Chemistry of fossil fuels and biofuels

Chemistry of Fossil Fuels and BiofuelsFocusing on today’s major fuel resources – ethanol, biodiesel, wood, natural gas,petroleum products, and coal – this book discusses the formation, c

Chemistry of Fossil Fuels and Biofuels

Focusing on today’s major fuel resources – ethanol, biodiesel, wood, natural gas,petroleum products, and coal – this book discusses the formation, composition andproperties of the fuels, and the ways in which they are processed for commercial use.The book examines the origin of fuels through natural processes such as photosynthesisand the geological transformation of ancient plant material; the relationships betweentheir composition, molecular structures, and physical properties; and the variousprocesses by which they are converted or refined into the fuel products appearing ontoday’s market Fundamental chemical aspects such as catalysis and the behaviour ofreactive intermediates are presented, and global warming and anthropogenic carbondioxide emissions are also discussed The book is suitable for graduate students inenergy engineering, chemical engineering, mechanical engineering, and chemistry,

as well as for professional scientists and engineers

Harold H Schobert is Professor Emeritus of Fuel Science, The Pennsylvania StateUniversity, and Extra-ordinary Professor, Coal Research Group, North-West University

A recognized leading authority on energy technology, he has over 30 years’ experience inteaching and research on fuel chemistry

Arvind Varma, Purdue University

Editorial Board

Christopher Bowman, University of Colorado

Edward Cussler, University of Minnesota

Chaitan Khosla, Stanford University

Athanassios Z Panagiotopoulos, Princeton University

Gregory Stephanopolous, Massachusetts Institute of Technology

Jackie Ying, Institute of Bioengineering and Nanotechnology, Singapore

Books in Series

Baldea and Daoutidis, Dynamics and Nonlinear Control of Integrated Process Systems

Chau, Process Control: A First Course with MATLAB

Cussler, Diffusion: Mass Transfer in Fluid Systems, Third Edition

Cussler and Moggridge, Chemical Product Design, Second Edition

Denn, Chemical Engineering: An Introduction

Denn, Polymer Melt Processing: Foundations in Fluid Mechanics and Heat Transfer

Duncan and Reimer, Chemical Engineering Design and Analysis: An Introduction

Fan and Zhu, Principles of Gas-Solid Flows

Fox, Computational Models for Turbulent Reacting Flows

Leal, Advanced Transport Phenomena: Fluid Mechanics and Convective Transport

Mewis and Wagner, Colloidal Suspension Rheology

Morbidelli, Gavriilidis, and Varma, Catalyst Design: Optimal Distribution of Catalyst in Pellets, Reactors, and Membranes

Noble and Terry, Principles of Chemical Separations with Environmental Applications

Orbey and Sandler, Modeling Vapor-Liquid Equilibria: Cubic Equations of State and their Mixing Rules

Petyluk, Distillation Theory and its Applications to Optimal Design of Separation Units

Rao and Nott, An Introduction to Granular Flow

Russell, Robinson and Wagner, Mass and Heat Transfer: Analysis of Mass Contactors and Heat Exchangers

Schobert, Chemistry of Fossil Fuels and Biofuels

Slattery, Advanced Transport Phenomena

Varma, Morbidelli, and Wu, Parametric Sensitivity in Chemical Systems

Chemistry of Fossil Fuels and Biofuels

H A R O L D S C H O B E R T

The Pennsylvania State University

and

North-West University

Cambridge University Press

The Edinburgh Building, Cambridge CB2 8RU, UK

Published in the United States of America by

Cambridge University Press, New York

www.cambridge.org

Information on this title: www.cambridge.org/9780521114004

© H Schobert 2013

This publication is in copyright Subject to statutory exception

and to the provisions of relevant collective licensing agreements,

no reproduction of any part may take place without

the written permission of Cambridge University Press.

First published 2013

Printed and bound in the United Kingdom by the MPG Books Group

A catalog record for this publication is available from the British Library

Library of Congress Cataloging-in-Publication Data

Schobert, Harold H., 1943–

Chemistry of fossil fuels and biofuels / Harold Schobert.

p cm – (Cambridge series in chemical engineering)

ISBN 978-0-521-11400-4 (Hardback)

1 Fossil fuels–Analysis 2 Biomass energy 3 Energy crops–Composition.

4 Fuelwood crops–Composition I Title.

TP318.S368 2012

553.2–dc23

2012020435

ISBN 978-0-521-11400-4 Hardback

Cambridge University Press has no responsibility for the persistence or

accuracy of URLs for external or third-party internet websites referred to

in this publication, and does not guarantee that any content on such

websites is, or will remain, accurate or appropriate.

“The book is a welcome modern update to the available literature regarding the genesis,characteristics, processing and conversion of fossil and bio-derived fuels Its compre-hensive coverage of the chemistry involved with each of these aspects makes it animportant source for upper-level undergraduates, graduate students, and professionalswho need a strong understanding of the field It is an interesting read for anyone whoreally wants to understand the nature of fuels.”

Robert G Jenkins, University of Vermont

“There is no other book like this in field of energy science It is the perfect introduction

to the topic; but Professor Schobert has packed so much in, that it is just as much avaluable reference for more experienced professionals It touches on all aspects of fuelformation, transformation and use as well as strategies for managing the end product,carbon dioxide I will be using it as a text in my own teaching to both senior under-graduate and graduate students.”

Alan L Chaffee, Monash University, Australia

“This is an excellent reference for the student of modern fuel science or the practitionerwishing to sharpen their ‘big-picture’ understanding of the field The book offers aseasoned balance between technical rigor and readability, providing many helpfulreferences for the reader interested in further study I found the text engaging andenlightening, with the end-of-chapter notes a particularly thought-provoking andentertaining bonus.”

Charles J Mueller, Sandia National Laboratories

4.4 Issues affecting possible large-scale production of fuel ethanol 47

6 Composition and reactions of wood 69

ixContents

13.4 Measures of catalyst performance 217

17 Composition, properties, and classification of coals 295

18.5 Behavior of inorganic components during coal utilization 334

19.3.1 Fundamentals of the carbon–steam and related reactions 346

About twenty years ago I wrote a short book, The Chemistry of Hydrocarbon Fuels*,that was based on lectures I had been giving at Penn State University for a course onChemistry of Fuels In the years since, that book has long been out of print, and theenergy community has seen a significant increase in interest in biofuels, and concern forcarbon dioxide emissions from fuel utilization It seemed time, therefore, for a newbook in the area While this present book owes much to the earlier one, the changes are

so extensive that it is not simply a second edition of its predecessor, but merits a newtitle and new organization of chapters

