bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcendental functions
Authors: Steiner Erich
Published: September 2023

This chapter takes a closer look at transcendental functions that are used for the mathematical description of physical phenomena. It describes trigonometric functions, which are important in the physical sciences for the description of periodic motion, including circular motion and wave motion, as well as in the description of systems with periodic structure. The chapter also explains exponential functions which are useful for the modeling of all types of first-order rate processes, in which the rate of change (growth or decay) of a property is proportional to the value of the property. The chapter moves on to discuss the logarithmic function, which is involved in the definition and representation of fundamental physical concepts in thermodynamics, such as entropy and chemical potential. It ends with a brief discussion about hyperbolic functions.
Methods of integration
Authors: Steiner Erich
Published: September 2023

This chapter explains the general methods for calculating integrals. The aim of these methods of integration is to reduce a given integral to standard form or in other words, to transform it into an integral whose value is given in a table of standard integrals. It first considers the use of trigonometric relations for the integration of some trigonometric functions. Then it looks at the method of substitution, describing both trigonometric and hyperbolic substitutions. The chapter also explains the method of integration by parts. It discusses the reduction formula and rational integrands before moving on to the parametric differentiation of integrals.
Probability and statistics
Authors: Steiner Erich
Published: September 2023

This chapter introduces probability theory—the mathematical theory of statistics—that gives the theoretical models and analytical tools for the organization, interpretation, and analysis of statistical data. Probability theory is applied in chemistry for the description of the collective behaviour of very large numbers of particles in statistical mechanics, the quantum mechanical descriptions of changes of state and of rate processes, the physical interpretation of wave functions, and the enumeration of the ways of assembling basic chemical units to form large molecules. The chapter starts with a brief discussion on descriptive statistics. Then it tackles frequency and probability, as well as the combinations of probabilities. Furthermore, the discussion covers the binomial distribution. It describes permutations and combinations, as well as continuous distributions, then explains the Gaussian distribution. Lastly, it discusses the method of least squares.
The weightlifter
Authors: Maughan Ronald J. , Gleeson Michael
Published: September 2023

This chapter discusses skeletal muscle structure and function. Muscular strength is, to a large extent, determined by the size of the muscles and the ability to fully activate the muscles in a coordinated manner. Successful weightlifting requires a large muscle bulk and the ability to generate high power for a very limited period, usually less than a few seconds. Technique is also obviously important because, in competition, the weightlifter is required to demonstrate control of the posture and stance when lifting and holding the weight above the head. Muscle proteins provide the framework of the contractile machinery, and the chapter considers the structural and functional characteristics of these important biomolecules. It also looks at the energy needs for lifting heavy weights, with emphasis on the role of adenosine triphosphate (ATP) as the energy currency of the muscle (and all other) cells.
The endurance athlete
Authors: Maughan Ronald J. , Gleeson Michael
Published: September 2023

This chapter assesses the energy and oxygen cost of prolonged submaximal exercise, looking at the endurance athlete. Based on the physiological and biochemical demands of the events, the runners' distinction between middle-distance and long distance is a realistic one. At the longer distances, lasting about thirty minutes or more, anaerobic metabolism plays only a small role in energy supply. In the longer events, successful performers are characterized by a high capacity to use fat as a fuel. This requires a highly developed cardiovascular system to supply oxygen to the working muscles and a high activity in the muscles of the enzymes involved in oxidative metabolism. The chapter then considers fat oxidation, the metabolism of pyruvate derived from glycolysis, and the mechanisms of fatigue in prolonged submaximal exercise.
Variables, functions, and equations
Authors: Reed Martin B
Published: September 2023

This chapter reviews the measurement or calculation of values of variables to produce data-points from a 'function' point of view. It looks at standard types of function that can be used to describe the relationships between continuous variables that are found in all fields of science, noting that the simplest relationships are of proportionality. It also discusses an algebraic expression, which is any valid combination of numbers, parameters, and variables, together with arithmetic operators. The chapter defines the concept of a function f(x) and shows how it can be depicted by a line or curve with equation y = f(x), using Cartesian x- and y-axes. It describes the inverse proportion function as nonlinear; hence, itrequires a larger set of data-points, which will be joined up with smooth curves.
The Pharmaceutical Solid Phase
Authors: Moynihan Humphrey A. , Crean Abina M.
Published: September 2023

