The Natural Selection of the Chemical Elements

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1 The Natural Selection of the Chemical Elements The Environment and Life's Chemistry R. J. P. WILLIAMS Emeritus Research Professor, University of Oxford and J. J. R. FRAÜSTO da SILVA Professor of Analytical Chemistry, Instituto Superior Teenico, Universidade Tecnica de Lisboa CLARENDON PRESS OXFORD 1996

2 v/ouccill!* List of units of energy and work and the values of some physical constants xxv Part I The principles of the natural selection of chemical elements into physical states and chemical combinations 1 The development of man's ideas concerning nature The early views The development of modern views The periodic table and the electronic structure of atoms Fields of force Secondary consequences of (orbital) motion restrictions: shapes of atomic combinations Fire (energy), temperature and pressure Light and radiant energy Fields and flow Order, disorder and Organisation of rest masses The evolving universe The limitations to understanding 27 2 Order in chemical Systems: elements and their combinations 32 A Elements and stoichiometric combination of elements Introduction to chemical binding The atomic and physical properties of the elements Atomic sizes and structures of the elements Ionisation potential and electron affinity Empirical covalent and van der Waals radii of atoms Shapes of molecules formed from Single elements The binding energies of the elements Summary of the properties of the elements and their natural selection The combination of different elements stoichiometric and non-stoichiometric Compounds General factors affecting the combination of two different atoms Electronegativity and size 47

3 xiv CONTENTS Combining ratios valence Variable valence in A/B Compounds Available Orbitals: structures Stoichiometric combination of two similar non-metal atoms Small covalent molecules: electronegativity and Charge distribution Shapes of small covalent molecules A m B Bond energy in covalent Compounds Assemblies of molecules: intermolecular forces Hydrogen bonding The formation of liquids: water The different kinds of liquids Hydrogen in Compounds other than water Summary of the outstanding features of non-metal Compounds Stoichiometric combination of very different elements: ionic Compounds Energetics of ionic Compounds Physical properties of ionic solids Variable valence and electronic conductivity in salts Partial covalence in ionic Compounds: coordination chemistry Ligand-fleld effects on structure Ligand-fleld energies 71 B Non-stoichiometric combination of elements Introduction Ternary salts and Silicates Intermediate cases between salts and covalent molecules: covalent solids A m B Combination of like metal atoms: alloys Liquids and Solutions Summary of order 77 3 The balance between order and disorder Introduction Order-disorder balance Spatial arrangements of the particles of a System Changes in entropy with changes in volume of a gas configurational entropy Temperature change and disorder thermal entropy Total entropy change of a System Physical states in balance latent heats Systems out of balance Thermodynamics of mixing Standard states of chemical substances Applications to chemical Systems: thermodynamic stability of Compounds Free energy and chemical equilibrium The equilibrium constant at different temperatures or pressures Chemical change and physical change 107

4 CONTENTS xv 3.6 Energy transfer: work Chemical energy transfer to mechanical energy (pv) Thermodynamic efficiency of transfer of energy: doing work Radiative energy and entropy Energy State distribution in materials: the construction of machines Summary of order/disorder equilibrium Phase equilibria Introduction Phases and chemicals in equilibrium The phase rule Chemical equilibria and components of chemical Systems The operational deflnition of component The number of phases Variability of chemical Systems: examples of Systems of more than one component Unitary Systems Binary Systems Ternary Systems Systems with more than three components Liquid crystals Summary of phase diagrams The effects of gravity The free-energy conditions and phases at equilibrium Stability of phases: free-energy changes with composition The co-operative character of phase transitions Supercooled phases glasses Summary of equilibrium conditions of phases Equilibria in dilute Solutions in water Introduction Factors that affect solubility generally Relative solubility in two liquid phases: partition coefficients Dilute Solutions containing more than one solute Equilibria between acids and bases in aqueous Solutions Formation of precipitates: solubility products Complex ion formation Selectivity of precipitation and complex ion formation Competitive equilibria Proton and hydroxide ion binding Conditional, apparent or effective stability constants Organic molecule associations Organic polymers in Solution Summary of solubility and complex association equilibria Acid-base equilibria and components in Solutions 174