The life cycle of any fuel begins with its formation in nature, followed by itsharvesting or extraction Many fuels then undergo one or more processes of refining,upgrading, or conversion to improve their properties or to remove undesirable impur-ities Finally, the fuel is put to use, usually in a combustion process, but sometimes byfurther conversion to useful materials such as carbon products or polymers Chemistry

of Fossil Fuels and Biofuels focuses primarily on the origins of fuels, their chemicalconstitution and physical properties, and the chemical reactions involved in theirrefining or conversion Most fuels are complex mixtures of compounds or have macro-molecular structures that are, in some cases, ill-defined But that does not mean that wethrow away the laws of chemistry and physics in studying these materials The compos-ition, molecular structures, and properties of fuels are not some curious, randomoutcome of nature, but result from straightforward chemical processes Any use ofthe fuels necessarily involves breaking and forming chemical bonds

This book has been written for several potential audiences: those who are new to thefield of fuel and energy science, especially students, who seek an introduction to fuelchemistry; practicing scientists or engineers in any field who feel that some knowledge

of fuel chemistry would be of use in their activities; and fuel scientists who have beenspecializing in one type of fuel but who would like to learn about other fuels I havepresumed that the reader of this book will have had an introductory course in organicchemistry, so is familiar with the basic principles of structure, nomenclature, andreactivity of functional groups I have also presumed that the reader is familiar withaspects of the descriptive inorganic chemistry of the major elements of importance infuels, and with some of the basic principles of physical chemistry As a textbook, thisbook would therefore be suitable for third- or fourth-year undergraduates or first-yeargraduate students in the physical sciences or engineering However, anyone with someelementary knowledge of chemistry and who is willing to refer to other appropriatetexts as needed could certainly derive much from this book

Our civilization once relied almost entirely on biomass fuel (wood) for its energyneeds Then, for about two centuries, the fossil fuels – coal, oil, and natural gas – havedominated the energy scene In recent decades biomass has experienced increasinginterest – a revival of interest in wood, as well as ethanol and biodiesel Anything that

we do in daily life requires use of energy, and, in most parts of the world, much of thatenergy derives from using fossil or biofuels Despite the critical importance of fuels,few, if any, texts in introductory chemistry or organic chemistry give more than passingmention to these resources So, I hope that this book might also be of use to chemists orchemical engineers curious to learn about new areas

This book does not intend, nor pretend, to provide encyclopedic coverage of fuelformation or of refining and conversion processes At the end of each chapter I haveprovided a number of suggested sources for those wishing to probe further Thematerial in the book is the distillation of having taught Chemistry of Fuels at leasttwenty times to students in fuel science, energy engineering, and chemical engineering.The course has changed somewhat each year, incorporating student feedback as appro-priate The person using this book, either as a textbook or for self-study, should becomeequipped with enough knowledge then to follow his or her interests with confidence inthe professional journals or monographs in the field

*The Chemistry of Hydrocarbon Fuels, London, Butterworths, 1990

I could not have done this without the help and support of my dear wife Nita, whoassisted in many, many ways This book has been developed from more than twentyyears’ worth of notes for a course, Chemistry of Fuels, that I taught at Penn StateUniversity Every year I started over again making entirely new notes for the lectures

My good friend and colleague, Omer Gu¨l, provided invaluable assistance in convertingmany of my hand-drawn sketches, used off and on for years, into diagrams for thisbook Two staff assistants, Carol Brantner and Nicole Arias, typed some of the versions

of hand-written notes and created some of the diagrams Their work was of great help

in pulling the manuscript together Lee Ann Nolan and Linda Musser, of the FletcherByrom Earth and Mineral Sciences Library at Penn State, helped in tracking downinformation, particularly biographical sketches of fuel scientists I am also indebted tothe staff of the Shakopee branch of the Scott County (Minnesota) Library, who made

me welcome and provided a quiet room to work on visits to Minnesota Many friendsand colleagues at Penn State, especially Gary Mitchell and Caroline Clifford, helped inmany different ways to provide information or ideas Professor Christien Strydom,Director of the School of Physical and Chemical Sciences, North-West University,Potchefstroom, South Africa, helped by providing office space and computer access,

as well as many splendid discussions Many other friends at North-West and at Sasolprovided assistance in various ways as well Mohammad Fatemi, President of MiddleEast PetroChem Engineering and Technology, generously provided the software used

to create the chemical structures and reactions The two people at Cambridge sity Press with whom I have worked, Michelle Carey and Sarah Marsh, deserve thanksfor their long-suffering perseverance that would make Job seem a pretty impatientfellow Finally, special thanks are due to the generations of students in Chemistry ofFuels, whose comments and suggestions were actually listened to, and often useful.Despite all this help, which I am very pleased to acknowledge and thank, any mistakesare my own

Univer-to use illustrations

Figure 1.1 U.S National Aeronautics and Space Administration, Greenbelt,

MarylandFigure 1.6 U.S National Oceanic and Atmospheric Administration, Boulder,

ColoradoFigure 2.1 Dr David Pearce, general-anesthesia.com

Figure 2.2 Dr Ian Musgrave, Adelaide, Australia

Figure 3.1 Lawrence Berkeley National Laboratory, Berkeley, CaliforniaFigure 6.1 Dr Wayne Armstrong, Palomar College, San Marcos, CaliforniaFigure 8.8 Dr Robert Sullivan, Argonne National Laboratory, Chicago, IllinoisFigure 12.4 Carmel Barrett, Marketing Director, Amistco, Alvin, Texas

Figure 13.6 Chris Hunter, Curator of Collections and Exhibitions, Schenectady

Museum and Suits-Bueche Planetarium, Schenectady, New YorkFigure 13.18 Bart Eggert, Aerodyne, Chagrin Falls, Ohio

Figure 14.1 Dean Rodina, German Postal History, Brush, Colorado

Figure 14.5 Jon Williams, Hagley Museum and Library, Wilmington, Delaware,

and Joseph McGinn, Sunoco Corporation, Philadelphia,Pennsylvania

Figure 14.8 Professor Carmine Collela, Facolta` d’Ingegneria, Universita` Federico,

Napoli, ItalyFigure 14.9 Dr Geoffrey Price, Department of Chemical Engineering, University

of Tulsa, Tulsa, OklahomaFigure 14.16 Dr Lars Grabow, Department of Chemical and Biomolecular Engin-

eering, University of Houston, Houston, TexasFigure 15.1 United Kingdom government (public domain)

Figure 15.3 David Aeschliman, Stamp.Collecting.World.com

Figure 16.7 Roger Efferson, Process Engineering Associates, Oak Ridge,

TennesseeFigure 16.8 Helmut Renner, Graphite COVA, Roethenbach/Pegnitz, GermanyFigure 16.9 Gareth Mitchell, The EMS Energy Institute, Penn State University,

University Park, PennsylvaniaFigure 17.1 Reprinted with permission from ASTM D720–91 (2010) Standard

Test Method for Free-Swelling Index of Coal, copyright ASTMInternational, West Conshohocken, Pennsylvania