This chapter evaluates the pharmaceutical solid phase. Pure pharmaceutical substances may be either crystalline or amorphous solids. Crystalline solids possess regular, repeating order in three dimensions, whereas amorphous solids possess no such order. In a crystalline solid, the three-dimensional repeating pattern of the crystal is defined by the unit cell. These dimensions can be used to assign crystals to one of seven crystal systems. For any molecular structure, more than one crystal structure may be possible; this is known as crystal polymorphism. The chapter then looks at the different methods of characterizing pharmaceutical solids, including X-ray diffraction and thermal analysis. It also considers pharmaceutical crystallization and the solid-state properties of powder particles.
From structure to metabolic function: the globins
Authors: Dobson C. M. , Gerrard J.A. , Pratt A.J.
Published: September 2023

This chapter uses globins as an example to introduce the role of proteins in metabolism. It explains that globins are responsible for transporting oxygen in many multicellular organisms, collecting oxygen from the atmosphere to be delivered to the cells. It also explains the molecular mechanism by which the process of oxygen transport takes place, which is one of the best understood examples of the relationship between a structure of a protein and its function. The chapter explores the structures of myoglobin and haemoglobin and examines their physiological roles. It provides specific examples of how the basic principles of protein structure can be used to understand the complex functions of large macromolecules..
Proteins as catalysts
Authors: Dobson C. M. , Gerrard J.A. , Pratt A.J.
Published: September 2023

This chapter reviews how proteins adopt well-defined three-dimensional structures and are capable of binding small molecules reversibly at one or more specific sites on their surfaces. It refers to enzymes that generally catalyse specific reactions of particular molecules and the enhancements of the reaction rate that are often remarkably high. It also emphasizes the efficiency of enzymes as the rate-limiting factor in the catalysed reaction is the diffusion of the reactants to the enzyme. The chapter focuses on the appreciation of the chemistry of enzyme catalysis that provides insights into the biochemical details of cells and chemical catalysis. It looks at features of enzyme catalysis by illustrating triose phosphate isomerase in great detail.
Electrons in simple molecules
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter explains electrons in simple molecules. It highlights the significance of understanding the activity of electrons in a molecule to understand chemical structures and reactions. Moreover, the chapter looks into the molecular orbital description of bonding in relation to simple diatomic and larger molecules. It also explores how molecular orbital helped rationalize bonding in molecules by referencing the bonding and anti–bonding molecular orbitals. The chapter then notes the labels given to molecular orbital in relation to symmetry. It discusses the general rules for forming molecular orbitals while expounding the bonding of heteronuclear diatomics. Additionally, the chapter uses diagrams to clarify its discussion of bonding.
Reactions
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter explains the relationship between molecular orbital and chemical reactions. It shows how energies of the orbitals help us understand why the reaction occurs. Knowing the shapes is vital in understanding how the reaction takes place. Moreover, the chapter uses the formation of lithium borohydride to showcase chemical reactions. It notes the nucleophilic addition to a carbonyl group as one of the most significant reactions in organic chemistry. The chapter also analyses nucleophilic attack on carbonyl, carbon–carbon double bond, and acyl chlorides. It then turns to the process of nucleophilic substitution. Finally, the chapter hints at the possibility of a reversible reaction between carboxylic acid and alcohol.
Rates of reaction
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter discusses the factors influencing the rates of reaction. It notes the necessity of molecules colliding with correct orientation and sufficient energy so they can overcome the energy barrier. The chapter also mentions the steric requirements wherein reactions need reactants to approach a particular orientation. It points out how the presence of an energy barrier means that products have lower energy than the reactants. Additionally, the chapter explores the equations and order of rate law. It looks at the Arrhenius equation. This is because studies indicate the temperature dependence of rate constants. The chapter then differentiates between elementary and complex reactions before tackling reversible reactions in relation to the equilibrium constant.
Substitution and elimination reactions
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter explores substitution and elimination reactions. It notes nucleophilic substitution by referencing the reaction between bromomethane and hydroxide alongside the carbon–bromine bond. The chapter notes the stabilization of positive charges, adjacent lone pairs, and adjacent bonds–conjugation. Additionally, it examines the elimination reactions by referencing the reaction between t–butyl bromide and hydroxide. It also includes the addition reactions–elimination in reverse while noting Markovnikov’s Rule. It demonstrates the equation behind the rate of elimination. Moreover, the chapter uses diagrams and equations to clarify the process of substitution and elimination.
The effects of the solvent
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter focuses on the effects of the solvent. It regards solvent as a crucial component of reactions while referencing the reaction of t–butyl chloride. The rate of formation of either the substitution or elimination product depends only on the rate of the initial step. The chapter highlights the importance of the solvent being a result of the solubility of one substance in another. It lists different types of solvent as they are classified through their polarity and relative permittivity. Types of solvents include hydrogen bonds, protic solvents, and aprotic solvents. Additionally, the chapter examines the solvating of different ions, acid strengths, and the role of solvents while noting the impact of solvents on the rate of reactions.
α-Carboxy protection
Authors: Jones John
Published: September 2023