5 xvi CONTENTS 5.7 Equilibria between oxidation states Oxidation-reduction potentials in water The H 2 /0 2 potentials in water at ph = Metal ion oxidation states at ph = C,N,0 and S oxidation states in aqueous Solutions Oxidation states, components and variance Combined acid-base and redox equilibria Redox potentials and complex ion formation The change from the H 2 S/S to the H 2 0/0 2 potential (or vice versa) Summary: variance in Solutions Limited phases, fields and compartments Introduction One-component Systems of limited volume Sizes of phases Shape of a limited phase alone and in contact with a bulk phase Surfaces and shapes of limited phases as variables Fields between limited phases in equilibrium Assemblies of limited phases Total variables in phase Systems of limited volume Factors governing phase interactions in fields: chemical selectivity of surface interactions Matching of shapes of elastic substances at equilibrium Further diversification through barriers: compartments Storage of free energy between compartments: an ability to do work Pressure and concentration gradients between compartments Chemical potential gradients between compartments Storage of mechanical energy (tension) Energy storage in a gravitational fleld The natural selection of chemical elements in compartments Energy storage by dilute components in compartments Osmotic pressure Electrical potential differences Equivalences of free energies Radiation energy stored in compartments Limited phases and compartments in biological Systems Very small phases: large molecules treated as phases 'Phase'behaviour of proteins and nucleotides Ordered sequences in polymers and assemblies An example of equilibrium self-assembly: viruses Summary: the incommensurate increase in variables The evolution of kinetic control and of Organisation 219 A Kinetic principles Introduction Change, time and flow The initial development in the natural selection of the atomic elements 222

6 CONTENTS xvii 7.3 Factors affecting reaction rates Kinetics and natural selection of chemical elements: functional value in living Systems 226 B Chemical kinetic controls Chemical barriers to reaction Molecularity and energy requirements Chemical selection of components for rate control Electron transfer The nature of water: a very special solvent for transport Selected chemical rates of diffusion in water and ion Channels: solvent exchange and message transmission The extension of the selectivity of chemical steps of diffusion: message reception and triggering Diversiflcation of element use through non-exchanging binding Slow exchange, structures and the requirements for catalysts: construction and reaction Systems Kinetics of organic Compounds in traps Chemical change in organic molecules Acid-base reactions: hydrolysis and condensation Oxidation/reduction reactions: further reaction Systems Two-electron changes Free-radical reactions Inorganic elements in organic and biological chemistry: summary of kinetic aspects Kinetic selection of the elements for survival Allosteric control of reactions: feedback to catalysts The effect of temperature Control of energy supply: synthesis Control over molecularity Chemicals and self-assembly of equipment 250 C Physical barriers Physical controls over reaction rates Introduction Diffusion in one phase in a Single compartment Restricted diffusion across boundaries between compartments Diffusion in media formed by different elements The nature of containing vessels: boundaries Control of diffusion in inorganic phases The flow of water The control of diffusion by organic phases Functional advantages of an increase in the number of (communicating) compartments Fields and flow Electronic and electrolytic circuits From simple flow to feedback control Feedback electronic circuits: an illustration Physical fields and feedback: a biological example Geological control and feedback: the physical water cycle on Earth 269

7 7.14 Physical control of diffusion and variance of Systems Physical feedback control in relation to chemical component feedback 2 72 D Organisation Linking metabolic change to creation of structure Nucleation of assemblies Shape Energy, radiation fields and flow in temperature gradients Energy capture and control Energy flow and shape Thermodynamics and Organisation Plans and Information Thermodynamic efficiency and the ability to change State The trapping of energy and the evolution of Organisation: a summary 284 Part II The observed natural selection of chemical elements in both abiotic and biotic Systems during their evolution 8 The evolution of inorganic chemicals on Earth Introduction The formation of the elements in the universe The abundance of elements in the universe The initial formation of Compounds and condensates The affinity of the elements for one another at different temperatures The formation of Earth The formation of sulphides The primitive atmosphere The nature of the early sea The early surface of the Earth Some non-equilibrated inorganic compartments of interest: an aside The later evolution of the Earth's chemicals The atmosphere today The nature of the sea today The nature of freshwater today The crust of Earth today Trace element fractionation in the rocks and soils of the crust The nature of soils and soil water Summary of element Separation in Earth's compartments today The elementary composition of living Systems Clays and sulphides: origins of early life? Conclusion: Earth's evolution 320

