bluuebunny/crossref_metadata_2025 huggingface dataset:
Differential equations II
Authors: Reed Martin B
Published: September 2023

This chapter introduces numerical methods that can be used on problems that are too hard to solve by standard algebra, such as finding roots of complicated equations. It demonstrates numerical methods for solving a first-order ordinary differential equations (ODE) with an initial condition. It also looks at problems involving two or more simultaneous ODEs, particularly the equations relating the growth of populations of different species in a predator–prey situation. The chapter explains how a numerical method produces a set of data-points that lie on or close to the true solution curve. It analyses the accuracy of Euler's method, which can be improved by reducing the steplength or taking shorter steps between data-points.
Conducting effective literature searches
Authors: Aysha Divan
Published: September 2023

This chapter aims to equip the student with the necessary skills to construct and implement a systematic search of the literature and retrieve information, which is most relevant to the topic of the search in a time-efficient way. It begins with a description of the key features of an effective literature search. The chapter argues that the ability to search and retrieve particular types of information is an essential part of academic work. The chapter elaborates on the search tools that we can use to locate particular types of publications: library catalogues, specialist databases, and gateways. Then, the chapter details the strategy for planning and implementing a comprehensive literature search. Finally, it explores how we can keep track of scientific literature using alerting services and RSS feeds.
Preparing tables and figures
Authors: Aysha Divan
Published: September 2023

This chapter highlights some general guidelines on presenting data in table and figure format. As research is likely to generate a significant amount of data, these data need to be presented in a format that is meaningful and comprehensible to the reader. The chapter discusses the main features of figures and tables and provides tips on preparing them. It emphasizes a number of software programs which are available to help the student produce high-quality tables and figures, and it also presents some basic guidance on how to use them. Finally, the chapter reviews the ethical reporting of data and gives a checklist for reviewing the quality of tables and figures.
Networking
Authors: Aysha Divan
Published: September 2023

This chapter looks at the benefits of networking and describes some of the ways in which a student can network. It argues that networking is an important part of the academic career as it involves developing and maintaining contact with people who work in the same field or in a related field. The chapter begins by explaining what networking is and why it is important to network. It then details the different ways in which a student can network, including face-to-face networking and the use of web-based technologies. Lastly, the chapter explores some web-based tools for collaborative authoring, and it investigates how to network effectively and ethically online.
Pharmaceutical Disperse Systems
Authors: Moynihan Humphrey A. , Crean Abina M.
Published: September 2023

This chapter assesses the use of disperse systems as pharmaceutical drug-delivery systems (dosage forms). There are a wide range of dosage forms that can be classified as pharmaceutical disperse systems, and their properties can vary widely depending on the type of disperse system. These include pharmaceutical suspensions and gels. Pharmaceutical suspensions injected intramuscularly and subcutaneously can be designed with extended drug-release characteristics. Meanwhile, gels can be formed from dispersed lyophobic or lypophilic colloidal material. The main factors that influence the stability of pharmaceutical gels are microbial growth, dehydration, changes in pH, and temperature. Other pharmaceutical disperse systems include pharmaceutical emulsions, microemulsions, micellar systems, liposomes, aerosols, and foams.
The chemicals of biological systems
Authors: Dobson C. M. , Gerrard J.A. , Pratt A.J.
Published: September 2023

This chapter provides a background on the chemistry processes that take place in the cells of living organisms, noting that cells consist of a semipermeable membrane that encloses an aqueous solution rich in a diverse range of chemicals. It describes cells as sophisticated machines that undertake a wide range of chemistry in an organized fashion. It also refers to the chemicals present in cells that appear to have been selected by the processes of evolution for their chemical utility. The chapter shows that many cellular processes can be understood in simple molecular terms. It introduces a series of examples to exemplify principles that are important for understanding the chemistry of cells.
Introduction to aminoacids and proteins
Authors: Dobson C. M. , Gerrard J.A. , Pratt A.J.
Published: September 2023

