the other hand, in the year 1921, they are 21 states. On the verge of the twenty-first century, 45 nationwide administrations observed, and 16 other ones were associated. In the era of the period 1950s, the Union started a massive interaction effort by printing the outcomes of its operations and suggestions: the specified colored documents, a Pure and Applied Chemistry specific journal, a news sheet, and far ahead of a Worldwide Chemistry publication. At the start of the year 1960s, together with The International Union of Pure and Applied Physics (IUPAP) at Ottawa in the year1960, the Union accepted the isotope carbon-12 at Montréal, Canada in the year 1961 as the exclusive reference for atomic weights. Then the two organizations, together with The International Organization for Standardization (ISO), attained in the year 1971 official acknowledgment of the mole as the base unit in the International System of Units (SI) for the quantity of element. The Union, with its international vocation, functioning in the direction of a common language in the field chemistry and a broadcast of its principles, is in continuousness with the initial congress in Karlsruhe in the year 1860, and the IACS since the year 1911 to the year 1919. Under its patronages, the initial international congress after-World War I took place in Madrid in the year 1934, together with the International

Nomenclature of Organic Molecules

Chemistry Conference. At the present times, it is called the General Assembly of the Union. Ever since, the custom remains.

3.3. BASIC STEPS FOR NOMENCLATURE OF THE ORGANIC MOLECULES 3.3.1. Cracking the Code A modern organic name is considered as simply a code. Every single portion of the name provides some valuable data regarding the organic compound. For example, to understand the name 2-methylpropan-1-ol you need to take the name to pieces. The “prop” that is used in the center expresses the individual that how many carbon atoms are present in the longest chain. The “an” which follows the “prop” communicates that there are no carbon-carbon double bonds present. The further two portions of the name communicate about the exciting things which are going on the initial and second carbon atom that is founded in the chain. Any name that the individual is possibly to come across can be shattered up in this similar method.

3.3.2. Counting the Carbon Atoms It is mandatory to recall the codes for the amount of the carbon atoms that are existing in a series up to six carbons. It has been detected that there occurs no unpretentious method around this; it is mandatory to be learned. If it

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cannot be completed appropriately, then no one will be capable of tagging any of the organic compounds (Figure 3.3).

Figure 3.3: There are certain guidelines that have to be followed in the naming of the organic molecules. Source: https://upload.wikimedia.org/wikipedia/ commons/thumb/0/0a/Prentice_Hall_Molecular_ Model_Set_for_General_Organic_Chemistry_8140. JPG/800px-Prentice_Hall_Molecular_Model_Set_ for_General_Organic_Chemistry_8140.JPG

In order to provide the organic compounds with a name or tag, there are a set of defined rules, and these certain rules must be followed. At the time of tagging or naming the organic compounds in the Organic Chemistry, the IUPAC nomenclature (naming scheme) is used. This is to give constancy to the names. It also allows every compound to have an exclusive name, which is not possible with the common names that are used, for instance, in any of the business. It is essentially required to look at some of the set of rules that are required to be followed at the time of giving a specific name to an organic compound, and after this, one needs to try to apply these set of rules to some specific instances.

Nomenclature of Organic Molecules

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3.4. HOW TO NAME ORGANIC COMPOUNDS USING THE IUPAC RULES In order to name or tag any of the organic compounds, it is initially required to remember a few basic names. These names are registered in the conversation of naming alkanes. In the general context, the base portion of the name replicates the number of carbon atoms in what it has been allocated to be the parent chain. The suffix of the name imitates the kinds of functional group(s) that are founded on or inside the parent chain. The other groups which are linked to the parent chain are known as the substituents.

3.4.1. Alkanes- Saturated Hydrocarbons The names of the straight chain saturated hydrocarbons for near about 12-carbon chain. The names or the tags of the substituents created by the elimination of one hydrogen from the end of the chain is attained by altering the suffix -ane to -yl. • Recognize the lengthiest carbon chain. This chain is known as the parent chain. • Recognize all of the substituents, the clusters that are joining from the parent chain). • Quantify the number of the carbon atoms that are present on the parent chain from the end that gives the substituents the lowermost numbers. When associating a sequence of

Alkanes are organic compounds that consist entirely of single-bonded carbon and hydrogen atoms and lack any other functional groups.

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•

•

•

a) b) c)

numbers, the sequence that is the “lowermost” is the one which comprises the lowermost number at the time of the initial change. If two or more side chains are in equal positions, allocate the lowermost number to the one which will come initially in the name. If the similar substituent happens more than on one occasion, the place of every single point on which the substituent happens is given. In addition to it, the quantity of times the substituent group arises is specified by a prefix, for instance, di, tri, tetra, etc. If there exist two or more diverse substituents, they are registered in arranged order using the base name. The only prefix which is used when pushing the substituents in sequential direction is “iso” as in isopropyl or isobutyl. The prefixes, for instance, sec-, and tert- are not utilized in defining arranged order excluding when it is associated with each other (Figure 3.4). If chains of equivalent length are opposing for selection as the parent chain, then the choice goes in sequence to: The chain which comprises of the highest number of side chains. The chain whose substituents have the lowermost- numbers. The chain which comprises of the

Nomenclature of Organic Molecules

d) •

utmost number of carbon atoms that is founded in the smaller side chain. The chain that is having the smallest branched side chains. A cyclic or ring form of hydrocarbon is selected by the prefix cyclo-, which looks directly in forward-facing of the base name.

Figure 3.4: As the saturated hydrocarbons, there is a different set of rules for the nomenclature of the alkanes. Source: https://upload.wikimedia.org/wikipedia/ commons/thumb/4/4f/Alkanes.svg/620px-Alkanes. svg.png

The name of the compound is inscribed out with the substituents in sequential order, which is followed by the base name that is consequent of the number of carbons that are present in the parent chain. There is the use of commas in between numbers. On the other hand, dashes are used in between letters and numbers. There exist no spaces in the name or tag of the organic compound.

3.4.2. Alkyl Halides The halogen atoms are treated as a substituent on an alkane chain. The halo- substituent is well-

Hydrocarbon is an organic compound consisting entirely of hydrogen and carbon.

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thought-out of equivalent rank with an alkyl substituent in the totaling of the parent chain.

3.4.3. Alkenes and Alkynes – Unsaturated Organic Compounds The dual bonds in hydrocarbons are designated by substituting the suffix -ane with -ene. If there is more than one dual bond presented, the suffix is extended to comprise a prefix that specifies the number of dual bonds available. For instance, adiene, -atriene, and many more. Tripartite bonds are called in an analogous way using the suffix -yne. The location of the several bonds in the interior of the parent chain is specified by engaging the number of the initial carbon of the several bonds directly in the obverse direction of the base name.

3.4.4. Alcohols

Hydroxyl group is the entity with the formula OH. It contains oxygen bonded to hydrogen. In organic chemistry, alcohol and carboxylic acids contain hydroxy groups.

Alcohols are termed by substituting the suffix -ane with -anol. In case if there exist more than just one hydroxyl group (-OH), the suffix is extended to comprise a prefix that specifies the number of hydroxyl groups that are presented, for instance, anediol, -anetriol, and many more. The location of the hydroxyl groups that are founded on the parent chain is specified by placing the number that is matching to the position on the parent chain directly in the front direction of the base name. It is similar to that of alkaline.

Nomenclature of Organic Molecules

3.4.5. Ethers It is just predictable to know how to give name or tag to ethers by their common names. The two alkyl groups that are associated with the oxygen are put in sequential order with spaces among the names, and they are followed by the term ether. The prefix di- is used if both the clusters of the alkyl are similar in nature.

3.4.6. Aldehydes Aldehydes are called by substituting the suffix -ane with -anal. In case, if there exists more than one -CHO group, the suffix is extended to contain a prefix that specifies the number of -CHO groups that are available. For instance, anedial – there must not be more than two of these clusters to be present on the parent chain as they must happen at the ends. It is not essential to specify the location of the -CHO group. This is because this group will be at the end point of the parent chain, and its carbon is robotically allocated as C-1.

3.4.7. Ketones Ketones are called by substituting the suffix -ane with -anone. In the case, if there is more than one carbonyl group (C=O), the suffix is extended to contain a prefix that specifies the number of carbonyl groups that are available, for instance, anedione, -anetrione, and many more.

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The location of the carbonyl group that is present on the parent chain is specified by placing the number that is matching to the location on the parent chain directly in the front direction of the base name. It is similar to that of the alkenes.

3.4.8. Carboxylic Acids Carboxylic acids are called by quantifying the number of carbons that are founded in the longest continuous chain that comprises of the carboxyl group and by substituting the suffix -ane of the equivalent alkane with -anoic acid. If there are two -COOH groups, the suffix is extended to contain a prefix that specifies the number of -COOH groups that are available, for instance, anedioic acid – there must not be more than two of these groups on the parent chain as they must happen at the ends. It is not essential to specify the location of the -COOH group. This is because this group will be at the end of the parent chain, and its carbon is robotically allocated as C-1.

3.4.9. Esters Carboxylic acid is an organic compound that contains a carboxyl group (C(=O) OH).

Organized names of esters are grounded on the name of the equivalent carboxylic acid. The alkyl group is called like a substituent which is making use of the -yl ending. This is trailed by a space. The acyl part of the name, what is left behind, is termed by substituting the -ic acid suffix of the equivalent carboxylic acid with -ate.

Nomenclature of Organic Molecules

3.4.10. Amines It is just predictable to know how to give tag or name to amines by their common names. They are termed similar to that of ethers, the alkyl (R) groups are associated to the nitrogen are put in sequential order with no spaces which are between the names and these are followed by the term amine. The prefixes di- and tri- are used if two or three of the clusters of alkyls are similar in nature.

3.5. GUIDELINES FOR THE NOMENCLATURE OF ORGANIC MOLECULES An improved general set of guidelines to follow is to start at the end, the suffix and work towards the back, starting from the direction of the right to left in the name (Figure 3.5). • Identify the functional group in the organic compound. This will decide about the suffix of the name. • Now, the task is to discover the lengthiest constant carbon chain that comprises of the functional group, and it won’t be a straight chain at all the times and sum total the number of carbon atoms that are present in this long chain. This number will decide about the prefix that is the beginning of the name of the organic compound. • Find the amount of the carbon atoms that are founded in the longest carbon chain. In case if the organic molecule

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•

is not an alkane, that means it has a functional group, then it is required to begin the totaling so that the functional group is on the carbon having the lowermost possible figure. Begin with the carbon at the termination, which is near to the functional group. Find any of the branched groups: Name or tag them by quantifying the number of carbon atoms that is founded in the branched group. The location of the branched group on the foremost carbon chain is to be noted.

Figure 3.5: While naming an organic molecule, it is important to recognize the number of branched chains. Source: https://upload.wikimedia.org/wikipedia/ commons/thumb/e/ec/Cobalamin.png/800px-Cobalamin.png

Nomenclature of Organic Molecules

In the case, if there are more than one of the similar kinds of the branched group available then both the numbers must be listed, for example, 2, 4, etc.), and one of the prefixes should be utilized. In the situation, if the molecule is an alkane, the branched group must be on the carbon, which is having the lowermost probable figure. The branched groups must be recorded prior to the name of the key chain in alphabetic order; di/tri/tetra should be overlooked. In case of the alkyl halides, the halogen atom is treated in much the similar method as that of the branched groups. Offer the halogen atom with a figure to display its location on the carbon chain. In case there is more than one halogen atom the figures should be recorded, and also, a prefix should be used. The halogen atoms must be registered prior to the name of the main chain in an arranged order. Also, if there are no halogen atoms founded in the long chain, then this phase can be overlooked. Join the elements of the name into an only word in the following order: branched groups/ halogen atoms in alphabetic order, the prefixes are overlooked. The prefix of the key chain name ending in accordance with the functional group and its location on the lengthiest carbon chain.

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Alkyl halides (also known as haloalkanes) are compounds in which one or more hydrogen atoms in an alkane have been replaced by halogen atoms (fluorine, chlorine, bromine or iodine).

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REVIEW QUESTIONS 1. 2. 3. 4. 5. 6. 7.

8. 9. 10.

What do you understand by the term of nomenclature? Explain the concept of the nomenclature used by the International Union of Pure and Applied Chemistry. Explain the basic steps for the nomenclature of the Organic Molecules. Explain the methods used for naming the unsaturated organic compounds. What is the difference between the naming a Carboxylic Acid and an Ester? How did the International Union of Pure and Applied Chemistry formulate the nomenclature of the organic molecules? In which year did the International Union of Pure and Applied Chemistry take over from its predecessor organization to initiate the nomenclature of the Organic Compounds? Which were the first five countries that begun the Union for the Nomenclature of the Organic Molecules? What are the different steps for properly naming the Organic molecules? How is the formation of the nomenclature of the alkyl halides different from forming the nomenclature of the other groups of Organic Molecules?

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REFERENCES 1.

2.

3.

4.

5. 6.

7.

8.

9.

Ashenhurst, J., (2014). Table of Functional Group Priorities for Nomenclature – Master Organic Chemistry. [online] Master organic chemistry. Available at: https://www.masterorganicchemistry. com/2011/02/14/table-of-functional-group-priorities-fornomenclature/ (Accessed on 15 June 2019). Ashenhurst, J., (2019). Organic Chemistry IUPAC Nomenclature Demystified With A Simple Puzzle Piece Approach – Master Organic Chemistry. [online] Master organic chemistry. Available at: https://www.masterorganicchemistry.com/2014/10/21/organicchemistry-iupac-nomenclature-demystified-with-a-simple-puzzlepiece-approach/ (Accessed on 15 June 2019). Chem.ucalgary.ca. (2019). Basic IUPAC Organic Nomenclature. [online] Available at: http://www.chem.ucalgary.ca/courses/351/ WebContent/orgnom/index.html (Accessed on 15 June 2019). IUPAC | International Union of Pure and Applied Chemistry. (2019). Our History – IUPAC | International Union of Pure and Applied Chemistry. [online] Available at: https://iupac.org/who-we-are/ourhistory/ (Accessed on 15 June 2019). IUPAC (2019). IUPAC | History. [online] Available at: https://www. iupac2019.org/iupac-history (Accessed on 15 June 2019). Kpu.ca. (2019). Chemistry 1110 – Organic Chemistry IUPAC Nomenclature. [online] Available at: https://www.kpu.ca/sites/ default/files/downloads/1110OrgNomen.pdf (Accessed on 15 June 2019). (2018). Naming Organic Compounds: Rules & Practice Chapter 15/Lesson 6 Transcript. [online] Study.com. Available at: https:// study.com/academy/lesson/naming-organic-compounds-rulespractice.html (Accessed on 15 June 2019). Siyavula.com. (2019). Iupac Naming and Formulae | Organic Molecules | Siyavula. [online] Available at: https://www.siyavula. com/read/science/grade-12/organic-molecules/04-organicmolecules-03 (Accessed on 15 June 2019). Toppr-guides, (2019). Nomenclature of Organic Compounds: Features, Drawbacks, Steps, Types. [online] Available at: https://www.toppr.com/guides/chemistry/organic-chemistry/ nomenclature-of-organic-compounds/ (Accessed on 15 June 2019).

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10. Utdallas.edu. (2019). Introduction to Organic Nomenclature. [online] Available at: https://www.utdallas.edu/~scortes/ochem/ OChem1_Lecture/Class_Materials/07_org_nomenclature1.pdf (Accessed on 15 June 2019). 11. Web.chemdoodle.com. (2019). IUPAC Naming | ChemDoodle Web Components. [online] Available at: https://web.chemdoodle.com/ demos/iupac-naming/ (Accessed on 15 June 2019).s

4 ACIDS AND BASES

LEARNING OBJECTIVES: In this chapter, you will learn about: • Acids, their properties, and uses. • Bases, their properties, and uses. • Neutralization. • Theories related to acids and bases.

KEY TERMS: • • • • • •

Acids Bases Hydroxides of alkali Inorganic substances Ionizable proton Litmus paper

• • • • •

Organic substances Properties of bases Types of acids Uses of acids Weak acids

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4.1. INTRODUCTION Any substance which tastes sour when mixed with water changes the color of some indicators like shows red color in blue litmus paper, reacts with base in order to form salts, reacts with metals in order to release hydrogen and promotes certain chemical reactions like acid catalysis are known as acids. Some examples of acids are: • Inorganic Substances: Nitric acid, Hydrochloric acid, Phosphoric acid, and Sulfuric acid. • Organic Substances: Sulfonic acid, phenol groups, and carboxylic acid. Any substance which when mixed with water offers slippery touch, tastes bitter, reacts with acids to form salts, changes the color of an indicator like turns red litmus blue and promotes certain analysis like base catalysis are known as bases. Some examples of bases are water solution of ammonia or its organic derivatives like amines and hydroxides of alkali and alkaline earth metals such as calcium, sodium, etc.

4.1.1. Identifying Acidity and Basicity •

Using pH Scale: The numeric value of the level of acidity or basicity of any substance can be estimated by using a pH scale where pH stands for ‘potential of hydrogen.’ In order to measure how acidic or basic any substance is pH scale is very helpful. In a pH scale, which can vary from 0 to 14, 0 is the most acidic, and 14 is the most basic (Figure 4.1).

Acids and Bases

Substance is matter which has a specific composition and specific properties.

Figure 4.1: pH scale with examples of every pH level. Source: https://commons.wikimedia.org/wiki/ File:PH_Scale.svg

•

Using Litmus Paper: Another method which can be used in order to check acidity and basicity of any substance is using litmus paper. There are mainly two types of litmus paper that are used – blue litmus paper and red litmus paper. When blue litmus paper comes in contact with an acid, it turns red and when red litmus paper comes in contact with a base it turns blue (Figure 4.2).

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Figure 4.2: Blue and red litmus paper. Source: https://en.wikipedia.org/wiki/File:Blue_ and_Red_litmus_papers.jpg

4.2. ACIDS

Hydroxide ions are molecular ions with the formula OH-, formed by the loss of a proton from a water molecule.

The word ‘acid’ has been originated from the Latin words ‘acidus’ or ‘acere,’ which means ‘sour’ and so one of the characteristics of acid is it tastes sour when mixed with water. When an acid is dissolved in water, there is a shift in the balance between hydrogen ions and hydroxide ions. This is because acids have a property of donating hydrogen ions. After the shift, there will be more hydrogen ions than hydroxide ions in the solution. This kind of solution will be referred to as acidic. An acid donates protons or hydrogen ions and accepts electrons. In order to yield cation or anion in water, the release of hydrogen atom bonds, which is contained by many of the acids. The acidity will be high and the pH of the

Acids and Bases

solution will be low, when the concentration of hydrogen ions produced by an acid is higher.

4.2.1. Types of Acids Strong Acids: The acids which completely segregates in water and thus forms H+ and an anion are known as strong acids. Strong acids include six acids. Other than these six acids, all are considered as weak acids. • HCl – Hydrochloric acid; • H2SO4 – Sulfuric acid; • HI – Hydroiodic acid; • HBr – Hydrobromic acid; • HNO3 – Nitric acid; and • HClO4 – Perchloric acid. An acid is referred to as strong acid, when its 100% dissociates in the solution of 0.1 M or less. In sulfuric acid, the dissociation occurs in first step only and thus it is considered as strong. H2SO4 → H+ + HSO4 2. Weak Acids: When an acid is partially segregated when dissolved in water in order to give H+ and the anion is the weak acid. Some examples of weak acid are Hydrofluoric acid – HF and acetic acid – CH3COOH. Some more substances can be included in weak base, and they are: • Organic acids which contain one or more carboxyl group – COOH where H is ionizable. • Transition metal cations. 1.

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• Ionization is the process by which an atom or a molecule acquires a negative or positive charge by gaining or losing electrons, often in conjunction with other chemical changes.

• •

Cations and anions that have an ionization proton, for example, HSO4 → H+ + SO42–. Those molecules are also included, which has an ionizable proton. Heavy metal cations that have a high charge.

4.2.2. General Properties of Acids • • • • •

The pH levels of acids are always less than 7; Acids are corrosive in nature; Acids are good conductors of electricity; Acids are the substances that are sour in taste; When acids are reacted with metals, they produce hydrogen gas.

4.2.3. Uses of Acids •

•

• •

The diluted solution of acetic acid is vinegar. Vinegar has various household applications. Generally, vinegar is used as a food preservative. In batteries, sulfuric acid is used. The batteries that are used in engines of automobiles contain this acid. In soft drinks, phosphoric acid is used. Sulfuric acid and nitric acid are used in industrial production of dyes, paints, fertilizers, and explosives.

Acids and Bases

•

In lemon juice and orange juice, citric acid is found majorly. It can also be used in food preservation.

4.3. BASES The word ‘base’ is generally attributed by French Chemist Guillaume – Francois Rouelle. As defined by Rouelle, a neutral salt is a product of the union of an acid with another substance that acted as a base for the salt. The substance, which accepts hydrogen ions, is referred to as the base. The balance between hydrogen ions and hydroxide ions shifts the opposite way when the base is dissolved in water. The result comes out with a solution with more hydroxide ions than hydrogen ions because of the fact that the base absorbs hydrogen ions. This kind of solution is termed as alkaline.

4.3.1. Types of Bases 1.

• • • •

Strong Base: The base that segregates 100% into cation and OH– (hydroxide ion) is referred to as strong bases. Strong bases get dissociated completely in the solution of 0.01 M or less. Strong bases include hydroxides of the Group I and Group II metals. Examples of strong bases include: LiOH – Lithium hydroxide; NaOH – Sodium hydroxide; RbOH – Rubidium hydroxide; Ca (OH)2 – Calcium hydroxide;

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• • • • 2. Aqueous solution is a solution in which the solvent is water. It is mostly shown in chemical equations by appending (aq) to the relevant chemical formula.

• •

KOH – Potassium hydroxide; Sr (OH)2 – Strontium hydroxide; CsOH – Cesium hydroxide; Ba (OH)2 – Barium hydroxide. Weak Bases: The bases that after dissociation does not provide OH– ions are weak bases. Weak base when getting in contact with an aqueous solution, they do not completely dissociate. In order to generate OH– ions, they have to react with water. Most weak bases are anions of weak acids. Some examples of weak bases include: NH3 – Ammonia; (CH3CH2)2NH – Diethylamine.