This chapter describes the amino groups of amino acids and peptides as more nucleophilic than their carbonyl groups when it comes to acylation. It explains how amino acids and peptides with unprotected carboxy groups can be used for peptide bond formation if separately preactivated carboxy components are employed. It also cites esterification as the usual means of carboxy protections, wherein the parent carbolic acid can be regenerated from the esters by acyl-oxygen or alkyl-oxygen fission. The chapter considers the fundamental alkyl-oxygen cleavage chemistry as qualitatively the same as that for alkoxycarboxyl groups, which are esters of a special kind. It notes that there is no significant distinction between methyl and ethyl esters.
Peptide bond formation
Authors: Jones John
Published: September 2023

This chapter considers the application of peptide bond forming procedures that involve the generation and aminolysis of reactive carboxy derivatives in peptide synthesis. It explains activation, which is the attachment of a leaving group to the acyl carbon of the carboxy component. This enables the attack by the amino group of the amino component. The chapter also discusses why activation is necessary, pointing out that ordinary carboxylic acids form salts with amines at ambient temperature, but that the heating required to transform these salts directly into amides is incompatible with the presence of other functional groups or any structural subtlety. The chapter highlights acidic catalysis, which is effective in bringing about the acylation of simple alcohols by carboxylic acids without the need for other activation. It mentions the activation in coupling that is achieved by the reaction of the carboxy component with an electrophilic reagent.
Solution peptide synthesis
Authors: Jones John
Published: September 2023

This chapter reviews the classical solution approach, wherein hundreds of peptides and proteins are synthesized. It discusses oxytocin, which is involved in the control of uterine contraction during labour and milk release afterwards. It considers oxytocin as the first peptide hormone to be synthesized in 1853 by Vincent du Vigneaud and his collaborators. The chapter refers to gastrins as peptide hormones that can be isolated from the antral region of the stomach. These hormones stimulate gastric secretion. The chapter looks at the first Liverpool synthesis of porcine gastrin as an example. It also discusses insulin, which is involved in the regulation of blood glucose levels and used clinically to control diabetes mellitus.
Organic Chemistry
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

