Organic Chemicals in the Environment: Mechanisms of Degradation and Transformation

1047 Pages·2012·0.86 MB·English

by  Alasdair H. Neilson

Chemistry Neilson
Allard
Organic Chemicals
in the Environment
i
Second Edition n O
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e
Addressing the persistent environmental threat of organic chemicals with a fresh approach to
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degradation and transformation processes, Organic Chemicals in the Environment:
Mechanisms of Degradation and Transformation, Second Edition examines a wide range E i
of compounds as well as abiotic and microbiological reactions mediated by microorganisms. c
n
It emphasizes the pathways used and the broad classes of enzymes involved, including
examples from the application of NMR, EPR, and x-ray crystallography. v C
Illustrated with detailed figures describing experimental procedures and their associated i h
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chemical intermediates, the book’s interdependent chapters cover:
o e
• Abiotic and biotic reactions, including the basic chemical and biochemical reactions
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• The reaction of bacteria to stress induced by the physical or chemical environment n
• Procedures for establishing the details of metabolic pathways using isotopes,
m
including the application of stable isotope probes and stable isotope fractionation to i
microbial populations c
• Application of physical methods to structure determination using NMR, EPR, and e a
x-ray crystallography
n l
• Biochemical reactions involved in the biodegradation of the major groups of aliphatic,
s
alicyclic, carbocyclic, aromatic, and heterocyclic compounds t

Broad and expansive, this fully updated second edition addresses the persistent environmental
threat of organic chemicals with a fresh approach to evaluating degradation and transformation
processes. It examines a wide range of chemical as well as abiotic and microbiological reactions
mediated by microorganisms. Emphasizing the pathways used and the broad classes of
enzyme involved, it provides an overview of experimental procedures with detailed coverage
of xenobiotic organic compounds. Second Edition
K11270
ISBN: 978-1-4398-2637-9
90000
9 781439 826379
K11270_Cover_mech.indd 1 7/27/12 1:36 PM
Organic Chemicals
in the Environment
Mechanisms of Degradation
and Transformation
Second Edition

Organic Chemicals
in the Environment
Mechanisms of Degradation
and Transformation
Second Edition
Alasdair H. Neilson and Ann-Sofie Allard
Boca Raton London New York
CRC Press is an imprint of the
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Contents
Preface....................................................................................................................................................xxv
Acknowledgment..................................................................................................................................xxvii
Authors...................................................................................................................................................xxix
Section I Degradation and Transformation Processes
1 Abiotic Reactions: An Outline.........................................................................................................3
1.1. Introduction..............................................................................................................................3
1.2. Photochemical.Reactions.in.Aqueous.and.Terrestrial.Environments.....................................3
1.3. The.Diversity.of.Photochemical.Transformations...................................................................4
1.3.1. The.Role.of.Hydroxyl.Radicals..................................................................................4
1.3.2. Illustrations.of.Photochemical.Transformations.in.Aqueous.Solutions....................5
1.3.2.1. Chloroalkanes.and.Chloroalkenes............................................................5
1.3.2.2. Arenes........................................................................................................5
1.3.2.3. Nitroarenes................................................................................................5
1.3.2.4. Heteroarenes..............................................................................................6
1.3.2.5. Organofluorines.........................................................................................7
1.3.2.6. Organochlorines........................................................................................8
1.3.2.7. Organobromines........................................................................................9
1.3.2.8. Miscellaneous............................................................................................9
1.4. Hydroxyl.Radicals.in.the.Destruction.of.Contaminants........................................................10
1.4.1. Fenton’s.Reagent......................................................................................................10
1.4.2. Polyoxometalates.(Heteropolyacids).........................................................................11
1.4.3. Photolytic.Degradation.on.TiO................................................................................11
2
1.5. Other.Photochemically.Induced.Reactions...........................................................................12
1.6. The.Role.of.Humic.Matter:.Singlet.Dioxygen........................................................................14
1.7. Interactions.between.Photochemical.and.Other.Reactions....................................................14
1.8. Reactions.in.the.Troposphere................................................................................................15
1.8.1. Survey.of.Reactions..................................................................................................16
1.8.2. Survey.of.Reactants..................................................................................................17
1.8.2.1. Aliphatic.Hydrocarbons...........................................................................17
1.8.2.2. Aromatic.Hydrocarbons...........................................................................18
1.8.2.3. Biogenic.Terpenes....................................................................................18
1.9. Reentry.of.Tropospheric.Transformation.Products...............................................................19