4.3.2. Properties of Bases • • •

•

•

Bases are bitter in taste. When a solution is basic, it will have a pH greater than 7. Molten bases or aqueous base solution conduct electricity when dissociated into ions. Strong bases and concentrated bases are corrosive in nature. They react strongly when gets in contact with acids or organic matter. A base turns red litmus paper blue, methyl turns it orange yellow, and phenolphthalein turns it pink. In the presence of a base, bromothymol blue remains blue.

Acids and Bases

4.3.3. Uses of Bases •

• •

•

• •

Calcium hydroxide is used to make dry mixes and hence these dry mixes that are used in decoration or painting. In laboratories, ammonium hydroxide is used as a very important component. Sodium hydroxide is used in the manufacturing soap and paper. And are also used in manufacturing of rayon. Ca (OH)2 is also named as calcium hydroxide and also slaked lime. This is also used in manufacturing of bleaching powder. By the use of slaked lime, excess acidity in the soils can be neutralized. Magnesium hydroxide is also known as milk of magnesia. It is commonly used as a laxative. It is used in reducing excess acidity produced in the human stomach and therefore also used as an antacid.

4.4. NEUTRALIZATION A reaction in which an acid and a base react with each other in order to form water and salt is known as neutralization reaction. It involves a combination of H+ ions and OH– ions in order to generate water. When neutralization of a strong acid and a strong base takes place then that has a pH equal to 7. When a strong acid is neutralized with a weak base then that will have a pH of less than

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Neutralization is a chemical reaction in which an acid and a base react quantitatively with each other.

7. When a strong base is neutralized with a weak acid then the pH is greater than 7. Salts are formed from equalized weights of acids and bases, then the solution is said to be neutralized. The amount of acid that is needed is the amount that will give one mole of protons that is H+ ions and the amount of base which is needed is the amount that would give one mole of OH– ions. This is because, with equivalent concentration of weights of acids and bases, salts can be formed from neutralization reactions. That means that N parts of acids always neutralize N parts of base. In a neutralization reaction, an acid and a base are placed together in order to neutralize the properties of acid and base and thus produces salt. In order to form water, the H+ cation of the acid is combined with the OH– anion. For example, when hydrochloric acid is reacted with sodium hydroxide, it produces sodium chloride which common salt and water. The reaction is given below: HCl + NaOH → H2O + NaCl

4.4.1. Strong Acid-Strong Base Neutralization As mentioned, consider the reaction between hydrochloric acid HCl and sodium hydroxide NaOH: HCl + NaOH → H2O + NaCl In terms of ions, the above reaction can be written as: H+ (aq) + Cl– (aq) + Na+ (aq) + OH– (aq) → Na+ (aq) + Cl– (aq) + H2O

Acids and Bases

The net ionic equation shows the H+ and OH− ions forming water in a strong acid, strong base reaction after the spectator ions are removed: H+ (aq) + OH– (aq) ⇋ H2O The pH level is neutral, when a strong acid and a strong base neutralize completely. Neutral pH means at the temperature of 25°C, the pH shown is 7. At this instant of neutralization, OH– and H3O+ are in equal amount and hence there will be no excess of NaOH. At the equivalence point, the solution is NaCl.

4.4.2. Weak Acid-Weak Base Neutralization Using a net ionic reaction which is mentioned below, a weak acid and a weak base reaction can be predicted. H+ (aq) + NH3 (aq) ⇋ NH4+ (aq) When both the acid and base in the reaction are completely consumed and neither of them is in excess then that instant is the equivalent point of a neutralization reaction.

4.4.3. Titration When one solution of a known concentration is slowly added to a known volume and unknown concentration of another solution until the reaction achieves neutralization, then this process is known as titration. It generally indicates color change. The solution which is added slowly is referred to as titrant (Figure 4.3).

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Figure 4.3: Titration using burette and beaker. Source: https://pixabay.com/vectors/beaker-liquidnumber-read-scale-1300637/ Titrant is the solution involved or used in a titration to determine the concentration of an unknown solution.

The titrant must satisfy the necessary requirements to be a primary or secondary standard. Titration is a technique which helps in determining the concentration of an unknown solution.

4.5. ARRHENIUS THEORY In 1884, a Swedish Chemist Svante Arrhenius proposed the Arrhenius theory of acids and base. He classified a particular number of compounds

Acids and Bases

into acids and bases which was based on the type of ions formed when it was added to water (Figure 4.4).

Figure 4.4: Swedish chemist Svante Arrhenius who gave Arrhenius theory. Sources: https://commons.wikimedia.org/wiki/ File:Svante_Arrhenius_01.jpg

When a compound is dissolved in an aqueous solution, certain ions release into the solution. The compound which increases the concentration of H+ ions that are present when added to water is known as Arrhenius acid. When these H+ ions get combine with water molecules they form the hydronium ion (H3O+).

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Arrhenius base is a substance that, when dissolved in an aqueous solution, increases the concentration of hydroxide, or OH-, ions in the solution.

The chemical reaction for the above will be given by: HCl (aq) → H+ (aq) + Cl– (aq) In the reaction mentioned above, hydrochloric acid that is HCl when dissolved in water, it gets completely segregated into hydrogen (H+) and chlorine (Cl–) ions and thus H+ ions are released into the solution. Chemical reaction involved in formation of the hydronium ion is: HCl (aq) + H2O → H3O+ (aq) + Cl– (aq) The Arrhenius theory includes acids such as HBr and HClO4 and bases such as NaOH and Mg (OH)2. For example, the reaction provided below gives complete dissociation of HBr gas into water and hence results in the generation of free H3O+ ions: HBr (g) + H2O → H3O+ (aq) + Br– (aq) A compound which increases the concentration OH– ions that are present, when the compound is added with water, is known as Arrhenius base. The chemical reaction provided below represents the dissociation: NaOH (aq) → Na+ (aq) + OH– (aq) This reaction represents the dissociation of sodium hydroxide into sodium and hydroxide ion that OH– ions when sodium hydroxide is dissolved in water.

4.5.1. Limitation of Arrhenius Theory •

Arrhenius theory was unable to explain the variation of ionic conductivity with concentration of the solution.

Acids and Bases

•

•

•

•

Arrhenius theory can provide a satisfactory explanation for the conduction of electricity by molten salts but failed to provide an explanation about what happens in water. When the degree of dissociation of strong electrolyte was obtained by using conduct-o-metric measurements, then the value obtained was different from colligative properties. Arrhenius theory assumes that the ionic form of electrolyte is only present in solution phase, but the X-ray diffraction study of crystalline alkali halides specifically proves that they exist in ionized form even in solid state. This theory was unable to provide any explanation about the variation of equivalent conductance with dilution for NaCl which exists in-full ionized form even in solid state.

4.6. BRONSTED-LOWRY THEORY Definitions of acids and bases were developed independently by Chemists Johannes Nicolaus Bronsted and Thomas Martin Lowry in 1923, based on the compound’s abilities to either donate or accept protons that are H+ ions. As per this theory, acids are referred to as proton donors whereas bases are defined as proton acceptors. Acid-base interactions are described in terms of proton transfer between chemical species by this Bronsted-Lowry theory. The

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Alkali halides are the family of inorganic compounds with the chemical formula MX, where M is an alkali metal and X is a halogen.

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Bronsted-Lowry acid can be described in terms of chemical structure that it can dissociate as H+. For accepting proton, Bronsted-Lowry base must have at least one lone pair of electrons to form a new bond with a proton (Figure 4.5).

Figure 4.5: 3D diagram of Bronsted and Lowry theory. Source: https://bn.wikipedia.org/wiki/%E0%A6%9 A%E0%A6%BF%E0%A6%A4%E0%A7%8D%E0 %A6%B0:Bronsted_lowry_3d_diagram.png

When a Bronsted-Lowry acid donates a proton, it forms its conjugate base. In the case of a Bronsted-Lowry base, conjugate acid is formed once it accepts a proton. The molecular formula for conjugate acid-base pair is same as the original acid-base pair, except those acids who have one more H+ compared to the conjugate base. As per this theory, water is amphoteric and is able to act as both BronstedLowry acids as well as Bronsted-Lowry base. For example, a basic salt, Na+F–, generates OH– ions by absorbing protons from water when dissolves in water and make HF: F– (aq) + H2O ⇌ HF (aq) + OH– The Bronsted acid when dissociated increases the concentration of hydrogen ions in the solution, H+. And when by taking protons from the solvent that is water, Bronsted bases dissociate to generate OH–.

Acids and Bases

• Acid dissociation: HA (aq) ⇌ A– (aq) + H+ (aq)

• Acid ionization constant: Ka = {[A–][H+]}/[HA] • Base dissociation: B (aq) + H2O (l) ⇌ HB+ (aq) + OH–(aq) • Base ionization constant: Kb = {[HB+] [OH–]}/[B]

4.6.1. Conjugate Base After the acid releases hydrogen ion H+, the particle which left is known as the conjugate base. Many times, conjugate bases have high pH values and hence, are negatively charged. There are many conjugate bases as well as acids. Whenever an acid loses a hydrogen ion, it produces its conjugate base. An acid and it’s conjugate base contain same formula except for the one minor difference that is acid has one more hydrogen ion than its conjugate base. For example, HCl is hydrochloric acid. When HCl is dissolved in water, being an acid, it produces hydrogen ions H+. The negatively charged chloride ion Cl– will be left after the acid releases its hydrogen ion. Then the chloride ion Cl– is the conjugate base of HCl (Table 4.1). HCl → H+ + Cl– Table 4.1: Some Acids and Their Conjugate Bases Acid

Conjugate Base

HF

F–

HBr

Br–

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NO3–

HC2H3O2

C2H3O2–

H2SO4

HSO4–

H2O

OH–

Source: https://study.com/academy/lesson/conjugate-base-definition-lesson-quiz.html

4.6.2. Amphoteric Substance

Neutral substance is a substance that shows no acid or base properties, has an equal number of hydrogen and hydroxyl ions and does not change the colour of litmuspaper.

The word ‘amphoteric’ is derived from a Greek prefix ‘amphi-,’ which means both. A substance that has the ability to act as both either as an acid or as a base is known as amphoteric substance. Acids can donate protons, and bases can accept protons. But amphoteric substance can do both that can accept protons and donate protons as well. So, it can be said that amphoteric substances can act as a double agent. It acts as either acid or base, and this depends on which substance it is reacting with. The best example of an amphoteric substance can be water. Water is generally considered as a neutral substance. If water comes in contact with a base like ammonia, then it will act as an acid and will donate proton that is a positively charged particle in the form of hydrogen ion to ammonia. But if the water is made to react with an acid like hydrochloric acid, then it will act as a base and will receive a proton in the form of a hydrogen ion from the acid like hydrochloric acid.

Acids and Bases

4.6.3. Limitations of Bronsted Lowry Theory •

Bronsted Lowry theory was unable to explain reactions between acidic oxides and basic oxides, which takes place even in the absence of the solvent like water. Acidic oxides like CO2, SO3, SO2, etc. and basic oxides like MgO, CaO, BaO, etc. For example, CaO + SO3 → CaSO4 No proton transfer is taking place in the above-given reaction. •

•

Substance which does not have any hydrogen, for example, BF, AlCl3, etc. and so they cannot give proton, but they are known to behave as acids. The definition for protons cannot be used in order to explain the reactions occurring in non-protonic solvents such as SO2, N2O4, COCl2, etc.

4.7. LEWIS THEORY In 1923, G. N. Lewis suggested one theory named as Lewis theory of acids and bases to get a different look at the reaction between H+ and OH– ions. According to Lewis Theory of acids and bases, acids act as electron pair acceptor and bases act as electron pair donor. This theory had nothing to do with the hydrogen atom. This theory only includes the transfer of electron pairs (Figure 4.6). Let’s take an example, NH3 (g) + BF3 (g) ⇌ H3NBF3 (g)

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Figure 4.6: Image shows the reaction between ammonia and boron trifluoride (BF3). Source: https://commons.wikimedia.org/wiki/ File:NH3-BF3-adduct-bond-lengthening-2D.png

The reaction mentioned above gives the chemical reaction between ammonia that is NH3 and boron trifluoride (BF3). Since no hydrogen atom transfer can be seen in this reaction so this is a Lewis acid-base reaction. NH3 has a lone pair of electrons, and since boron do not have enough electrons around it in order to form an octet, BF3 has an incomplete octet. Boron can hold two more electrons as it has only 6 electrons around it. BF3 will act as Lewis acid and accept the pair of electrons from nitrogen in NH3. After that, a bond will be formed between the nitrogen and the boron. A reaction where NH3 behaves as a base and donate a pair of electrons to BF3 which is acting as an acid and so BF3 is accepting those electrons in order to form a new compound H3NBF3. As per Lewis theory, acid can be defined as the species that has vacant orbital and therefore, it has the ability to accept a pair of electrons. Similarly, the base can be defined as the species that holds a lone pair of electrons and so act as an electron pair donor.

Acids and Bases

Lewis acid possesses electrophilic nature, whereas Lewis Bases are nucleophilic in nature. A Lewis acid accepts an electron pair from a Lewis base, which thus forms a coordinate covalent bond in the process. The compound thus formed is known as Lewis adduct. Examples of Lewis acids are Fe3+, Cu2+and BF3, and examples of Lewis bases are NH3, C2H4 (ethylene) and F–. This concept has a noteworthy advantage that many compounds can be defined as either acids or bases by it.

4.7.1. Limitations of the Lewis Theory • • •

•

Many of the Lewis acids do not have catalytic property. For the acid-base reaction concept, Lewis concept does not fit in. Some of the protonic acids like H2SO4, HCl, etc. are not regarded as acids as per this Lewis theory because they do not form coordination bonds with bases. Lewis theory does not explain the relative strengths of acids and bases.

Lewis acid is therefore any substance, such as the H+ ion, that can accept a pair of nonbonding electrons.

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REVIEW QUESTIONS 1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

Briefly explain the methods used for identifying acidity and basicity. What are acids? Give examples and uses. What are bases? Give examples and uses. Define neutralization. Name its types. What is titration? Write down the general chemical reaction acid dissociation and base dissociation. What is the general equation for acid ionization constant and base ionization constant? Give examples of some acids with their conjugate base. Define the amphoteric substance. Give its example. Name the theories of acids and bases.

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REFERENCES 1.

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(Nikki) Wyman, E., (2018). Conjugate Base: Definition & Overview – Video & Lesson Transcript | Study.com. [online] Study.com. Available at: https://study.com/academy/lesson/conjugate-basedefinition-lesson-quiz.html (Accessed on 15 June 2019). Byjus.com. (2019). Acids and Bases – Definition, Properties, and Uses with Examples. [online] Available at: https://byjus.com/ chemistry/acids-and-bases/ (Accessed on 15 June 2019). Chemistry Libre Texts, (2019). Neutralization. [online] Available at: https://chem.libretexts.org/Bookshelves/Physical_and_ Theoretical_Chemistry_Textbook_Maps/Supplemental_Modules_ (Physical_and_Theoretical_Chemistry)/Acids_and_Bases/ Acid%2F%2FBase_Reactions/Neutralization (Accessed on 15 June 2019). Chemistry Libre Texts, (2019). Overview of Acids and Bases. [online] Available at: https://chem.libretexts.org/Bookshelves/ Physical_and_Theoretical_Chemistry_Textbook_Maps/ Supplemental_Modules_(Physical_and_Theoretical_Chemistry)/ Acids_and_Bases/Acid/Overview_of_Acids_and_Bases (Accessed on 15 June 2019). Emedicalprep.com. (2010). Limitations of Bronsted, Lowry Concept, Chemistry Study Material @eMedicalprep.Com | eMedicalPrep. [online] Available at: https://www.emedicalprep. com/study-material/chemistry/ionic-equillibrium/limitations-ofbronsted-lowry-concept/ (Accessed on 15 June 2019). Garcia, N., (n.d.). Amphoteric: Definition, Properties & Examples. [online] Available at: https://study.com/academy/lesson/amphotericdefinition-properties-examples.html (Accessed on 15 June 2019). Helmenstine, A., (2019). What is a Base in Chemistry? [online] ThoughtCo. Available at: https://www.thoughtco.com/definitionof-base-604382 (Accessed on 15 June 2019). Khan Academy, (2019). Acids and Bases | Chemistry | Science |Khan Academy. [online] Available at: https://www.khanacademy. org/science/chemistry/acids-and-bases-topic/acids-and-bases/a/ bronsted-lowry-acid-base-theory?modal=1 (Accessed on 15 June 2019).

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Rogers, K., (2019). Acid | Definition & Examples. [online] Encyclopedia Britannica. Available at: https://www.britannica.com/ science/acid (Accessed on 15 June 2019). 10. Science Buddies, (2002). Acids, Bases, & the pH Scale. [online] Available at: https://www.sciencebuddies.org/science-fair-projects/ references/acids-bases-the-ph-scale#acidicorbasic (Accessed on 15 June 2019). 11. Tikkanen, A., (2019). Base | Chemical Compound. [online] Encyclopedia Britannica. Available at: https://www.britannica.com/ science/base-chemical-compound (Accessed on 15 June 2019). 9.

5 UNDERSTANDING ORGANIC REACTIONS LEARNING OBJECTIVES: In this chapter, you will learn about: • To understand the importance of the Organic Reactions in the Organic Chemistry. • To gain knowledge about the different kinds of the Organic Reactions that take place at the molecular level. • To understand the different rules that is to be followed while writing down an organic reaction. • To understand the role of the Organic Reactions in the Modern World and the impact of the Organic Reactions at the Molecular Level. • To gain knowledge about the role and importance of the catalyst and the effect of the catalyst on the Organic Reactions.

•

To understand the involvement of the organic reactions in the materials and different fields of industry in the world.

KEY TERMS: • • • • • •

Catalytic agent Chemical abstracts Electrophilic addition reactions Elimination reactions Hypervalence Nucleophilic reactions

• • • •

Organic reactions Polymerization Radical reactions Surfactants

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5.1. INTRODUCTION Organic reactions deliver a composing of a commanding instant of a preoperatively valuable organic reaction from the principal works. Experts absorbed in implementing such kinds of the reaction, or merely gaining knowledge about the structures, benefits, and drawbacks of the organic reaction, therefore have a valued supply to give direction to their research. Extracting services, like the Chemical Abstracts and Beilstein, enables for the expert to position all of the literature on the subject, but in the absence of offering perception into the value of any of the specific reference (Figure 5.1).

Figure 5.1: According to many researchers, the life and all the life-related functions were started on the planet earth after the initiation of organic reactions. Source: https://cdn.pixabay.com/photo/2015/03/18/17/46/organic-679701_960_720.jpg

Organic reactions comprise of the process of distillation of this avalanche of data into the information that is required to properly execute an organic reaction and are much more as compared to that of a surfeit of primary references.

Understanding Organic Reactions

This volume, specifically to offer engrossed, academic, and wide-ranging impressions of a specific data, that organic reactions takes on even bigger importance for the exercise of chemical investigation in the twenty-first century. The appropriateness of a specified reaction for an unidentified application is umpired in the best method from the informed vantage point that is offered by example and guiding principle provided by a writer who is having the knowledge as it is offered in the case of organic reactions.

5.2. TYPES OF ORGANIC REACTIONS 5.2.1. Free Radical Reactions Free radical substitution reactions are usually seen in the alkanes and alkyl groups. The process of Free radical addition throughout the process of polymerization of ethene and the reaction amongst the compounds of HBr and alkenes in the existence of the compounds of organic peroxides.

5.2.2. Electrophilic Addition Reactions The addition reactions that take place in the family of the organic compounds alkenes such as ethene and propene is one of the most common reactions.

Ethene is the most important organic chemical, by tonnage, that is manufactured. It is the building block for a vast range of chemicals from plastics to antifreeze solutions and solvents.

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5.2.3. Electrophilic Substitution Reactions The electrophilic substitution reactions occur in the organic molecules such as benzene and other simple arenes. In this kind of chemical reaction, an electrophile usually displaces a functional group present in a compound.

5.2.4. Nucleophilic Substitution Reactions Substitution reactions of halogenoalkanes like the alkyl halide of bromoethane explain the Nucleophilic Substitution Reaction.

5.2.5. Elimination Reactions Halogenoalkanes are compounds in which one or more hydrogen atoms in an alkane have been replaced by halogen atoms (fluorine, chlorine, bromine or iodine).

The creation of alkenes from halogenoalkanes is the examples of Elimination Reactions. For example, the formation of 2-bromopropane, and also the formation of halogenoalkanes by the process of the dehydration of alcohols.

5.2.6. Nucleophilic Addition Reactions Addition reactions of the organic compounds of the carbonyl family such as ethanal and propanone. These reactions are known as central to the organic chemistry. They actually aids in the formation of complex organic chemicals.

5.2.7. Nucleophilic Addition/Elimination Reactions The reactions of acyl chlorides (acid chlorides) with water, alcohols, ammonia, and amines.

Understanding Organic Reactions

5.3. PRINCIPAL METHODS OF FORMING THE ORGANIC REACTIONS The capability to write an organic reaction mechanism in the correct method is most important to achieve in organic chemistry lessons. Organic chemists make use of a method which is known as arrow pushing to show the flow or movement of electrons at the time of chemical reactions. Arrow pushing helps the organic chemists to keep the record of the way in which electrons and their linked atoms rearrange as bonds are formed and fragmented.

5.3.1. The Correct Use of Arrows to Indicate Electron Movement The initial vital regulation to keep in mind is the following, which includes: • First Rule: In this, arrows are used to specify the flow of the electrons. A regular arrow that is the doublesided arrowhead is used in order to specify the flow of two electrons. On the other hand, a line with a singlesided arrowhead which is also known as “fish hook arrow” at times is used to specify the flow of a single electron movement that is involved with fundamental reactions (Figure 5.2).

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Figure 5.2: The direction of arrow plays a very crucial role in displaying the direction of the reaction. Source: https://upload.wikimedia.org/wikipedia/ commons/thumb/5/52/SolGelTechnologyStages. svg/2000px-SolGelTechnologyStages.svg.png

In the case of the chemical reactions, electrons, as well as atoms, vary the locations as both π as well as σ bonds are created and fragmented. Arrow pushing is used to maintain the record of the flow of all electrons that are included with every single step of the complete conversion. This is because the electrons are positioned in orbitals that is neighboring atoms, when bonds are made or fragmented, the flow of electrons between orbitals is essentially gone together by the flow of the connected atoms, which give rise to the second rule of arrow pushing at the time of showing chemical reaction mechanisms.