This chapter introduces proteins as biological polymers that play important roles in the chemical processes of life and represent 15% of the total cell mass. It explains the chemistry of amino acids and how their properties change when they are polymerized in a protein, which are important in the analysis of the molecular basis of the is properties of proteins. It also describes proteins as linear polymers that are derived from α-amino acid monomers, noting that α-amino acids are carboxylic acid with an amino group, a hydrogen atom, and a further substituent attached to the α-carbon. The chapter looks at the distinguishing feature of proteins as they are composed of a variety of monomer units linked together in a defined sequence. It analyses the variety of possible proteins that underpins the diverse roles for which they are suited.
The structures of proteins
Authors: Dobson C. M. , Gerrard J.A. , Pratt A.J.
Published: September 2023

This chapter analyses the properties of a protein that are determined by its shape and its chemical functionality, noting that proteins form well-defined three-dimensional structures. It reviews the role of some proteins as structural materials, which can be understood in terms of their molecular architecture. It also elaborates how proteins adopt compact globular structures. The text uses an illustration of an enzyme called triose phosphate isomerase. The chapter discusses the overall structure of a protein that is related to the order of the monomer units in the chain and the conformation that each monomer residue adopts. It outlines the appreciation of the three-dimensional structures of proteins that is achieved by considering the stereochemical preferences of a short stretch of a polypeptide chain.
Lipids: cells as compartments
Authors: Dobson C. M. , Gerrard J.A. , Pratt A.J.
Published: September 2023

This chapter examines the molecular components of the membranes enclosing compounds, looking at compartments of living organisms that are bounded by semipermeable membranes. It discusses how organic compounds are immiscible with water and tend to associate in aqueous solution, which is exploited by cells with the use of compounds and lipids to form the basic structures of cell membranes. It also develops an awareness of the intrinsic chemistry of phospholipids. The chapter analyses the membranes found in biological systems. These are formed by the spontaneous association of relatively small organic molecules called lipids. It explains that membrane structures arise because of the amphiphilic nature of lipid molecules, wherein one end is hydrophilic and the remainder is a hydrophobic tail.
Ionic interactions
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter discusses ionic interactions. It focuses on the interaction between ions in solid materials. The chapter notes the usage of X–ray diffraction to measure the distance between ions in the lattice while referencing a lattice diagram of NaCl. It explains the force between oppositely charged objects attracted to one another. This is called electrostatic interaction. Additionally, the chapter explains the process and equations used in the formation of ion pairs and lattice. It refers to the Born–Landé equation as an expression for the energy of interaction between the ions in a crystal lattice. The chapter also mentions the Kapustinskii equation before exploring the application of other equations dealt with in the chapter.
Electrons in atoms
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter explores electrons in atoms. It mentions how a chemical bond involves the sharing of electrons. The chapter refers to the concept behind quantum mechanics as the behaviour of electrons in atoms and molecules. It notes the significance of atomic energy levels, atomic orbitals, and electronic configuration by explaining hydrogen orbitals. Photoelectron spectroscopy (PES) provides a particularly direct way of looking into the energy levels of electrons in atoms and molecules. The chapter explores how wavefunctions predict the spatial distribution of electrons. It also includes the usage of radial distribution functions to work out the total probability of finding the electron at a set distance from the nucleus. In addition, electronegativity is related to the atom which attracts more of the electron density.
α-Amino acid synthesis
Authors: Jones John
Published: September 2023