1.9.1. Halogenated.Alkanes.and.Alkenes..........................................................................20
1.9.2. Arenes.and.Nitroarenes...........................................................................................21
1.9.3. Alkylated.Arenes.....................................................................................................22
1.9.4. Sulfides.and.Disulfides.............................................................................................22
1.10. Chemically.Mediated.Transformations.................................................................................23
1.10.1. Hydrolysis................................................................................................................23
1.10.2. Reductive.Displacement:.Dehalogenation.and.Desulfurization..............................26
1.11. Reductive.Dehalogenation.....................................................................................................26
1.11.1. Zero-Valent.Metals..................................................................................................26
v
vi Contents
1.11.2. Chromous.Chloride..................................................................................................27
1.11.3. Porphyrins.and.Corrins............................................................................................27
1.12. Thiol.and.Sulfide.Reductants.................................................................................................28
1.12.1. Homogeneous.Dechlorination.................................................................................28
1.12.2. Heterogeneous.Dechlorination................................................................................28
1.13. Reductive.Desulfurization.....................................................................................................29
1.13.1. Reductions.Other.than.Dehalogenation...................................................................29
1.13.2. Nucleophilic.Reactions............................................................................................30
1.13.3. Oxidations.................................................................................................................31
1.13.3.1. Anodic.Oxidation.....................................................................................31
1.13.3.2. Ozone........................................................................................................31
1.13.3.3. Hydrogen.Peroxide..................................................................................33
1.13.3.4. Manganese.Dioxide.................................................................................33
1.13.3.5. Sulfate.Radicals.......................................................................................33
1.13.4. Halogenation............................................................................................................33
1.13.5. Thermal.Reactions...................................................................................................35
1.13.5.1. Gas.Phase.................................................................................................35
1.13.5.2. In.Water...................................................................................................36
1.13.6. Electrocatalytic.Reactions.......................................................................................38
1.14. Sonication..............................................................................................................................39
1.15. References..............................................................................................................................39
2 Biotic Reactions: An Outline of Reactions and Organisms........................................................53
Part.1:.Microbial.Reactions...............................................................................................................53
2.1. Introduction............................................................................................................................53
2.2. Definitions:.Degradation.and.Transformation.......................................................................53
2.3. Biodegradation.of.Enantiomers:.Racemization.....................................................................56
2.3.1. Enantiomers.and.Racemases...................................................................................56
2.3.1.1. Biodegradation.of.Enantiomers...............................................................56
2.3.2. Racemization...........................................................................................................57
2.3.2.1. d-Amino.Acids........................................................................................57
2.3.2.2. Additional.Roles.for.d-Amino.Acids......................................................58
2.3.2.3. Cofactor-Independent.Racemization.......................................................58
2.4. Sequential.Microbial.and.Chemical.Reactions.....................................................................59
2.5. The.Spectrum.of.Organisms...................................................................................................61
2.5.1. Bacteria.in.Their.Natural.Habitats............................................................................61
2.5.2. Marine.and.Oligotrophic.Bacteria...........................................................................63
2.5.3. Lithotrophic.Bacteria...............................................................................................64
2.5.4. Phototrophic.Organisms..........................................................................................65
2.5.4.1. Oxygenic.Algae.and.Cyanobacteria........................................................65
2.5.4.2. Phototrophic.Anaerobic.Bacteria............................................................68
2.5.4.3. Aerobic.Nonoxygenic.Phototrophs..........................................................68
2.5.5. Aerobic.and.Facultatively.Anaerobic.Bacteria........................................................70
2.5.5.1. Gram-Positive.Aerobic.Bacteria..............................................................70
2.5.5.2. Gram-Positive.Facultatively.Anaerobic.Organisms................................75
2.5.6. Gram-Negative.Aerobic.Bacteria.............................................................................76
2.5.6.1. Azotobacter..............................................................................................76