5.3.2. Arrows Are Never Used to Indicate the Movement of Atoms Directly The arrows just display the flow of the atom in an indirect manner as an outcome of the flow

Understanding Organic Reactions

of the electron when covalent bonds are formed and fragmented. Arrow pushing is used to display the transmission of the proton numerous times.

5.3.3. Arrows Always Start at an Electron Source and End at an Electron Sink An electron cause is a link or a single pair of electrons. It might be a pi bond or a single pair on an atom of comparatively high electron density in a molecule or ion. Moreover, this could be a bond that might discontinue in the middle of a reaction. An electron sink is an atom on a molecule or ion that can receive or accepts a newly formed bond or single pair of electrons. This results in another kind of normally type of procedure that is usually seen in the Organic Reactions. It is quite evident that creating a new bond to the newly formed electron sink generally needs the concurrent infringement of one of the bonds existing at the sink atom in order to evade the situation of the overfilling of the valence orbitals of that particular atom or molecule or ion. In Organic Chemistry, this condition is generally called as hypervalence.

5.3.4. Breaking a Bond Will Happen to Evade Overfilling Valence (Hypervalence) on an Atom Helping as an Electron Sink In these kinds of cases, the electron causes for the arrow is the actually bond that is being shattered, and the electron sink is an atom that is capable enough to house the electrons as a lone

Electron density is the measure of the probability of an electron being present at a specific location.

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pair. This lone pair is usually an electronegative atom like an oxygen atom or a halogen. If an ion is formed, that ion is often alleviated by the method of resonance delocalization or some other methods that could be used for stabilizing reactions. This is also the same as the proton transfer reaction amongst acetic acid and hydroxide.

5.4. ROLE OF ORGANIC REACTIONS IN THE MODERN WORLD In its understanding, organic chemistry has its partners and opponents, all of them perform the necessary functions in cooperation, and this is done for the common good. Segregation and organizational classification of natural goods is another kind of such discipline. Accompanying in the newly formed molecules from the nature with unnaturally thought-provoking molecular structures and promising organic characteristics, the discovery of the Quinine, penicillin, and Taxol are three examples of the listed findings. Numerous organic approaches and the compounds that are being used as the catalysts are found by the synthetic organic scientists that are utilized to form every kind of these products. Most significantly, the organic reactions in the organic chemistry are used to form the new compounds and products, by this means increasing their claims and performance.

Understanding Organic Reactions

The organic reactions are of utmost, and specific importance in the application of the organic reactions is the chance to use the expectedness and exactness of organic chemistry to yield things that are well demarcated at the molecular level. Such knowledge and understanding of the organic chemistry will positively upsurge the predictivity of function as an importance of the construction of the compound that is grounded on the basis of the molecular structure.

5.5. IMPORTANCE OF CATALYST IN ORGANIC REACTIONS A catalytic agent is an element which can be added to a reaction to raise the rate of the reaction without getting consumed in the procedure. Catalytic agent characteristically increases the rate of the reaction by lessening the activation energy or altering the reaction mechanism. Enzymes are considered as the proteins that act as a catalytic agent in biological reactions. The catalytic agent frequently functions by decreasing the rate of energy of the transition state, therefore dropping the activation energy, and/or Altering the mechanism of the reaction. This also alters the nature (and energy) of the transition state. The catalytic agent is found at every place. There are several biological procedures, like the oxidation reaction of glucose, are profoundly relies on enzymes, proteins that act as a catalytic agent (Figure 5.3).

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Figure 5.3: The role of the catalyst is to alter the rate of the reaction and assist in the completion of the reaction. Source: https://upload.wikimedia.org/wikipedia/ commons/7/71/Catalysis-_Reaction_progress.png

Epoxyethane is a colourless gas at room temperature. The bonds in the ring are easily broken so epoxyethane is very reactive.

The other common categories of catalytic agent comprise of acid-based chemical agent and varied catalytic agent. A catalyst agent that rises the rate of reaction by changing the reaction mechanism. A true catalytic agent is redeveloped at some point of time in the process of the reaction mechanism, and need only be founded in sub-stoichiometric quantity. It comprises of the creation of epoxyethane from ethene, and numerous reactions from benzene chemistry – Friedel-Crafts reactions and halogenation. The process of catalysis and the detection and expansion of the innovative synthetic approaches are definitively allowing those who create particles. The inventions from these activities improve the devices of the art of synthesis.

Understanding Organic Reactions

They manifest themselves as unequal catalytic reactions and green chemical procedures for creating new organizational ideas. These kinds of findings feed into actions in the process of complete synthesis and industrial practices. This field of synthetic organic chemistry is accountable for several numbers of inventions that interpret into thoughtful assistances for investigation, technology, and the atmosphere. The rise in the power of synthetic organic chemistry all over the twentieth century was overburdened in order to allow and ease biology. Therefore, synthetic peptides and nucleosides were made eagerly available by the automatic approaches for all intentions and resolutions. The rare geologically active natural and planned particles were manufactured in great amounts, which empowered environmentalists to study about these particles in a more careful manner. These research or studies have further added to the consideration of human ecology and directed the invention of the medicine and its growth. These efforts done have strengthened in the past few decades, giving rise to fields of investigations at the interface of chemistry and biology below the umbrella of what came to be termed as bio-organic chemistry, and then it was termed as chemical biology, and also, besides the biochemistry (or organic chemistry) and medicinal chemistry, standards that had already been definitely recognized and progressed on the molecular level. Depending on the approaches and devices of synthetic organic chemistry, chemical biology, and the associated field’s main objective is to investigate the organic systems with small

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biological particles. The produced consideration of biology covers the method for the invention of the medicine and its growth, in that way decisively impacting the well-being of the human and health. The combination is also used in the organic reactions to form mixtures of the biomolecules like that of proteins or nucleic acids with minor organic molecules for the purpose of biomedical researches such as the molecule imaging, drug distribution, path clarification, target separation and authentication, and analytical and healing tenacities.

5.6. ORGANIC CHEMISTRY IS ALL AROUND US

Acrylic is a transparent plastic material with outstanding strength, stiffness, and optical clarity.

Polymers comprise of long chains and divisions of particles. The common polymers that the individual come across on day-to-day basis are biological particles. For instance, it comprises of nylon, acrylic, PVC, polycarbonate, cellulose, and polyethylene. Petrochemicals are the types of chemicals that are the outcomes of the crude oil or petroleum. Fractional distillation split up the raw substance into biological composites in accordance with their diverse scorching points. The individual come across substances that are made from petrochemicals on day to day basis. For instance, it comprises of petrol, plastic material, detergents, soaps, cleanser, dyes, food flavors, natural gas, and drugs.

Understanding Organic Reactions

Even though both chemicals are utilized for the purpose of washing, detergent, and soap are two diverse instances of organic chemistry. Soap is created by the saponification reaction, which reacts as a hydroxide with a biological particle, for instance, an animal fat to make glycerol and basic soap. Though soap is considered as an emulsifier, on the other hand, detergents tackle oily, slimy (biological) dirtying mostly because they are considered as surfactants. Whether the scent of a perfume arises from a flower head or a test center, the particles that the individual smell and adore are an instance of organic chemistry. The cosmetics business is a money-spinning segment in the field of organic chemistry. Chemists observe the alterations in the skin in retort to metabolic and ecological issues, frame products to address the issues that are related to the skin and help in improving the beauty, and examine how cosmetics cooperate with the skin and the other variety of products.

5.6.1. Importance of Organic Chemistry •

Medicine: It is the most important uses of organic compounds. However, not all but there exist many of the medications that are made of organic substances. For instance, antibiotics, anticancer medications, painkiller drugs, anti-depressant, general anesthetic, cardiac medicines, and many more (Figure 5.4).

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Figure 5.4: The understanding of the organic reaction is very necessary in the medicine industry. Source: https://c.pxhere.com/photos/cc/d9/organic_ chemistry_chemistry_science_laboratory_chemical-1086886.jpg!d

•

Food: Diet resources are completely comprised of carbon composites that is to say carbohydrates (CHO), proteins (NH2-CH-COOH), and fats (CH-COO-CH). The vitamins are also biological in nature. Grounded on the study of the body necessities at the time of prenatal period, sickness state, body capability, authorities recommend the usage of proteins, vitamins, and some other substituents. For instance, folic acid is suggested at the time of prenatal period to lessen the probabilities of anemia in mother. For the patient suffering from heat diseases, doctors or medics suggests for negligible consumption of fat food. And for those people who are interested in bodybuilding, the doctors suggest for high consumption of food which is rich in protein.

Understanding Organic Reactions

•

Textiles and Clothing: Cloth or fabric is comprised of materials like cotton, wool, silk, polyester, and many more. All these materials are biological in nature. This field of chemistry helps in the research of textiles material, their enhancement for robustness, dye, and washing procedure. • Cleansing Agents: In manufacturing industries and test center, the solvents which are biological in nature are extensively used for the purposes of washing. For instance, in the abstraction of medicines from plants, the substance which is full of fat from the fleshy tissue is detached by the use of the petroleum ether. At household and other places of existing, there is the use of compounds like phenols and other agents in order to wash the ground and walls. These cleaning agents’ function on the guideline of organic chemistry to get rid of the dirt and it also destroys the microorganisms. Therefore, the field of organic chemistry by its information of polarization, solubility, divider aspects makes use solvents for the improved usage. •

Sterilizing Agents: Majority of the disinfecting agents and antiseptics such as phenol, formaldehyde, and many more are termed as carbon compounds. Because of their characteristic such as solubility, pH they can destroy the microorganisms and even they can destroy the cells of the human body.

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Ethylene oxide is a colorless and flammable gas with a faintly sweet odor.

They destroy the microorganisms and the other bacteria by either liquefying the microbe cell wall or destroying the protein coatings. Their effectiveness is improved by creating small segments in the field of compound chemistry. In addition to these solvents, there also exist gases such as ethylene oxide which are used for purification of medications and other manufactured materials. • Analytic Materials: The chemical materials such as the medications, insect repellent, cosmetics are verified as a portion of quality control. This verification of the chemical material is performed by using several diverse kinds of titrations, chromatography methods, and the process of spectrophotometry. Here the substances such as acids, or bases, reducing, and oxidizing agents used are biological in nature. In addition to it, the endpoint pointers in the titration are also biological composites. • Valuables: It comprises of diamonds, graphite, and petroleum. Stimulatingly the carbon compounds are considered to be extremely valued, robust, and solidest all over the world. The carbon compounds such as Diamond as well as graphite are both pure carbon alone compound in the absence of any other material within (Figure 5.5).

Understanding Organic Reactions

Figure 5.5: Various variable materials comprise majorly of the organic compounds and are formed by the organic reactions. Source: https://live.staticflickr.com/7012/65354119 31_4dfe796009_b.jpg

In addition to it, diamond as well as graphite is both enormously utilized and affluent. Their characteristics are studied in the field of the organic chemistry. Petroleum is the other utmost treasured resources on the earth for fuels requirements all over the world. These petroleum products are further branch out for several numbers of uses. And petroleum is one of the features which affect the economy of the world.

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Explain the term organic reactions in context with the Organic Reactions. What are the major types of the Organic Reactions that have been observed? What is the difference between the Electrophilic substitution Reactions and the Nucleophilic substitution Reactions? Explain the significance of the electron sink in the organic reactions. What is the difference between the Elimination Reaction and the Nucleophilic Elimination Reaction at the functionality level? How does the absence of catalyst affect the rate of the Chemical Reaction and the products that are to be formed at the end of the Chemical Reaction? Define the role of the Organic Reactions in the products that are being produced in the modern world. Explain the role of the catalyst in the organic reactions and how they affect the formation of the products that are being linked to the Human Health. What is the role of the Organic Reactions in Medicine Industry? How does the involvement of the Organic reactions affect the production of the Sterilizing and Analytical Materials that are being used in daily life of the Human Being?

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Berger, D., (1999). Understanding organic reaction mechanisms (Jacobs, Adam). Journal of Chemical Education, [online] 76(2), p. 167. Available at: https://pubs.acs.org/doi/abs/10.1021/ed076p167.2 (Accessed on 15 June 2019). Bhowmick, S., (2016). 6 Tips to Master Organic Chemistry – Learn More Here! [online] Toppr bytes. Available at: https://www.toppr. com/bytes/master-organic-chemistry/ (Accessed on 15 June 2019). Chem.ucla.edu. (2019). Illustrated Glossary of Organic Chemistry – Catalyst. [online] Available at: http://www.chem.ucla.edu/~harding/ IGOC/C/catalyst.html (Accessed on 15 June 2019). Chemistry Libre Texts, (2019). Chapter 6: Understanding Organic Reactions. [online] Available at: https://chem.libretexts.org/ Bookshelves/Organic_Chemistry/Map%3A_Organic_Chemistry_ (Smith)/Chapter_06%3A_Understanding_Organic_Reactions (Accessed on 15 June 2019). Clark, J., (2002). More Examples of Catalysis in Organic Chemistry. [online] Chemguide.co.uk. Available at: https://www.chemguide. co.uk/physical/catalysis/organic.html (Accessed on 15 June 2019). Clark, J., (2012). Understanding Chemistry – Organic Mechanisms Menu. [online] Chemguide.co.uk. Available at: https://www. chemguide.co.uk/mechmenu.html (Accessed on 15 June 2019). Clark, J., (2019). 5. Examples of Other Catalytic Reactions in Organic Chemistry. [online] Chemistry LibreTexts. Available at: https://chem.libretexts.org/Bookshelves/Inorganic_Chemistry/ Supplemental_Modules_(Inorganic_Chemistry)/Catalysis/ Examples/Examples_of_Catalysis/5._Examples_of_Other_ Catalytic_Reactions_in_Organic_Chemistry (Accessed on 15 June 2019). DePuy, C., (2002). Understanding organic gas-phase anion molecule reactions. The Journal of Organic Chemistry, [online] 67(8), pp. 2393–2401. Available at: https://pubs.acs.org/doi/abs/10.1021/ jo0163593 (Accessed on 15 June 2019). Evans, P., Press, D., & Weinreb, S., (2019). Organic Reactions Volumes | ACS Division of Organic Chemistry. [online] ACS division of organic chemistry. Available at: https://www.organicdivision.org/

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organicreactions/ (Accessed on 15 June 2019). Iverson.cm.utexas.edu. (2019). [online] Available at: http:// iverson.cm.utexas.edu/courses/310N/Mechanism%20Sheets/ MechanismExplanation.pdf (Accessed on 15 June 2019). Khan Academy, (2019). Types of Catalysts. [online] Available at: https://www.khanacademy.org/science/chemistry/chem-kinetics/ arrhenius-equation/a/types-of-catalysts (Accessed on 15 June 2019). Master Organic Chemistry, (2019). Reaction Guide – Master Organic Chemistry. [online] Available at: https://www. masterorganicchemistry.com/reaction-guide/ (Accessed on 15 June 2019). Medlin, J., (2017). The catalysis of organic reactions. Organic Process Research and Development, [online] 21(3), pp. 277–278. Available at: https://pubs.acs.org/page/oprdfk/vi/catalysisorganicreactions (Accessed on 15 June 2019). Nicolaou, K., (2016). Catalyst: Synthetic organic chemistry as a force for good. Chem., [online] 1(3), pp. 331–334. Available at: https:// www.sciencedirect.com/science/article/pii/S2451929416301085. Organic Chemistry Help, (2016). Learning Reactions FAST! [online] Available at: https://www.studyorgo.com/blog/learning-reactionsfast/ (Accessed on 15 June 2019). Organic chemistry: Catalysts cooperate, (2010). Nature International Journal of Science, [online] 463, pp. 986–990. Available at: https:// www.nature.com/articles/4631003a (Accessed on 15 June 2019). Organic-chemistry.org. (2019). Organic Reactions. [online] Available at: https://www.organic-chemistry.org/reactions.htm (Accessed on 15 June 2019). Stradling, S., (1999). Understanding organic reaction mechanisms (Jacobs, Adam). Journal of Chemical Education, [online] 76(2), p. 167. Available at: https://pubs.acs.org/doi/abs/10.1021/ed076p167.1 (Accessed on 15 June 2019). Understanding organic reactions in water: From hydrophobic encounters to surfactant aggregates, (2001). Chemical Communications, [online] 1(18), pp. 1701–1708. Available at: https://pubs.rsc.org/en/content/articlelanding/2001/cc/b104537g/ unauth#!divAbstract (Accessed on 15 June 2019).

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20. Winter, A., (2019). Important Concepts of Organic Chemistry – Dummies. [online] dummies. Available at: https://www.dummies. com/education/science/chemistry/important-concepts-of-organicchemistry/ (Accessed on 15 June 2019). 21. Winter, A., (2019). Organic Chemistry Mechanisms. [online] Chemhelper.com. Available at: https://www.chemhelper.com/ mechanisms.html (Accessed on 15 June 2019).

6 STEREOCHEMISTRY

LEARNING OBJECTIVES: In this chapter, you will learn about: • Concept of stereochemistry. • A brief history of stereochemistry. • The fundamentals of stereochemistry. • The notion of chirality, stereoisomers, and its types. • R and S configuration system. • Fischer projections along with its interpretation and examples.

KEY TERMS: • • • • • •

Chiral carbon Chirality Diastereomers Enantiomers Fischer projection Optical activity

• • • •

Organic compounds R&S configuration Stereochemistry Stereoisomers

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6.1. INTRODUCTION Stereochemistry is defined as the study of three-dimensional arrangement of atoms and molecules together with the properties that follow from such kind of arrangement. Molecules having identical molecular structure but different spatial arrangement of the component parts are known as stereoisomers. Identical molecule structures are those that is of same kind, have same number and sequential arrangement of atoms. Organic as well as inorganic compounds show stereoisomerism. Stereochemistry is a field of chemistry, which is mainly concerned with the molecules as entities by means of shape and structure. This fact actually poses several questions regarding the legitimacy of science as neither structure nor shape is taken any longer in the form of solid scaffold on which to make scientific as well as philosophical as well as scientific arguments. The field of stereochemistry comprises the study of isomers along with the stereochemical reactions. The study of isomers majorly focuses on the static features of molecules and is greatly associated with the geometrical as well as topological arrangement of atoms in the molecules. For example, n-propanol, and isopropanol, and cis- and trans-butenes. In addition, they are concerned with the spatial character of atoms in molecules as demonstrated by enantiomers. Enantiomers are the mirror images of each other. According to Le Poidevin, enantiomorphy raises ethical issues related to the relationship between chemistry and the nature of space. The study of stereochemical reactions concentrates on the control of stereoselective reactions or stereo-specific reactions. According to the shape and structure of molecules, the trajectory of reacting molecules is measured to produce one isomer over another. This type of study is chiefly related to the dynamic aspects of molecules. Stereoisomers are defined as those molecules that have identical atomic connectivity but three-dimensional arrangement of atoms in space is not. This has extensive effects in biological systems. For

Stereochemistry

instance, most of the drugs are generally made of a single stereoisomer of a compound. While one of the stereoisomers may have positive impact on the body as it has the correct three-dimensional shape for binding of the protein receptor, another stereoisomer may not bind to the protein receptor or could even be very toxic. A key example of this is thalidomide drug. This drug was used during the phase of 1950s. It was mainly used to suppress the morning sickness. Unfortunately, the drug was recommended as a mixture of stereoisomers and though one of the stereoisomers vigorously worked to control morning sickness, the other stereoisomer caused several birth defects. At the end, the drug was banned from the market. Due to such kind of effects, a major deal of work done by the organic chemists is in formulating different methods of synthesizing compounds that are completely one stereoisomer. The capability of visualizing and modifying molecules in three dimensions is very important to study as well as understand the structural aspects that are the main reason behind stereoisomerism.

6.2. HISTORICAL PERSPECTIVE OF STEREOCHEMISTRY Viktor Meyer in year 1878 originated the term ‘Stereochemistry’ for the study of stereoisomers. In year 1848, Louis Pasteur had demonstrated that tartaric acid comprises optical activity and it is basically based on the molecular asymmetry.

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Stereoisomerism is a form of isomerism in which molecules have the same molecular formula and sequence of bonded atoms (constitution), but differ in the three-dimensional orientations of their atoms in space.

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In 1874, Jacobus H. van’t Hoff and JosephAchille Le Bel had individually clarified how a molecule, which has a carbon atom bonded to four different groups, has two mirror-image forms. Stereochemistry in general deals with the study of stereoisomers along with their asymmetric synthesis. The history of stereochemistry along with the traits of modeling practice, which developed at the time of its evolution, is directly related to each other. Not like most of the concepts and chemical theories that can be considered as empirical generalizations of the chemical process, those of the stereochemistry require the type of mathematical abstraction that van ‘t Hoff described on for his theory of the tetrahedral carbon atom. The concept of a bond, which is rigid and not able to change the directions, could not be obtained by inductive inference from the chemical experience. Furthermore, an exact understanding of the association between the physical shape and chemical structure of the molecule had not been recognized before this day. The distance between the empirical knowledge and understanding of compounds and the idea of stereoisomerism was much beyond the imagination. In the year 1848, Pasteur demonstrated the paratartrate salt of sodium ammonium paratartrate consists of an identical number of left-handed and right-handed crystals by optical resolution technique. He further tested each and every crystal of sodium ammonium paratartrate for its impact on the polarized light. What he found was

Stereochemistry

the optical inactivity of paratartrate could be endorsed to the equal number of left-handed and right-handed molecules. Each of these molecules canceled the effect of the others. Pasteur was the first person to show a different kind of relationship between optical activity, asymmetry, and crystalline form at the molecular level. However, the latent origin of asymmetry was not followed in context to the structure of the molecule. It was left for others to further explain. In the year 1869, Johannes Wislicenus recommended that the main cause of optical isomerism could lie in the difference in the spatial arrangement of atoms. At that time, he was occupied in the categorization of isomeric lactic acids. However, he was influenced that some kind of physical cause was required to demonstrate the difference observed in the optical rotation of α-lactic acid, but Johannes Wislicenus could not make any actual claims regarding it. It is valuable to note that, he could draw the structures of α- and β-lactic acid by using Crum Brown’s formula which is an episode recommending how tough it was to control the epistemological hurdle between the physical shape and the chemical structure. This may be attributed to the understanding of 19th century of the structural formula. It was considered as a symbolic representation that shows the theoretical concepts of the chemical combination inferred by valence. The structural formula being a conventional and symbolic image had no dimensionality at all. It was Jacobus Henricus van ‘t Hoff who

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provided the physical reality to the structural formula. He transformed it into iconic from symbolic. During the period of explaining lactic acid isomerism, Jacobus Henricus van ‘t Hoff tested specific arrangements of atoms by trial and error method. He compared the number of probable hypothetical isomers with the number of known isomers. In year 1874, he came up with the notion that the reason behind optical activity in a compound could be accredited to the existence of at least one asymmetric carbon atom in the structure of that compound. By supposing the tetrahedral arrangement of the valences in carbon atoms, the optical activity of the molecules could be concluded from the structural formulas. According to van’t Hoff, the tetrahedron was graphic and accurate representation of the valence arrangement around the carbon atom. In this context, it put up in the marked difference to the tetrahedron that Le Bel projected as the molecular type. Le Bel illustrated on the French tradition of crystallography, and on track from Pasteur’s discovery that optical activity was a kind of asymmetry indicator at the molecular level. As a result, though the two models are alike in appearance, they were different in their modal structure. As compared with Le Bel’s, the model given by van’t Hoff was much easier to use at a large scale. Huge research programs were organized to test the hypothesis related to the asymmetric carbon atoms in directing the stereoisomerism of saturated as well as unsaturated compounds.