This chapter examines proteinogenic α-amino acids that are produced industrially by fermentation methods and chemical synthesis on a vast scale. It highlights the principal application of α-amino acids as food additives and cheap starting materials for laboratory work. It also considers the synthesis of α-amino acids as an active field wherein there is demand for specifically labelled, unnatural, and unusual amino acids. The chapter explores the general methods of synthesis of α-amino acids, including the displacement reactions on α-halo acids, Strecker synthesis, approaches through hydantoins, and via oxazolones. It describes reactions that lead to racemic products and reviews the traditional general approach to the resolution of racemates, which is to derivatize an optically active reagent.
Determining organic structures
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter examines the determination of organic structures, looking at three different methods of spectroscopy: mass spectrometry, nuclear magnetic resonance (NMR) spectroscopy, and infrared spectroscopy. It is not easy to weigh a neutral molecule, and a mass spectrometer works by measuring the mass of a charged ion instead: the charge is used because the molecule controllable by an electric field. A mass spectrometer therefore has three basic components: something to volatilize and ionize the molecule into a beam of charged particles; something to focus the beam so that particles of the same mass–charge ratio are separated from all others; and something to detect the particles. Meanwhile, NMR allows us to detect atomic nuclei and say what sort of environment they are in within the molecule. Finally, infrared spectroscopy detects the stretching and bending of bonds rather than any property of the atoms themselves.
Delocalization and conjugation
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter focuses on delocalization and conjugation. Colours result from the interaction of light with the pigments in different things—some frequencies of light are absorbed, others scattered. Inside our eyes, chemical reactions detect these different frequencies and convert them into electrical nerve impulses sent to the brain. All these pigments have one thing in common—lots of double bonds. The chapter looks at the properties, including colour, of molecules that have several double bonds. These properties depend on the way the double bonds join up, or conjugate, and the resulting delocalization of the electrons within them. The chapter then considers the structure of ethane, the UV–visible spectrum, the allyl system, and aromaticity.
Stereochemistry
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter reviews stereochemistry. It begins by differentiating between enantiomers and chiral compounds. Two structures that are not identical but are mirror images of each other are called enantiomers. Structures that are not superimposable on their mirror image, and can therefore exist as two enantiomers, are called chiral. Meanwhile, structures that are superimposable on their mirror images are called achiral. The chapter asks: what is the essential difference between these two compounds that means one is superimposable on its mirror image and one is not? The answer is symmetry. The chapter then looks at diastereoisomers and stereoisomers. It also considers chiral compounds with no stereogenic centres.
Aromatic heterocycles 1: reactions
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter investigates the reactions of aromatic heterocycles. Benzene is aromatic because it has six electrons in a cyclic conjugated system. Most organic compounds belong to the class of aromatic heterocycles, and they number among them some of the most significant compounds for human beings. The chapter begins by considering how aromaticity survives when parts of benzene’s ring are replaced by nitrogen atoms. How can we insert a heteroatom into the ring and retain aromaticity? What kind of atom is needed? If we want to replace one of the carbon atoms of benzene with a heteroatom, we need an atom that can be trigonal to keep the flat hexagonal ring, and that has a p orbital to keep the six delocalized electrons. Nitrogen fits all of these requirements. This is what happens if we replace a CH group in benzene with a nitrogen atom. The chapter then looks at reactions of five-membered heterocycles, as well as benzo-fused heterocycles.
Aromatic heterocycles 2: synthesis
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter evaluates the synthesis of aromatic heterocycles. There are three major strategies in the synthesis of heterocycles: ring construction by ionic reactions; ring construction by cycloadditions; and modification of existing rings by electrophilic or nucleophilic aromatic substitution or by lithiation and reaction with electrophiles. The first strategy one should try out when faced with the synthesis of an aromatic heterocyclic ring is the disconnection of bonds between the heteroatom or atoms and carbon, with the idea of using the heteroatoms as nucleophiles and the carbon fragment as a double electrophile. The chapter looks at the Hantzsch pyridine synthesis and the Fischer indole synthesis. It also considers quinolines and isoquinolines.
Pericyclic reactions 2: sigmatropic and electrocyclic reactions
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter explores two other classes of pericyclic reactions: sigmatropic rearrangements and electrocyclic reactions. The original sigmatropic rearrangement occurred when an aryl allyl ether was heated without solvent and an ortho-allyl phenol resulted. This is the Claisen rearrangement. This is a one-step mechanism without ionic intermediates or any charges, just like a cycloaddition. The difference between this and a cycloaddition is that one of the arrows starts on a σ bond instead of on a π bond. In an electrocyclic reaction, a ring is always broken or formed. Rings may, of course, be formed by cycloadditions as well, but the difference with electrocyclic reactions is that just one new σ bond is formed (or broken) across the ends of a single conjugated π system.
The first forests
Authors: Willis K. J. , McElwain J. C.
Published: September 2023