Figure 17.6 Dr Caroline Clifford, The EMS Energy Institute, Penn State

University, University Park, Pennsylvania

Figure 17.10 Dr Atul Sharma, Energy Technology Research Institute, National

Institute of Advanced Industrial Science and Technology, Tsukuba,Ibaraki, Japan

Figure 17.11 Dr Mhlwazi Solomon Nyathi, Indiana Geological Survey, Indiana

University, Bloomington, IndianaFigure 17.12 Public domain

Siemens AG

Figure 19.17 Dr Fred Starr, Claverton Energy Group, www.claverton-energy

com/energy-experts-online

Figure 21.16 Manuela Gebhard, Max-Planck-Gesselschaft zur Fo¨rschung der

Wissenschaften, Mu¨nchen, GermanyFigure 22.5 Permission granted by www.dullophob.com

Figure 23.8 Jeannie Van Lew, Arizona Trailblazers Hiking Club, Chandler,

ArizonaFigure 23.9 U.S Library of Congress

Figure 25.1 Catherine Gatenby, US Fish and Wildlife Service

xixAcknowledgments for permissions to use illustrations

1 Fuels and the global carbon cycle

Fuels are substances that are burned to produce energy In many practical situations,

it can be advantageous first to carry out one or more processing steps on a fuel before

it is burned This might be done to improve the yield of the fuel from its source, toimprove the performance of the fuel during combustion, or to mitigate potentialenvironmental problems resulting from using the fuel Examples include processes toenhance the yield of gasoline from petroleum, to improve gasoline performance inengines, and to convert solid coal into cleaner gaseous or liquid fuels Some fuels,particularly natural gas and petroleum, also serve as important feedstocks for theorganic chemical industry, for producing a host of useful materials So, fuels can beused in at least three different ways: burned directly to release thermal energy;chemically transformed to cleaner or more convenient fuel forms; or converted tonon-fuel chemicals or materials These uses might appear quite different at first sight,but all have in common the making and breaking of chemical bonds and transform-ation of molecular structures The ways in which we use fuels, and their behaviorduring conversion or utilization processes, necessarily depend on their chemical com-position and molecular structure

The world is now in a transition state between an energy economy that, in mostnations, has an overwhelming dependence on petroleum, natural gas, and coal, to

a new energy economy that will be based heavily on alternative, renewable sources

of energy, including fuels derived from plants This book covers both Thedominant focus is on wood, ethanol, and biodiesel among the plant-derived fuels,and on coal, petroleum, and natural gas as traditional fuels If we were toassemble a collection of examples of each, at first sight they would appear to bewildly different Natural gas, a transparent, colorless gas, commonly containsmore than ninety percent of a single compound, methane, at least as delivered

to the user Ethanol, a transparent, volatile, low-viscosity liquid, is a singlecompound Petroleum is a solution of several thousand individual compounds.Depending on its source, the color, viscosity, and odor can be very variable.Biodiesel, a lightly colored, moderate viscosity liquid, contains only perhaps ahalf-dozen individual compounds Wood, a heterogeneous solid, is usually of lightcolor, but varies in density, hardness, and color, depending on its source Coalsusually are black or brown heterogeneous solids of ill-defined and variable macro-molecular structure

Despite these apparent differences, there are two very important points of ality First, all of these fuels occur directly in nature or are made from materials thatoccur in nature The second point becomes apparent when we consider the chemicalcompositions of representative samples, see Table 1.1

common-In every case the predominant element, on a mass basis, is carbon These two pointsestablish a starting place for a study of the chemistry of fuels: the transformations ofcarbon in natural processes We will see also that all of these have something else incommon – they represent stored solar energy.

The transformations of carbon in nature are conveniently summarized in a diagram

of the global carbon cycle, see Figure 1.1

The global carbon cycle establishes the fluxes of carbon among various sources thatintroduce carbon into the total environment, and among sinks, which remove or

Table 1.1 Chemical compositions, in weight percent, of representative samples of the major fuelscovered in this book The data for wood and coal do not include moisture that might be present in thesematerials, or ash-forming inorganic constituents

Carbon Hydrogen Oxygen Nitrogen Sulfur

get covered up and become Sedimentary Rock

Livestock (produce methane – CH4)

Agriculture – uses

CO2 and produces O2but also a source of CH4

sequester carbon An understanding of the directions of flow and annual fluxes amongthe sources and sinks has become especially important in recent decades, with increas-ing concern and focus on atmospheric carbon dioxide concentration and its conse-quence for global climate change The world can be thought of as consisting of: theatmosphere; the hydrosphere, dominated by the global ocean; the lithosphere, the crustand upper mantle of solid Earth; and the biosphere, living organisms on, and in, Earth.For the purpose of fuel chemistry, Figure 1.1 can be simplified to the cyclic process ofFigure 1.2.

Two equilibria of atmospheric carbon dioxide with natural systems will henceforth

be neglected: incorporation of carbon dioxide into carbonate rocks and its release whenthese rocks are transformed or destroyed; and dissolution of carbon dioxide into theocean, or its coming back out of solution Both processes have great importance in theglobal carbon cycle, but neither has a significant role in formation and use of fuels

In principle one can start at any point in a cycle and work through it, eventually toreturn to the start For this simplified global carbon cycle (Figure 1.2), the atmospheremakes the most convenient starting point A single compound, carbon dioxide, repre-sents 99.5% of the carbon in the atmosphere (though CO2itself is a minor component

of the atmosphere, about 0.035% by volume) Green plants remove carbon dioxidefrom the atmosphere by the process of photosynthesis The energy in sunlight drivesphotosynthesis, hence the prefix “photo.” (Chapter 2 discusses the chemical details ofphotosynthesis.) Arguably, photosynthesis is the most important chemical reaction onthe planet Though some life forms do not depend in some way on photosynthesis [endnote A], the majority certainly do Almost all living organisms either use photosynthesisdirectly or, like us, rely on other organisms that are capable of photosynthesis Ourfood consists of plants, or of parts of animals that themselves ate plants Direct use ofplants (e.g wood) or plant-derived substances (e.g ethanol and biodiesel) as fuelsmeans that we utilize the solar energy accumulated in the plants during their growth.Plants proceed through their life cycles and eventually die, or might be eaten byanimals that, in turn, live through their life cycles and die [B] The convenient euphem-ism “organic matter” denotes the accumulated remains of dead plants and animals.Eventually, organic matter decays, usually as a result of action of aerobic bacteria,releasing its carbon back to the atmosphere as carbon dioxide and closing the carboncycle The decay process is responsible for the fact that dead organisms disappear fromthe environment [C] On a walk in a forest, for example, we do not wade hip-deep in the

CO2dissolved in the ocean CO2in the atmosphere Carbonate rocks

Dead organisms Life cycle

to the atmosphere as CO2

3Fuels and the global carbon cycle

accumulated fallen leaves from decades’ worth of autumns – leaves from years past aregone because they have decayed.