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However, it should be noticed that, model given by Le Bel appeared equally favorable in year 1874 when a quite low number of optically active compounds was recognized. Neither van’t Hoff’s nor Le Bel’s model was of true-or-false character in an accurate sense, as they were not predictable outcomes derived from the chemical experiences.

6.3. FUNDAMENTALS OF STEREOCHEMISTRY Presuming that all of the reactants are present, inorganic reactions are mainly administered by the temperature. Temperature is critical to determine whether a specific reaction will take place or not. In the case of biological reactions, the shape and structure of the molecules becomes the crucial factor, however. Little amount of changes in the structure or alignment of the molecules can govern whether or not a reaction will take place. Actually, one of the significant roles of enzymes in the field of biochemistry is to decrease the requirements for temperature in chemical reactions. Assuming that accurate and sufficient enzymes are present in the reaction mixture, biological temperatures are generally enough to permit the reaction to proceed. Due to this reason, the stereochemistry of molecules is regarded as the controlling factor in organic and biological reactions along with the shape and alignment of the reactants. The molecular geometry around any kind of atom depends on the quantity of bonds to some other atoms as well as the presence or absence

Stereochemistry is a subdiscipline of chemistry, involves the study of the relative spatial arrangement of atoms that form the structure of molecules and their manipulation.

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of lone pairs of electrons linked with the atom. The chemical formula of a specific molecule is a simple representation of the arrangement of atoms in a molecule. It does not represent the three-dimensional structure of the molecule. Usually, it is on the reader to transform the chemical formula of any compound into its geometric arrangement. For instance, the chemical formula for methane is CH4. This formula shows that a central carbon atom is bonded to four hydrogen atoms. To transform this formula into threedimensional molecular arrangement, a person should know that when a carbon atom comprises four single bonds to four atoms, every bond point toward a distinct corner of the tetrahedron. Another way of visualizing a carbon atom having four single bonds is to regard the central carbon atom at the center of pyramid in threedimensional structure. A hydrogen atom is located at each point in the pyramid. The threedimensional arrangement of each carbon atom comprising four single bonds is always the same and identical. The angle between any two bonds is 109.5° always.

6.4. CHIRALITY The word “chirality” is a Greek word, which refers to the property of “handedness.” For example, the left and right hands are mirror images of each other that cannot be superimposed on each other. Molecules that do not have a mirror plane as well as an inversion center can have non-superimposable mirror images. These molecules are known as chiral.

Stereochemistry

Usually, a chiral center is a tetrahedral carbon along with four different groups attached to it. Chiral carbons are referred as stereocenters, asymmetric centers or stereogenic centers. For example, 1-Bromo-1-chloroethane is a chiral molecule (Figure 6.1).

Figure 6.1: 1-Bromo-1-chloroethane. Source: https://www.molport.com/shop/ moleculelink/1-bromo-1-chloroethane/6111992

Stereocenter: the most common reason behind chirality in organic molecules is presence of a tetrahedral atom, commonly carbon, which is bonded to four different groups. A carbon bonded to four different groups is known as chiral center. All of the chiral centers are stereocenters, but not all stereocenters are chiral centers.

6.5. STEREOISOMERS Stereoisomers are defined as the chemicals having the same connections but different orientations. In general, there are mainly two categories of stereoisomers. These are enantiomers and diastereomers.

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Chiral molecule is a molecule that is not superimposable on its mirror image.

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•

•

An enantiomer is a type of stereoisomer which is a non-superimposable mirror image of each other. A diastereomer is a type of stereoisomer having two or more stereocenters, and the isomers are not mirror images of each other.

6.5.1. Enantiomers For two molecules to be enantiomers, each of the stereocenter is required to be in the opposite alignment of each other. The designation to these stereocenters can be R or S. in a molecule which comprises three stereocenters with all of them in R designation, and then the enantiomer will require comprising all of the stereocenters in the S designation. For instance, if a molecule ‘A’ comprises two stereocenters, the first one in the R alignment while second in S alignment, then the enantiomer will require to have the first stereocenter in the S alignment and the second one in R alignment. Each stereocenter requires being in the opposite direction. Based on the R and S orientation of the last stereocenter, the sugar molecules are named. If the last stereocenter comprise the OH group on the right side in Fischer projection, or in the R alignment, then the whole molecule is categorized as D sugar. On the other hand, if it is on the left side, then the molecule is categorized as an L sugar. For instance, there are mainly two forms of glucose as D-glucose and L-glucose. In the nature, L-glucose is not available. Though both

Stereochemistry

of them are glucose molecules as it is not only that the last stereocenter that has been converted around. Every stereocenter is on the opposite side, which makes them enantiomers of each other (Figure 6.2).

Figure 6.2: Orientation of D-glucose and L-glucose. Source: https://www.quora.com/What-are-the-structures-of-L-+-and-D-+-glucose

6.5.2. Diastereomers Diastereomers are defined as the kind of stereoisomers that are not mirror images of each other as well as non-superimposable on one another. Stereoisomers having two or more than two stereocenters are diastereomers. Sometimes, it is quite tough to determine if the two molecules are diastereomers. For example, consider the molecules given in Figure 6.3. These molecules are not mirror images of each other. In addition to that, these molecules are non-superimposable as one of these molecules is rotated around 180°, the stereochemistry is different at one carbon and the same at another carbon. Thus, these molecules are known as diastereomers.

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Figure 6.3: Orientation of D-glucose and D-altrose. Source: https://commons.wikimedia.org/wiki/ File:Diastereomers-Glucose_Altrose.png

6.5.3. Meso Compounds

Superimposable is the ability for an object to be placed over another object, usually in such a way that both will be visible.

A meso compound is known as a molecule having multiple numbers of stereocenters that are superimposable on its mirror image. These specific features lead to particular qualities that meso compounds do not really share with most of other stereoisomers. One of such qualities is the internal mirror plane. All of the meso compounds comprise something known as an internal mirror plane. This internal mirror plane is a line of symmetry that cuts the molecule in half. Each of the half molecules is a mirror image of the other half. A meso compound cannot have an enantiomer, as it is achiral. When a molecule is observed to be superimposable on its mirror image, then the molecule and mirror image of this molecule are almost identical. Given below is an example of a meso compound and nonmeso compound (Figure 6.4).

Stereochemistry

Figure 6.4. A meso compound and a regular chiral compound. Source: https://socratic.org/questions/how-do-youcalculate-how-many-stereoisomers-a-compoundhas

6.6. ABSOLUTE CONFIGURATION AND THE (R) AND (S) SYSTEM 6.6.1. The Cahn-Ingold-Prelog (CIP) Rules of Priority To clearly name the enantiomers of a compound, their names must consist of the ‘handedness ‘of the molecule. The letters ‘R’ and ‘S’ are decided by applying the rules of the Cahn-Ingold-Prelog (CIP). In addition, the optical activity can be represented in the name of the molecules but should be empirically derived. There are some biochemical conventions for amino acids and carbohydrates. The method of allocating the handedness of molecules was initially originated by three chemists named as R. S. Cahn, C. Ingold, and V. Prelog and, as such, is often called the CIP rules.

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Enantiomer is one of the two molecules that are mirror images of each other and are nonsuperposable.

There are two other ways of experimentally defining the absolute configuration of an enantiomer in addition to the CIP system: • X-ray diffraction analysis: There is no connection between the sign of rotation as well as the structure of a particular enantiomer; and • Chemical connection with a molecule whose structure has previously been determined through X-ray diffraction. Although, it is valuable to concentrate on the R/S system in case of non-laboratory purposes. The sign of optical rotation, which is different for the two enantiomers of a chiral molecule at an identical temperature cannot be utilized, determine the absolute orientation of an enantiomer. The main reason behind this is, the sign of optical rotation for a specific enantiomer may modify when the temperature changes. The CIP rules of priority are mainly dependent on the atomic numbers of the atoms. For chirality, the atoms of interest are those atoms that are bonded to the chiral carbon. • The atom having higher atomic number has higher priority. For example, I > Br > Cl > S > P > F > O > N > C > H. • While comparing isotopes, the atom having the higher mass number has higher priority. For example, 18O > 16 O or 15N > 14N or 13C > 12C or T (3H) > D (2H) > H. • When there is a tie in two of the above points, create relative priority by continuing with the next atom(s)

Stereochemistry

present along the chain until the first variance is observed. Multiple bonds are dealt as if each of the bonds in a multiple bond is bonded to any exclusive atom. For instance, the ethenyl group (CH2=CH) has higher priority as compared to the ethyl group (CH3CH2). The priority of ethenyl carbon is two bonds with carbon atoms and one bond with a hydrogen atom as compared to ethyl carbon that comprise only one bond with a carbon atom and two bonds with two hydrogen atoms (Figure 6.5).

Figure 6.5: Relative priority as per the Cahn-IngoldPrelog (CIP) rules. Source: https://commons.wikimedia.org/wiki/ File:CIP_priority_diagram.png

6.6.2. Stereocenters Are Labeled R or S The left hand and right-hand nomenclature are applied to name the enantiomers of a chiral compound. The stereocenters are designated as R or S. Consider the diagram given below. A curved arrow is drawn counter-clockwise (c-cw) from the highest priority substituent (1) to the lowest priority substituent (4) in the S-configuration.

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Chiral center is an atom that has four different groups bonded to it in such a manner that it has a nonsuperimposable mirror image.

The left movement when leaving the position of 12 o’ clock can identify the counterclockwise direction. Now, consider the next diagram on the right where a curved arrow is drawn clockwise (cw) from the highest priority substituent (1) to the lowest priority substituent (4) in the R configuration. The R and S are added to the name of the enantiomer as a prefix. A locator number is needed if there is more than one chiral center (Figure 6.6).

Figure 6.6: The stereocenters are labeled as R or S. Source: https://chem.libretexts.org/Bookshelves/ Organic_Chemistry/Supplemental_Modules_ ( O rg a n i c _ C h e m i s t r y ) / C h i r a l i t y / A b s o l u t e _ Configurationpercentage2C_R-S_Sequence_Rules

6.7. FISCHER PROJECTIONS The objects present in the surrounding are in a three-dimensional state. Generally, people try to represent them on paper that only permits for a two-dimensional representation. This conversion from a three-dimensional state to a two-dimensional state results in some kind of disfiguration of the object. Exactly same things

Stereochemistry

tales place with the chemical compounds also. The molecules are in three-dimensional state but to represent them on a sheet of paper, a unique approach is needed to represent them in a two-dimensional state. There are various methods for this, one of which is Fischer Projections. Fischer projections use vertical and horizontal lines to represent the three-dimensional state. The vertical lines demonstrate the attachments directing out to the back of paper and horizontal lines demonstrate the attachments directing in front of the paper. The intersection demonstrates the central carbon.

6.7.1. Fischer Projection Examples Normally, Fischer projections are used for the representation of amino acids and monosaccharides. They are very useful in the representation of monosaccharides as they entail a great number of stereocenters or carbons with four different bonds. Different kinds of monosaccharides are identical; the difference is just about the stereocenter orientation. The Fischer Projection permits to rapidly observe the orientation of each monosaccharide.

6.7.2. Fischer Projection Interpretation For drawing the Fischer projections, first start by converting the three-dimensional conformation of the molecules into dashes and wedges. Then the dashes and wedges becomes the horizontal line while other lines become the vertical ones.

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Galactose is a simple sugar, which belongs to simple carbohydrates. Galactose is composed of the same elements as glucose, but has a different arrangement of atoms.

The second step is the toughest part to visualize. In Fischer projections, the molecules are being rotated clockwise around the carboncarbon bond. The actual position or order of any bonds is not being changed in the process. These are just being observed from distinct angles. On comparing glucose and galactose, it is observed that the key difference is only at one specific stereocenter. Once the right and left horizontal line is converted, it can be observed that the main difference between glucose and galactose is that: in glucose, the OH group is present in the front while the hydrogen is present in the back. On the other hand, in galactose, the OH group is present in the back and the hydrogen is in front. No matter how these molecules are rotated, the attachments will remain in the same order and hence there are two distinct molecules (Figure 6.7).

Figure 6.7: Comparison of glucose and galactose. Source: http://www.nutrientsreview.com/carbs/ monosaccharides-galactose.html

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REVIEW QUESTIONS 1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

Define stereochemistry with example. Discuss the contribution of van’t Hoff in the field of stereochemistry. State the definition of stereocenter. What do you mean by chirality? Give some examples. Explain different kinds of stereoisomers. What is the difference between enantiomers and diastereomers? Illustrate the Cahn-Ingold-Prelog rules of Priority. Explain the R and S configuration system in detail. What are Fischer projections? State one example also. How Fischer projections are interpreted?

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REFERENCES Chapter 4 Stereochemistry and Chirality, (n.d.). [eBook] p. 41. Available at: http://ww2.chemistry.gatech.edu/class/2311/marder/ Stereochem.pdf (Accessed on 15 June 2019). 2. Chemeddl.org. (n.d.). Definitions: Diastereomers. [online] Available at: http://www.chemeddl.org/resources/stereochem/definitions17. htm (Accessed on 15 June 2019). 3. Chemistry LibreTexts, (2019). 6.3: Absolute Configuration and the (R) and (S) System. [online] Available at: https://chem.libretexts. org/Courses/Sacramento_City_College/SCC%3A_Chem_420_-_ Organic_Chemistry_I/Text/06%3A_Stereochemistry_at_ Tetrahedral_Centers/6.03%3A_Absolute_Configuration_and_the_ (R)_and_(S)_System (Accessed on 15 June 2019). 4. Encyclopedia Britannica, (2009). Stereochemistry. [online] Available at: https://www.britannica.com/science/stereochemistry (Accessed on 15 June 2019). 5. Foist, L., (2019). What is the Difference Between Enantiomers & Diastereomers? – Video & Lesson Transcript | Study.com. [online] Study.com. Available at: https://study.com/academy/lesson/what-isthe-difference-between-enantiomers-diastereomers.html (Accessed on 15 June 2019). 6. Hirofumi, O., (2015). Philosophical foundations of stereochemistry. [eBook] International Journal for Philosophy of Chemistry, p. 18. Available at: http://www.hyle.org/journal/issues/21-1/ochiai.pdf (Accessed on 15 June 2019). 7. Meso Compounds, (2019). [eBook] p. 4. Available at: http://www. chem.ucla.edu/~harding/ec_tutorials/tutorial17.pdf (Accessed on 15 June 2019). 8. Science.jrank.org. (n.d.). Stereochemistry – Fundamentals of Stereochemistry. [online] Available at: https://science.jrank.org/ pages/6511/Stereochemistry-Fundamentals-stereochemistry.html (Accessed on 15 June 2019). 9. Stereochemistry, (n.d.). [eBook] p. 14. Available at: https:// www.ccdc.cam.ac.uk/support-and-resources/ccdcresources/ stereochemistry_teaching_subset.pdf (Accessed on 15 June 2019). 10. Stereochemistry, (n.d.). Access Science. [online] Available at: 1.

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https://www.accessscience.com/content/654900 (Accessed on 15 June 2019). 11. Stereoisomerism and Chirality, (n.d.). [eBook] p. 23. Available at: http://colapret.cm.utexas.edu/courses/Chap3.pdf (Accessed on 15 June 2019). 12. Study.com. (n.d.). Fischer Projections in Organic Chemistry: Definition, Examples & Interpretation | Study.com. [online] Available at: https://study.com/academy/lesson/fischer-projectionsin-organic-chemistry-definition-examples-interpretation.html (Accessed on 15 June 2019).

7 AMINO ACIDS AND PROTEINS

LEARNING OBJECTIVES: In this chapter, you will learn about: • Significance of amino acids and proteins. • Classification of the amino acids and proteins. • Structure of the amino acids and proteins. • Properties of the amino acids and proteins. • Types of amino acids. • Role of amino acids in the structure of proteins. • Difference between a protein and an amino acid. • Essential amino acids. KEY TERMS: • • • • • •

Alanine Amino acids Cysteine Glycine Isoleucine Leucine

• • • • •

Proline Proteins Threonine Tyrosine Valine

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7.1. INTRODUCTION Proteins are complicated and large-sized molecules that are very important with respect to the normal working of the human body. Proteins are very important for the regulation, function, and structure of the tissues and organs of the human body. Proteins are constructed with the help of several numbers of smaller units which is called as amino acids. Amino acids are linked or connected to one another with the help of bonds which is known as peptide bonds, these peptide bonds are forming a long chain. For example, it could be said that protein as a string of beads where each bead is an amino acid. Proteins are the polymers of amino acids, which is connected with the help of amide groups known as peptide bonds. An amino acid can be thought of as having two elements which is a ‘backbone,’ or ‘main chain,’ derived from a group of ammonia, an ‘alpha-carbon,’ and a carboxylate, and a variable ‘side chain’ which is linked to the alphacarbon (Figure 7.1).

Figure 7.1: General structure of amino acid. Source: https://upload.wikimedia.org/wikipedia/commons/4/46/Amino_ acid_general_structure.png

There are 20 several side chains, which is occurs naturally inside the amino acids, and it is the distinctiveness of the side chain that determines the distinctiveness of the amino acid. For instance, if the side chain is a -CH3 group, the amino acid is alanine, and if the side chain is a -CH2OH group, the amino acid is serine.

Amino Acids and Proteins

Several types of amino acid side chains are consisting of a functional group (the side chain of serine, for instance, consist of a primary alcohol), on the other hand, similar to alanine, deficiency a functional group, and consist of only a simple alkane. Amino acids are very important, up till now basic unit of protein, and they are consisting of an amino group and a carboxylic group. Amino acids act as a widespread part in the genetic factor expression process, which consist of an adjustment of protein functions that make it more ease messenger RNA (mRNA) translation, according to the researcher named as Scot, in the year 2006. There are more than 700 kinds of amino acids that have been discovered in nature. Not quite all of them are α-amino acids. They have been found in: • Algae; • Bacteria; • Plants; • Fungi. Proteins are more complicated, organic compounds which is derived from several numbers of amino acids which are associated with each other with the help of peptide bonds and cross-linked between chains with the help of sulfhydryl bonds, hydrogen bonds, and van der Waals forces. There is a greater variety of chemical configuration in proteins as compared to any other group of biologically active complexes. The proteins in the several numbers of animal

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Alanine is an important source of energy for muscles and central nervous system, strengthens the immune system, helps in the metabolism of sugars and organic acids, and displays a cholesterol-reducing effect in animals.

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and plant cells discuss on these tissues their biological specificity (Figure 7.2).

Figure 7.2: General structure of alpha-amino acid. Source: https://upload.wikimedia.org/wikipedia/ commons/7/74/Alpha-amino-acid-general-2D.png

Proteins are the end products of the decoding process that starts with the information in cellular Deoxyribonucleic Acid (DNA). As workhorses of the cell, proteins which are derived from the structural and motor elements in the cell, and they aid in the form of catalysts for virtually every biochemical reaction that took place in living things. This incredible set or collection of purposes derives from a startlingly simple code that postulates an enormously varied set of structures. Proteins are very important nutrients which are found in any healthy diet. All type of proteins is made of building blocks which are known as called amino acids, but not all of the proteins in the diet are consisting of all the amino acids it necessitates. Nutritionists categorize the proteins as vital or nonessential and also contemplate some type of source of protein more high quality as compared to others. Amino acids are the molecules which are made of an amine group (NH2), a carboxylic acid group (R-C=O-OH) and a side-chain (more

Amino Acids and Proteins

commonly signified with a symbol R) which diverges among several types of amino acids. The main or most important component of an amino acid is oxygen, hydrogen, nitrogen, and carbon. They are more specifically are very crucial in the field of biochemistry, where the term commonly mentions to alpha-amino acids. Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form in a biologically functional way. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues. The series of amino acids in a protein is defined with the help of the series of a genetic factor, which is prearranged in the genetic code. More commonly, the genetic code postulates an amount of 20 standard amino acids. Never the less, in particular organisms, the genetic code can be consisting of selenocysteine, and in certain archaea in the form of pyrrolysine.

7.2. PROTEINS 7.2.1. Classification of Proteins There are several types of proteins, which are categorized as below: • Simple Proteins: During the course of the process of hydrolysis, they produce only the amino acids and occasional small of compounds carbohydrate.

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Selenocysteine is an unusual amino acid of proteins, the selenium analogue of cysteine, in which a selenium atom replaces sulphur.

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Some example is albumins, glutelin, globulins, protamine, histones, and albuminoids. • Conjugated Proteins: These are simplest form of the proteins which is linked with some non-protein material which are present in the body. Some examples are nucleoproteins, phosphoproteins, lactoproteins, glycoproteins, and hemoglobin. • Derived Proteins: These are proteins which are made from simple or conjugated proteins with the help of physical or chemical means. Some examples are denatured proteins and peptides. An amino acid is consisting of both a carboxylic group and an amino group. Amino acids that have an amino group linked directly to the alpha-carbon are denoted to as alpha amino acids. Specialists or professional categorize amino acids on the basis of a several numbers of features; consist of whether people can obtain them with the help of diet (Figure 7.3). Consequently, scientists identify three types of amino acid which are mentioned below: • Conditionally essential; • Essential; and • Nonessential.