Organic Chemistry begins with the question: what is organic chemistry? Topics covered include organic structures, molecular structures, organic reactions, nucleophilic substitution, and stereochemistry. There are also chapters on conformational analysis, elimination reactions, formation and reactions of enols and enolates, and chemoselectivity. The text moves on to consider regioselectivity, alkylation and reaction of enolates, retrosynthetic analysis, and aromatic horocycles. There is also coverage of stereoselectivity, diastereoselectivity, pericyclic reactions, and radical reactions. Finally, towards the end, the text looks at synthesis and reactions of carbenes, how to determine reaction mechanisms, organometallic chemistry, asymmetric synthesis, and organic chemistry today.
What is organic chemistry?
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter provides an overview of organic chemistry. Organic chemistry started as the chemistry of life, which was once thought to be different from the chemistry in the laboratory. Then it became the chemistry of carbon compounds, especially those found in coal. But now, it is both. It is the chemistry of the compounds formed by carbon and other elements such as those found in living things, in the products of living things, and other places where carbon is found. The chapter then looks at organic compounds before considering the relationship between organic chemistry and industry. It also presents the periodic table.
Organic structures
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter discusses the process of interpreting organic structures and drawing organic molecules. Organic chemistry is the study of compounds that contain carbon. Nearly all organic compounds also contain hydrogen; most also contain oxygen, nitrogen, or other elements. Organic chemistry concerns itself with the way in which these atoms are bonded together into stable molecular structures, and the way in which these structures change in the course of chemical reactions. The chapter then looks at hydrocarbon frameworks and functional groups. It also considers how carbon atoms carrying functional groups can be classified based on oxidation levels, before explaining the process of naming compounds.
Using organometallic reagents to make C–C bonds
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter addresses one of the most important ways of making carbon–carbon (C–C) bonds: using organometallics, such as organolithiums and Grignard reagents, in combination with carbonyl compounds. Carbon dioxide reacts with organolithiums and Grignard reagents to give carboxylate salts. Protonating the salt with acid gives a carboxylic acid with one more carbon atom than the starting organometallic. Meanwhile, aldehydes and ketones react with organometallic reagents to form secondary and tertiary alcohols, respectively. The chapter then looks at the oxidation of alcohols. Oxidation of primary alcohols gives aldehydes and then carboxylic acids, while oxidation of secondary alcohols gives ketones. It is important to note that we cannot oxidize tertiary alcohols without breaking a C–C bond.
Conjugate addition and nucleophilic aromatic substitution
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter addresses conjugate addition and nucleophilic aromatic substitution. Conjugate additions occur only when the C=C double bond is immediately adjacent to the C=O group. They do not occur to C=C bonds that are not conjugated. Compounds with double bonds adjacent to a C=O group are known as α,β-unsaturated carbonyl compounds. Most types of nucleophiles can be made to undergo conjugate additions with α,β-unsaturated carbonyl compounds. Conjugate addition is also known as Michael addition. The chapter then demonstrates why alkenes conjugated with carbonyl groups behave differently from unconjugated alkenes. It also looks at conjugate substitution reactions, nucleophilic epoxidation, and diazonium compounds.
Alkylation of enolates
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter studies the alkylation of enolates. The alkylations in the chapter each consists of two steps. The first is the formation of a stabilized anion—usually (but not always) an enolate—by deprotonation with base. The second is a substitution reaction: attack of the nucleophilic anion on an electrophilic alkyl halide. All the factors controlling SN1 and SN2 reactions are applicable here. Problems that arise from the electrophilicity of the carbonyl group can be avoided by replacing C=O by functional groups that are much less electrophilic but are still able to stabilize an adjacent anion. The chapter then looks at the alkylation of nitriles and nitroalkanes.
Retrosynthetic analysis
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter examines retrosynthetic analysis. The best synthetic route to a molecule cannot be predicted with certainty. Retrosynthetic analysis allows us to suggest several different strategies for any given target molecule, and thorough literature searching plus experimentation in the laboratory will allow us to whittle the possibilities down to the most likely to succeed. Thinking like this underpins the design of syntheses of molecules, from the relatively simple molecules forming the next generation of drugs or agrochemicals to the most complex molecules known. Retrosynthetic thinking also reinforces the concept that the combination of electrophile and nucleophile is the basis for the understanding of organic reactions.
Pericyclic reactions 1: cycloadditions
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter describes pericyclic reactions. In pericyclic reactions, electrons move round a circle and there are no positive or negative charges on any intermediates, indeed, there are no intermediates at all. The most famous example is the Diels–Alder reaction, which goes in a single step simply on heating. The electrons do not really rotate at all; in reality, two π bonds disappear and two σ bonds take their place by the electrons moving smoothly out of the π orbitals into the σ orbitals. Such a reaction is called a cycloaddition. The chapter then looks at regioselectivity in Diels–Alder reactions, and other thermal and photochemical cycloadditions.
The evolutionary record and methods of reconstruction
Authors: Willis K. J. , McElwain J. C.
Published: September 2023

This chapter provides a background to the main evolutionary changes that have occurred in the plant kingdom within a framework of environmental changes. It reviews the predominant evolutionary patterns in the plant fossil record over the past 3.5 billion years, from the first prokaryotes to the present flora. It also presents evolutionary trends apparent from morphological, genetic, and metabolic data alongside evidence in geological records for global environmental change. The chapter synthesizes the evidence for the timing of evolutionary innovations and the origin of the major plant groups and considers these in the environmental context in which they were occurring. It looks at evidence for mass extinctions and persistent plant populations in the fossil record.
The past 66 million years
Authors: Willis K. J. , McElwain J. C.
Published: September 2023

This chapter reviews the past 66 million years, which provides a vital understanding of the evolution and distribution of the present-day flora. It describes how continental plates moved into their present arrangement or prominent mountain ranges were formed, such as the Himalayas, Alps, Carpathians, Caucasus, Zagros, and Rockies. It also talks about the angiosperm groups that continued to diversify and modernize throughout the Cenozoic, the grass lineages that evolved, the long-term decline in the aerial extent of forests, and the expansion of grasslands. The chapter regards the past 66 million years as the period of time that the precursors of most modern taxa and plant communities must be observed. It mentions hypotheses that account for the appearance of grasses in the fossil record, emphasizing that the evolution was closely linked with the increasing aridity in the higher latitudes, the rise in wildfire occurrence, and the emergence of hoofed mammals.
Introduction and orientation
Authors: Atkins Peter , Friedman Ronald
Published: September 2023