Photosynthesis converts atmospheric carbon dioxide to glucose [D]:

6 CO2þ 6 H2O ! C6H12O6þ 6 O2:

Glucose is an example of a simple sugar Its molecular formula could be rewritten as

C6(H2O)6 as if it were some sort of compound of carbon and water The apparentcompositional relationship of sugars to a hydrated form of carbon gives the name ofthis class of compounds – carbohydrates These sugars play an important role in thebiochemistry of plants, acting as an energy source and chemical starting material for thebiosynthesis of many other compounds involved in the life processes of the plant Althoughthe net equation for photosynthesis appears to be fairly simple, the chemistry of photosyn-thesis is vastly more complicated than implied by this simple equation Unraveling thechemistry of photosynthesis produced at least one Nobel Prize in chemistry Oxygen

is also a product of photosynthesis The evolution of photosynthetic organismsabout three billion years ago allowed oxygen to accumulate in the atmosphere; that

in turn made possible the development of life forms that utilize oxygen (including us).Any organism can consist of hundreds, thousands, possibly tens of thousands ofindividual chemical components Decay of accumulated organic matter involves theoxidation reactions of these thousands of compounds For simplicity, though, considerthe oxidative decay of glucose:

CO2 in atmosphere

Plants

photosynthesis

biomass utilization

Figure 1.3 Use of biofuels represents a “short-circuit” in the global carbon cycle CO2

produced by burning biofuels is removed from the atmosphere by photosynthesis when thenext crop of biomass is grown In principle there should be no long-term net increase inatmospheric concentrations of CO2

Most of the focus on biomass energy and biofuels is on plants or plant-derivedmaterials In part, this is because of the vastly greater mass of plant materialavailable, compared to animals However, in the developing world, animal dunghas been, and still is, dried and used as fuel; animal fat, lard, offers a superbreplacement for petroleum-derived fuel oils Two major considerations drive thecurrent interest in biofuels: First, in principle, biofuels are renewable For instance,

a crop of soybeans harvested this year for production of biodiesel fuel could be grown next year to produce more biodiesel, and again the year after that, and onand on Second, again in principle, biofuels have no net impact on atmosphericcarbon dioxide; i.e they are said to be CO2-neutral The amount of CO2released byburning a biofuel would be absorbed from the atmosphere during the growth of nextyear’s crop Both considerations can be challenged in practice Concerns can beraised about prospects of soil depletion and about the danger of long-term reliance

re-on mre-onocultures Over the whole life cycle of a biofuel, petroleum and natural gaswould probably be used in farming and transportation of the biomass, and in itsprocessing Despite these concerns, biofuels enjoy both increasing public interest andincreasing use

Currently, though, the mainstay of the energy economy in industrialized nations isenergy from coal, petroleum, and natural gas In the United States, about half of theelectricity used is produced in generating plants that burn coal All of the coke used asfuel and reducing agent in iron-making blast furnaces is made from coal Natural gasdominates for home heating, except in all-electric homes, and is growing in importance

in electricity generation About 98% of the transportation energy comes from eum products Oil sands, especially those in Canada, are rapidly increasing in import-ance Nothing in Figure 1.2, however, accounts for the world’s enormous deposits ofcoal, petroleum, natural gas, oil sands, and oil shales Multiple lines of evidence,especially for coals and petroleum, show that they derived from once-living organisms.This evidence is discussed in Chapter 8 Because these substances derive from organ-isms, commonly they are referred to as fossil fuels, from the definition of a fossil asbeing a remnant of past life preserved in the Earth’s crust Fossil fuels occur because thedecay process is not perfectly effective Some 98–99% of accumulated organic matterindeed decays as indicated in Figure 1.2 The remaining small fraction is preservedagainst decay, and, over geological time, turns into the materials that we recognizetoday as the fossil fuels Formation of fossil fuels can be considered as a detour in theglobal carbon cycle, see Figure 1.4

petrol-CO2dissolved in the ocean CO2in the atmosphere Carbonate rocks

Organic matter

Fossil Fuels

Life cycle Animals

Plants

Photosynthesis

Decay

Figure 1.4Formation of fossil fuels is a “detour” in the global carbon cycle About one percent

of accumulated organic matter does not decay, but is preserved in the Earth, where a succession

of biochemical and geochemical processes transforms the organic matter to fossil fuels

5Fuels and the global carbon cycle

Thus the origin of the vast deposits of fossil fuels on which we depend so much forour energy economy lies in the fact that a seemingly simple reaction – decay – goes

“only” 98–99% to completion Since the fossil fuels derive from once-living plants thathad accumulated energy from sunlight, fossil fuels themselves represent a reservoir ofstored solar energy

However, Figure 1.4 is not complete Even if <1% of the carbon proceeded throughthe detour to fossil fuels, running the cycle enough times eventually would result in allthe carbon being locked up in fossil fuels The missing link in Figure 1.4 is the eventualfate of the fossil fuels: they are extracted from the Earth and burned

Burning fossil fuels (Figure 1.5) inevitably liberates carbon dioxide Combustion ofmethane, the dominant ingredient of natural gas, provides an example:

CH4þ 2 O2! 2 H2O þ CO2:For the global carbon cycle to be at steady state, the rates of removing CO2from theatmosphere and adding it to the atmosphere must be equal The important step for CO2

removal is photosynthesis CO2 returns to the atmosphere from burning biomass orbiofuels, decay of organic matter, and burning fossil fuels When the flux of carbondioxide into the atmosphere exceeds the flux of carbon into the sinks, concentration of

CO2in the atmosphere necessarily must increase A wealth of solid evidence shows thatatmospheric CO2 has been increasing for some time, Figure 1.6 being an example.Carbon fluxes from the sources are indeed outrunning fluxes back into the sinks

In recent decades, multiple, independent observations from geology, meteorology,and biology show that profound changes are occurring on the planet These observa-tions include partial melting of the polar ice caps, shrinkage of glaciers, increasingdesertification, spreading of tropical diseases, and setting of new records for hightemperatures and for frequency of severe storms All of these observations are consist-ent with the notion that our planet is warming

The principal source of warmth on Earth is incoming radiation from the sun Tomaintain a heat balance, heat is radiated from Earth back into space, largely as infraredradiation Carbon dioxide is one of a number of gases, others including water vapor,methane, nitrous oxide, and chlorofluorocarbons, that trap infrared Increasing atmos-pheric CO2concentration acts to retain more heat, by reducing the amount of infraredenergy radiated back to space [E] Hence increasing CO2links with increasing warming.While global temperatures and atmospheric CO2 concentrations appeared to havecycled up and down a long way back into Earth’s history – long before humans evenevolved – a profound piece of circumstantial evidence connected with the present