Amino Acids and Proteins

Figure 7.3: Classification of the amino acid and proteins.

Never the less, the categorization as essential or nonessential does not actually imitate their significance as all 20 types of amino acids play an important factor for human health. Eight of these amino acids are very crucial (or indispensable) and cannot be produced by the body. They are listed below: • Leucine; • Threonine; • Lysine; • Isoleucine; • Phenylalanine; • Tryptophan; • Valine; and • Methionine. Histidine is an amino acid that is considered or characterized as semi-essential from the time of the human body does not always require it to appropriately function consequently nutritional sources of it are not always important as much. In the intervening time, conditionally essential amino acids are not commonly compulsory in

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Asparagine is a nonessential amino acid in humans, Asparagine is a beta-amido derivative of aspartic acid and plays an important role in the biosynthesis of glycoproteins and other proteins.

the diet of the human but do become very crucial under the particular conditions. In the conclusion, nonessential amino acids are made up with the help of the human body either from essential amino acids or from the normal protein breakdowns. Nonessential amino acids are consisting of: • Asparagine; • Cysteine; • Arginine; • Alanine; • Aspartic acid; • Glutamic acid; • Tyrosine; • Proline; • Glutamine; • Glycine; • Serine. An additional, the categorization of the amino acids depends on the side chain structure, and professional identify these five as: • Cysteine and Methionine (amino acids containing sulfur); • Leucine, Isoleucine, Glycine, Valine, and Alanine (aliphatic amino acids); • Phenylalanine, Tryptophan, Tyrosine, and Histidine (aromatic amino acids); • Asparagine, Serine, Threonine, and Glutamine (neutral amino acids); and • Glutamic acid and Aspartic acid (acidic); and Arginine and Lysine (basic).

Amino Acids and Proteins

One ultimate amino acid arrangement is characterized with the help of the side chain structure that splits the list of 20 amino acids into four divisions, in that, two of which are the major division and two that are the subdivisions. They are mentioned as follow: • Polar; • Basic and polar; • Acidic and polar; and • Non-polar. For instance, side chains which are having pure type of hydrocarbon alkyl or aromatic groups, which are well thought-out as non-polar, and these types of amino acids are consisting of phenylalanine, leucine, glycine, valine, alanine, tryptophan, proline, methionine, and isoleucine.

7.2.2. Structure of Amino Acids and Proteins The potential formation of the molecules of the protein is so complicated that several types of molecules of the protein can be created and are found in the biological materials with various physical aspects or features. Globular proteins are found in the blood and tissue fluids in amorphous globular form with very thin or nonexistent membranes. Collagenous proteins are bringing into the being in connective tissue, for example, skin or cell membranes. Fibrous proteins are found inside the hair, muscle, and connective tissue. Crystalline proteins are demonstrated with the help of the lens of the eye and alike tissues. Enzymes are proteins with particular chemical

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Tryptophan is an α-amino acid that is used in the biosynthesis of proteins. Tryptophan contains an α-amino group, an α-carboxylic acid group, and a side chain indole, making it a non-polar aromatic amino acid.

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functions and mediate most of the physiological processes of life.

7.2.3. Properties of Amino Acids and Proteins Proteins can also be branded in accordance of their chemical reactions. Most types of proteins are solvable in water, in alcohol, in weak base or in numerous concentrations of salt solutions. Proteins have the typical coiled construction which is strong-minded by the order of amino acids in the main polypeptide chain and the stereo shape of the radical groups being linked to the alpha carbon of each amino acid. Proteins are warmth labile showing numerous degrees of lability basically held responsible upon kind of protein, solution, and temperature outline. Proteins can be rescindable or permanent, denatured by boiler, by salt attentiveness, by cold, by ultrasonic stress or by elderly. Proteins undergo characteristic bonding with other proteins in the so-called plastering reaction and will combine with free aldehyde and hydroxy groups of carbohydrates to form Maillard type compounds.

7.3. THE 20 AMINO ACIDS AND THEIR ROLE IN PROTEIN STRUCTURES Each of the 20 most shared amino acids has its exact chemical features and its sole role in a protein construction and function. For instance, solely based on the tendency of the side chain

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to be in interaction with water, amino acids are then characterized as hydrophobic low tendency to be in relation with water, polar, and charged energetically favorable in relation with water. The emotional amino acids comprise two basic, lysine, and arginine which have positive charge, and two acidic, aspartate, and glutamate which have basically negative charge. Polar amino acids comprise serine and threonine which consists of a hydroxyl collection, asparagine, and glutamine which contain amide group. Histidine is also a polar residue, although its behavior depends on the polarity of its environment. It has two –NH group with a pKa value of around 6. When both groups are protonated, the side chain has a charge of +1. However, the pKa may be modulated by the environment inside the protein, and when raised the side chain may give away a proton, losing its positive charge and becoming neutral. By additional words, histidine may effortlessly stretch away and receive a proton, creation it particularly useful within enzyme active locations. The aromatic remains tyrosine and tryptophan and the non-aromatic methionine are often called amphipathic all because to their ability to have both polar and non-polar charm. These remains are often found close to the surface of proteins. The –OH group of tyrosine is talented to both give and accept a hydrogen bond. The lateral chains of histidine, tyrosine, phenylalanine, and tryptophan are also able to form weak hydrogen bonds of the types, OH-π and CH-O, by other arguments using electron clouds within their ring constructions.

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Methionine is an amino acid. Amino acids are the building blocks that our bodies use to make proteins. Methionine is found in meat, fish, and dairy products.

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The hydrophobic amino acids comprise alanine, valine, leucine, isoleucine, proline, phenylalanine, cysteine, and methionine. These remains contribute in van der Waals type of interactions. The arrangement above is based on the type of the amino acid side chain. Though, glycine, existence one of the common amino acids, does not have a side chain and for this reason, it is not straightforward to allocate it to one of the above classes. Usually, glycine is often found at the superficial of proteins, within loop- or coil deprived of clear secondary construction regions, if high suppleness to the polypeptide chain at these sites. This proposes that it is rather hydrophilic. Proline, on the other hand, is usually non-polar and is typically found suppressed confidential the protein, though likewise to glycine, it is frequently found in loop districts. In difference to glycine, proline delivers inflexibility to the polypeptide chain by impressive certain torsion angles on the section of the structure. • Glycine (G/Gly): Shares DNA and produces different amino acids. One of the three most significant glycogenic amino acids (Figure 7.4).

Figure 7.4: Structure of glycine. Source: https://aminoacidsguide.com/

Amino Acids and Proteins

•

Alanine (A/Ala): An essential source of the energy for muscle. One of the three most crucial glycogenic amino acids (Figure 7.5).

Figure 7.5: Structure of alanine. Source: https://aminoacidsguide.com/

•

Valine (V/Val): It plays a very crucial part in the development of the muscle (Figure 7.6).

Figure 7.6: Structure of valine. Source: https://aminoacidsguide.com/

•

Leucine (L/Leu): This is very important for skin, bone as well as tissue wound healing (Figure 7.7).

Figure 7.7: Structure of leucine. Source: https://aminoacidsguide.com/

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• Hemoglobin is the protein molecule in red blood cells that carries oxygen from the lungs to the body›s tissues and returns carbon dioxide from the tissues back to the lungs.

Isoleucine (I/Ile): This is very important factor for the synthesis of hemoglobin (Figure 7.8).

Figure 7.8: Structure of isoleucine. Source: https://aminoacidsguide.com/

•

Proline (P/Pro): This is a very important element of cartilage; it helps in joint health, tendons, and ligaments. Proline help to keep the heart muscle strong (Figure 7.9).

Figure 7.9: Structure of proline. Source: https://aminoacidsguide.com/

•

Phenylalanine (F/Phe): This is very helpful or profitable for healthy nervous system. It boosts memory and learning (Figure 7.10).

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Figure 7.10: Structure of phenylalanine. Source: https://aminoacidsguide.com/

•

Tyrosine (Y/Tyr): This is parent part of the dopamine, norepinephrine, and adrenaline. Tyrosine helps to increases the energy, enhances the mental clarity as well as concentration. Tyrosine can treat some depressions to an extent (Figure 7.11).

Figure 7.11: Structure of tyrosine. Source: https://aminoacidsguide.com/

•

Tryptophan (W/Trp): It is very crucial for the process of synthesis of neurotransmitter serotonin. Tryptophan is an effective sleep support, because of the conversion to serotonin. Tryptophan helps in decrease the anxiety and some sort of depression as well (Figure 7.12).

Cartilage is a resilient and smooth elastic tissue, a rubber-like padding that covers and protects the ends of long bones at the joints, and is a structural component of the rib cage, the ear, the nose, the bronchial tubes, the intervertebral discs, and many other body components.

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Figure 7.12: Structure of tryptophan. Source: https://aminoacidsguide.com/

•

Serine (S/Ser): This is one of the three most crucial glycogenic amino acids, the others being alanine and glycine (Figure 7.13).

Figure 7.13: Structure of serine. Source: https://aminoacidsguide.com/

• Collagen is the most abundant protein in your body. It is the major component of connective tissues that make up several body parts, including tendons, ligaments, skin and muscles.

Threonine (T/Thr): It is compulsory for the formation of collagen. Threonine is very helpful in preventing the fatty deposits in liver. Threonine also helps in the production of the antibodies (Figure 7.14).

Figure 7.14: Structure of threonine. Source: https://aminoacidsguide.com/

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•

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Cysteine (C/Cys): It is a protective against radiation, pollution as well as ultra-violet light. Detoxifier, necessary for growth and repair of skin (Figure 7.15).

Figure 7.15: Structure of cysteine. Source: https://aminoacidsguide.com/

•

Methionine (M/Met): This is an antioxidant. Methionine also helps in the breakdown of fats and also support in the decrement of muscle degeneration (Figure 7.16).

Figure 7.16: Structure of methionine. Source: https://aminoacidsguide.com/

•

Asparagine (N/Asn): This is one of the two main excitatory neurotransmitters (Figure 7.17).

Neurotransmitters are endogenous chemicals that enable neurotransmission. It is a type of chemical messenger which transmits signals across a chemical synapse, such as a neuromuscular junction, from one neuron (nerve cell) to another «target» neuron, muscle cell, or gland cell.

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Figure 7.17: Structure of asparagines. Source: https://aminoacidsguide.com/

•

Glutamine (Q/Gln): This is very important for helping to keep normal and stable levels of the blood sugar. Glutamine also aids in the muscle strength as well as endurance (Figure 7.18).

Figure 7.18: Structure of glutamine. Source: https://aminoacidsguide.com/

•

Lysine (K/Lys): It is an element of muscle protein which is needed in the synthesis of enzymes and hormones (Figure 7.19).

Figure 7.19: Structure of lysine. Source: https://aminoacidsguide.com/

Amino Acids and Proteins

•

Arginine (R/Arg): This is one of the two main excitatory neurotransmitters. Arginine can also elevate endurance and can reduce the fatigue (Figure 7.20).

Figure 7.20: Structure of arginine. Source: https://aminoacidsguide.com/

•

Histidine (H/His): It is found in the high concentrations in hemoglobin. Histidine help to treat anemia and it has been used to treat issues such as rheumatoid arthritis (Figure 7.21).

Figure 7.21: Structure of histidine. Source: https://aminoacidsguide.com/

•

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Aspartate (D/Asp): It helps to elevate the stamina and also, it helps to protect the liver; DNA and RNA metabolism, immune system function (Figure 7.22).

Histidine is used for rheumatoid arthritis, allergic diseases, ulcers, and anemia caused by kidney failure or kidney dialysis.

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Figure 7.22: Structure of aspartate. Source: https://aminoacidsguide.com/

•

Glutamate (E/Glu): This is a type of Neurotransmitter that took participation in the synthesis of DNA (Figure 7.23).

Figure 7.23: Structure of glutamate. Source: https://aminoacidsguide.com/

7.4. WHAT IS THE DIFFERENCE BETWEEN A PROTEIN AND AN AMINO ACID? Amino acids are the most important factor which is present in the proteins or it can be said that amino acids are the building blocks of proteins. Another way of thinking of this is to relate the amino acids to the beads of a necklace. Without the help of string to clutch them together, they are just beads. The amino acids in formula are diverse as compared to the amino acids in the food because they are already bro-

Amino Acids and Proteins

ken down. Because amino acids are already disconnected from each other, amino acids are absorbed quickly and all at once, giving the body a small amount of time to use them (Figure 7.24).

Figure 7.24: Chemical structure of amino acid. Source: https://upload.wikimedia.org/wikipedia/ commons/thumb/7/7d/Amino_acid.svg/2000pxAmino_acid.svg.png

A protein is a chain of amino acids are linked to each other. People can think of this like a beaded necklace. The beads (amino acids) are linked with each other with the help of a string or bond, which contracts a long chain or protein. Consequently, a protein is “intact” or “whole.” Proteins are linked with each other; free amino acids are not.

7.5. WHAT ARE ESSENTIAL AMINO ACIDS? Amino acids are organic compounds are derived with the help of nitrogen, hydrogen, oxygen, and carbon, along with a flexible side chain group. Human body requires 20 several types of amino acids to prosper and function appropriately. Even though all of these 20 are very crucial for the health of the human, only nine amino acids are categorized as an important factor.

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Isoleucine is one of nine essential amino acids in humans (present in dietary proteins), Isoleucine has diverse physiological functions, such as assisting wound healing, detoxification of nitrogenous wastes, stimulating immune function, and promoting secretion of several hormones.

These are histidine, methionine, lysine, isoleucine, phenylalanine, leucine, valine, tryptophan, and threonine. Dissimilar to the nonessential amino acids, essential amino acids cannot be made with the help of human body and must be found with the help of the diet of the human. The best causes of the essential amino acids are animal proteins such as poultry, eggs, and meat. When human eat protein, it is broken down into the amino acids, which are then utilized to support the human body with several number of processes, for example, building muscle and regulating immune function.

7.5.1. Conditionally Essential Amino Acids There are various types of nonessential amino acids which are categorized in the form of conditionally essential. These nonessential amino acids are well thought-out to be essential only under specific conditions, for example, illness or stress. For instance, even though arginine is well thought-out nonessential, human body cannot meet the demands when fighting particular diseases such as cancer. That is why arginine must be accompanied with the help of the diet in order to meet the requirements of the human body in particular states.

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REVIEW QUESTIONS 1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

What is the significance of amino acids and proteins? Explain the classifications of the proteins and amino acids. Describe the structure of amino acids and proteins. Explain the properties of the amino acids and proteins. What are the several types of amino acids? Explain the role of the amino acids in the proteins. What is the main difference between a protein and amino acids? What are the essential amino acids? What do you mean by the conditionally essential amino acids? How proteins and amino acids play a vital role in the functionality of a human body and why they are necessary?

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Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., & Walter, P., (2019). The Shape and Structure of Proteins. [online] Ncbi. nlm.nih.gov. Available at: https://www.ncbi.nlm.nih.gov/books/ NBK26830/ (Accessed on 15 June 2019). Amino acids guide, (2019). Amino Acids – Structure, Advantages, Properties, Classification. [online] Aminoacidsguide.com. Available at: https://aminoacidsguide.com/ (Accessed on 15 June 2019). Biology.arizona.edu., (2003). Amino Acids. [online] Available at: http://www.biology.arizona.edu/biochemistry/problem_sets/aa/ aa.html (Accessed on 15 June 2019). Briggs, M. G., & Howes, C. D., (1984). How Amino Acids Relate to Protein in Your Diet – Dummies. [online] dummies. Available at: https://www.dummies.com/health/nutrition/how-amino-acidsrelate-to-protein-in-your-diet/ (Accessed on 15 June 2019). Cambrooke, A., (2019). Protein versus Amino Acids | Ajinomoto Cambrooke. [online] Cambrooke.com. Available at: https://www. cambrooke.com/products/glytactin/protein-vs-amino-acid.php#. XOzfUogzbtR (Accessed on 15 June 2019). Google classroom, (2019). Chemistry of Amino Acids and Protein Structure. [online] Khan Academy. Available at: https://www. khanacademy.org/test-prep/mcat/chemical-processes/amino-acidspeptides-proteins-5d/a/chemistry-of-amino-acids-and-proteinstructure (Accessed on 15 June 2019). Google classroom, (2019). Introduction to Proteins and Amino Acids. [online] Khan Academy. Available at: https://www. khanacademy.org/science/biology/macromolecules/proteins-andamino-acids/a/introduction-to-proteins-and-amino-acids (Accessed on 15 June 2019). Halver, J., (2019). Chapter 3: Proteins and Amino Acids. [online] Fao.org. Available at: http://www.fao.org/3/x5738e/x5738e04.htm (Accessed on 15 June 2019). Kubala, J., (2019). Essential Amino Acids: Definition, Benefits and Food Sources. [online] Healthline. Available at: https://www. healthline.com/nutrition/essential-amino-acids (Accessed on 15

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June 2019). Lodish, H., Berk, A., Zipursky, S., Matsudaira, P., Baltimore, D., & Darnell, J., (2019). Hierarchical Structure of Proteins. [online] Ncbi.nlm.nih.gov. Available at: https://www.ncbi.nlm.nih.gov/ books/NBK21581/ (Accessed on 15 June 2019). Ncbi.nlm.nih.gov. (1989). Protein and Amino Acids. [online] Available at: https://www.ncbi.nlm.nih.gov/books/NBK234922/ (Accessed on 15 June 2019). Reddy, K. M., (2019). Amino Acid | Definition, Structure, & Facts. [online] Encyclopedia Britannica. Available at: https://www. britannica.com/science/amino-acid (Accessed on 15 June 2019). Reusch, W., (2013). Proteins. [online] Www2.chemistry.msu.edu. Available at: https://www2.chemistry.msu.edu/faculty/reusch/ VirtTxtJml/proteins.htm (Accessed on 15 June 2019). Scitable, (2014). Protein Structure | Learn Science at Scitable. [online] Nature.com. Available at: https://www.nature.com/scitable/ topicpage/protein-structure-14122136 (Accessed on 15 June 2019). Soderberg, T., (2019). Introduction to Amino Acids and Proteins. [online] Chemistry LibreTexts. Available at: https://chem. libretexts.org/Bookshelves/Organic_Chemistry/Book%3A_ Organic_Chemistry_with_a_Biological_Emphasis_(Soderberg)/ Chapter_01%3A_Chapter_1%3A_Introduction_to_organic_ structure_and_bonding_I/1.3%3A_Structures_of_some_ important_biomolecules/Introduction_to_amino_acids_and_ proteins (Accessed on 15 June 2019). Wampler, J., (2019). The 20 Amino Acids: Hydrophobic, Hydrophilic, Polar and Charged Amino Acids. [online] Proteinstructures.com. Available at: https://proteinstructures.com/Structure/Structure/ amino-acids.html (Accessed on 15 June 2019). Wikibooks, (2019). Principles of Biochemistry/Amino Acids and Proteins – Wikibooks, Open Books for an Open World. [online] En.wikibooks.org. Available at: https://en.wikibooks.org/wiki/ Principles_of_Biochemistry/Amino_acids_and_proteins (Accessed on 15 June 2019).

8 CARBOHYDRATES

LEARNING OBJECTIVES: In this chapter, readers will get an opportunity: • To understand the concept of carbohydrates. • To know the history of carbohydrates. • To understand the classification and nomenclature of carbohydrates. • To understand the monosaccharides. • To learn about the disaccharides. • To gain knowledge on three characteristics to classify monosaccharides.

KEY TERMS: • • • • • •

Aldopentose Carbohydrates Carbon molecules Disaccharides Polysaccharides Stereocenters

• • •

The carbohydrate chirality The Fischer projections Tollen’s reagent

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8.1. INTRODUCTION The three carbons molecules and more that include minimum one carbonyl set and one alcohol set is called Carbohydrates or saccharides. The set of aldehydes that are found in carbohydrates are called as are aldoses, and the set of ketones that are found in carbohydrates are called as ketoses. The stereochemistry is present in the universe, and it is a normal happening like all molecules are found in the universe. Recall that chiral, non-superimposable, mirror images will rotate the plane-polarized light will be moved to the left or right, which are known as S and R by chiral, non-superimposable mirror images. In carbohydrate chemistry, left-, and right- rotation is referred to as The L or levorotary and D or dextrorotary left and right movement is also called in chemistry as carbohydrate and the concept is the same. The animal cells have the capability of using the D-isoforms of saccharides, although the L-isoforms cannot be digested and chirality is the source of life, and it is common knowledge. The glyceraldehyde or C=3 contain one stereo enter, so it has two enantiomers is contain in simple carbohydrate. The erythrose has two stereocenters that are found in C=4 carbons and has two diverse arrangements of the OH groups, and Threose diastereomers, but enantiomers have a mirror image, four stereoisomers are finally created. The three stereocenters are found in C=5 carbons, and ribose, arabinose, xylulose, and lyxose will contain eight stereoisomers and the four diastereomers respectively. There is only one mirror image; enantiomer D or L is present for each OH arrangement.

8.1.1. Cyclization of Carbohydrates The reaction of aldehydes or ketones by putting in alcohol to manufacture the hemiacetal functional group, and this process is known as the creation of hemiacetal. The hemiacetal reactions that are that inter-molecular are not suitable. Though in carbohydrates the creation of intra-molecular hemiacetal is good. The Hayworth projection is used to draw the carbohydrates.

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The molecule pyran or 5 carbon cyclized ether or furan or 4 carbon cyclized either is the same in the display as cyclized aldose or ketose. The D-glucopyranose has a cyclic Diastereomers are structure known as D-glucose. In the language stereoisomers that of biochemistry, the pyran is not important. are not mirror

8.1.1.1. Anomers In the organic chemistry, the alcohol created from the hemiacetal reaction is the essential functional group of carbohydrates. The anomeric place is defined as the carbon center, normally at position C1 or C2. It is also a stereocenter, and the subsequent enantiomers, also known as anomers are also a stereocenter. The OH is placed up of the plane of the ring, it is known as beta configuration and the alphaposition is represented by OH place below the ring. The anomeric carbon is found in all monosaccharides.