This chapter introduces two approaches to quantum mechanics, one is to follow the historical development of the theory from the first indications that the whole fabric of classical mechanics and electrodynamics should be held in doubt to the resolution of the problem. The other approach is to stand back at a point late in the development of the theory and see its underlying theoretical structure. The chapter shows that in the first approach the theory is seen gradually emerging from confusion and dilemma, while the second is a more formal approach that can still be exciting and compelling in a different sense. The chapter highlights the logic and elegance in a scheme that starts from only a few postulates, yet reveals a rich, experimentally verifiable structure. It traces some of the most fundamental concepts of the nature of matter and its behaviour that were overthrown and replaced by a puzzling but powerful new description.
Molecular rotations and vibrations
Authors: Atkins Peter , Friedman Ronald
Published: September 2023

This chapter reviews the primary goals of molecular quantum mechanics, which is to solve the time-independent Schrödinger equation. It determines the electronic structures of atoms and molecules, with the modern emphasis on molecules of ever greater complexity. It also introduces some of the computational techniques that are used to solve the Schrödinger equation for electrons in molecules, such as establishing the equations that are used and describe some of the approximations that make the computations feasible. The chapter talks about the Born–Oppenheimer approximation, focusing on the solution of the electronic Schrödinger equation. In an ab initio calculation, a model is chosen for the electronic wavefunction and is solved using as input only the values of the fundamental constants and the atomic numbers of the nuclei.
Glycomics and analysis of glycan structures
Authors: Taylor Maureen E. , Drickamer Kurt
Published: September 2023

This chapter focuses on glycomics and provides an analysis of glycan structures. The analysis of glycomes provides a basis for understanding the functions of glycans in cell differentiation and disease. The analysis of glycans on specific glycoproteins and glycolipids is needed to establish their roles as targets for receptor binding. This chapter surveys the most commonly used methods for glycan structure determination and oligosaccharide synthesis, including nuclear magnetic resonance (NMR), glycosidases, and mass spectrometry. Because common sets of glycans are attached to many glycoproteins, the structures that are present can often be identified through routine profiling. Lectins and antibodies can also be used to detect specific sugar structures and are particularly useful for localizing glycans in cells and tissues. Experimental and bioinformatics approaches are being developed to link this information to knowledge about the enzymes that synthesize the glycans and the glycan-binding receptors that recognize them.
Glycoprotein trafficking in cells and organisms
Authors: Taylor Maureen E. , Drickamer Kurt
Published: September 2023

This chapter explores lectins that function in the trafficking of glycoproteins by recognizing endogenous glycans. It first looks at the intracellular recognition events that involve glycans common to all proteins that are N-glycosylated. Glycans of this type tag many different glycoproteins that serve a variety of different functions at the cell surface. Similarly, the asialoglycoprotein and mannose receptor clearance systems can handle a multitude of different glycoproteins as long as they bear the correct glycans. However, two of the systems, the mannose 6-phosphate receptor and the binding of glycans containing 4-O-sulphated GalNAc residues to the mannose receptor, involve unusual glycans that are attached to specific subsets of glycoproteins. These special glycans allow targeting of selected glycoproteins in ways that are different from the bulk of glycoproteins. Attachment of special glycans to the selected subset of glycoprotein targets is directed by information in the amino acid sequence of the glycoprotein.
Electrons in atoms
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter discusses the behaviour of electrons in atoms. Quantum mechanics provides a complete description of the behaviour of electrons in atoms and molecules. Each electron is described by a wavefunction; the square of the wavefunction gives the probability distribution of the electron. In the hydrogen atom, the familiar orbitals are the electron wavefunctions. In multi-electron atoms, the electrons can be assigned to hydrogen-like orbitals. The energies and sizes of the orbitals in multi-electron atoms are affected by electron–electron repulsion in a way which can be understood using the concepts of screening and penetration. Meanwhile, trends in ionization potentials can be rationalized using orbital energies.
Symmetry
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter examines how molecules possess certain symmetry elements, and each symmetry element gives rise to one or more symmetry operations. A symmetry operation, when applied to a molecule, leaves it in an identical position. The possible symmetry elements include axis of symmetry, mirror plane, centre of symmetry, and improper rotation axis. Symmetry considerations can be used to identify which atoms in a molecule are equivalent; determine whether or not a molecule has a dipole; and determine whether or not a molecule is chiral. Ultimately, orbitals can be classified as being symmetric or anti-symmetric with respect to the symmetry operations possessed by the molecule.
Describing reactions using orbitals
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter looks at how to describe chemical reactions using orbitals. During a reaction, as bonds are formed and broken, the electrons are redistributed. The redistribution of electrons may be followed by calculating how the molecular orbitals change as the reaction proceeds. ‘Curly arrow mechanisms’ summarize the way in which electrons are redistributed during a reaction. Ultimately, the way in which two reactants may react can often be understood by considering the interaction between the highest energy occupied MO (the HOMO) and the lowest energy unoccupied MO (the LUMO). The chapter then looks at the role of protonation in reactions before considering intramolecular orbital interactions and rearrangement reactions.
Organic chemistry 2: three-dimensional shapes
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter examines three-dimensional shapes adopted by organic molecules. It begins by looking at the phenomenon of isomerism, which is where a compound with a given molecular formula can exist as various isomers in which the constituent atoms are joined up or arranged in space in different ways. Sometimes there are large differences between isomers. They might, for example, contain different functional groups, but the distinction can be much more subtle than this. The chapter then considers how different shapes or conformations of molecules may be obtained by rotating about single bonds. Different conformations which are energy minima for that compound are called conformational isomers, or conformers. The chapter also covers enantiomers, chirality, and cyclic molecules.
Dimensions, units and some key mathematical ideas
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter reviews dimensions, units, and some key mathematical ideas. It begins by looking at dimensional analysis, which provides a way of checking the consistency of an expression. The use of SI units provides a consistent and reliable way of calculating quantities. The exponential function, and the related natural logarithm, appears frequently in the mathematical analysis of chemical processes. Differentiation can be used to find the maxima and minima of functions, while integration can be thought of in terms of finding the area under a graph. Ultimately, the mathematical analysis of some chemical processes leads to differential equations, simple examples of which can be solved straightforwardly.
Why did evolution explode in the Cambrian?
Authors: Bromham Lindell , Cardillo Marcel
Published: September 2023

