Taylor & Francis - Hydrogen as a Fuel - Learning from Nature 0748401032

Table of contents :
0415242428FM.PDF......Page 2
Hydrogen as a Fuel: Learning from Nature......Page 3
Contents......Page 6
List of figures......Page 8
List of tables......Page 13
List of contributors......Page 14
Preface......Page 18
Table of Contents......Page 0
1.1. Life and oxidation–reduction processes......Page 20
1.1.1. Hydrogen as a microbial energy source......Page 21
1.2. Technological implications......Page 26
2.2.1. Overview......Page 28
2.2.2. The species coverage......Page 30
2.3.1. Functions of hydrogenases: An overview......Page 31
2.3.2. The multiplicity of hydrogenases......Page 32
Group 1. The Fe-only hydrogenases......Page 33
Group 3. The NiFe-(thylakoid) uptake hydrogenases of Cyanobacteria......Page 34
Group 4. The bidirectional-NAD(P)-reactive hydrogenases in Cyanobacteria......Page 36
Group 5. The NAD(P)-reactive hydrogenases from bacteria......Page 38
Group 7. The F420-non-reducing hydrogenase of methanogens......Page 39
Group 10. NiFe hydrogenase in the formate hydrogen lyase complex......Page 40
2.4.1. Describing the genetic diversity......Page 41
2.5.2. Revealing hydrogenase evolution by protein comparison......Page 43
Relationships in the NiFe(Se) enzyme family......Page 44
Relationships amongst the Fe-only hydrogenases......Page 47
2.5.5. Relationships amongst accessory (hyp) genes......Page 48
Hyp genes in the Eubacteria......Page 49
2.6. Extending the horizons......Page 50
3.1. Hydrogenase regulation is guided by environmental factors and physiological requirements......Page 52
3.2. Diversity of hydrogenase operons and their transcriptional control......Page 55
3.3.1.1. H2-specific signal transducing system......Page 63
3.3.2.1. A multicomponent signal transduction system controls H2-dependent hydrogenase gene expression in R. eutropha......Page 66
3.3.2.2. The H2 sensor of R. eutropha belongs to a distinct subclass of [NiFe] hydrogenases......Page 71
3.4. Concluding remarks and perspectives......Page 73
4.2. General mechanisms of metal incorporation into proteins and enzymes......Page 76
4.3.1. Iron......Page 77
4.3.2. Nickel......Page 78
4.4.1. The role of housekeeping genes......Page 79
4.4.4. The hypC proteins (the HypC family)......Page 81
4.4.7. The hypF protein (HypF)......Page 83
4.4.9. The hydrogenase specific endopeptidases (HybD, HyaD, HyI, HoxM, HupM, HupD)......Page 84
4.5.2. Early events in maturation prior to C-terminal cleavage......Page 85
4.6.1. N-terminal twin-arginine leader sequences......Page 88
4.6.2. Involvement of the tat genes......Page 89
4.7. Conclusions, future directions and biotechnological implications......Page 90
5.1. Isolation of hydrogenase from cells: Desulfovibrio gigas......Page 92
5.2. Anaerobic techniques......Page 95
5.3.1. Evolution and oxidation of H2......Page 96
5.3.3. Interconversion of ortho- and para-H2......Page 97
5.3.4. Mechanistic implications of isotopic effects on rates......Page 98
5.4. Activation and activity states......Page 99
5.5. Multiple hydrogenases in the same species......Page 100
5.7. The hydrogen-consumption activity of the [NiFe] hydrogenase of Allochromatium vinosum in different redox states......Page 101
5.8.1. Mediated measurements of redox potentials......Page 103
5.8.2. Titrations with H2 pressure......Page 105
5.8.3. Direct electrochemistry......Page 106
5.9. The active inactive interconversion of an [NiFe]-hydrogenase at an electrode......Page 107
5.9.1. Energetics of reductive activation......Page 108
5.9.2. Probing kinetics initiated by a potential step......Page 109
6.1.1. Growing crystals......Page 112
6.1.2. From X-ray diffraction to electron density......Page 114
6.1.3. Building the atomic models......Page 115
6.1.4. Identification of metal atoms by X-ray diffraction......Page 116
6.1.5. Modelling the non-protein ligands......Page 118
6.2.1. An overall view......Page 120
6.2.2. Hidden at the centre of the molecule: The catalytic site......Page 122
6.2.3. Accessibility of the [NiFe] active site......Page 123
6.3. Hydrogen channels......Page 124
6.4.2. The active site......Page 126
6.4.3. Access......Page 128
7.1.1. FTIR spectroscopy: The diatomic ligands......Page 129
7.2. [Fe] hydrogenases......Page 130
7.2.1. FTIR......Page 132
7.3.1. Hydrogenases and oxygen......Page 134
7.3.2. Activation of H2: A heterolytic process......Page 135
7.4.1. Probing the behaviour of the NiFe(CN)2(CO) site in an enzyme solution......Page 136
7.4.2. Oxidized enzyme in air (inactive)......Page 137
7.4.3. Enzyme with one electron added to the active site (inactive)......Page 140