8.1.1.2. Reducing Sugars The Tollen’s reagent contains silver nitrate causes oxidation of the aldose or ketose and makes the carbonyl. This reaction converts the carbonyl in saccharides to a carboxylic acid. The silver settles to create the mirror-like left substance on the beaker in this process. The anomeric position is found in any saccharide that found positive in test and can make equal to the aldose or ketose formation and also known as reducing sugar. The polysaccharides are formed by useful carbohydrates that are known as reducing sugar and glycosidic bonds are formed by polymers of units of carbohydrate. The anomeric position

images of one another and are nonsuperimposable on one another.

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Glycosidic bond is a type of covalent bond that joins a carbohydrate (sugar) molecule to another group, which may or may not be another carbohydrate.

that is also known as the decreasing end on both sugar units is not found when the anomeric position between two saccharides is connected. The glucose and fructose are disaccharide of sucrose and is also known as table sugar. However, since both reducing ends are used in the glycosidic bond, they will not react with Tollen’s Reagent; thus the sucrose is defined as non-reducing sugar as it cannot react with Tollen’s reagent and in glycosidic bond, both reducing ends are used.

8.2. HISTORY OF CARBOHYDRATES The human body obtains energy from the just eaten food by oxidation of foods, and it was found and that is first by German chemist Justus von Liebig in the mid of the year 1800, AntoineLaurent Lavoisier has stated that Leibig was first to announce that it was carbohydrates and fats that increase the process of the oxidationnot carbon and hydrogen. In the year of 1891, the French physiologist Claude Bernard documented that the matter that looks like starch is produced in the liver of mammals is named glycogen. The glucose derived from the blood and it could be broken down further into sugar whenever it was required was discovered later by him. In the year of 1891, Karl von Voit documented that the mammals can produce glycogen when they eat sugars more intrinsic than glucose. In the year of 1919, Otto Meyerhof has documented that that glycogen is converted into lactic acid in active muscles.

Carbohydrates

In the year of 1930, the Czech-American biochemists Carl Cori and Gerty Cori stated the complicated process by which glycogen, stored in the liver and muscle, and are broken down in the body. The Fritz Lipmann was able to work further to found the method carbohydrates can be transformed into the forms of chemical energy most usable by the body. In the year of 1884 the German biochemist Emil Fischer started his work on the chemical structure of the various sugars in welldocumented form and won Nobel Prize. He not only produced glucose and 30 other sugars; he also displayed the outline of the molecules was most essential than their chemical composition.

8.3. CARBOHYDRATES The variety of naturally occurring compounds and derivatives create together carbohydrates. The things like the wood, starch, and linen was discovered that it is made up of molecules containing atoms of carbon, hydrogen, and oxygen and to have the general formula C6H12O6; other molecules of organic form with the same formulas were discovered to have the same ratio of hydrogen to oxygen in the early 19th century. The carbohydrates that are also known as watered carbon is represented by general formula Cx(H2O) y. The most plentiful and organic substances found in large amount in nature are carbohydrates and are necessary building blocks of all living things. In the process of photosynthesis the carbon dioxide and water together build carbohydrates.

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Chemical composition is the arrangement, type, and ratio of atoms in molecules of chemical substances.

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The source of energy and necessary structural components in organisms is carbohydrates and additionally found in the structure of nucleic acids that include genetic information, made up of carbohydrate.

8.4. CLASSIFICATION AND NOMENCLATURE There are many schemes of categorization of carbohydrates, but the carbohydrates are mainly divided into four main sets of common types that is monosaccharides, disaccharides, oligosaccharides, and polysaccharides. In the fruits, in grapes and most monosaccharides, or simple sugars are found. The most common representatives include five or six chain-like molecules joined together, though it can include three to nine carbon atoms. Three of the most important simple sugars The glucose also called as dextrose, grape sugar, and corn sugar, fructose or fruit sugar, and galactose are thee of most essential simple sugar and have the same molecular formula C6H12O6, and isomers have different features as their atoms have diverse structural arrangements. The change in structural arrangement affects the biological reputation of isomeric compounds. The hydroxyl group’s ―OH that build part of the molecular structure and its placement has impacted the extent of sweetness in different varieties of sugar. This concept has not been proved but the direct relationship that can exist between taste and any particular structural arrangement, possible to predict the taste of a sugar by knowing its and by knowing the particular structural arrangement.

Carbohydrates

The large part of the energy that the living thing needs and is essential for them to perform their daily activities is supplied by chemical bonds of glucose though indirectly. The mixture with other simple sugars in a way to build large molecules of galactose that is not found normally in shape of normal sugar. The disaccharide that is also known as double sugar is consisting of two molecules of simple sugar that are connected to each other. The molecule of glucose and one molecule of fructose together build the disaccharide sucrose or table sugar. The sugar beets and cane sugar are the most common sources of disaccharide. The disaccharide is also found in Milk sugar, lactose, and maltose. The molecules should be broken into the corresponding monosaccharides before the living organism use the energy contained in disaccharides. Oligosaccharides, which consist of the three to six monosaccharide units that are rarely present in natural sources through the few plant derivatives have been recognized together, form the oligosaccharides.

8.4.1. Classification of Carbohydrates Based on the number of forming units, mainly there are three distinct classes of carbohydrates: monosaccharides, oligosaccharides and polysaccharides. However, there are some other classifications also. In addition, the hydrolysis is the key criteria behind the classification of carbohydrates. It is divided as follows.

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Disaccharide is the sugar formed when two monosaccharides (simple sugars) are joined by glycosidic linkage.

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8.4.1.1. Monosaccharides In this form the carbohydrate is modest that cannot be hydrolyzed any more. Its general formula is (CH2O)n. Glucose and Ribose are some general examples.

8.4.1.2. Oligosaccharides The hydrolysis of 2 to 10 small pieces or monosaccharides gives carbohydrates that are oligosaccharides. It is a large classification and it can be divided into various subcategories. Hydrolysis is a chemical reaction in which water is used to break down the bonds of a particular substance.

8.4.1.3. Disaccharides The hydrolysis of two units of the same or different monosaccharides gives disaccharides. For example, the one molecule of glucose and fructose each is produced on hydrolysis of sucrose while maltose on hydrolysis gives two molecules h on hydrolysis of glucose produce maltose.

8.4.1.4. Trisaccharide The three molecules of monosaccharides on hydrolysis give carbohydrates and it can be the same or different. For example, Raffinose.

8.4.1.5. Tetra Saccharides The four molecules of monosaccharides on hydrolysis produce carbohydrates. For example, stachyose.

8.4.1.6. Polysaccharides The hydrolysis of them in large amount gives monosaccharides. They are also known as nonsugars and are not sweet in taste and are called

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carbohydrates. For example, starch, glycogen. They are the last classification of carbohydrates.

8.5. CARBOHYDRATES AS THE MONOSACCHARIDES The hydrates of carbon that has empirical formula CH2O is specially used to define the compounds that are commonly known as carbohydrates. The carbohydrates have been divided on the basis of their structures and not on the basis of a formula. It is also described as polyhydroxy aldehydes and ketones. The cellulose, starch, glycogen, and most sugars are compounds that belong to this category. The monosaccharides, disaccharides, and polysaccharide are all three groups of carbohydrates. The white crystalline solids that include the single aldehyde or ketone functional class is called monosaccharides. The aldoses and ketoses are the two subcategories of monosaccharides on the origin of whether they are aldehydes or ketones. It as a triose, tetrose, pentose, hexose, or heptose on the basis of whether they contain the three, four, five, six, or seven carbon atoms form the basis of division on being found in triose, tetrose, pentose, hexose, or heptose. They are optically active compounds with one omission. The monosaccharides are in D shape that exists in nature though there is the possibility of D and L isomers. The Emil Fischer in the year of 1880 and 1890 first discovered the structures of a large number of monosaccharides and the rules innovated by him are still used to write them.

Stachyose is a tetrasaccharide consisting of two Dgalactose units, one D-glucose unit, and one D-fructose unit sequentially linked.

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The molecule will display in shape of threedimensional structure projected onto a piece of paper by the Fisher projection. The Fischer projections are written vertically, with the aldehyde or ketone on the top according to established rules. The fisher projection that is displaying -OH group on the second-to-last Fischer projections can be derived from the skeleton figure by imaging. The carbon atom is written on the right side of the in the skeleton structure on the right-side carbon atom is present on the D isomer and L isomer is present on the left. The imaging is used in Fischer projections for the skeleton structures to know the result if the model of each isomer is put on an overhead projector so that the CHO and CH2OH groups are on the glass and then by looking at the images of these models that will be shown on a computer screen it is obtained that If the carbon chain is long enough, The alcohol at one end of a monosaccharide can attack the carbonyl group at the other end to create a cyclic compound if the carbon chain is not long sufficiently. The pyranose is obtained as a product from the reaction of six-membered rings. The furanose is formed as the product that is obtained from the reaction of the five-membered ring. The creation of a pyranose or a furanose is caused by reversible reactions. If one starts with a pure sample of a-D-glucopyranose or b-Dglucopyranose, it is no more a concern. The balanced mixture that is 63.6% of the b-anomer and 36.4% of the a-anomer can be converted to get the anomer in the span of a few minutes.

Carbohydrates

The six-membered ring planes consist of the bulky -OH or -CH2OH contents that are inside more or less in the b-anomer. In the a-anomer, In the six-membered ring plane one of the -OH groups are perpendicular to the plane in a-anomer, in an area it gets strong opposite forces from the hydrogen atoms that are in ring sitting in the same place. The b-anomer is firmer than the a-anomer as the conclusion.

8.6. DISACCHARIDES The condensing a pair of monosaccharides produce disaccharides. The starch breaks down to produce the malt sugar or maltose, is an important element of the barley malt that is used to make the beer. The disaccharide found in milk is called milk sugar or lactose. Very young children have the special enzyme known as lactase that helps to digest lactose is found inside the stomach of toddlers and young children. There are people that lost the ability to digest lactose and cannot bear milk or milk products as they grow due to lactose that is inside the human milk and is twice in an amount in comparison to milk from cows. The children are given cow’s milk or a manmade milk formula based on sucrose that forms intolerance to lactose instead of mother milk. The disaccharide sucrose that is obtained from sugar cane or beetroot is a matter that is known as sugar in general. The disaccharides that are sweetest in taste are sucrose. They are sweet as thrice as maltose and as sweet as six times of lactose. In recent years, sucrose has been replaced the corn syrup is being used in

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many commercial products, that is produced when in corn-starch the polysaccharides are broken down in place of sucrose from last decade. In taste, the corn syrup is 70 percent as sweet as sucrose is mainly the glucose. In comparison to glucose, the fructose is less than two and a half times. A commercial process has therefore been developed that uses the isomerase enzyme is used to change the amount of half of the glucose in corn syrup into fructose in the process on a commercial level. In soft drinks on a large scale, the high-fructose corn sweetener is used, and it is as sweet as sucrose. The carbohydrates that are found in natural conditions are huge in amount, and only the miniscule amount is represented by monosaccharides and disaccharides. The polysaccharides contain a large amount of carbohydrates found in nature that have comparatively large molecular weights. There are basically two different tasks of polysaccharides. They are used by both plants and animals to store glucose as a source of future food energy, and then it supplies the few of the mechanical structure of cells and is used to store glucose as the source of energy to be used in future. In the environment, few living beings get a regular amount of energy. The cells in plant and animal have been modified to save the energy for the future in times of abundance so that they can survive in the times of scarcity. The polysaccharides contained in starch are the form of food energy stored by plants.

Carbohydrates

The amylose and amylopectin are mainly two varieties of starch. In the plant lower varieties and in algae amylose is present. In the structure of maltose, the a-D-glucopyranose rings are added to forecast the structure of linear polymer of approx. 600 glucose remains. In the higher plants, the dominant form of starch is amylopectin. It is a branched polymer of about 6000 glucose residues with branches on 1 in every 24 glucose rings. The glycogen is defined as a polysaccharide that is used as a storehouse for short term energy by animals. The amylopectin has approximately the same structure with two small differences as glycogen. In comparison to amylopectin, the glycogen molecule is approximately as large as the same in size, and it has unevenly twice as many branches. The branched polysaccharides like the amylopectin and glycogen have many advantages. During times of shortage, the enzymes take one end of the polymer chain and take glucose molecules one by one in times of scarcity of energy. The polysaccharide that is suitable in a great way for the fast secretion of glucose in comparison of linear polymer is highly branched. The walls of plant and bacterial cells are created by the Polysaccharides. The solution in which the amount of salt dissolved is either too low that is hypotonic or too high that is hypertonic often causes the breakdown of the cells that do not have a cell wall. The osmotic pressure is responsible for pushing water into the cell to balance the system that causes the cell to break down, and it happens

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Amylopectin is a water-soluble polysaccharide and highly branched polymer of α-glucose units found in plants. It is one of the two components of starch, the other being amylose.

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in situations when the ionic strength of the solution is very less than the cell. The osmotic pressure is responsible for pushing water out of the cell, and the cell decrease in size and ruptures if the ionic strength of the solution is very much. The plant cells are kept safe by the strength it gets from the cell wall that lives in fresh-water ponds containing very less salt or seawater containing very much salt from the tremor of osmotic nature. The cell wall also provides the mechanical strength that allows the plant cells to take the weight of other cells from the strength it gets from the cell wall. Polysaccharides are The cellulose is a most rich structural polymeric carbopolysaccharide. In all the biological molecules, hydrate molecules the large amount is of cellulose and in large composed of long chains of monosacquantity in the cell wall of plants. The residue charide units bound of glucose has a linear polymer that is known together by glycoas cellulose, and has a shape that looks like sidic linkages, and on amylose more in comparison to amylopectin. hydrolysis give the constituent monosacThe inconsistency in the shape of cellulose charides or oligosacand amylose is clearly visible by comparing the charides. images of amylose and cellulose. The joining of b-glucopyranose rings together creates the cellulose, instead of the joining of the rings in starch and glycogen to form glucopyranose. In the starch and glycogen, the -OH substituent works as the basic connector between -glucopyranose rings and is in a perpendicular position to the plane of the six-membered ring plane. The carbohydrate that contains the glucopyranose rings builds the shape that looks like the stairs of a ladder. The -OH substituent that links the b-glucopyranose rings are connected by -OH substituent in cellulose that is found in the plane

Carbohydrates

of the six-membered ring. In the rectilinear style, the molecule is stretched. The tough hydrogen bonds build between the -OH groups of nearby molecules in a possible easy manner. The cellulose gets the toughness that is essential for it to supply and act as the source of the mechanical shape of cells of the plant. There is a connection between the shape and working of biomolecules, and the good example is cellulose and starch. At the turn of the century, The Emil Fischer has stated that the enzyme shape is first matched to the matter on that it works in large in the same order as the lock and key works. The glucose molecules in starch do not do work on the b-linkages in cellulose as the a-connector got broken by amylase enzymes. The absence of an enzyme that can cut b-linkages between glucose molecules is the reason behind most animals is not been able to digest cellulose. The fiber or roughage can act as an essential part of cellulose. The digestive tracts of some animals, such as the animals such as cows, horses, sheep, and goats include bacteria that have enzymes that cut the b-linkages, are found in the stomach of some animals that digest cellulose.

8.6.1. The Three Characteristics Are Used to Classify Monosaccharides • • • •

The molecule containing a number of carbon atoms; The carbonyl group location; and The carbohydrate chirality. Aldose: The carbonyl group is an aldehyde in monosaccharide.

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•

Ketone: The carbonyl group is a ketone in monosaccharide. • Triose: The monosaccharide containing three carbon atoms. • Tetrose: The four carbon atoms that are found in monosaccharide. • Pentose: The five carbon atoms that are found in monosaccharide. • Hexose: The six carbon atoms that are found in monosaccharide. • Aldohexose: It is also known as the 6-carbon aldehyde. For example, glucose. • Aldopentose: The 5-carbon aldehyde. For example, glucose. • Ketohexose: The -6-carbon hexose. For example, fructose. The unequal carbon found away from the carbonyl group decides the direction of monosaccharide to be D or L. According to Fisher projection, the hydroxyl group is on the right of the molecule in D sugar. If the hydroxyl group is on the left of the molecule, then it is an L sugar.

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REVIEW QUESTIONS 1. 2. 3. 4. 5. 6. 7. 8. 10. 11.

What are carbohydrates? Explain the history of carbohydrates? Explain the carbohydrates in detail with examples? What are the classification and nomenclature of carbohydrates? Explain Monosaccharides? Explain oligosaccharides? Define in detail disaccharides? Explain trisaccharide? Define the three characteristics used to classify monosaccharides? Define tetrasaccharides?

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REFERENCES 1.

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Chemed.chem.purdue.edu. (n.d.). Carbohydrates. [online] Available at: https://chemed.chem.purdue.edu/genchem/topicreview/ bp/1biochem/carbo5.html (Accessed on 15 June 2019). Davidson, E., (n.d.). Carbohydrate | Definition, Classification, & Examples. [online] Encyclopaedia britannica. Available at: https:// www.britannica.com/science/carbohydrate (Accessed on 15 June 2019). Helmenstine, A., (2019). What is the Science Behind Carbohydrates? [online] ThoughtCo. Available at: https://www.thoughtco.com/ chemistry-of-carbohydrates-603878 (Accessed on 15 June 2019). Organic Chemistry Help, (2015). Carbohydrates in Organic Chemistry. [online] Available at: https://www.studyorgo.com/blog/ carbohydrates-in-organic-chemistry/ (Accessed on 15 June 2019). Science.jrank.org. (n.d.). Carbohydrate. [online] Available at: https://science.jrank.org/pages/1197/Carbohydrate.html (Accessed on 15 June 2019). Toppr-guides, (n.d.). Carbohydrates: Definition, Formula, Classification, Importance, Examples. [online] Available at: https:// www.toppr.com/guides/chemistry/biomolecule/carbohydrates/ (Accessed on 15 June 2019).

9 ALCOHOLS AND ETHERS LEARNING OBJECTIVES: In this chapter you will learn about: • Basic nomenclature of alcohol and ether. • Physical properties of alcohol. • Physical properties of ether. • Chemical properties of alcohol. • Chemical properties of ether. • Basic idea about the preparation of alcohol. • How alcohol is being prepared. • How ether is being prepared. • Williamson’s synthesis. KEY TERMS: • • • • • •

Acetone Alcohol Alkyl halides Asymmetrical ether Benzene Carbon atoms

• • • • • •

Dehydration of alcohols Ether Methyl Metronidazole Regular ether Williamson’s synthesis

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9.1. INTRODUCTION We have understood that replacement of one or more hydrogen atom(s) from a hydrocarbon by an additional atom or a collection of atoms end up in the production of a completely new composite having overall dissimilar possessions and requests. Alcohols are produced when a hydrogen atom in a hydrocarbon, aliphatic, and aromatic correspondingly, is substituted by –OH group. These lessons of mixes find wide requests in manufacturing as well as in day-to-day life. For example, have you ever saw that normal spirit being used for improving wooden furniture is primarily a compound containing hydroxyl group, ethanol. The sugar we consume, the cotton with usage for fabrics, the chapter we require for writing, are all created up of compounds containing –OH groups. Just think of our daily life without paper; no notebooks, books, newspapers, currency notes, cheques, certificates, etc. The magazine’s resonant beautiful photos and stimulating stories would vanish from our life. It would have been actually a dissimilar world. An alcohol consists of one or more hydroxyl (OH) group or groups which is directly in relation to carbon atom or atoms, of an aliphatic system which basically consists of CH3OH while a phenol consists of –OH group or groups straight being linked to carbon atom or atoms of an aromatic system which basically consists of C6H5OH (Figure 9.1).

Figure 9.1: Nomenclature of alcohol. Source: https://upload.wikimedia.org/wikipedia/commons/thumb/c/cb/Butan_Lewis.svg/2000px-Butan_Lewis.svg.png

The replacement of a hydrogen particle in a hydrocarbon by an alkoxy or aryloxy collection (R–O/Ar–O) harvests another session

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of mixes known as ‘ethers,’ for instance, CH3OCH3 which is the chemical formula of dimethyl ether. One may also visualize ethers as mixes created by relieving the hydrogen atom of hydroxyl collection of an alcohol or phenol by an alkyl or aryl collection. In this section, we shall talk about the chemistry of two classes of compounds, namely alcohols, ethers. The organization of mixes makes their education methodical and hence simpler. The hydroxyl collection is one of the most vital useful groups of obviously being occurring organic particles. All carbohydrates and their offshoots, counting nucleic acids, have hydroxyl collections. Some amino acids, most steroids, many terpenes, and plant pigments have hydroxyl groups. These materials serve many diverse determinations for the provision and conservation of life. One dangerous instance is the strong toxin tetrodotoxin, which is inaccessible from puffer fish and has clear usage for protection against marauders. This compound has superior biochemical attention, having six different hydroxylic purposes decided on a cage-like construction. On the additional practical side, vast amounts of simple alcohols – methanol, ethanol, 2-propanol, 1 -butanol and numerous Ethers are constitutes from petroleum-derived hydrocarbons. These alcohols are extensively used as solvents and as intermediates for the fusion of more complex materials. The reactions which consist of the hydrogens of the alcoholic OH class are predictable to be equal to those of H2o, HOH, and the simplest

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Tetrodotoxin is a potent neurotoxin. Its name derives from Tetraodontiformes, an order that includes pufferfish, porcupinefish, ocean sunfish, and triggerfish; several of these species carry the toxin.

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hydroxylic compound. Alcohols, ROH, can be stared in this admiration as replacement products of H2o. Though, with alcohols one shall its focus on not only in reactions that continue at the 8-H bond but also with procedures that end up in cleavage of the C-0 bond, or vicissitudes in the organic class R. The simple ethers, ROR, do not consist of 0-H bonds, and maximum of their reactions are incomplete to the substituent collections. The chemistry of ethers, so, is less diverse than that of alcohols. This detail is twisted to benefit in the extensive usage of ethers as thinners for a diversity of organic responses, as one already has observed for Grignard reagents. However, cyclic ethers with minor rings projects improved reactivity because of ring strain and, for this aim, are valued intermediates in organic mixture.