This chapter evaluates the Cambrian explosion. This burst of animal diversity has been interpreted as marking an unusually inventive period of evolution, with a greater rate of change in fundamental features of body plan than has ever occurred before or since. The Cambrian explosion presents two challenges to Darwinian gradualism: explaining evolution of novel features for which we have little direct evidence of intermediate forms, and explaining why animal phyla appear in a particular time period and not before or since. One proposed solution to both these challenges is that body plans evolved not by a long series of gradual changes but by relatively few changes to developmental genes that allowed new distinct new forms to be generated without intermediates. The chapter then assesses whether such ‘macromutations’ are possible, and if it is plausible that they could give rise to a successful lineage of animals with a novel body plan.
Was the diversification of mammals due to luck?
Authors: Bromham Lindell , Cardillo Marcel
Published: September 2023

This chapter assesses the diversification of mammals, which is often considered a classic example of ecological opportunity prompting evolutionary radiation. The fossil record shows a dramatic increase in the diversity of placental mammals as they evolved to occupy the niches left vacant by the extinction of the dinosaurs. But date estimates based on DNA analysis have been used to question the assumed timing of this radiation, suggesting that the major placental mammal lineages diverged from each other long before the dinosaurs' demise. Given that different molecular dating analyses give very different estimates for the timing of the mammalian radiation, the quetsion is, how reliable are these molecular dates? Can we estimate the timing of divergence events from DNA sequences when rates of molecular evolution vary between lineages? The chapter finally considers the Bayesian molecular dating methods.
How pathogens escape innate immunity
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter narrates how a pathogen escapes the powerful defence mechanisms of innate immunity. It follows the principal ways in which pathogens achieve this, then details how they are classified according to the immune component they are designed to avoid. The chapter also investigates how pathogens can circumvent the initial recognition of microbial surfaces in several ways, and how capsules can prevent activation of the alternative complement pathway. The chapter then shifts the focus to the phagocytic cell, noting it is the deadliest enemy for bacteria, fungi, and protozoa, particularly when it is assisted by complement and/or antibody. Next, the chapter explains the three main categories of pathogen survival strategies. It then considers the vital role of dendritic cell in T-cell activation, the interference of pathogens with the cytokine network, and the role of vectors.
B cells and antibody
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter stresses the function of B lymphocytes (or B-cells), essentially little antibody factories, able to switch on high-rate synthesis and secretion of antibody molecules when stimulated by recognition of the right antigen. It tracks the coordinated recognition and response in B-cells, then explains the diversity of the antibody repertoire. The chapter then describes the antibody molecule and its classes and subclasses. All antibody molecules using a particular heavy-chain constant-region gene are defined as belonging to the same class. The differences between different classes are fairly major, but there are smaller differences within classes, which are referred to as subclasses. The chapter also investigates what exactly do antibodies recognize, then studies the antigenic determinant or epitope. Finally, the chapter elaborates on the affinity of the antibody-antigen bond, then emphasizes the functions of the antibody. It also considers another useful role of antibodies in the monitoring and treatment of disease.
Cell-mediated responses
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter considers T-cell responses that do not involve B-cells and antibodies. It begins with examining the points of resemblance of the activation of macrophages by CD4 (helper) T-cells to the activation of B-cells, then explores the CD8 (cytotoxic) T-cell response. The chapter argues that both involve the selection and expansion of clones of effector cells from a tiny number of precursors and both result in the long-term survival of a population of memory cells that ensure a more vigorous secondary response to the same pathogen. The chapter analyzes how T-cells become activated for these responses. Next, the chapter highlights a more drastic approach to kill both the virus and its host-cell with the help of cytotoxic T lymphocytes (CTLs). It also elaborates on the t-cell memory and t-cell responses at mucosal surfaces.
Regulation of immune responses and memory
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter focuses on subtle processes to regulate the size of lymphocyte responses to somewhere near the optimum. It reviews these regulatory processes, and considers some aspects of memory. The chapter begins with discussing the elimination of antigen,: since antigen is a requirement for the initiation of lymphocyte proliferation. It then explains the process of apoptosis once a population of lymphocytes has responded. The chapter also examines inhibitory receptors, then illustrates how lymphocytes induce inhibition of proliferation and/or function, particularly of B-cells. The chapter next defines the concept of regulatory cells (mainly T-cells). Finally, the chapter looks at one of the major virtues of adaptive immunity: the generation of specific memory. It further describes the generation of memory cells, then analyzes the activation, response, and maintenance of memory cells.
Rotational motion in two dimensions
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