8 CONTENTS xix 9 The evolution of organic Compounds Introduction The evolution of carbon chemistry: thermodynamics and kinetics The basic reactions of organic chemistry Major small organic chemicals: abiotic organic chemistry Saturated linear fatty chains (alkanes) Unsaturated and non-linear C/H chains Substitutional derivatives of C/H Compounds Shapes of organic molecules Handedness within shape: optical activity A general summary of organic chemical constructions Basic practices of organic and biological organic chemistry Introduction The apparatus of biological organic chemistry General introduction to bioorganic chemistry Condensation reactions in bioorganic chemistry Polyfunctional condensation Peptides and proteins Nucleic acids Weak bonds and the folded structures of polymers The properties of folded polymers Summary of condensation reactions fntermediates: carriers of fragments: cofactors and coenzymes Driving energy for biological reactions including condensation Introduction Energy from chemicals: disproportionation Initial sources of energy Phosphorus bioorganic chemistry Sulphur bioorganic chemistry Relative thermodynamic and kinetic stability of organic molecules in water Summary of the origins of acid-base organic chemistry Organic redox chemistry Redox reactions at low redox potential Organic redox chemistry and sulphur Free-radical reactions and polymerisations A note on selenium organic chemistry Summary of redox organic chemistry Nature's need for catalysts in organic chemistry Metal organic Compounds in biological catalysts Organometallic and co-ordination Compounds in organic chemistry Organic chemicals in Condensed phases Introduction Self-assembly of organic molecules The phase rule and organic molecules Abiotic organic chemical cycles Summary: the diversity of organic and biological chemistries 374

9 CONTENTS 10 Early biological chemistry: the uptake and incorporation of elements in anaerobic organisms Introduction The biological selection of major elements: general introduction Biological selection of minor elements Examples of essential functions of inorganic elements Osmotic pressure control Electrical neutrality Cross-linking and precipitation Electronic conduction Catalysis Energy capture synthesis and gradients Triggering of mechanical action Summary of required elements Uptake and incorporation mechanisms of the major elements Hydrogen and oxygen uptake and incorporation Uptake and incorporation of carbon and nitrogen: introduction C/H/O incorporation Nitrogen incorporation The uptake and incorporation of sulphur and selenium Interrelationships of C/H/O/N Compound incorporation The incorporation of phosphate Final stages of the incorporation of the major elements in polymers Summary of major element incorporation The uptake and incorporation of electrolytes Introduction to pumps Proton and other ion pumps Biological centres in proteins for metal ion incorporation Incorporation of metals into cofactors Elements in different oxidation states Summary of early element uptake and incorporation and of developing functional use Catalysis and metal ions Fitness of individual sites: the entatic State The incorporation of proteins into compartments Primitive development of energy sources Summary of uptake and incorporation of elements in anaerobic organisms Early cellular Organisation in anaerobes Introduction Co-operative stability in dissipative Systems The beginning of molecular copying Coded polymers: RNA life Syntheses of matching sequences of different polymers The beginnings of translation The selected elements for the coded polymers Control and regulation: introduction 428

