Organic Geochemistry: Methods and Results

850 Pages·1969·20.617 MB·English

by  G. Eglinton, M. T. J. Murphy (auth.), Geoffrey Eglinton, Mary T. J. Murphy (eds.)

Organic Geochemistry
Methods and Results
Edited by
G. Eglinton and M. T.J. Murphy
Springer-V erlag Berlin Heidelberg GmbH 1969
With 246 Figures
ISBN 978-3-642-87736-0 ISBN 978-3-642-87734-6 (eBook)
DOI 10.1007/978-3-642-87734-6
This work is subiect to copyright. AII rights are reserved, whether the whole or part of the material is concerned,
specifically those of translation, reprinting, re-use of illustrations, broadcasting, reproduction by photocopying
machine or similar means, and storage in data banks.
Under § 54 of the German Copyright Law where copies are made for other than private use, a fee is payable to the
publisher, the amount of the fee to be determined by agreement with the publisher.
© by Springer-Verlag Berlin Heidelberg 1969
Originally published by Springer-Verlag Berlin· Heidelberg in 1969
Library of Congress Catalog Card Number 70-107318
Softcover reprint of the hardcover lst edition 1969
The use of general descriptive names, !rade names, trade marks etc. in this publication, even if the former are not
especially identified, is not be taken as a sign that such names, as understood by the Trade Marks and Merchandise
Marks Act, may accordingly be used freely by anyone. Title No. 1576.
Foreword
For many years, the subject matter encompassed by the title of this book
was largely limited to those who were interested in the two most economically
important organic materials found buried in the Earth, namely, coal and petroleum.
The point of view of any discussions which might occur, either in scientific
meetings or in books that have been written, was, therefore, dominated largely
by these interests. A great change has occurred in the last decade. This change
had as its prime mover our growing knowledge of the molecular architecture
of biological systems which, in turn, gave rise to a more legitimate asking of the
question: "How did life come to be on the surface of the Earth?" A second
motivation arose when the possibilities for the exploration of planets other than
the Earth-the moon, Mars, and other parts of the solar system-became a
reality. Thus the question of the possible existence of life elsewhere than on
Earth conceivably could be answered.
In the search for the answers to these questions the role of the organic com
pounds found amongst the various types of geological structures buried in the
Earth became a more central source of knowledge. It became necessary for the
geologist who could recognize and define the nature of the rock to consult with
the organic chemist who could isolate and determine the ultimate architecture of
the organic molecules in the rock; and the two together to listen to the biologist
as to the possible significance of their findings with regard to the basic questions
of evolution. Thus, what had once been the primarily economic motive for trying
to determine the origin of petroleum or of coal, that is, to facilitate further discovery
and use is giving way to a much broader and deeper question which will require
the best efforts of all three kinds of scientists.
This book constitutes really the first textbook to attempt to bring together
all three of the aspects-chemistry, geology and biology-which have a bearing
on the subject, following this new motivation. The last book bearing the same
title, that of Breger, was written in 1962 and was a sort of transition volume
between the older interest and the new. While the present volume is a multiple
authored one, its prime editors are to be congratulated on having produced a
selection of essays which form a comprehensive whole in a way that no other
such collection that I know of has done. Each of the essayists have written a
thoroughly authoritative piece of work in an area in which he is competently
working, and Drs. EGLINTON and MURPHY have organized them so as to make
them a unitary whole. In fact, the first chapter, which is called "Introduction",
is an extended table of contents containing a brief statement about the nature
of each chapter as well as an extensive table from which one can immediately
comprehend the place of each essay in the system.
VI Foreword
There is no doubt in my mind that this field will continue to grow and expand,
both in depth and in breadth, as well as in interest, and that this book may very
well provide the first textbook for an organized academic study of the subject.
October, 1969. MELVIN CALVIN
Laboratory of Chemical Biodynamics
University of California
Berkeley, California, USA
Preface
This book has proved to be a much bigger and more difficult enterprise than
we had foreseen and we thank the authors and publishers for their patience in
seeing it through to completion. The overall scheme was drawn up in Glasgow
in 1965 but various events, notably trans-Atlantic moves of both editors, delayed
the gathering and processing of the manuscripts. Most of the editing of the
manuscripts was handled at Glasgow University. Since then we have worked
on the book in Hartford (Connecticut), Berkeley (California), Austin and Houston
(Texas) and Bristol (England). During this time, several authors have moved
their laboratories and we are sorry to report that Dr. R. 1. MORRISON, the author
of the chapter on "Soil Lipids", has died.
Initially we set ourselves the task of gathering in the chapters within the space
of about six months. This, not unexpectedly, proved to be over-optimistic and
it was not until the middle of 1968 that most of the chapters were in our hands
and in their final form. In fact, the majority of the chapters cover the literature
up to about the end of 1967 and some to the end of 1968. In several cases the
authors have provided recent addenda.
In inviting contributors and in our editorial procedures, we have attempted
to bring about some uniformity in format and approach throughout the book.