CO2 dissolved in the ocean CO2 in the atmosphere Carbonate rocks

Organic matter

Fossil Fuels Fossil fuel combustion

Life cycle Animals

warming cycle is that the increase in atmospheric CO2 over the past several centuriesbegan at about the same time as the Industrial Revolution, which marked the beginning

of large-scale use of fossil fuels It took millions of years to form fossil fuels We havebeen burning them on a large, and ever-increasing, scale only for about 250 years Thusthe rate of CO2addition to the atmosphere currently outstrips the rate of CO2removal.Buttressing this circumstantial evidence [F], recent years have seen further evidenceadded for a link between increased atmospheric carbon dioxide and human use of fossilfuels Certainly, anthropogenic CO2emissions from fossil fuel combustion are not thesole cause of global warming Nevertheless, connections between global warming,atmospheric CO2, and fossil fuel use confront us with several energy policy options.One, of course, is to do nothing At the other end of the spectrum lies the argument that

we must stop using fossil fuels right now

History teaches us that some 60 to 70 years are needed for one fuel to replace another

as the dominant energy source In 1830, renewable fuels (mainly wood) dominatedworldwide primary energy sources, accounting for more than 90% of total energy Coalmade up most of the rest By 1900, the contribution from wood had dropped, and that

of coal had increased, to a point at which both energy sources were accounting fornearly 50% of world energy use, with a very small contribution from petroleum Coaldominated the world energy scene until 1965, when coal and petroleum each contrib-uted about 30%, with natural gas and renewables about 15% each Since 1965 petrol-eum has dominated the world energy scene Perhaps at the end of another 70 year cycle,sometime around 2035, we will witness a resurgence of renewable energy sources, notjust biomass, but also solar, wind, and other forms that do not involve combustion

It is likely that we are now somewhere in the “transition state” between an energyeconomy heavily dominated by fossil fuels and a new one based on alternative energysources Plants, or fuels derived from plants, will contribute to the alternativeenergy mix We need to understand the chemistry of these biofuels, but also torecognize that fossil fuels will be with us for decades to come, so we should be

380

Scripps Institution of Oceanography

NOAA Earth System Research Laboratory

Atmospheric CO2 at Mauna Loa Observatory

7Fuels and the global carbon cycle

concerned with their conversion to clean, efficient fuel forms Furthermore, we shouldrecognize that, at the end of the transition, fossil fuels will be important sources ofgraphite, activated carbon, and other carbon-based materials.

Notes

[A] The recently discovered Desulfatomaculum bacteria provide an example Theseremarkable organisms exist by reducing sulfate ions to hydrogen sulfide They haveflourished for several million years at depths to four kilometers in a gold mine nearJohannesburg Organisms able to manufacture their own compounds for use asenergy sources are called autotrophs By far the most familiar autotrophs are thegreen plants Microorganisms living near deep-sea vents, where conditions areextremely hostile for ordinary life (such as 400

C, 25 MPa, and pH 3), obtainenergy by using heat from the vents for oxidizing inorganic sulfides or methane.Organisms that rely entirely on chemical reactions to manufacture their biochem-ical energy sources are chemoautotrophs Especially weird are the radiotrophs,fungi found growing inside reactors at Chernobyl, Ukraine, that seem to utilize theenergy in radiation to help synthesize needed biochemical energy sources Organ-isms that must rely on eating other organisms to obtain a supply of energy areheterotrophs We are heterotrophs

[B] Sooner or later, biology catches up to all of us The expression “Mother Nature batslast,” the origin of which has been attributed to numerous individuals, has appeared

on bumper stickers for at least a decade Or, as the American author Damon Runyon(1880–1946) said, “in life, it’s 6 to 5 against,” meaning the odds are against us.[C] We will not consider the decay process in detail, because it destroys the rawmaterial (organic matter) needed eventually to produce coal, petroleum, and nat-ural gas For learning more about the decay process in nature, the book Life in theSoil (James B Nardi, University of Chicago Press) is an excellent place to start.[D] Note that oxygen is a co-product The first organisms using water as the source ofelectrons in photosynthesis – the cyanobacteria – evolved approximately threebillion years ago This development in the history of life allowed O2to accumulate

in the Earth’s atmosphere Chemically, this converted the atmosphere from areducing environment to an oxidizing one, with profound implications for thefurther evolution of life

[E] While it is common to speak of the greenhouse gases acting to trap infraredradiation, they neither trap all of the radiation nor trap it permanently Absorption

of infrared by a greenhouse gas molecule excites the molecule to a higher tional energy state Energy is released when the molecule returns to its ground state,but the energy is released in all directions, re-radiating a portion of it back to Earth.[F] Two of the finest minds of the nineteenth century provide contrasting opinions onthe validity of circumstantial evidence Henry David Thoreau tells us that, “Somecircumstantial evidence is very strong, as when you find a trout in the milk.” ButSherlock Holmes cautions that, “Circumstantial evidence is a very tricky thing

vibra-It may seem to point very straight to one thing, but if you shift your point of view alittle, you may find it pointing in an equally uncompromising manner to somethingentirely different.”

Recommended reading

Cuff, David J and Goudie, Andrew S The Oxford Companion to Global Change OxfordUniversity Press: New York, 2009 This is a very handy one-volume reference book withseveral hundred short articles, including useful material on the global carbon cycle, biomassand biofuels, and fossil fuels

McCarthy, Terence How on Earth? Struik Nature: Cape Town, 2009 An introductory book

on geology with superb color illustrations Chapter 3, on the Earth’s atmosphere andoceans, is relevant to the material in this chapter

Richardson, Steven M and McSween, Harry Y Geochemistry: Pathways and Processes.Prentice-Hall: Englewood Cliffs, NJ, 1989 A book on geochemical principles presented inthe context of thermodynamics and kinetics Chapter 4, on the oceans and atmosphere, andChapter 6, on weathering of rocks, are useful for understanding the global carbon cycle.Schobert, Harold H Energy and Society Taylor and Francis: Washington, 2002 An introduc-tory text surveying various energy technologies and their impacts on society and on theenvironment Chapter 34 discusses the global carbon cycle and introduces the concept ofbiomass energy being a short-circuit in the cycle

Vernadsky, Vladimir I The Biosphere Copernicus: New York, 1998 This book was firstpublished in 1926, and provides a remarkable discussion of how living organisms havetransformed the planet, including the geochemical cycling of elements and the ways in whichorganisms utilize geochemical energy The edition listed here is extensively annotated withexplanations and findings through the 1990s

Williams, R.J.P and Frau´sto da Silva, J.J.R The Natural Selection of the Chemical Elements.Clarendon Press: Oxford, 1996 This book presents aspects of the physical chemistry ofdistribution of chemical elements between living and non-living systems Chapter 15 onelement cycles includes a discussion of the global carbon cycle; other chapters also containuseful discussions of the partitioning of carbon between various natural systems