This chapter examines the evidence for environmental and evolutionary changes and discusses the possible evolutionary pathways from the earliest vascular plants to trees. It reviews the biogeographical distribution of the first multi-storied forests and the factors influencing their distribution. It also describes the global vegetation that evolved from one dominated by small, weedy plants, most less than 1 metre in height, to fully forested ecosystems with trees towering up to 35 metres during the period spanning the early Devonian to late Carboniferous. The chapter discusses biogeographic reconstruction that indicates that provinciality of the global vegetation increased markedly through the Carboniferous. It highlights biomes, including tropical everwet, tropical summerwet, subtropical desert, warm temperate, cool to cold temperate, and arctic and glacial.
Mass extinctions and persistent populations
Authors: Willis K. J. , McElwain J. C.
Published: September 2023

This chapter describes ‘the big five’-the mass extinction events viewed observed in the marine faunal record, -comparing the nature and magnitude of these events to changes apparent in the plant fossil record. It examines the evidence for mass extinction in the plant fossil record, particularly to the physiological characteristics that enable plants to be resilient to the types of environmental change associated with mass extinction events. It also cites examples of the long-term persistence of various families in the plant fossil record and the implications of this in terms of understanding the driving mechanisms behind plant evolution. The chapter explains mass extinctions that are characterized by the relatively rapid extinction of groups of organisms. It points out the reasons for the lack of mass extinction in the fossil plant record relatesd to the mechanisms that enable plants to withstand a certain amount of environmental stress.
Evolutionary theories and the plant fossil record
Authors: Willis K. J. , McElwain J. C.
Published: September 2023

This chapter outlines several of the main evolutionary theories that are part of the current and lively debate and examines them in light of the plant fossil record. It analyszes evidence from the plant fossil record that indicates a broadening spectrum of diversity and morphological and developmental complexity through time. It also cites suggestions in the plant fossil record concerning the major evolutionary change and innovation on the broadest scale, which concentrated into relatively short intervals in geological time. The chapter discusses biological interactions which played a role in terrestrial diversification and which have been responsible for the decline in species diversity of incumbent groups or clades of plants as new ones evolved. The chapter identifies potential drivers of the macroevolutionary pattern, such as plate movements, changes in land mass area, climate, and alterations to atmospheric concentrations and chemistry.
Group theory
Authors: Atkins Peter , Friedman Ronald
Published: September 2023

This chapter discusses how solving the Schrödinger equation leads to the conclusion that orbital angular momentum is quantized and how the same conclusion can also be reached from the angular momentum operators without solving the Schrödinger equation explicitly. It analyses the commutation properties of the angular momentum operators, noting that the same conclusions apply to observables that are described by operators with the same commutation properties. Angular momentum has many more mundane applications, including being central to the discussion of the structures of atoms and the rotation of molecules, as well as to virtually all forms of spectroscopy. The chapter mentions classical mechanics that puts no constraints on the magnitude of the angular momentum, which is consistent with the kinetic energy of rotation being continuously variable. The property of hermiticity can be demonstrated explicitly in the position representation.
The electric properties of molecules
Authors: Atkins Peter , Friedman Ronald
Published: September 2023

This chapter examines the complexity of the electronic spectra of molecules, which occur in the visible and ultraviolet regions of the electromagnetic spectrum and arise in part from the stimulation of simultaneous vibrational and rotational transitions. It mentions electronic transition that changes the distribution of the electrons, and the nuclei respond to the new force field by breaking into vibration. In turn, the stimulation of vibration results in rotational transitions, just as ice skaters change the speed of their rotation by pulling in or throwing out their arms. The chapter deals with diatomic molecules, reviewing how the concepts generalize to polyatomic molecules. Computational chemistry has a considerable role to play in the prediction and interpretation of electronic absorption spectra.
Introduction to Glycobiology
Authors: Taylor Maureen E. , Drickamer Kurt
Published: September 2023