2.5.6.2. Burkholderia............................................................................................76
2.5.6.3. Rhizobia...................................................................................................77
2.5.6.4. Sphingomonads.......................................................................................77
2.5.6.5. Gram-Negative.Facultatively.Anaerobic.Bacteria...................................78
2.6. Microbial.Metabolism.of.C.Compounds..............................................................................81
1
2.6.1. Metabolism.of.C.Substrates....................................................................................81
1
Contents vii
2.6.1.1. Organisms................................................................................................81
2.6.1.2. CO.Assimilation.....................................................................................85
2
2.7. Anaerobic.Bacteria................................................................................................................90
2.7.1. Clostridia..................................................................................................................91
2.7.2. Anaerobic.Sulfate-Reducing.Bacteria.....................................................................91
2.7.3. Other.Anaerobic.Bacteria........................................................................................91
2.8. Organisms.from.Extreme.Environments:.Extremophiles.....................................................92
2.8.1. Psychrophiles...........................................................................................................92
2.8.2. Thermophiles...........................................................................................................94
2.8.3. Acidophiles..............................................................................................................96
2.8.4. Alkaliphiles..............................................................................................................98
2.8.5. Halophiles................................................................................................................98
2.9. Eukaryotic.Microorganisms..................................................................................................99
2.9.1. Metabolism.by.Fungi...............................................................................................99
2.10. References.............................................................................................................................101
Part.2:.Reactions.Mediated.by.Other.Biota.....................................................................................130
2.11. Aquatic.and.Terrestrial.Biota...............................................................................................130
2.11.1. Introduction............................................................................................................130
2.12. Metabolism.by.Fish...............................................................................................................132
2.13. Metabolism.by.Other.Organisms..........................................................................................135
2.13.1. Mussels....................................................................................................................135
2.13.2. Insects.....................................................................................................................135
2.13.3. Invertebrates............................................................................................................135
2.13.3.1. Isopods...................................................................................................136
2.13.3.2. Oligochaetes..........................................................................................136
2.13.3.3. Polychaetes............................................................................................136
2.13.4. Other.Organisms....................................................................................................136
2.14. References............................................................................................................................137
Part.3:.Plants.and.Their.Microbial.Interactions..............................................................................140
2.15. Introduction..........................................................................................................................140
2.16. Primary.Roles.of.Plants........................................................................................................141
2.16.1. Plant.Wax................................................................................................................141
2.16.2. Metabolism.............................................................................................................141
2.17. Secondary.Role.of.Plants.....................................................................................................144
2.17.1. Introduction............................................................................................................144
2.17.2. Degradative.Enzymes............................................................................................144
2.17.3. The.Role.of.Plant.Exudates.in.Degradation...........................................................145
2.18. Plant.Metabolites.as.Antagonists.........................................................................................146
2.18.1. Introduction............................................................................................................146
2.19. Group.1.................................................................................................................................147
2.19.1. Saponins..................................................................................................................147
2.19.2. Steroidal.Glycoalkaloids.........................................................................................147
2.19.3. Cyclic.Hydroxamates..............................................................................................148
2.19.4. Acetoxyalkenes.and.Acetoxyalkadienes.................................................................148
2.20. Group.II.Phytoalexins...........................................................................................................149