10 CONTENTS xxi 11.5 Feedback control of element and small molecule concentrations The cell as a chemostat: feedback to pumps Feedback in metabolic pathways of the elements hydrogen, carbon and oxygen Feedback control of the incorporation of the element nitrogen and of amino acid synthesis Feedback control of nucleotides: incorporation into polymers Different pathways for degradation and synthesis in metabolism Phosphate metabolism and its feedback Additional elements in controls over pathways Redox potential controls Summary of acid-base and redox control The control of shape: mechanical controls Fields, flow and shape Early mineralisation Regulation: introduction Phosphate regulation of genes Other examples of regulation by non-metal elements Regulation by metal cations Redox regulation of protein production: sulphur and iron Control plus regulation an example: nitrogen fixation The different pathways of polymer synthesis and degradation Cross-talk in regulation The Integration of element chemistry in control and regulation: summary The cell cycle: introduction Developmental evolution of anaerobic cells Intracellular vesicles and their membranes Contents of internal vesicles Symbiosis and differentiation Summary The structure and chemistry of organisms after the advent of dioxygen Introduction Developing Organisation The geological record of evolution Development of intracellular compartments in aerobic cells The chemical problems of evolution The introduction of new metabolism Changing element availability with rising dioxygen partial pressure The chemical and biological reactions to dioxygen increase with time Coevolution of the use of new non-metal Compounds and metal elements Energy transduction from dioxygen 484

11 xxii CONTENTS 12.5 New uptake and incorporation of elements The new handling of iron uptake The linking of new iron uptake to phosphate: controls and regulation Iron uptake in higher organisms and its connections The uptake, distribution and incorporation of other elements Changes in the uses of some non-metals The distribution of elements in compartments Element distribution in eukaryote cells New small organic Compounds New proteins and enzymes Metabolite and protein distribution Putting together cells with filaments: multicellular Systems The redox metabolism outside cells Biomineralisation: introduction Biominerals: examples Summary Organisation in advanced organisms Introduction Control and regulation: a reminder The elements in message transmission Single eukaryotic cells: control and regulation The extended use of calcium as a messenger Phosphate metabolic and signalling changes Messages to mechanical devices Multicellular organisms Maintained cell shape: Single nerve cells The functional shapes of multicellular organisms and communication Extracellular fluids and multicellular communication Zinc and its organic messenger network Summary of acid-base messengers Redox Communications: free iron and the new messenger networks Haem iron and the new networks Copper and new messengers Other elements in messenger Systems 531 Interactions between and complexity of messenger Systems The integration of element messages in networks Total integration of element functions Organs and their elements 535 The problem of development Adaptability, differentiation and morphogenesis The problem of the development of an element network Conclusions concerning the element content of organisms The brain: a phenotypical Organisation centre Cellular dependencies: genetic management towards an ecosystem Summary: complexity, management and survival stability The ecosystem and man 547

12 CONTENTS xxiii 14 Man's selection of the chemical elements Introduction The internal chemistry of man The evolution of man's industrial inorganic chemistry Inorganic agricultural developments Catalysis and inorganic materials Man's development of energy sources using chemical elements Culture and inorganic materials The development of industrial organic materials Organometallic and complex ion chemistry: homogeneous catalysts Compartments, catalysts and energy Transfer of material Organisation and control in chemical change Genetic manipulation: a new industry? The parallel and the orthogonal activities of man and biology Element cycles and their evolution Introduction The nature of'cycles' The cycles of the rocks The cycle of water The cycle of air The cycle of oxygen The cycle of hydrogen The cycle of carbon The cycle of nitrogen The cycles of sulphur and phosphorus The cycles of light elements and metal ions The cycling of other elements The birth of cycles Life and the cycles Man's input to cycles The evolving natural selection of the chemical elements and the senses Introduction: summary ofprevious chapters The bases of the initial chemical selection Summary of variance at equilibrium Co-operativity and selected phase formation on Earth Steady states and their survival Flow Systems of many elements Coded Systems: DNA Natural selection and element fitness Optimal co-operativity in a steady State Summary of survival values Changes in components and evolution 616

13 16.11 Development rates and complexity DNA, development and evolution The environment and evolution Assumptions underlying the steady State Resources General considerations concerning waste products Selfish protection by individual species: population increase The natural selection of the elements and the nature of man Understanding Thesenses Thebrain Future selection of the chemical elements 632 Index 635

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