A particle on a ring 103

Brief illustration 13.1: The moment of inertia 104

The qualitative origin of quantized rotation 105 Brief illustration 13.2: The rotational energies 106

The solutions of the Schrödinger equation 106

Example 13.1: Using the particle-on-a-ring model...
Periodicity
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The building-up principle 176

Brief illustration 20.1: The building-up principle 176

The configurations of the elements 177

Brief illustration 20.2: The configurations of ions 178

The periodicity of atomic properties 178

Atomic radii 178

Ionization energies 179

Electron...
Atomic spectroscopy
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The spectrum of hydrogen 181

The spectral series 181

Example 21.1: Calculating the shortest and longest wavelength lines in a series 182

Selection rules 182

Brief illustration 21.1: Selection rules 182

Term symbols 183

The total orbital angular momentum...
Vectors
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

A scalar physical property (such as temperature) in general varies through space and is represented by a single value at each point of space. A vector physical property (such as the electric field strength) also varies through space, but in general...
Semi-empirical methods
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The Hückel approximation revisited 248

Brief illustration 28.1: The Hückel method 248

Differential overlap 249

Brief illustration 28.2: Neglect of differential overlap 249

Checklist of concepts 250

Checklist of equations 250

Why do you need to know this material?

Modern computational...
Interactions between molecules
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Interactions between partial charges 309

Brief illustration 35.1: The interaction energy of two partial charges 310

The interactions of dipoles 310

Charge–dipole interactions 310

Brief illustration 35.2: The energy of interaction of a point charge and a point dipole 311
General features
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Spectrometers 378

Sources of radiation 378

Spectral analysis 378

Example 40.1: Calculating a Fourier transform 379

Detectors 380

Absorption spectroscopy 381

The Beer–Lambert law 381

Example 40.2: Determining a molar absorption coefficient 382

Special techniques 382
Features of NMR spectra
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The chemical shift 464

Brief illustration 48.1: The δ scale 465

Example 48.1: Interpreting the NMR spectrum of ethanol 465

The origin of shielding constants 466

The local contribution 466

Example 48.2: Using the Lamb formula 467

Neighbouring group contributions...
The Third Law
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The calorimetric measurement of entropy 620

Example 63.1: Evaluating a change in entropy 621

Example 63.2: Calculating the entropy at low temperatures 621

The Nernst heat theorem and the Third Law 622

Brief illustration 63.1: The Nernst heat theorem 622

Example 63.3:...
Spontaneous processes
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Criteria of spontaneity 625

Changes at constant volume 626

Brief illustration 64.1: Spontaneous changes at constant volume 626

Changes at constant pressure 626

Brief illustration 64.2: Spontaneous changes at constant pressure 626

The Helmholtz and Gibbs energies 626

Criteria...
Physical transformations
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Partial molar quantities 670

Partial molar volume 670

Example 69.1: Determining a partial molar volume 671

Partial molar Gibbs energies 672

The chemical potential 673

Changes in the Gibbs energy 673

Brief illustration 69.1: The Gibbs–Duhem equation 673
Colligative properties
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The origin of colligative properties 687