9Notes

2.1 Catalysis

The topic of catalysis recurs throughout fuel chemistry A catalyst increases the rate

of a chemical reaction without itself being permanently altered by the reaction, orappearing among the products The key word is rate Catalysts affect reactionkinetics A catalyst affects reaction rate by providing a different mechanism forthe reaction, usually one that has a markedly lower activation energy than that ofthe non-catalyzed reaction Catalysts do not change reaction thermodynamics; they

do not alter the position of equilibrium [A], but they can help reach equilibriummuch more quickly And, they cannot cause a thermodynamically unfavorablereaction to occur

Catalysts can be classified as homogeneous, in the same phase as the reactants andproducts, and heterogeneous, in a separate phase Homogeneous catalysts mix intim-ately with the reactants This good mixing often leads to enormous rate enhancements,

in some cases by more than eight orders of magnitude But, because they are in thesame phase as the reactants and products, industrial use would require a separationoperation for catalyst recovery downstream of the reaction, unless one were willing tothrow away the catalyst (possibly allowing it to contaminate the products) as it passesthrough the reactor For many catalytic processes, the catalyst costs much more thanthe reactants do, so loss of the catalyst would result in a significant economic penalty.Usually, heterogeneous catalysts have no major separation problems, thanks to theirbeing in a separate phase from reactants and products However, because of their being

in a separate phase, mass-transfer limitations can hold up access of the reactants to thecatalyst, or hold up departure of products Heterogeneous catalysis can also be affected

by various problems at the catalyst surface (discussed in Chapter 13) Large-scaleindustrial processing almost always favors use of heterogeneous catalysts, to avoidpossibly difficult downstream separation issues Nevertheless, steady progress is beingmade in finding ways to overcome separation problems with homogeneous catalysts,including, as examples, membrane separation, selective crystallization, and use ofsupercritical solvents

While, by definition, a catalyst remains unchanged at the end of a reaction, it can,and often does, change during a reaction Mechanisms of many catalytic reactions ofteninvolve many steps, which collectively comprise the catalytic cycle The catalyst mightundergo change during one or more of the elementary reaction steps of the mechanism,but at the end, when its action is complete, the catalyst must emerge in its original form,ready for another catalytic cycle

Most homogeneous catalytic reactions occur in the liquid phase Some reactionscan be catalyzed in the gas phase by homogeneous catalysts (which, because theyare homogeneous, must be gases themselves) Probably the most important example

of homogeneous catalysis in the gas phase is the chlorine-catalyzed decomposition

of ozone, the reaction responsible for the so-called ozone hole in the atmosphere [B].Various parameters can be used to describe quantitatively the quality or “goodness”

of a catalyst Turnover number, and the related turnover frequency, compare theefficiency of different catalysts Turnover number indicates the number of molecules

of reactant that one molecule of catalyst can convert into product The term “turnover”comes from the notion that the catalytic conversion is “turning over” reactant mol-ecules into product molecules Turnover frequency is the turnover number expressedper unit time Selectivity expresses the fraction of the desired product, usually in weightpercent or mole percent, among all products of the reaction Ideally, selectivity should

be as close to 1, or 100%, as possible Catalyst activity can be broadly defined in terms

of rate of consumption of the reactant(s) or rate of formation of products (These termshave slightly different meanings in the field of heterogeneous catalysis, and are revisited

in Chapter 13.) Ideal catalysts are those with high selectivity and high activity

2.2 Proteins

Biochemical reactions in living organisms rely on homogeneous catalysts calledenzymes Enzymes provide superb activity and selectivity Because most enzymes areproteins [C], we consider composition and structure of proteins first, leading into adiscussion of enzymes and their catalytic behavior

The building blocks of proteins are amino acids These compounds contain both anamine and a carboxylic acid functional group All naturally occurring amino acids ofbiochemical significance are 2-aminocarboxylic acids Derivatives of carboxylic acidshave sometimes been named using Greek letters to identify the positions on the carbonchain starting from the atom attached to the carboxylic group, with a- indicating thecarbon attached to the carboxylic acid, b- the next carbon in the chain, and so on.Hence 2-aminocarboxylic acids can be, and usually are, referred to as a-amino acids.Twenty naturally occurring a-amino acids are known, which differ in the nature ofthe organic substituent, generically called R, attached to the a-carbon atom [D].Alanine (2.1), leucine (2.2), and cysteine (2.3), provide examples

H3C

CH32.2 Leucine

CH C

O

OH

H2N

CH2 SH 2.3 Cysteine

112.2 Proteins

Amines can react with carboxylic acids to form amides, e.g the reaction of methylaminewith acetic acid:

CH3

O HO

O

N H

CH

CH C

CH

CH3CH

C O

of natural silk, has perhaps the simplest protein structure

C HN

O

O C

O O

[

]x

2.4 FibroinFibroin is a co-polymer of alanine and glycine, the two simplest amino acids.Proteins have numerous vital roles in living organisms Certainly their role as enzymecatalysts is one of the most important

Protein structure is considered at three levels The number and kind of the individualamino acids in the protein, and the way that they are linked together, determines

the primary structure Even small proteins are likely to contain more than 50 peptidelinkages The secondary structure of proteins arises from a very specific pattern offolding of the chain of amino acids into a helix or a pleated sheet Secondary structureindicates how various segments of the protein molecule become oriented Formation

of secondary structure comes from an attempt to maximize the number of possibleintramolecular hydrogen bonds between C¼O and H–N groups With large proteins,several secondary-structure helices might be joined together into a tertiary structurethat could arise from intramolecular electrostatic interactions, further hydrogenbonding, or even formation of covalent bonds such as the disulfide linkage, – S–S –.The tertiary structure describes how the whole protein molecule acquires its three-dimensional shape Folding the protein into its tertiary structure occurs so as to involvethe greatest possible loss of energy Of all possible tertiary structures of a protein, theone that actually forms is the one having the lowest DG of formation Disruption ofthe secondary or tertiary structure of the proteins, such as by heating or a change in pH,destroys their physiological functioning, a process known as denaturation Cooking eggwhites provides a familiar example of denaturation; the antiseptic action of “alcohol”(i.e isopropanol) on the skin comes from its ability to denature the proteins in bacteria.Proteins are further classified, based on structure, as either fibrous or globular.Fibrous proteins have long, thread-like structures that often lie adjacent to each other

to form fibers Strong intermolecular forces facilitate this structural arrangement.Fibrous proteins are usually insoluble in water They make the structural materials

in organisms, including muscle, skin, and tendons In contrast, globular proteins haveroughly spherical structures that result from strong intramolecular forces, but haveweak intermolecular forces Globular proteins dissolve in water and in many aqueoussolutions Enzymes that are proteins are invariably globular proteins