7.4.4. The Nia-S Nia-C* reaction......Page 141
7.4.6. Involvement of Fe-S clusters in the redox reaction with H2......Page 142
Why do the equilibrium reactions with H2 not show a change of redox state of the Fe-S clusters?......Page 143
7.5.2. Reduction and activation of the active site......Page 144
7.6. Reaction of [NiFe] hydrogenases with H2 and CO on the millisecond timescale......Page 146
7.7. Modifications in the H2-activating site of the NAD-reducing hydrogenase from R. eutropha......Page 149
7.8. FTIR spectroscopy of hydrogenases......Page 151
7.9. Using EPR and Mössbauer spectroscopies to probe the metal clusters in [NiFe] hydrogenase......Page 153
What about the hetero-dinuclear Ni-Fe centre?......Page 154
7.10. Spin–spin interactions in [NiFe] hydrogenases......Page 156
7.10.1. Intercentre spin–spin interactions......Page 157
7.11.1. EPR analysis of the Ni-Fe site of the Vhu and Fru hydrogenases......Page 159
7.11.2. A model explaining the spectroscopic characteristics of the active reaction centre......Page 161
7.12.1. Basic principles......Page 163
7.12.2. Applications in hydrogenase research......Page 164
7.13. The application of X-ray absorption spectroscopy (XAS) to [NiFe] hydrogenases......Page 166
7.13.1. Edge-energy shifts as a probe of Ni redox chemistry......Page 167
7.13.2. Coordination number and geometry from XANES analysis......Page 168
7.13.3. Metric details from EXAFS analysis......Page 169
7.14. Chemical and theoretical models of the active site......Page 171
Theoretical calculations......Page 172
7.15.2. Hartree–Fock versus DFT......Page 173
7.15.4. The electronic structure of [NiFe] hydrogenase......Page 174
7.15.5. Outlook......Page 177
8.1. Significant features of the active sites of hydrogenases......Page 178
8.2. Connections to the active site......Page 179
8.2.2. The electrical connection......Page 181
Electrostatic neutrality: Hydrons go with the electrons......Page 182
8.2.3. How H2 gets to the active site......Page 183
8.3.1. Hydride formation......Page 184
8.4. The metal-free hydrogenase from methanogenic archaea......Page 186
8.5.1. Hydrogenase biomimetics as substitutes for platinum......Page 189
8.6. Synthetic model compounds – how chemists mimic nature......Page 190
8.6.1. Models of the hydrogenase active sites......Page 192
8.7. A dinuclear iron(II) compound mimicking the active site of [Fe] hydrogenases......Page 197
8.7.1. A nickel disulfonato complex obtained by oxidation of a mononuclear nickel dithiolate complex......Page 198
9.1. Utilization of hydrogen metabolism in biotechnological applications......Page 200
9.1.1. Bioremediation: Generation of reductant......Page 201
9.1.2. Biogas production from wastes......Page 202
9.1.3. Denitrification for removal of nitrate from water......Page 204
9.2. Nitrogen fixation......Page 208
9.3. A novel anaerobic thermophilic fermentation process for acetic acid production from milk permeate......Page 212
9.4. Electron production by hydrogenase for bio-remediation of Se-oxoanions......Page 214
9.5. Hydrogenase in the reduction of halogenated pollutants......Page 215
9.6. Microbial recovery of platinum group metals......Page 216
9.7. Hydrogenases in water-in-oil microemulsions......Page 217
10.1.1. The hydrogen economy......Page 220
10.1.2. Biological hydrogen production......Page 221
10.2. Technologies to produce hydrogen by biological systems......Page 223
10.3.2. Enzymes for photosynthetic hydrogen production......Page 225
Nitrogenase......Page 226
Uptake hydrogenase......Page 227
10.3.3. Oxygen sensitivity and how to avoid it......Page 228
10.3.4. Cyanobacterial hydrogen production: Present status and future potential......Page 230
10.5.1. Photoheterotrophic bacteria......Page 232
10.5.2. Heterotrophic microorganisms......Page 237
10.6. The road to the hydrogen future: R&D in the US Hydrogen Program......Page 239
10.6.1. Biological systems......Page 240
10.6.3. Photoelectrochemical systems......Page 241
10.6.4. Indirect hydrogen production technologies......Page 242
Carbon-based storage systems......Page 243
10.6.6. End use technologies......Page 244
10.7. Japan: International cooperations/networks......Page 245
10.8.1. Improving the performance of the production organism......Page 246
10.8.2. Improving the performance of hydrogenases in technical systems......Page 247
10.8.4. Economic and ecological assessments parallel to experimental R&D......Page 248
10.9. Concluding remarks......Page 249
Appendix 1: List of names of microorganisms......Page 250
Appendix 2: Glossary......Page 251
Appendix 3: Websites for hydrogen research......Page 256
References......Page 257