The authors, though mainly from Great Britain and the United States of America,
belong to eight countries. Consequently, we have not been able to introduce an
entirely systematic presentation or bring about a consistent style. In any case,
differences would be expected in view of the range of disciplines represented in
the volume.
We thank Miss DEE WITNEY for her assistance in copy-editing, Miss ISABEL
MCGEACIDE, Mrs. WENDY HARRISON and Mrs. SUE SNEDDON for coping with
the seemingly interminable correspondence and Dr. K. DOURAGID-ZADEH,
Dr. A. G. DOUGLAS, Mr. W. HENDERSON, B. Sc., Mr. D. H. HUNNEMAN, B. Sc.,
Dr. A. MCCORMICK, Dr. 1. MACLEAN, and Mr. B. J. URQUHART, B. Sc., for their
assistance in preparing the manuscripts for publication.
We are especially grateful to BRENDA KIMBLE, B. Sc., for the extensive and
detailed copy-editing of the galley and page proofs at Bristol during 1969. We
also thank Dr. J. R. MAXWELL for the Subject Index.
Finally, we are most grateful to Professor CALVIN for the foreword, which
puts so neatly into words what we have tried to do.
November 1969
GEOFFREY EGLINTON, Sister MARY T. J. MURPHY,
University of Bristol, St. Joseph College,
Bristol, England. Hartford, Connecticut, USA.
Contents
CHAPTER 1
G. BoumON and M. T. J. MURPHY
Introduction
Layout 2
Analytical Methods . . . . . . . . . . . . . . . . . . . . 2
General Geological Processes and Principles . . . . . . . . . 2
Geological Abundance of Specific Classes of Organic Compounds 2
Specific Geological Situations . 3
Individual Chapters . . . . . . . . . . . . . . . . . . . . 3
CHAPTER 2
G.BoUNTON
Organic Geochemistry. The Organic Chemist's Approach
I. Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . 20
II. Organic Chemistry: Significance of Molecular Structure and the Representation of
Formulae . . . . . . 22
A. Carbon Compounds . 22
B. Stereochemistry . . . 25
C. Structural Isomerism . 26
III. Elucidation of Molecular Structure by Chemical and Physical Methods 26
A. Isolation and Separation of Lipids . . . . . . . . . . . . . . . 26
B. Characterization and Identification of Lipids . . . . . . . . . . 29
IV. Special Significance of Molecular Structure in Relating Geolipids to Biolipids 31
A. Carbon Skeleton Philosophy. Chemical Fossils and Biological Markers. . 31
B. Possible Relationships between BioIipids and GeoIipids. Alkanes of the Formula
C31H64(CnH2n+2; n= 31) . . . . . . . . . . . . . . . . . . . . . . . 33
C. Possible Relationships between BioIipids and GeoIipids. Cycloalkanes of the
Formula C27H4S(CnH2n-6; n= 27) . . . . . . . . . . . . . . . . . . . 34
D. Possible Relationships between BioJipids and GeoIipids. Branched Chain Carb
oxylic Acids of the Isoprenoid Type . . . . . . . . . . . . . . . . . . . . 35
E. Possible Relationships between Biolipids and Geolipids. Biopolymers. Proteins
and Polypeptides . . . . . . . . . . . . . . . . . . . . 39
V. Biosynthetic Rationalization of Biolipid Patterns . . . . . . . . 43
A. Main Biosynthetic Pathways and Resulting Biological Patterns 43
B. "Natural Product" Chemistry. . . . . . . . . . . . . . . 45
C. Chemotaxonomy, Paleochemotaxonomy, Chemosystematics, and Evolutionary
Processes . . . . . . . . . . . . . . . 46
VI. Organic Chemistry of Natural Environments . 46
A. Path of Carbon Compounds in Nature 46
B. Pollution of Environments . 49
VII. Organic Chemistry of Sediments . . . . 50
A. The Time-Scale . . . . . . . . . . 50
B. State of Organic Matter in Sediments 52
x Contents
C. Collection of Geological Samples and Extraction and Separation of Geolipids 53
D. Recent Sediments . . . . . . . . . . . . . 57
E. Ancient Sediments . . . . . . . . . . . . . 59
VIII. Geolipids - Biological or Non-Biological Origin? 63
A. The Problem . . . . . . . . . . . . . 63
B. Pre-Biological Era and the Origin of Life. 63
C. Biogenic-Abiogenic: The Present Situation 64
D. Biogenic-Abiogenic: Possible Criteria 67
E. Meteorites, the Lunar Sample, and Extraterrestrial Planetary Analysis 69
Acknowledgements 70
References . . . . . . . . . . . . 71
CHAPTER 3
M. T. J. MURPHY
Analytical Methods
I. Introduction 74
II. Extraction 75
III. Separation Methods 76
A. Clathration. . 79
B. Derivatives. . 80
C. Saponification 81
D. Esterification . 82
E. Special Derivatives 82
F. Ozonolysis . . . . 83