Brief illustration 71.1: Cryoscopic and ebullioscopic effects 688

Osmosis 688

The van ’t Hoff equation 689

Brief illustration 71.2: The van ’t Hoff equation 689

Osmometry 690

Example 71.1: Using osmometry to determine the...
The statistical description of equilibrium
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The relation between K and the partition function 723

Example 74.1: Calculating an equilibrium constant 725

Contributions to the equilibrium constant 725

Brief illustration 74.1: Interpretation of the equilibrium constant 727

Checklist of concepts 727

Checklist of equations 727

Why do...
Electrochemical cells
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Half-reactions and electrodes 734

Brief illustration 76.1: Half-reactions 734

Brief illustration 76.2: The reaction quotient of a half-reaction 734

Varieties of cells 734

Brief illustration 76.3: Cell notation 735

The cell potential 736

Brief illustration 76.4: The cell reaction 736
Standard electrode potentials
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The conventions 740

The determination of standard electrode potentials 741

Example 77.1: Determining a standard electrode potential 741

Combining electrode potentials 742

Example 77.2: Evaluating a standard potential from two others 742

Applications of standard potentials 743

The electrochemical...
The kinetic theory of gases
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The kinetic model 757

Pressure and molecular speeds 758

Brief illustration 78.1:The number of molecules with a range of speeds 760

Mean values 761

Example 78.1: Calculating the mean speed of molecules in a gas 762

The collision frequency...
Motion in liquids
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Pure liquids 774

Brief illustration 80.1: Liquid viscosity 775

Electrolyte solutions 775

Conductivity 775

Example 80.1: Determining the limiting molar conductivity 776

The mobilities of ions 777

Brief illustration 80.2: Ion mobility 777

Mobility and conductivity 778

The...
Reaction mechanisms
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Elementary reactions 821

Brief illustration 86.1: The rate laws of elementary steps 822

Consecutive elementary reactions 822

Example 86.1: Analysing consecutive reactions 823

The steady-state approximation 823

Example 86.2: Using the steady-state approximation 824

The rate-determining step 825

Brief illustration...
Introduction
Authors: Campbell Iain D.
Published: September 2023

This chapter talks about the identification of molecules, the measurement of their concentrations and interaction partners, and the definition of their structure and location in the cell. It reviews extraordinarily powerful sets of physical and mathematical tools that can be used to study molecules. It also analyses molecular assemblies which need appropriate dynamic and energetic properties and the correct location and structure in order to function properly. The chapter describes diverse, powerful, and complementary biophysical tools, which exploit developments in technology and apply insights from the laws of physics and chemistry to all aspects of molecular and cellular biology. It reviews the key role of biophysical techniques in the exploration of other properties of cellular components.
Molecules and interactions
Authors: Campbell Iain D.
Published: September 2023

Introduction

We have learned a great deal in the last 100 years about the molecules that assemble to make a living cell. Their nature and composition are largely known (Tutorial 1). A major remaining challenge facing the molecular biologist in the 21st...
X-ray spectroscopy
Authors: Campbell Iain D.
Published: September 2023

Introduction

This chapter gives a brief description of techniques that involve absorption and emission of high-energy X-rays. These X-ray spectra, which arise from transitions involving core electron energy levels, give information about metal ion environments and the elemental composition of a sample. We have previously...
Manipulation and observation of single molecules
Authors: Campbell Iain D.
Published: September 2023

Introduction

The last two decades have seen the development of a number of ultrasensitive biophysical methods that allow the manipulation and study of individual molecules. Most techniques measure the properties of an ensemble of many molecules. The ability to watch one molecule at a...
Thermodynamics
Authors: Campbell Iain D.
Published: September 2023

The aim of this tutorial is to introduce some key concepts about thermodynamics, which is the study of the energetics of a system.

Life depends on the redistribution of energy. The study of thermal energy (heat) has a fascinating history; the first and second...
Mathematical representation of waves
Authors: Campbell Iain D.
Published: September 2023

The aim of this tutorial is to show how waves can be represented and summed. These ideas are important for understanding electromagnetic radiation, scattering, and spectroscopy experiments (Tutorial 8, Sections 4 and 5).

As shown in Figure T5A, a wave can be...
Atomic and molecular orbitals, their energy states, and transitions
Authors: Campbell Iain D.
Published: September 2023

The aim of this tutorial is to introduce ideas about the shapes and energies of the wave functions that describe the distribution of electrons in atoms and molecules. This is important for understanding many of the properties described elsewhere, especially Section 5, which is concerned...