9.2. PHYSICAL PROPERTIES OF ALCOHOLS AND ETHERS Now that we all know fairly enough about alcohols and phenols, over how many of scholars know about the physical properties of alcohol? One may also request why it is vital? Well, one required to analyze the physical possessions of these organic mixes to be able to have use for them for everyone’s’ benefit. Envisage how would it be if alcohol be situated miscible in water? So, in this chapter, one will analyze at the idea of physical possessions of alcohols and ethers, one after the other. By the end of this chapter, one will be in a great position to observe

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about the basic possessions of these compounds (Figure 9.2).

Figure 9.2: Isomeric representation. Source: https://upload.wikimedia.org/wikipedia/ commons/1/1b/Isomeren.png

9.2.1. Physical Properties of Alcohol Alcohols are carbon-based compounds where a hydroxyl collection swaps the hydrogen atom of an aliphatic carbon. Thus, an alcohol molecule contains of two sections. The first one has the alkyl group and the other has the hydroxyl group. They consume a sweet odor and exhibition an exclusive set of physical and chemical possessions. The non-absence of hydroxyl collection is the chief factor in deciding the possessions of alcohol. Let one now observe at some of the protuberant physical possessions of alcohol. • The Boiling Point of Alcohols: Alcohols usually have advanced boiling points as likened to additional hydrocarbons consuming equal molecular masses. One can qualify this to the attendance of intermolecular hydrogen linkage between hydroxyl groups of alcohol molecules. In

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Alkoxide is the conjugate base of an alcohol and therefore consists of an organic group bonded to a negatively charged oxygen atom.

adding to this, the boiling point of alcohols upsurges with a hike in the amount of carbon atoms in the aliphatic carbon chain. • The Solubility of Alcohols: The hydroxyl collection chooses the solubility of alcohol in water. The hydroxyl collection in alcohol takes portion in the creation of intermolecular hydrogen bonding. Thus, hydrogen bonds amid water and alcohol particles make alcohol solvable in water. The solubility of alcohol reductions with the upsurge in the size of the alkyl class because of the water fearing nature of the alkyl class. • The Acidity of Alcohols: Alcohols respond with active metals which consist of sodium, potassium etc. and procedure the consistent alkoxide. These responses of alcohols are revealing of their acidic character. The acidic character of alcohol is partly due to the divergence of –OH bond. The acidity of alcohols reductions when an electron giving class is devoted to the hydroxyl group. This is owing to the detail that it upsurges the electron thickness of the oxygen atom. Thus, the main alcohols are usually more acidic. • Hydrogen Bonding: It happens amid molecules in which a hydrogen atom is devoted to a powerfully electronegative component fluorine, oxygen or nitrogen. In the

Alcohols and Ethers

circumstance of alcohols, hydrogen bonds occur amid the partly-positive hydrogen atoms and lone pairs on oxygen atoms of other particles. • The Effect of Van Der Waals Forces: a. Boiling Points of the Alcohols: Hydrogen linkage is not the only the most of intermolecular force alcohols knowledge. There are also van der Waals dispersal forces and dipole-dipole connections. The hydrogen bonding and dipole-dipole connections are abundant the same for all alcohols, but dispersal forces increase as the alcohols get better. These magnetisms get sturdier as the particles get lengthier and have more electrons. These upsurges the sizes of the provisional dipoles shaped. This is why the boiling facts hike as the amount of carbon atoms in the chain’s upsurges. It takes more vigor to overwhelmed the dispersal forces, and thus the boiling points rise. b. Comparison Between Alkanes and Alcohols: Even deprived of any hydrogen bonding or dipole-dipole connections, the boiling point of the alcohol would be greater than the consistent alkane with a similar amount of carbon atoms. • Solubility of Alcohols in Water: Minor alcohols are totally solvable in a water solution of the two in any amount generate a solitary solution. Though, solubility decreases as the length of the hydrocarbon chain in the alcohol upsurge. At four carbon atoms and outside, the reduction in

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solubility is obvious a two-covered material may seem in a test tube when the two are mixed. Reflect ethanol as a typical small alcohol. In both pure water and pure ethanol, the main intermolecular magnetisms are hydrogen bonds. In instruction to combine the two, the hydrogen linkage amid water particles and the hydrogen linkages between ethanol particles must be defamed. Energy is obligatory for both of these procedures. However, when the particles are being mixed, new hydrogen bonds are shaped amid water molecules and ethanol molecules. The vigor free when these new hydrogen bonds form about recompenses for the vigor required to defame the original connections. In adding, there is an upsurge in the complaint of the system, an upsurge in entropy. This is an additional sector in deciding whether chemical processes occur. Consider a hypothetical situation involving 5-carbon alcohol molecules. The hydrocarbon chains are forced between water molecules, breaking hydrogen bonds between those water molecules. The -OH ends of the alcohol molecules can form new hydrogen bonds with water molecules, but the hydrocarbon “tail” does not form hydrogen bonds. This means that many of the original hydrogen bonds being broken are never replaced by new ones. In place of those original hydrogen bonds are merely van der Waals dispersion forces between the water and the hydrocarbon “tails.” These attractions are much weaker, and unable to furnish enough energy to compensate for the

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broken hydrogen bonds. Even allowing for the increase in disorder, the process becomes less feasible. As the length of the alcohol increases, this situation becomes more pronounced, and thus, the solubility decreases.

9.2.2. Ethers and Their Physical Properties Ether is an organic compound that has an oxygen particle fused to two alike or dissimilar alkyl or aryl collections. The overall formulation for ethers can be R-O-R, R-O-Ar, or Ar-O-Ar. Now, the term R opinions in direction an alkyl collection and Ar deal with an aryl collection. Ethers exhibition a wide variety of physical and chemical possessions. Physical properties of ethers are: • An ether molecule consumes a net dipole moment. This dipole moment is mostly due to the schism of C-O bonds. • The boiling point of ethers is similar to the alkanes. Though, it is much decreased than that of alcohols of similar molecular form notwithstanding the schism of the C-O bond. The miscibility of ethers with water is on the same appearances as that of alcohols. • Ether molecules are easily mixed in water. Ethers are a section of organic mixes that have an oxygen molecule being attached to two same or dissimilar alkyl or aryl collections. One

Dipole moment is a quantity that describes two opposite charges separated by a distance.

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can analyze down the general formula for ethers as R-O-R, R-O-Ar or Ar-O-Ar. From our information of organic nomenclature, one observes that in the above formula, R shows an alkyl group and Ar signifies an aryl group. One can categorize these mixes into two major kinds or categories. This categorization be contingent on the substituent groups devoted to the multiple. So, we can classify them into: • Regular Ether: It has binary undistinguishable collections devoted to the oxygen atom. • Asymmetrical Ether: It has two dissimilar groups devoted to the oxygen atom. Ethers exhibition a wide variety of bodily and chemical possessions. Let us now deliberate some of the physical and chemical possessions of ethers. An ether particle has a net dipole instant. One can attribute this to the schism of C-O bonds. The boiling point of ethers is being to the alkanes. Though, it is much lower likened to that of alcohols of similar molecular mass. This is notwithstanding the detail of the schism of the C-O bond. The mixing of ethers with water look like those of alcohols. Ether particles are mixing in water. One can characteristic this to the detail that like alcohols, the oxygen particle of ether can also procedure hydrogen bonds with an H2o molecule.

Alcohols and Ethers

•

•

•

Polar Nature of Ether: Meanwhile, the electronegativity of oxygen is higher than that of carbon, ethers are glacial in nature. Furthermore, the binary C-O bonds in ether are tinted towards each other at an angle of 110°, and so, the two dipoles do not cancel each other, subsequent in a net dipole moment. Boiling Point of Ether: The boiling point of ethers is inferior to that of isomeric alcohols just because ethers do not create H-bonds within the array. For instance, the boiling point of methoxymethane whose chemical formula is CH3OCH3 is inferior to that of ethanol whose scientific formula is CH3CH2OH even though both have the same nomenclature C2H6O. Solubility of Ether: Inferior ethers up to three carbon particles are solvable in water since they form hydrogen linkage with water particles. The mixture of ethers in water reductions with upsurge in form since the hydrocarbon part develops larger and fights the creation of hydrogen bonds with water molecules. Ethers are fairly solvable in organic thinners such as alcohols, benzene, and acetone.

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Acetone is the organic compound with the formula (CH3)2CO. It is a colorless, volatile, flammable liquid and is the simplest and smallest ketone.

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9.3. CHEMICAL PROPERTIES OF ALCOHOLS AND PHENOLS 9.3.1. Chemical Properties of Alcohols • Combustion: Alcohols burns in oxygen to produce carbon dioxide and water. Alcohols blister easily and cleanly, and do not yield soot. It grows increasingly more difficult to injury alcohols as the particles get bigger (Figure 9.3).

The over-all molecular comparison for the reaction is: CnH2n+1OH + (1.5n) O2 → (n+1) H2O + nCO2

Figure 9.3: 3-methyl-2-pentanone synthesis. Source: https://upload.wikimedia.org/wikipedia/ commons/thumb/e/e0/3-Methyl-2-pentanone_synthesis.svg/2000px-3-Methyl-2-pentanone_synthesis.svg.png

•

Dehydration: alcohol to alkene— dehydration of alcohols is being done

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by heating with focused sulfuric acid, which performances as the desiccating agent, at 180°C. This response uses alcohols to harvest consistent alkenes and water as by-product. • Oxidation: alcohol to carboxylic acid—Alcohols can be oxidized into carboxylic acids. e.g., oxidation of ethanol: C2H5OH + [O] → CH3COOH + H2O Corrosion can be complete by means of oxidizing agents such as acidified potassium dichromate (VI), acidified potassium manganate (VII) or atmospheric oxygen. Ethanol, if left unattended to air, can oxidize and develop ethanoic acid. An instance is wine rotating sour as the alcohol content, which is ethanol, is oxidized by atmospheric oxygen. • Esterification: Alcohols can be responded with a carboxylic acid to procedure esters. Additional of this will be clarified under the creation of esters.

9.3.2. Chemical Properties of Ethers Ethers usually experience chemical reactions in two habits. One will discuss them in the below section. Cleavage of C-O bond: Ethers are usually very unreactive in character. When one adds an extra of hydrogen halide to the ether, cleavage of C-O bond happens place. It leads up to the creation of alkyl halides. The instruction of reactivity is as mentioned below:

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Friedel-Crafts reaction provides an easy method for the introduction of alkyl and acyl groups in the benzene ring.

HI > HBr > HCl R-O-R + HX → RX + R-OH Electrophilic substitution: The alkoxy collection in ether triggers the aromatic circle at ortho and para positions for electrophilic replacement. Common electrophilic substitution responses are halogenation, Friedel Craft’s reaction, etc. Halogenation reaction of ethers: Perfumed ethers experience halogenation, for instance, brominating, when we add a halogen in the nonpresence or absence of a catalyst. Friedel Craft’s reaction of ethers: Aromatic ethers goes through Friedel Craft’s response, for instance, adding of alkyl or acyl group when one introduces it to an alkyl or acyl halide in the attendance of a Lewis acid as catalyst.

9.4. PREPARATION OF ALCOHOLS Numerous of the shared laboratory approaches for the groundwork of alcohols have been discussed already in the previous sections or will be analyzed for later thus to evade unwarranted recurrence one shall not contemplate them in detail at this duration of time. Comprised among these approaches are hydration and hydroboration, adding of hypohalous acids to alkenes, S,1 and S,2 hydrolyzes of alkyl halides and of allylic and benzylic halides, adding of Grignard substances to carbonyl compounds, and the discount of carbonyl mixes. These approaches are summarized in this section. Most of these reactions that this chapter

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stated are being used for large-scale industrial manufacturing. For instance, ethanol is produced in quantity by the hydration of ethene, with the usage of an excess of steam under high pressure at temperatures around 300°C in the non-absence of phosphoric acid: A weak solution of ethanol is created, which can be focused by concentration to a constantboiling point mixture that contains 95.6% ethanol by weight (Figure 9.4).

Figure 9.4: Synthesis of metronidazole. Source: https://upload.wikimedia.org/wikipedia/ Isopropyl alcohol commons/0/09/Synthesis_of_metronidazole.png

Dryness of the residual few portions of water to provide “total alcohol” is attained either by chemical means or by concentration with benzene, which ends up in special parting of the water. Ethanol also is completely in great quantities by fermentation, but this way is not modest for manufacturing uses with the hydration of ethene. Isopropyl alcohol and tert-butyl alcohol also are manufactured by hydration of the corresponding alkenes.

is a compound with the chemical formula CH3CHOHCH3. It is a colorless, flammable chemical compound with a strong odor.

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9.5. NUCLEOPHILIC PROPERTIES: ETHER FORMATION Alkoxide ion creation is vital as an income of creating a strong nucleophile that will willingly create C-0 linkages in SN2 reactions. Thus, ethanol responds very slowly with methyl iodide to give methyl ethyl ether, but sodium ethoxide in ethanol mixture reacts quite fastly:

In fact, the response of alkoxides with alkyl halides or alkyl sulfates is a vital overall technique for the groundwork of ethers, and is basically known as the Williamson mixture. Problems can happen because the rise of nucleophilicity related with the change of an alcohol to an alkoxide ion always is escorted by an even better upsurge in removing power by the E2 mechanism. The reaction of an alkyl halide with alkoxide then may be one of elimination rather than substitution, depending on the temperature, the structure of the halide, and the alkoxide. For instance, if one wishes to prepare isopropyl methyl ether; better yields would be obtained if one were to make use of methyl iodide and iso-proxied ion rather than isopropyl iodide and methoxide ion because of the occurrence of E2 elimination with the latter combination.

9.5.1. Williamson’s Synthesis In Williamson’s synthesis, alkyl halides (primary and secondary) react with R’ONa (Sodium

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alkoxide) or R’OK (Potassium alkoxide) to produce ethers. (Figure 9.5)

Figure 9.5: Williamson-ether-synthesis. Source: https://upload.wikimedia.org/wikipedia/ commons/7/72/Williamson-ether-synthesis-2D.png

Tertiary alkyl halides are not used in Williamson’s synthesis because tertiary alkyl halides prefer to undergo elimination (example of elimination is given in nucleophilic substitution reaction of haloalkanes) instead of substitution. Hence, if one were to prepare t-Butyl methyl ether, we will use (CH3)3ONa and CH3Br; and not (CH3)3Br and CH3OH.

9.5.2. Preparation of Ethers by Dehydration of Alcohols When alcohols are heated with concentration H2SO4 at 413 kelvins, ethers (ROR’) are created (Figure 9.6).

Figure 9.6: Ether peroxide formation. Source: https://upload.wikimedia.org/wikipedia/ commons/1/1d/Ether_peroxide_formation.png

Nucleophilic substitution is the reaction of an electron pair donor (the nucleophile, Nu) with an electron pair acceptor (the electrophile).

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9.5.3. Preparation of Ether from Alkyl Halides Alkyl halides are heated with dry silver oxide to form ether (Figure 9.7).

Figure 9.7: Ether. Source: https://upload.wikimedia.org/wikipedia/ commons/thumb/3/32/Addition_Alkohol_an_Doppelbindungen.svg/2000px-Addition_Alkohol_an_ Doppelbindungen.svg.png

9.6. SOME COMMERCIALLY IMPORTANT ALCOHOLS Methanol and ethanol are among the two commercially important alcohols. • Methanol, CH3OH, also known as ‘wood spirit,’ was shaped by the destructive concentration of wood. Presently, most of the methanol is created by catalytic hydrogenation of carbon monoxide at high pressure and temperature and in the non-absence of ZnO – Cr2O3 catalyst. Methanol is a colorless liquid and boils at 300 and 37 K. It is extremely toxic in nature. Digestion of even minor amounts of methanol can reason blindness and large amounts cause even demise. Methanol is being used as a solvent in

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paints, varnishes, and primarily for producing formaldehyde. • Ethanol, C2H5OH, is gained commercially by fermentation; the eldest technique is from sugars. The sugar in molasses, sugarcane or fruits such as grapes is being changed to glucose and fructose, both of which have the same formulation of C6H12O6, in the non-absence of an enzyme, invertase. Glucose and fructose knowledge fermentation in the non-absence of another enzyme, zymase, which originates in yeast. In wine creation, grapes are the basis of sugars and yeast. As grapes ripen, the amount of sugar upsurges and yeast produces on the outer skin. When grapes are crumpled, sugar, and the enzyme come in contact and fermentation starts. Fermentation takes place in anaerobic circumstances that are in nonappearance of air. Carbon dioxide is unconfined during fermentation.

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Methanol is the simplest alcohol, consisting of a methyl group linked to a hydroxyl group. It is a light, volatile, colorless, flammable liquid with a distinctive odor similar to that of ethanol (drinking alcohol).

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REVIEW QUESTIONS 1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

Explain nomenclature of alcohol and ethers. State different physical properties of alcohol. State different physical properties of ether. Explain and discuss chemical properties of alcohol. Explain and discuss chemical properties of ether. How alcohol gets prepared? How ether gets prepared? Explain Williamson’s synthesis. How ether is prepared with the help of dehydration? How ether is prepared with the help of alkyl halides?

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REFERENCES Alcohols and Ethers, (2019). (2nd edn., p. 3) [eBook] https://authors. library.caltech.edu. Available at: https://authors.library.caltech. edu/25034/16/BPOCchapter15.pdf (Accessed on 15 June 2019). 2. Alcohols, Phenols and Ethers, (n.d.). (5th edn., p. 2) [eBook] New Delhi: Ncert. Available at: http://www.ncert.nic.in/ncerts/l/lech202. pdf (Accessed on 15 June 2019). 3. Chem.latech.edu. (n.d.). Alcohols, Phenols, Thiols, and Ethers. [online] Available at: http://www.chem.latech.edu/~deddy/ chem121/Alcohols.htm (Accessed on 15 June 2019). 4. Clark, J., (2019). 9.4: Physical Properties of Alcohols, Ethers and Epoxides. [online] Chemistry LibreTexts. Available at: https://chem. libretexts.org/Courses/University_of_Illinois%2C_Springfield/ UIS%3A_CHE_267_-_Organic_Chemistry_I_(Morsch)/ Chapters/Chapter_09%3A_Alcohols%2C_Ethers%2C_and_ Epoxides/9.04%3A_Physical_Properties (Accessed on 15 June 2019). 5. Embibe.com. (2019). Alcohols and Ethers. [online] Available at: https://www.embibe.com/study/alcohols-and-ethers-chapter (Accessed on 15 June 2019). 6. Horrocks, M., (2019). Alcohols and Ethers. [online] 4college. co.uk. Available at: http://www.4college.co.uk/as/df/alcohols.php (Accessed on 15 June 2019). 7. Opentextbc.ca. (n.d.). 20.2 Alcohols and Ethers – Chemistry. [online] Available at: https://opentextbc.ca/chemistry/chapter/20-2alcohols-and-ethers/ (Accessed on 15 June 2019). 8. Organicmystery.com. (2018). Physical Properties of Ether. [online] Available at: http://www.organicmystery.com/Ether/ PhysicalPropertiesEther.php (Accessed on 15 June 2019). 9. Organicmystery.com. (2018). Preparation of Ether. [online]Available at: http://www.organicmystery.com/Ether/PreparationOfEther.php (Accessed on 15 June 2019). 10. Shrestha, B., (2016). Physical Properties of Ether. [online] Chemistry LibreTexts. Available at: https://chem.libretexts. org/Bookshelves/Organic_Chemistry/Supplemental_Modules_ 1.

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(Organic_Chemistry)/Ethers/Properties_of_Ethers/Physical_ Properties_of_Ether (Accessed on 15 June 2019). 11. Sites.google.com. (n.d.). 2. Properties of Alcohols – Alcohol, Carboxylic Acid and Esters. [online] Available at: https://sites. google.com/site/chemistryolp/properties-of-alcohols (Accessed on 15 June 2019). 12. Sydney.edu.au. (n.d.). Alcohols, Phenol and Ethers. [online] Available at: https://sydney.edu.au/science/chemistry/~george/ alcohols.html (Accessed on 15 June 2019). 13. Toppr-Guides. (n.d.). Physical Properties of Alcohol, Phenols and Ethers: Concepts, Video, Q&A. [online] Available at: https://www. toppr.com/guides/chemistry/alcohols-phenols-and-ethers/physicalproperties-of-alcohols-phenols-and-ethers/ (Accessed on 15 June 2019).

10 SPECTROSCOPY

LEARNING OBJECTIVES: After studying this chapter, you should be able to: • • • • • • • •

Describe in detail the meaning of spectroscopy. Explain the various types of spectroscopy for chemistry analysis. Explain the meaning of atomic spectroscopy. Examine the different basic components of spectroscopic instruments. Explain the meaning of infrared spectroscopy. Describe the spectroscopy based on absorption. Examine the meaning of electromagnetic radiation. Explain the meaning of nuclear magnetic resonance.

KEY TERMS: • • • • •

Electromagnetic radiation Mass spectrometry Spectroscopy Surface-enhanced Raman spectroscopy (SERS) Terahertz techniques

• • • •

Ultraviolet (UV) spectroscopy Vibrational frequency Visible (Vis) spectroscopy X-ray crystallography

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10.1. INTRODUCTION Until the mid-20th century, the only way available with the researchers to distinguish between most of the organic compounds from one another is on the basis of its chemical and physical properties. The understanding of these physical and chemical properties only resulted in basic hints about a compound’s molecular structure, and the determination of that structure was not an easy task (at least for large molecules) that requires in-depth examination of certain reaction pathways. There are no methods or approach available with the chemists to see how molecules looked like. Because these are so small in size that no device was developed at that time such as microscope that would give a complete image of a molecular structure. There one technique available called X-ray crystallography can help in giving accurate details of structural data for some molecules, but for only those molecules that can be gathered in crystalline and solid form. It is generally seen that using a full X-ray structure determination is time-consuming, expensive that is only applicable at most puzzling structures. In this case, the spectroscopic technique is the best technique available presently that can help in obtaining enough information to interpret a molecule structure. Spectroscopy is a general term used for the instrumental processes by which the complete details and information regarding the molecular structure are gained through careful analysis of the scattering, absorption, or emission of electromagnetic radiation (EMR) by compounds. According to a group of researchers EMR is defined as “the continuous spectrum of energy-bearing waves ranging from extremely short waves, such as high-energy X-rays (with wavelengths of about 10 nanometers [nm]), to very long, low-energy waves such as radio waves (with wavelengths of one meter [m] or more).” The light that can be easily seen is the variety of EMR having wavelengths of approximately 400 to 700 nm. When the light of certain wavelength is passing through the objects, then the object absorbs that light and appears in color, and those absorbed wavelengths are

Spectroscopy

not present from light that passes through the colored object to the eyes. Molecules have the capacity to absorb light up to a certain limit of different wavelengths because there is need to predict the accurate value of the energy content of the absorbed light as it enables the molecule to shift from one energy state to higher one. The countless energy levels that are present in a molecule are said to be quantized because there is a significant difference between one another on the basis of different computable energy value and each can be calculated step by step. Thus, as it allows calculating the wavelengths of the EMR that is absorbed by a molecule, no one can easily get enough information about the different types of energy levels within it. The valuable information generated from this process can then be used to interrelate with specific details of molecular structure. Instruments called spectrometers play a very important role in measuring the value of the wavelength of light that the molecules absorbed in different types of regions of the electromagnetic spectrum. There are various spectroscopic techniques such as visible spectroscopy, ultraviolet (UV), infrared (IR) spectroscopy, and nuclear magnetic resonance (NMR) that are very useful for structure determination. One another technique called mass spectrometry does not rely on EMR absorption, but it is of high importance to researchers because it provides valuable information about the number and type of atoms present in a molecule.