IV. Identification Methods 83
V. Contamination 85
References . . . . . . . 86
CHAPTER 4
A. L. BURLINGAME and H. K. SCHNOES
Mass Spectrometry in Organic Geochemistry
I. Introduction 89
II. Instrumentation and Techniques . . . . . . . 90
A. Conventional Instrumentation . . . . . . 90
B. Sample Handling and Introduction Systems 93
C. Principles of High Resolution Mass Spectrometry and Techniques of Data Acquisi-
tion and Processing . . . . . . . . . . . . . . . . . . . . . . . . . . 95
D. High Resolution Mass Spectra: Their Nature, Presentation and Interpretation 99
E. Application of High Resolution Mass Spectrometry . . 110
F. Gas Chromatograph-Mass Spectrometer Coupling. . . III
III. Characterization of Organic Matter from Geologic Sources 116
A. Hydrocarbons . . . . . . . . . . . . . . . . . . 116
1. Normal Hydrocarbons ............. 117
2. Branched Alkanes: Iso-, Anteiso-, Isoprenoidal Alkanes 117
3. Cyclic Hydrocarbons . . 125
4. Steranes and Triterpanes . 126
5. Olefins . . . . . . . 130
6. Aromatic Compounds . 132
B. Carboxylic Acids . . . . 133
C. Nitrogen Compounds . . 140
D. Porphyrins and Pigments. 143
Contents XI
E. Sulfur Compounds . . . . . . . . . . . 146
F. Other Classes of Compounds . . . . . . . 147
IV. Application to the Analyses of Extraterrestrial Materials 148
References . . . . . . . . . . . . . 149
CHAPTER 5
A. G. DOUGLAS
Gas Chromatography
I. Introduction 161
II. Definition of Terms 162
III. Apparatus . . . . 164
IV. Columns and Column Packings 167
V. Application of Gas-Liquid Chromatography to Organic Geochemistry 170
Bibliography 173
References 173
Addendum . 180
CHAPTER 6
W. E. ROBINSON
Isolation Procedures for Kerogens and Associated Soluble Organic Materials
I. Introduction . . . . . . . 181
II. Isolation of Kerogen . . . 182
A. Modified Quass Method 183
B. Sink-Float Method 184
C. Acid Treatment . 185
D. Pyrite Removal .. 186
III. Isolation of Bitumen . 186
A. Extraction Technique 187
B. Fractionation Technique 188
IV. Isolation of Acids 188
A. Extraction Techniques . 189
B. Fractionation Techniques . 189
V. Isolation of Porphyrins . 190
VI. Isolation of Amino Acids . . 191
A. Extraction Technique 191
B. Fractionation Techniques . 191
VII. Isolation of Carbohydrates 191
A. Extraction Techniques . 192
B. Fractionation Technique 192
VIII. Concluding Remarks 192
References . . . . . . . . . . 193
CHAPTER 7
M. O. DAYHOFF and R. V. ECK
Paleobiochemistry
I. Introduction ..... . 196
II. Biochemical Unity of Life . 200
III. Biochemical Evolution . . 203
IV. Increase in Genetic Material 205
V. Before the Proto-Organism . 207
XII Contents
VI. Evolution of Chemical Organization 209
A. Biochemical Inferences. . . . . 209
B. Astronomical and Geological Considerations 210
C. Fossil Evidence . . . . . . . 210
D. Model Laboratory Experiments 210
References . . . . . . . . . . . . 211
CHAPTER 8
W. D. I. ROLFE and D. W. BRETT
Fossilization Processes
I. Introduction . . . . . . . . . . . . 213
II. Taphonomy: The Study of Fossilization 215
III. Biostratinomy . . . . . . . . . . . 217
A. Biological Factors in Biostratinomy 218
1. Structure and Composition . 218
2. Autolysis . . . . . . . . 219
3. Viability. . . . . . . . . 220
4. Attack by Other Organisms 221
B. Physico-Chemical Factors in Biostratinomy . 224
1. Dynamic Selection and Mechanical Destruction. 224
2. Oxidation-Reduction and Hydrogen Ion Potentials 225
3. Microenvironment of the Decaying Organism 228
4. Salinity . . . . . . 229
5. Temperature Effects. 230
6. Selective Dissolution 230
IV. Diagenesis . . . . . . . 232
A. Diagenesis and Metamorphism 232
B. Geochemical Phases of Diagenesis . 233
C. Syndiagenesis. . . . . . 233
D. Later Diagenetic Processes 234
1. Cementation . . . . . 235
2. Recrystallization . . . 236
3. Replacement (Metasomatism) 236
4. Compaction 237
V. Weathering 237
References 238
Addendum .. 244
CHAPTER 9
B. J. BLUCK
Introduction to Sedimentology
I. Introduction 245
II. Clastic Rocks 246
III. Non-Clastic Rocks . 247
A. Siliceous Sediments 247
B. Iron-Bearing Sediments 248
C. Phosphatic Sediments 249
D. Evaporites ..... . 249
IV. Diagenesis . . . . . . . 250
A. Early Diagenesis: The Sediment-Water Interface 251
B. Early Diagenesis: Newly Buried Sediment 251
C. Late Stage Diagenesis . . . . . . . . . . . . 252