The excellent catalytic properties of enzymes derive from their molecular ation, which provides a site at which, usually, only a single kind of molecule canenter and react Enzymes are so specific that they catalyze reactions not just of oneparticular set of chemical bonds, but a set of bonds in a specific stereochemical configur-ation Emil Fischer [E] (Figure 2.1) was probably the first scientist to use the analogy of areactant fitting very specifically into the catalytic site on an enzyme in the way that a key fitsinto a lock

configur-In addition to great selectivity, many enzymes also demonstrate phenomenal activity, inexceptional cases enhancing reaction rates by 17 orders of magnitude Of all the substancesknown to catalyze reactions, whether homogeneous or heterogeneous, enzymes are themost effective Turnover frequencies can be of the order of 103 s 1, exceptional incomparison with many heterogeneous catalysts, for which values might be in the range

102–104hr 1 The very great enhancement of reaction rates by enzymes means that theycan have a noticeable effect even at very low concentrations, e.g 10 3 10 4mole percent.The compound on which the enzyme acts as a catalyst is known as the substrate.The nomenclature of enzymes involves adding the suffix –ase to a word that indicatesthe function of the enzyme, or its substrate As an example, the enzyme lactatedehydrogenase catalyzes the dehydrogenation (i.e oxidation) of the lactate ion

132.3 Enzymes

Enzymes fall broadly into six classes, summarized in Table 2.1 Almost every knowntype of organic reaction has an enzyme-catalyzed counterpart.

During the reaction, the enzyme interacts with the substrate molecule(s), bindingthem to a specific location, the active site, in the enzyme molecule Enzymatic reactionsoccur in three steps: formation of a complex between the substrate and the enzyme;converting the enzyme-substrate complex into an enzyme-intermediate complex, inwhich the configuration of the substrate molecule has changed; and finally formation

of an enzyme–product complex, from which the product dissociates

Interaction of enzyme with substrate could occur via hydrogen bonding, ionicattraction, or reversible covalent bonding Whatever the interaction that occursbetween the active site and the substrate, it is very specific for the substrate Further,

if the reaction is catalyzed by acid or by base, the active site must be capable ofsupplying the needed acidic or basic reactant The secondary or tertiary structure

of the enzyme strongly controls the orientation of the reactant molecules, such thatthey are stereochemically oriented for rapid reaction, and lead to a product having thebiochemically correct stereochemistry That is, the active site in the enzyme moleculehas to be a perfect stereochemical fit for the substrate – the lock has to be able to acceptthe key The sketch in Figure 2.2 shows this The complex formed between the enzymeand its substrate provides the optimum molecular orientation for reaction Usuallythe product detaches immediately from the enzyme, making the enzyme available for

Table 2.1 Classes of enzyme catalyst

Type of enzyme catalyst Reaction being catalyzed

Ligase linking two smaller molecules together

Lysase removing a small segment of a larger molecule

Oxidoreductase oxidation or reduction

Transferase transfer of a structural group from one molecule to another

Figure 2.1 Emil Fischer made enormous contributions to our understanding of proteinchemistry and of sugar chemistry in the late nineteenth and early twentieth centuries

another reaction A product tightly bound to the enzyme active site would effectivelyblock that site from participating in further reactions, shutting down the catalyticactivity of the enzyme The turnover frequency is often 103s 1per reactive site in theenzyme; the best enzymes might reach 105s 1.

Just as a lock will only accept the correct key, enzymes are usually extremely specific

in their action, such that any one particular biochemical reaction has its own ponding particular enzyme catalyst In some cases enzyme catalysis is so specific thatonly one compound will react with the enzyme For example, urease catalyzes hydroly-sis of urea, H2NCONH2, extremely well, yet has no effect for hydrolysis of methylurea,

corres-CH3NHCONH2 However, many enzymes can catalyze the reactions of substratesother than the desired one, provided that the changes in structure relative to the normalsubstrate occur in regions of the substrate molecule that do not affect the key-in-lock fit

of substrate to active site The catalytic activity of the enzyme might be reduced what, but the reaction still proceeds Situations occur in which a substrate binds strongly,often irreversibly, to the active site but does not undergo whatever reaction the enzymecatalyzes Substrates of this kind make the enzyme unable to perform its normal catalyticfunction Such substances are catalyst poisons; the analogous problem in heterogeneouscatalysis is discussed in Chapter 13 [F]

some-Rates of enzymatic reactions can be expressed in several ways The maximumvelocity, VMAX, represents the theoretical maximum rate when substrate concentration

is high enough such that the active site in the enzyme would be constantly occupied bysubstrate Maximum velocity is a specific property of a given enzyme, a function only ofthe amount of enzyme present in the system The Michaelis constant [G], KM, is thesubstrate concentration at which the measured rate of reaction is half the maximumvelocity Enzymatic reactions involving a single substrate follow Michaelis–Menten [H]kinetics, given by

n¼VMAXS=ðKMþSÞwhere n is the rate of reaction and S the concentration of the substrate When n isplotted as a function of S, in the initial stages of reaction the rate increases rapidly

as substrate concentration is increased, but, at some point, the rate becomes nearlyconstant and essentially independent of substrate concentration Figure 2.3 illustratesMichaelis–Menten kinetics for a hypothetical enzymatic reaction This behaviorreflects, first, a situation in which there is more available enzyme than substrate, sothat as substrate concentration increases, more and more of the enzyme can participate

in catalysis; but, second, at some point all of the enzyme is engaged in the reaction andfurther increases in substrate concentration can have no effect

Figure 2.2The way in which one specific key fits into a lock provides a model for the veryspecific structural relationships between an enzyme and its substrate

152.3 Enzymes

Since the majority of enzymes are proteins, it is worth considering why some, but

by no means all, protein molecules can act as catalysts (i.e enzymes) In other words,why aren’t all proteins enzymes? The answer lies in molecular structure, especially inthe secondary and tertiary structure that sets up the appropriate spatial conformation

of C¼O, NH, or other groups that, collectively, provide a site capable of modating and binding a specific substrate molecule The side chains on the individualamino acids may also be configured to create stronger intermolecular interactions withthe desired substrate molecules Stronger interactions between the substrate and the sidechains of the amino acids in the enzyme could enhance bond-breaking reactions in thesubstrate For some, not all, proteins, the secondary and tertiary structure is geometric-ally such that it forms the “lock” into which a specific biochemical “key” just fits In themany proteins that do not serve as enzymes, the secondary and tertiary structure may notprovide an appropriately configured binding site, or possibly cannot provide the acid orbase needed to complete a reaction

accom-Because enzyme activity depends on secondary or tertiary structure, denaturation

of an enzyme destroys its catalytic activity In most cases, denaturation cannot bereversed Exact conditions triggering denaturation are specific to each enzyme, buttypically denaturation occurs about 10–15