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Electromagnetic spectrum is all the wavelengths of light and reveals an otherwise invisible universe.

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10.2. WHAT IS SPECTROSCOPY

Radiation is the emission or transmission of energy in the form of waves or particles through space or through a material medium.

Spectroscopy can be defined by the form of radiative energy involved. The frequency and intensity of the radiation play an important role in measuring spectrum. EMR is one of the most common radiation types, and it was first used in spectroscopic studies. It is important to note that both IR and near IR make use of EMR, as well as a microwave and terahertz techniques. Both neutrons and electrons are also considered as a source of radiation energy because of the presence of their de Broglie wavelength. There are some of the mechanical methods that are useful in case of solids for radiation, and acoustic spectroscopy uses radiated pressure waves.

10.3. DIFFERENT TYPES OF SPECTROSCOPY FOR CHEMICAL ANALYSIS There are different ways to categorize the different spectroscopy methods depending on the interaction between the materials and energy, the types of radiation, the nature of the material, and the applications technique used. Presently, there are so many types of spectroscopy available, but some of them that are mostly used for chemical analysis are IR spectroscopy, atomic spectroscopy, UV and visible spectroscopy, and NMR and Raman spectroscopy.

10.3.1. Classifications There are also various other ways and criteria available to classify spectroscopy, such as by

Spectroscopy

analyzing the nature of the interactions between the material and energy. These interactions include emission, absorption, resonance spectroscopy, inelastic, and elastic scattering. The materials used can also help in identifying the spectroscopy type, including molecules, atoms, crystals, and nuclei.

10.3.1.1. Atomic Spectroscopy Atomic spectroscopy was recognized as the first method of spectroscopy developed, and it can be further categorized into emission, atomic absorption, and fluorescence spectroscopy. Most of the atoms of different types of elements have distinct spectra. Therefore it is possible for atomic spectroscopy to identify and quantify a sample’s composition. The various different types of atomic spectroscopy comprise of atomic emission spectroscopy (AES), atomic absorption spectroscopy (AAS), and atomic fluorescence spectroscopy (AFS). In AAS atoms absorb either visible light or UV to shift to higher levels of energy. AAS helps in measuring the volume of absorption of ground state atoms that are in the gaseous state. AAS also play an important role in detecting certain types of metals. In AES, atoms are emitted from the heat of a flame, arc, plasma, or spark to emit light. AES generally works by analyzing the intensity of light being released in order to examine the amount of an element in a sample. There are various techniques that AES use in its working. Some of them are an arc or spark AES, inductively coupled plasma AES and flame emission spectroscopy. In AFS, it is a beam of light that

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Fluorometer is a device used to measure parameters of visible spectrum fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light.

emits the analytes, resulting in realizing light. The fluorescence from a sample is then used for examination using a fluorometer, and it is commonly used to analyze organic compounds.

10.3.1.2. Ultraviolet (UV) and Visible Spectroscopy UV and visible (Vis) spectroscopy generally works by using the EMR spectrum that varies from the range10 nm to 700 nm to analyze compounds. There are various types of atoms that can absorb or emit visible light, and it is this reflectance or absorption that produces an indifferent color of the chemicals being analyzed (Figure 10.1).

Figure 10.1: Ultraviolet visible spectroscopy. Source: https://upload.wikimedia.org/wikipedia/ commons/5/5c/Ultraviolet-visible_spectroscopy_ of_Dichlorobis%28ethylenediamine%29cobalt%28 III%29_chloride.png

The absorption of UV radiation and visible light primarily depends on the excitation of electrons that shifts from the state of low energy grounds into a high-energy excited state. There

Spectroscopy

are mainly two ways to absorb the energy, such as by using π-electrons within a molecular orbital and non-bonding n-electrons. There are different levels of energy associated with the wavelengths of light, and the light having the exact quantity of energy is the only one that causes transitions from one to another level for absorption. In case, when there is a wider gap between energy levels, a large amount of energy is required for shifting to the higher energy level, in a way to ensure that the higher frequency and shorter wavelength absorbed. UV and visible spectroscopy also play an important role in measuring the concentration of samples, and it is possible with the help of BeerLambert Law principles, which states that there is a direct relationship between the absorbance and the concentration of the substance in path length and solution. In addition, the measurement of the concentration of UV, sample, and visible spectroscopy is helpful in finding the existence of the free electrons and double bonds within a molecule. Apart from an analytical technique that can work independently, a UV/Vis spectrometer is also helpful in identifying high-performance liquid chromatography.

10.3.1.3. Infrared (IR) Spectroscopy IR analyzes compound using the IR spectrum that can be categorized into near IR, mid-IR, and far IR. Near IR is considered as having the highest level of energy and can pierce a sample much deeper as compared to mid or far IR, but because of this, it is also the least sensitive

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Spectroscopy is the study of how light interacts with matter. We can use spectroscopy to determine the structure and functional groups in organic compounds.

one. IR spectroscopy is not as sensitive as UV/ Vis spectroscopy because of the small amount of energy released in the vibration of atoms as compared to the energies of the transitions (Figure 10.2).

Figure 10.2: Infrared spectroscopy. Source: https://upload.wikimedia.org/wikipedia/ commons/c/c5/IR_spectroscopy_apparatus.jpg

IR based on the assumption that molecules vibrate, along with bonds bending and stretching, when the IR radiation is absorbed by them. IR spectroscopy primarily works by throwing a beam of IR light through a sample, and in order to detect the transition, it is essential for the molecule of sample experience dipole moment change during vibration. When the vibrational frequency of the bonds is identical to the frequency of the IR, absorption occurs, and it became possible to record a spectrum. Various types of functional groups absorb heat at a different rate depending upon their structure, and thus, a vibrational spectrum can be helpful in examining the functional groups present in a sample. When analyzing the available that is gathered by an IR, results from the process can be used for comparison

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to a frequency table in a way to identify which types of functional groups are present to help determine the structure.

10.3.1.4. Raman Spectroscopy Raman spectroscopy is mostly identical to IR primarily because it is a vibrational spectroscopy technique, but it uses inelastic scattering. The spectrum of Raman spectroscopy shows different types of lines such as the Stoke lines, a scattered Rayleigh lines and anti-Stoke lines, which is not similar as compared to irregular absorbance lines of IR. Raman spectroscopy mainly works by identifying and detecting the inelastic scattering, also known by the name Raman scattering, of monochromatic light from a laser in the visible, UV or near IR range. In order to ensure that transition should be Raman active, there is a need to change the polarizability of the molecule during the time of vibration activity, and the electron cloud should witness a positional change. The technique is very useful as it delivers a molecular fingerprint of the structures of samples and chemical composition, but signal given by Raman scattering is not strong. Some of the techniques, such as Surface Enhanced Raman Spectroscopy (SERS) have been developed in order to increase the sensitivity at the time of using Raman spectroscopy.

10.3.1.5. Nuclear Magnetic Resonance (NMR) NMR is a very useful technique that works by using nuclear spin states and resonance

Polarizability is the ability to form instantaneous dipoles. It is a property of matter.

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spectroscopy for spectroscopic analysis. It is important to note that all of the nuclei currently available have a nuclear spin, and the spin behavior of the nucleus of every atom primarily relies on the externally applied field and on its intramolecular environment (Figure 10.3).

Figure 10.3: Nuclear magnetic resonance spectroscopy. Source: https://upload.wikimedia.org/wikipedia/ commons/thumb/9/9d/19F-NMR_yne-6AmF5. svg/2000px-19F-NMR_yne-6AmF5.svg.png

It is often seen that whenever nuclei of a specific element are in unfavorable chemical environments within the same molecule, there is a variety of magnetic field benefits witnessed because of shielding and de-shielding of electrons nearby, resulting in different types of resonant frequencies and defines the changed chemical values. Spin-spin coupling is of the view that the spin states of one nucleus always result in affecting the magnetic field, which further altered the neighboring nuclei through intervening bonds. Spin-spin coupling results in absorption peaks

Spectroscopy

of different groups of nuclei that are further divided into a number of components.

10.4. WHAT IS ELECTROMAGNETIC RADIATION (EMR)? EMR (light) is considered as a form of energy whose actions are determined by the properties of both particles and waves. There are certain properties of EMR that are best explained by recognizing light as a wave such as its refraction when it transfers from one object to another. Some of the other properties, such as emission and absorption are explained in a better way by considering light as a particle. It is not easy to analyze the actual nature of EMR because still now there is not enough information available on it because of the limited research and development in this field. Nevertheless, the current information and knowledge on the dual models of particle and wave behavior provide a detailed description for EMR

10.4.1. Wave Properties of Electromagnetic Radiation (EMR) EMR comprises of magnetic fields and oscillating electric that passes through space with a similar velocity along a linear path. It is important to note that in a vacuum, EMR travels as fast as the speed of light, denoted by c, which is 2.997 92 × 108 m/s. When there is a change in a medium of EMR other than a vacuum, its velocity, denoted by v, is less than the speed of light in a vacuum (Figure 10.4).

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Velocity is a vector expression of the displacement that an object or particle undergoes with respect to time.

Figure 10.4: Electromagnetic wave. Source: https://upload.wikimedia.org/wikipedia/ commons/9/99/EM-Wave.gif

10.5. BASIC COMPONENTS OF SPECTROSCOPIC INSTRUMENTS The spectroscopic techniques primarily work by using certain instruments in which most of the components are similar such as a source of energy, a detector for determining the signal strength, a method to eradicate a narrow range of wavelengths, and a signal processor that analyze and shows signals to an analyst for further action. In this section, some of the basic components of spectroscopic instruments is discussed.

10.5.1. Sources of Energy It is worth noticing that all types of spectroscopy require a source of energy. In scattering and absorption spectroscopy, photons play

Spectroscopy

an important role in supplying this energy. Photoluminescence and emission spectroscopy use radiant (photon), thermal, or chemical energy to encourage the analyte to a suitable excited state. • Sources of Electromagnetic Radiation (EMR): A source of EMR must deliver an output that is both stable and intense. Sources of ER are mainly categorized into line and continuum sources. In case of a continuum source, radiation is released over a different types and varieties of wavelengths, with a smooth range of intensity. While on the other hand, a line source releases radiation at predetermined wavelengths. • Sources of Thermal Energy: There is basically two important sources of thermal energy that is plasmas and flames. Plasmas, which are high in temperature level and comprises of ionized gases deliver temperature in between 6000 to 10000K. While on the other hand, Flames sources use the mixture of an oxidant and fuel to control the level of temperature between 2000 to 3400 K.

10.5.2. Wavelength Selection In a method designed by Nessler for ammonia, various types of standard solutions and samples are put in separate big, flat-bottomed tubes. In this, reagents are added and after then wait for a while in order to allow the color to develop.

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When the color is developed, then the analyst assesses the color by transferring ambient and natural light through the bottom of the tubes and after then looking downwards through the solutions. During the comparison of the sample’s color with that of a standard set, the analyst can be able to examine the concentration of ammonia in the sample. It is noticed that each wavelength of light from the source passes through the sample. At a time when there are only one absorbing objects, then it is not a problem at all. Suppose, in a sample, if there are two components that absorb different wavelengths of light, then it is not possible to do quantitative analysis with the help of Nessler’s original method. Ideally, there is a need to select wavelength that only the analyte absorbs. Unfortunately, it is not possible to separate a single wavelength of radiation from a continuum source. A researcher who is handling a wavelength passes a small band of radiation influenced by a nominal wavelength, a maximum throughput and an effective bandwidth of radiation. The bandwidth is called effective when the width of the radiation is approximately half at its maximum throughput.

10.5.3. Signal Processors An electrical signal by the transducer is supplied to a signal processor and it is displayed in such a manner that the analysts can examine the result efficiently and effectively. Some of the examples of signal processors are digital or analog meters, computers, and recorders enhanced with digital acquisition boards.

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There are many uses of a signal processor. For example, it can be used to regulate the detector’s response, to eliminate unnecessary noise through the filtration process, to amplify the transducer’s signal, or to mathematically calculate the value of the signal.

10.6. SPECTROSCOPY BASED ON ABSORPTION In absorption spectroscopy, there is a beam of EMR that transferred through a sample. During the transfer process, most of the radiation passes, without any loss in strength, through the sample. While, at a certain wavelength, the intensity of the radiation weakened. The process of weakening of intensity of radiation is called absorption.

10.6.1. Absorbance Spectra It is generally seen that there are two basic conditions for an analyte’s absorption of EMR. Firstly, there should be proper predefined criteria or way by the radiation’s magnetic field or electric field interacts with the analyte. In case of visible and ultraviolet radiation, the absorption process of a photon varies the energy of the analyte’s valence electrons. Moreover, the vibrational energy of a bond is changed or differed, when there is the absorption of IR radiation. The second condition that needs to be met is that the photon’s energy, hν, should be equal to the difference in energy, ΔE, between two of the quantized energy states of the analyte.

Photon is a type of elementary particle, the quantum of the electromagnetic field including electromagnetic radiation such as light and radio waves, and the force carrier for the electromagnetic force (even when static via virtual particles).

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The basic process of a photon’s absorption plays an important role as it ensures that the photon’s energy must able to equalize the difference in energy between a high state of energy and lower state of energy. There is certainly important information that is not available in this case such as information about what types of energy states are involved, the arrival of the resulting spectrum, and which transitions are likely to occur.

10.7. CONCLUSION In the end, it is concluded that since spectroscopy primarily depends on the interaction of EMR with a molecule, there is a need to have a good level of understanding of EMR is a must. Spectroscopy is basically concerned with controlling the changes in energy states of a molecule; it is therefore, important to have enough information about the important energy states and concept of quantization of energy within a molecule. One of the most important topics of the EMR spectrum that most of the researchers are aware of is “visible light,” but this is just a small portion of all the possible types. In a molecule, there are various types of energy states. Of particular interest to the organic chemist will be those that are similar to the energy associated with the vibration of a bond, the nuclear spin state, or an electronic energy levels (orbitals) When the atoms or molecules absorb the energy, then it allows them to shift from an initial state of energy (the ground state) to

Spectroscopy

another higher state of energy (an excited state). The energy changes can also be explained with the help of the energy level diagram. The energy states are said to be quantized because there are only certain discrete values that are possible; there is not a continuous spread of energy levels available.

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REVIEW QUESTIONS 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11.

What do you mean by spectroscopy? Explain in detail? Describe the meaning of nuclear magnetic resonance? Explain the various types of spectroscopy for chemistry analysis? What do you mean by Raman spectroscopy? Explain in detail the meaning of atomic spectroscopy? Explain the term electromagnetic radiation? What are the various components of spectroscopy instruments? What do you mean by infrared spectroscopy? Explain the spectroscopy based on absorption? What do you mean by ultraviolet and visible spectroscopy? Explain in details the wave properties of electromagnetic radiation?

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REFERENCES 1.

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Chem.ucalgary.ca. (2019). Chapter 13: Theory of Spectroscopy. [online] Available at: http://www.chem.ucalgary.ca/courses/350/ Carey5th/Ch13/ch13-1.html (Accessed on 15 June 2019). Encyclopedia Britannica, (2019). Chemical Compound – Spectroscopy of Organic Compounds. [online] Available at: https:// www.britannica.com/science/chemical-compound/Spectroscopyof-organic-compounds (Accessed on 15 June 2019). Louise, S. M., (2019). The Different Types of Spectroscopy for Chemical Analysis. [online] AZoOptics.com. Available at: https:// www.azooptics.com/Article.aspx?ArticleID=1382 (Accessed on 15 June 2019). Phy.pmf.unizg.hr. (2019). [online] Available at: https://www.phy. pmf.unizg.hr/~dandroic/nastava/fem/temp/00/Handbook%20 Of%20Spectroscopy%20-%20G.%20Gauglitz%20,%20T.%20VoDinh.pdf (Accessed on 15 June 2019). Resources.saylor.org. (2019). [online] Available at: https:// resources.saylor.org/wwwresources/archived/site/wp-content/ uploads/2012/07/Chapter1011.pdf (Accessed on 15 June 2019). Scilearn.sydney.edu.au. (2019). Spectroscopy in Organic Chemistry: Introduction. [online] Available at: https://scilearn.sydney.edu.au/ OrganicSpectroscopy/ (Accessed on 15 June 2019).

INDEX Atomic absorption spectroscopy (AAS) 201 Absorption spectroscopy 201, 208, Atomic emission spectroscopy 211 (AES) 201 Acetic acid 67, 68 Atomic fluorescence spectroscopy Acid donates protons 66 (AFS) 201 Alcoholic compounds 31 B Alcohols reduction 180 Aliphatic carbon 179, 180 Biological composites 98, 102 Alkoxide ion creation 190 Biological reactions 95 Alpha-amino acids 135 Biological specificity 134 Amino acid 131, 132, 133, 134, Bronsted-Lowry acid 78 135, 136, 137, 138, 139, 140, C 141, 142, 151 Amphoteric substance 80, 84 Carbohydrates 157, 158, 159, 160, Amylopectin 169, 170 161, 162, 163, 164, 165, 168, Analytical chemistry 1, 4 173, 174 Analyze compounds 202 Carbon atom 24, 28, 30, 35, 36 Analyze organic compounds 202 Carbon-based compounds 179 Animal protein 152 Carbon compounds 101, 102 Appropriately function 137 Carbon-containing compounds 9 Aqueous solution 70 Carbon dioxide 161 Aromatic system 176 Carbon skeleton 35 Arrhenius base 76 Carboxylic acid group 134, 139 Arrhenius theory includes acids 76 Carboxylic acids 36, 37, 38 A

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Carboxylic group 133, 136 Chemical composition 161 Chemical compounds 17 Chemical configuration 133 Chemical material 102 Chemical nomenclature 46 Chemical reaction 76 Chemical reaction mechanisms 92 Comparison of linear polymer 169 Complex carbohydrates 24 Crystalline 198 Crystallography 114, 197, 198 D Deoxyribonucleic Acid 134 Digest cellulose 171 Drug manufacturer 18

(DNA)

E Electromagnetic Radiation (EMR) 207, 209 Electromagnetic spectrum 199 Electron distribution 12 Electronegativity 31, 33 Electrophilic nature 83 Electrophilic substitution 188 Electrophilic substitution reactions 90 Emission of electromagnetic radiation (EMR) 198 Emotional amino acids 141 Energy security 8 Environmental chemistry 5 Ethylene oxide 102 Excitatory neurotransmitters 147, 149

F Fundamental reaction 91 G Glucose molecule 169, 171 H Halogenation reaction 188 Halogen atom 43, 59 Halogen atoms 53, 59 Hemiacetal reaction 159 Human body obtains energy 160 Human ecology 97 Hybridization 37 Hydrocarbon group 39 Hydrocarbons 25 Hydrochloric acid 72, 76, 79, 80 Hydrogen atom 66, 81, 82, 116, 123, 176, 177, 179, 180 Hydrogen ions 66, 67, 69, 78, 79 Hydroxyl collection 177, 179, 180 Hydroxyl group 30, 36 I Immune function 152 Initial vital regulation 91 Innovative synthetic approach 96 Inorganic chemistry 3, 19 International Standard Organization (ISO) 43 International system of units (SI) 43 International Union of Pure and Applied Chemistry (IUPAC) 43, 44

Index

L Laboratory approach 188 Liquid chromatography 203 M Methanol 192, 193 Microwave 200 Modern pharmacology 10 Molecular geometry 115 Molecular structure 198, 199 Monochromatic 205 N Natural gas 98 Neutralization reaction 71, 72, 73 Neutral substance 80 Nomenclature system 45 Nonessential amino acids 138, 152 Nuclear magnetic resonance (NMR) 199 Nucleic acids 23, 24, 25, 29 Nucleophilic substitution 191 Nucleophilic substitution reaction 191 Numeric value 64

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Organic molecules 24 Organic nomenclature 184 Organic reaction mechanism 91 Organic reactions comprise 88 Organic reactions deliver 88 Oxygen molecule 183 P Petrochemicals 98 Phenylalanine 139, 141, 142, 145, 152 Pneumonia 6 Polysaccharides 159, 162, 163, 168, 169 Produce carbon dioxide 186 Produces sodium chloride 72 R Raman spectroscopy 205, 214 Rational method 44 Reflect ethanol 182 Ribonucleic acid 24

197, 200,

S

Signal processor 208, 210, 211 Single electron movement 91 Single stereoisomer 111 Organic chemistry 1, 4, 5, 9, 10, Sodium hydroxide 72, 76 14, 15, 16, 18, 19, 20 Spatial arrangement 110, 113, 115 Organic compound 43, 44, 45, 50, Spectroscopic techniques 199, 208 51, 60, 133, 151, 183, 185 Spectroscopy 197, 198, 199, 200, Organic compound nomenclature 201, 202, 203, 204, 205, 206, 30 208, 209, 212, 214, 215 Organic compounds 26, 28, 33, Spin-spin coupling 206 34, 39 Stereochemistry 109, 110, 111, Organic mixture 178 112, 115, 128 Stereoisomerism 111, 129 O

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Structural polysaccharide 170 Surface Enhanced Raman Spectroscopy (SERS) 205 Synthetic organic chemistry 97

U Unfavorable chemical environments 206 V Vibrational energy 211