2.20.1. Cyanogenic.Plants...................................................................................................149
2.20.2. Rice.........................................................................................................................149
2.20.3. Grapevine................................................................................................................149
2.20.4. Potato.....................................................................................................................150
2.20.5. Crucifers.................................................................................................................150
2.20.5.1. Arabinopsis thaliana.............................................................................150
2.20.5.2. Brassica.spp............................................................................................151
2.20.6. Legumes..................................................................................................................151
viii Contents
2.21. Roles.of.Bacteria.Including.Biocontrol.Agents....................................................................151
2.21.1. Volatile.Metabolites................................................................................................152
2.21.2. Plant–Bacteria.Associations...................................................................................152
2.22. Plant.Endophytes..................................................................................................................153
2.22.1. Positive.Effects.on.Plants........................................................................................153
2.22.2. Biodegradation.of.Xenobiotics..............................................................................154
2.22.3. Nitrogen-Fixing.Bacteria.......................................................................................154
2.22.4. Solubilization.of.Phosphate...................................................................................156
2.22.5. Bacterial.Synthesis.of.Plant.Hormones.................................................................156
2.22.6. Ethylene.and.ACC.Deaminase..............................................................................158
2.22.7. Polyamines.............................................................................................................159
2.23. Microorganisms.with.Activity.as.Biocontrol.Agents..........................................................159
2.23.1. General.Mechanisms.............................................................................................159
2.23.1.1. Burkholderia cepacia sensu lato...........................................................160
2.23.1.2. Pseudomonas.spp...................................................................................161
2.23.1.3. Lysobacter.spp........................................................................................162
2.23.1.4. Streptomyces.spp....................................................................................163
2.23.1.5. Serratia marcescens..............................................................................164
2.23.2. Biocontrol.Agents.against.Bacterial.Infection.......................................................164
2.24. Siderophores.in.Plants:.Roles.of.Iron..................................................................................164
2.25. The.Role.of.Mycorrhizal.and.Other.Fungi...........................................................................165
2.25.1. Fungi.and.Yeasts.as.Control.Agents......................................................................166
2.25.1.1. Trichoderma.spp....................................................................................166
2.25.1.2. Yeasts......................................................................................................167
2.26. Conclusions...........................................................................................................................168
2.27. References.............................................................................................................................168
3 Mechanisms....................................................................................................................................185
Part.1:.Oxidation,.Dehydrogenation,.and.Reduction.......................................................................185
3.1. Introduction...........................................................................................................................185
3.2. Monooxygenation..................................................................................................................186
3.2.1. Monooxygenases.....................................................................................................186
3.2.2. Monooxygenation....................................................................................................186
3.2.3. Hydroxylation.of.Alkanes.......................................................................................187
3.2.3.1. Soluble.Diiron.Monooxygenases............................................................187
3.2.3.2. Membrane-Integral.Monooxygenases....................................................187
3.2.4. Flavoprotein.Monooxygenases...............................................................................188
3.2.4.1. Epoxidation.of.Alkenes..........................................................................188
3.2.4.2. Cycloalkanone.Monooxygenation..........................................................189
3.2.4.3. Thioamide.Monooxygenation.................................................................189
3.2.5. Other.Monooxygenases..........................................................................................190
3.2.6. Aromatic.Hydroxylases..........................................................................................193
3.2.6.1. Monooxygenation.of.Aromatic.Alkyl.Side.Chains...............................193
3.2.6.2. Ring.Hydroxylation.of.Aromatic.Hydrocarbons...................................194
3.2.6.3. Monooxygenation.of.Phenols.and.Related.Compounds........................195
3.2.6.4. Other.Hydroxylations/Monooxygenations............................................198
3.2.7. Hydroxylation.of.Hydroxybenzoates.and.Related.Compounds.............................198
3.2.7.1. Mechanisms.of.Hydroxylation..............................................................200