Introduction to Glycobiology considers the impact of sugars on biological systems, explaining their function at the molecular, cellular, and organismal level. It is made up of two parts. Part 1 looks at the structures and biosynthesis of glycans and includes chapters that examine concepts of glycobiology, N-linked glycosylation, O-linked glycosylation, and glycolipids and membrane protein glycosylation. There are also chapters on enzymology and the cell biology of glycosylation, analysis of glycan structures, and conformations of oligosaccharides. Part 2 focuses on glycans in biology. This section looks at the following topics: the effects of glycosylation on protein structure and function; carbohydrate recognition in cell adhesion and signalling; glycoprotein trafficking in cells and organisms; glycobiology of plants, bacteria, and viruses; glycobiology and development; glycosylation and disease; and the future of glycobiology.
Concepts of glycobiology
Authors: Taylor Maureen E. , Drickamer Kurt
Published: September 2023

This chapter provides an overview of concepts within the field of glycobiology. Because glycan structures are created by glycosyltransferases and are recognized by lectins, glycobiology encompasses the study of these proteins as well as the glycans themselves. There are a large number of possible hexoses and related structures, but only a small fraction of these monosaccharide units are found in glycoconjugates. Similarly, the monosaccharide units could potentially be combined in many different ways through different linkages, but the glycosyltransferases catalyse synthesis of only a limited number of the possible structures. Nevertheless, there is great diversity in the glycan portions of glycoconjugates. It is often difficult to assign functions to specific glycans because the functions may only be evident in an organismal context, and gene knockout approaches may be required to probe these roles.
Glycolipids and membrane protein glycosylation
Authors: Taylor Maureen E. , Drickamer Kurt
Published: September 2023

This chapter evaluates glycolipids and membrane protein glycosylation. Animal cell surfaces are rich in glycoconjugates. Glycans displayed on glycoproteins and glycolipids of the plasma membrane create a meshwork that projects up to 100 Å from the surface. This meshwork, called the glycocalyx, represents the outermost surface of the cell and plays a defining role in interactions between cells. However, a good deal more is known about the structure and biosynthesis of membrane-associated glycans than is known about their functions. The finding that membrane glycosylation is not essential for cell viability confirms the notion that many glycans function in an organismal rather than a cellular context. It is also clear that membrane glycoconjugates can mediate and modulate cell–cell interaction, both by affecting the physical properties of cell surfaces and by engaging in specific recognition events.
Enzymology and cell biology of glycosylation
Authors: Taylor Maureen E. , Drickamer Kurt
Published: September 2023

This chapter details the enzymology and cell biology of glycosylation. Our knowledge of the complement of glycosyltransferases and sugar nucleotide transporters, as well as other enzymes required for glycan modification in eukaryotic cells, is derived from a very sophisticated set of protein chemistry and molecular and cell biology tools that only became available in the past 25 years. Increases in our understanding of the spatial and temporal organization of glycosylation in cells have similarly been tied closely to progress in understanding the organization and function of the Golgi apparatus. Moreover, modification of the pathways of glycoconjugate biosynthesis has provided key evidence for the essential roles of glycosylation in cells and organisms. The chapter presents a summary of some key steps in identifying the enzymes that form glycan biosynthesis pathways, followed by a discussion of how these steps are integrated in the secretory pathways of cells.
Effects of glycosylation on protein structure and function
Authors: Taylor Maureen E. , Drickamer Kurt
Published: September 2023

This chapter addresses the effects of glycosylation on protein structure and function. In particular, it looks at how glycoprotein functions are modulated by glycosylation, which usually affects their stability or surface properties. While the attachment of sugars usually does not alter a stable, folded protein conformation, sugars can stabilize this conformation by adding hydrogen bonding and hydrophobic interactions. Because sugars are not uniquely able to cause this type of stabilization, it is unlikely that this function of glycosylation was the driving force for evolution of the glycosylation machinery. However, with the machinery in place, natural selection has taken advantage of the stabilization that glycosylation can afford. Sugars also serve to shield various portions of protein surfaces from the aqueous solvent and from proteases. In many cases, it is the core structures and the overall bulk of the glycans that provides these functions, so variability in terminal structures is tolerated.
The future of glycobiology
Authors: Taylor Maureen E. , Drickamer Kurt
Published: September 2023