C above the temperature normally found inthe cell The temperature at which denaturation occurs can be reduced if major changes

in pH happen at the same time

In some enzymatic reactions, the enzyme must be activated by the addition, orpresence, of a second substance, the cofactor Some cofactors are inorganic ions, such

as Feþ2or Znþ2[I] Other cofactors are organic molecules, called coenzymes During thecatalytic process, the cofactor also attaches to the enzyme, and may experience eitheroxidation or reduction For us, the most important of the coenzymes are the vitamins.Interest in using enzymes in industrial processes is increasing Reactions using enzymesare not limited to occurring in living organisms Many enzymes have been isolated fromorganisms and are commercially available They can be used to catalyze reactions inaqueous solution or sometimes in organic solvents Enzymatic catalysis of reactionsrepresents an important component of the emerging field of green chemistry, which

includes among its goals using renewable raw materials, minimizing extra reagents orsolvents, and designing processes with very low energy requirements Green chemistry inturn is an important component of the broader field of sustainable development, which isintended to meet our present needs – certainly including energy, chemicals, and materials –without compromising society’s ability to meet the needs of future generations.

be alternately exposed to the reacting gases or shielded from them If the catalystcould alter the equilibrium composition of the mixture, the piston would move up ordown with the shift in equilibrium, creating a perpetual-motion machine

[B] The ozone “hole” is not, of course, a hole in the atmosphere, but the termdescribes a region of considerably diminished ozone concentration in the southernhemisphere, particularly over the Antarctic Ozone in the stratosphere helpsabsorb incoming ultraviolet radiation from the sun Exposure to high levels ofultraviolet radiation has been implicated as a cause of health problems such asskin cancer and cataracts Chlorine atoms from the breakdown of chlorofluoro-carbon gases, released as aerosol propellants, or from refrigeration and air condi-tioning units, act as homogeneous catalysts to facilitate ozone decomposition The

1995 Nobel Prize in chemistry was awarded to Paul Crutzen of the Netherlandsand the American scientists Mario Molina and Sherwood Rowland for their work

in understanding the formation and decomposition of ozone This award cameexactly one week after a prominent member of the United States Congressdenounced the concept of the ozone hole as “pseudoscience.”

[C] While the great majority of enzymes are proteins, this is not true of all enzymes

A particularly important exception is the ribosomes, cell components that ble proteins from amino acids

assem-[D] In solution, the simple amino acids exist in a dipolar structure formed by transfer

of a proton from the carboxyl group to the amino group, e.g RCH(NH3)þ

COO–.This type of structure is known as a zwitterion However, for convenience we usethe formula RCH(NH2)COOH, which seems to be a long-standing convention inmany organic chemistry textbooks

[E] Emil Fischer (1852–1919, Nobel Prize 1902) is probably best known for enormouscontributions to understanding the structure and chemistry of sugars He was alsoamong the first to determine that proteins form from the reaction of amino acids.While the lock-and-key model remains an excellent way of thinking about enzym-atic catalysis, it is not always correct Daniel Koshland (1920–2007) showed in 1960that some enzymes first accept the substrate molecule and then structurallyrearrange to fit the substrate, the induced-fit model

17Notes

[F] Many catalyst poisons harm both homogeneous and heterogeneous catalysts,because the basic effect is the same for either type of catalyst: the poison bindsstrongly to the active sites on the catalyst, blocking them from interacting with thedesired reactant molecules In fact, many catalyst poisons also poison us, examplesbeing carbon monoxide and hydrogen sulfide The underlying catalytic chemistry

is exactly the same These substances poison us because they destroy the activity ofthe enzymes on which our bodily functions depend

[G] Named in honor of Leonor Michaelis (1875–1949), a German biochemist whosecareer in the German scientific system was destroyed when, as a young man, hepublished work questioning the validity of a pregnancy test devised by a scientist verysenior in the establishment Michaelis first moved to Japan, and then to America,where he worked at Johns Hopkins University and at The Rockefeller Institute.[H] Maud Menten (1879–1960) was a Canadian biochemist who worked with Michaelis

in Berlin Also an excellent artist and musician, her contributions to science

in addition to her work on enzyme kinetics included studies of hemoglobin andthe regulation of blood sugar content She also participated in several expeditions tothe Arctic

[I] Many inorganic species serve as enzyme cofactors; other examples include copperand manganese Inorganic ions that serve as cofactors are sometimes calledessential minerals Their presence in the diet is critical for good health, specificallybecause of their role as cofactors

McMurry, John Organic Chemistry Brooks/Cole: Pacific Grove, CA, 2000; Chapter 26 Thediscussion of proteins and enzymes in this chapter is intended to focus on the roles of enzymecatalysis in biosynthesis and in fermentation; i.e to provide a background for the material

in the next several chapters Necessarily, an enormous amount of other information onenzymes and proteins was left out A good place to start to explore further is in the relevantchapters in modern introductory texts on organic chemistry Many good ones are available;this text by McMurry is a fine example

Palmer, Trevor and Bonner, Philip Enzymes Horwood Publishing: Chichester, UK, 2007

A comprehensive look at enzymes, including much useful information on their behavior anduses in both biochemistry and biotechnology

Rothenberg, Geri Catalysis: Concepts and Green Applications Wiley-VCH: Weinheim,Germany, 2008 An excellent introduction to catalysis, particularly as it applies to greenchemistry and sustainable development Chapters 3 and 5 are particularly relevant here

3 Photosynthesis and the formation

of polysaccharides

Photosynthesis is the single most important chemical process on Earth Almost all lifedepends on photosynthesis, directly in the case of plants, or indirectly, in the case ofanimals that eat plants, or that eat other animals that in turn eat plants In thegeochemical history of Earth, the rise of green plants and their production of oxygenfrom photosynthesis converted the atmosphere from chemically reducing to oxygen-rich, making life as we know it able to evolve As a carbon dioxide sink in the globalcarbon cycle, photosynthesis consumes about one hundred billion tonnes of carbonannually

Photosynthesis converts atmospheric carbon dioxide to glucose:

6 CO2þ 6 H2O ! C6H12O6þ 6 O2:Few other chemical processes appear so simple when written as a single equation,but are so extremely intricate in detail [A] The American chemist Melvin Calvin(Figure 3.1) received the 1961 Nobel Prize in chemistry for work in elucidating thereaction pathways in photosynthesis [B]

The remarkable nature of photosynthesis is further highlighted by the fact that thesimple photosynthesis reaction, as written above, is quite strongly endergonic Thechange in Gibbs energy, DG, is þ2720 kJ per mole of glucose (or þ454 kJ/mol CO2)

at 298 K The corresponding equilibrium constant would be predicted to be far to theleft-hand side Photosynthesis can only proceed with the input of a significant amount

Figure 3.1Melvin Calvin, who made enormous contributions to understanding the chemistry ofphotosynthesis Image courtesy of Lawrence Berkeley National Laboratory