3.2.7.2. Cytochrome.P450.Hydroxylation..........................................................202
3.3. References............................................................................................................................207
3.4. Dioxygenation.......................................................................................................................217
3.4.1. Dioxygenases.in.Dihydroxylation.of.Arenes..........................................................217
Contents ix
3.4.2. Dihydroxylation.Enzymes......................................................................................217
3.4.2.1. Group.I....................................................................................................217
3.4.2.2. Group.II..................................................................................................218
3.4.3. Other.Reactions.Catalyzed.by.Dioxygenases........................................................220
3.4.3.1. Ring-Fission.Dioxygenases...................................................................222
3.5. References............................................................................................................................233
3.6. Oxidases,.Peroxidases,.and.Haloperoxidases......................................................................241
3.6.1. Oxidases.................................................................................................................241
3.6.2. Peroxidases.............................................................................................................244
3.6.3. Haloperoxidases.....................................................................................................245
3.7. References............................................................................................................................246
3.8. .Incorporation.of.Oxygen.from.Water:.Hydrolases,.Oxidoreductases,.and Hydratases.......250
3.8.1. Hydrolases..............................................................................................................250
3.8.1.1. Sulfatases...............................................................................................250
3.8.1.2. Amidases................................................................................................251
3.8.2. Oxidoreductases......................................................................................................251
3.8.2.1. Five-Membered.Heteroarenes...............................................................252
3.8.2.2. Pyridine.................................................................................................252
3.8.2.3. Quinoline...............................................................................................252
3.8.2.4. Isoquinoline...........................................................................................252
3.8.2.5. Purines...................................................................................................252
3.8.3. Hydratases..............................................................................................................253
3.9. References............................................................................................................................255
3.10. Electron.Acceptors.Other.than.Oxygen...............................................................................258
3.10.1. Inorganic................................................................................................................258
3.10.1.1. Nitrate.and.Related.Compounds............................................................258
3.10.1.2. Sulfate.and.Related.Compounds...........................................................260
3.10.1.3. Selenate.and.Arsenate...........................................................................262
3.10.1.4. Arsenite.................................................................................................264
3.10.1.5. Chlorate.and.Perchlorate.......................................................................265
3.10.1.6. V(V),.Mn(IV),.Fe(III),.Co(III),.Tc(VII),.and.U(VI).............................267
3.10.2. Organic.Acceptors.................................................................................................269
3.10.2.1. Dehalorespiration..................................................................................269
3.10.2.2. Dimethylsulfoxide.................................................................................271
3.10.2.3. Fumarate.as.Electron.Acceptor.............................................................271
3.10.2.4. Caffeate.as.Electron.Acceptor...............................................................273
3.10.2.5. Carnitine.as.Electron.Acceptor.............................................................273
3.10.2.6. Alkane.Sulfonates.as.Terminal.Electron.Acceptor...............................273
3.10.2.7. Nitroalkanes.as.Electron.Acceptor........................................................273
3.10.2.8. Humic.Substances.in.Redox.Reactions.................................................273
3.11. References............................................................................................................................275
3.12. Dehydrogenation..................................................................................................................286
3.12.1. Loss.of.H :.Desaturation........................................................................................286
2
3.12.1.1. Short-Chain.Alkanol.Dehydrogenases..................................................286
3.12.1.2. Degradation.of.Primary.Amines...........................................................288
3.12.1.3. Pyrroloquinoline.Quinone.(PQQ).Dehydrogenation............................288
3.12.1.4. Acyl-CoA.Dehydrogenases...................................................................289
3.12.1.5. Dehydrogenation.of.3-Oxosteroids........................................................289
3.12.1.6. Dehydrogenation.of.Arene.cis-1,2-Dihydrodiols..................................289
3.12.1.7. Aromatization.of.Cyclohexane.Carboxylate.........................................289
3.12.1.8. Formate.Dehydrogenase:.Distribution.and.Mechanism........................290
3.12.1.9. Anaerobic.Conditions.............................................................................291
3.12.1.10.Desaturases............................................................................................292