This chapter reflects on the future of glycobiology, considering biochemistry, cell biology, genetics, glycomics, and genomics. While the general question ‘What is the function of glycosylation?’ has probably been answered satisfactorily, specific questions of the form ‘What is the function of this particular glycan on this particular glycoconjugate?’ will be the basis for future work. A great deal has been learned about the roles of glycans, but there are also many indications that glycans have functions that we do not yet understand. A range of approaches, from glycan and lectin structure analysis to the physiological study of knockout mice, will be needed to provide convincing evidence for these roles. As our understanding of glycobiology broadens to encompass more examples, new routes to the application of this knowledge in the diagnosis and treatment of disease will undoubtedly emerge.
The liquid–liquid interface: emulsions; membranes
Authors: Barnes Geoffrey , Gentle Ian
Published: September 2023

This chapter talks about interest in the liquid-liquid interface that is concerned with the topic of emulsions, which is closely related to the study of food science. It explains that the liquid-liquid interface consists of liquid drops dispersed in another liquid, which are normally thermodynamically unstable and are usually stabilized by the adsorption of an emulsifier. It also considers the movement of a solute from one liquid phase to another. This is important with processes such as liquid-liquid extraction in the chemical industry and in many biological situations. The chapter highlights the role of membranes that can be significant in solute transport and is an essential feature of many biological processes. It reviews emulsions that are concerned with water or an aqueous solution as one phase and a water-insoluble organic liquid as the other phase.
The surfaces of solids
Authors: Barnes Geoffrey , Gentle Ian
Published: September 2023

This chapter reviews fluid interfaces that are characterized by the ability to flow readily and have the ability to rapidly deform and achieve equilibrium in response to surface tension forces. It describes principle solids that are susceptible to the forces of capillarity as the relative immobility of atoms in a solid. It also refers to the energy required to create a unit area of surface that is always positive. The chapter points out that the outer layers of any surface exposed to air contain a variety of contaminants, causing the top layers to have very different composition to the bulk. It mentions an example of the layer of fluorocarbon polymer that adheres well to metal or oxide surfaces and provides a non-stick coating for applications such as cooking.
Molecules and molecular structures: an overview
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter provides an overview of the key concepts that are commonly used in describing bonding and molecular structures, together with some related ideas, such as delocalization, oxidation state, and formal charge. It looks at the different types of bonding (covalent, ionic, and metallic) and their particular characteristics. The bonding in simple covalent molecules can be described using Lewis structures in which the focus is on bonding and non-bonding pairs of electrons. The shapes of simple molecules can often be predicted using the valence shell electron pair repulsion (VSEPR) model. Meanwhile, molecular structures are determined using X-ray diffraction. The chapter then considers the different types of solid materials, and the behaviour of the ideal gas.
Bonding in solids
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter focuses on bonding in solids, particularly metallic bonding. In solids, the overlap between orbitals on different atoms can give rise to crystal orbitals which extend throughout the material; these orbitals are analogous to delocalized molecular orbitals. The crystal orbitals which arise from a particular set of atomic orbitals form a band, which can hold a certain number of electrons. The electrical conductivity of metals is the result of partially filled bands; insulators have full bands, but in semiconductors there is a small gap between a filled and an empty band. The lattice enthalpy of an ionic solid can be estimated using a simple electrostatic model. It depends on the size (radii) of the ions and their three-dimensional arrangement in the crystal.
Transition metals
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter assesses the d-block elements, which form Groups 3–11 and are collectively often referred to as the transition metals. The common feature of these elements is the presence of a partially filled d sub-shell. It is the presence of this partly filled shell which is responsible for most of the special properties which set the transition metals apart from main-group metals. These special properties include: the existence of compounds in which a particular element shows a range of oxidation states; the presence of unpaired electrons associated with the metal; the formation of coloured compounds and solutions; the formation of a large number of complexes in which the metal is surrounded by typically between four and six electron-donating ligands; and the formation of organometallic complexes in which the ligands have π systems. The chapter focuses mainly on transition metal complexes.
Chemical kinetics
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter explores how rate laws are determined. This will involve looking at experimental methods, as well as at how the form of the rate law can be determined from data of concentration as a function of time. Concentration can be measured as a function of time by using various physical methods such as the measurement of absorbance, conductance, or pressure. The chapter then looks at two fundamental theories about the rates of reactions: collision theory, which is based on gas kinetic theory, and the more sophisticated transition state theory. Gas kinetic theory can be used to estimate the collision rate and hence the rate constant; however, in its simplest form, the theory massively overestimates the rate constant. Reactions can be thought of as taking place on a potential energy surface.
Electrochemistry
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter studies electrochemistry. The cell potential is very simply related to the Gibbs energy change of the reaction taking place in the cell. Measuring the cell potential is a straightforward process: attaching a digital voltmeter to the cell enables one to make a precision measurement in seconds. As a result, such measurements give access to thermodynamic properties in a particularly simple way. Since cell reactions generally involve ions, these measurements of cell potentials are especially useful for finding the standard thermodynamic functions of ions in solution. Data derived from cells, in the form of standard electrode potentials, are very useful for understanding the relative oxidizing or reducing power of different species. The cell potential is related in a simple way, given by the Nernst equation, to the concentration of the species in the cell. This leads to important practical applications in which cell potentials are used to measure concentrations.
Does evolution make everything bigger and better?
Authors: Bromham Lindell , Cardillo Marcel
Published: September 2023

This chapter examines the importance of studying the evolution of size and complexity. Trends in the fossil record can provide an informative view of evolutionary change over time, but they can often be interpreted in a number of different ways. The evolution of horses, which has long been a classic case of an evolutionary trend in size and specialization, provides a convenient illustration of the influence of data incompleteness on views of evolutionary change. Proposed explanations for 'Cope's rule' (increase in body size) include microevolutionary advantage to larger individuals, macroevolutionary advantage to lineages with larger size in diversifying or avoiding extinction, and stochastic (undirected) evolution of body size resulting in an overall increase in the maximum size over time. Meanwhile, complexity is hard to define and measure. The chapter then presents a case study on whether biodiversity has increased over time.
Why are most species small?
Authors: Bromham Lindell , Cardillo Marcel
Published: September 2023

This chapter explores body size and diversity. An organism's body size places severe constraints on its fundamental architecture and physiology, and therefore the way it obtains energy and resources from the environment, assimilates energy into body tissue, and uses it for growth and reproduction. The frequency distribution (histogram) of body sizes for large groups of species is often right-skewed on a logarithmic scale. This indicates a strong bias in species numbers towards species of smaller size. But it also requires us to explain the low species richness at the very smallest sizes. There are many hypotheses for this uneven distribution of body size, some focusing on the relative lack of small species, and others on the low numbers of both very small and very large species.
Matter
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Atoms 2

The nuclear model 2

The periodic table 2

Ions 3

Molecules 3

Lewis structures 3

Brief illustration 1.1: Octet expansion 4

VSEPR theory 4

Brief illustration 1.2: Molecular shapes 4

Polar bonds 4

Brief...
Differentiation and integration
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Two of the most important mathematical techniques in the physical sciences are differentiation and integration. They occur throughout the subject, and it is essential to be aware of the procedures involved.

Differentiation: definitions

Differentiation is concerned with the slopes of functions, such as the...
Predicting the outcome of experiments
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Wavefunctions as linear combinations 53

Brief illustration 7.1: The measurement of an observable 54

Mean values as expectation values 54

Example 7.1: Calculating an expectation value 55

The orthogonality of eigenfunctions 55

The expectation value of a linear combination of...
The uncertainty principle
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Complementarity 58

Brief illustration 8.1: Uncertainty in position and momentum 1 59

The Heisenberg uncertainty principle 59

Example 8.1: Calculating the uncertainty in linear momentum 60

Brief illustration 8.2: Uncertainty in position and momentum 2 60

Commutation and complementarity 61

Example...
Complex numbers
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

We describe here general properties of complex numbers and functions, which are mathematical constructs frequently encountered in quantum mechanics.

Definitions

Complex numbers have the general form

where i=(−1)1/2. The real...
Time-independent perturbation theory
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Perturbation expansions 132

Brief illustration 15.1: The corrections to the energy and wavefunction 133

The first-order correction to the energy 134

Example 15.1: Evaluating the first-order correction to the energy 134

The first-order correction to the wavefunction 135

Example 15.2: Evaluating...
Valence-bond theory
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Diatomic molecules 202

The basic formalism 202

Brief illustration 22.1: A valence-bond wavefunction 202

Resonance 203

Brief illustration 22.2: Resonance hybrids 204

Polyatomic molecules 204

Brief illustration 22.3: A polyatomic molecule 204

Promotion 205

Brief illustration 22.4: Promotion 205...
The principles of molecular orbital theory
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Linear combinations of atomic orbitals 209

The construction of linear combinations 210

Example 23.1: Normalizing a molecular orbital 210

Brief illustration 23.1: A molecular orbital 210

Bonding orbitals 211

Brief illustration 23.2: Molecular integrals 212

Antibonding orbitals 213

Brief illustration...
Density functional theory
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The Kohn–Sham equations 256

The exchange–correlation energy 257

The exchange–correlation potential 257

Example 30.1: Deriving an exchange–correlation potential 257

Solution of the equations 258

Example 30.2: Applying the DFT method 258

Checklist of concepts 259

Checklist of equations 259
Vibrational spectroscopy: diatomic molecules
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Vibrational motion of diatomic molecules 405

Brief illustration 43.1: The vibrational frequency of a diatomic molecule 407

Infrared spectroscopy 407

Brief illustration 43.2: The gross selection rule for infrared spectroscopy 407

Anharmonicity 408

Example 43.1: Estimating an anharmonicity constant 409
General principles
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Nuclear magnetic resonance 457

The energies of nuclei in magnetic fields 458

Brief illustration 47.1: The resonance condition in NMR 459

The NMR spectrometer 459

Brief illustration 47.2: Nuclear spin populations 460

Electron paramagnetic resonance 461

The energies of...
Probability theory
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Probability theory deals with quantities and events that are distributed randomly and shows how to calculate average values of various kinds. We shall consider variables that take discrete values (as in a one-dimensional random walk with a fixed step length) and continuous values (as...
Enthalpy
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The definition of enthalpy 552

Brief illustration 56.1: The change in enthalpy 553

Heat capacity at constant pressure 553

Example 56.1: Evaluating an increase in enthalpy with temperature 554

Changes in enthalpy with pressure and temperature 555

Brief illustration 56.2: The...
Multivariate calculus
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

A thermodynamic property of a system typically depends on a number of variables, such as the internal energy depending on the amount, volume, and temperature. To understand how these properties vary with the conditions we need to under stand how to manipulate their derivatives. This...
Real solutions
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Activities 694

The solvent activity 694

Brief illustration 72.1: The solvent activity 695

The solute activity 695

Example 72.1: Measuring activity 696

Model systems: regular solutions 696

Brief illustration 72.2: Regular solutions 697

Brief illustration 72.3: The Margules equations 698...
Chemical transformations
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The reaction Gibbs energy 714

Brief illustration 73.1: The reaction Gibbs energy 715

The thermodynamic description of equilibrium 715

Perfect gas equilibria 716

Brief illustration 73.2: The equilibrium constant 1 716

The general case of a reaction 717

Brief illustration...
Reaction rates
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Monitoring the progress of a reaction 799

General considerations 799

Example 82.1: Monitoring the variation in pressure 800

Special techniques 800

The rates of reactions 801

The definition of rate 801

Brief illustration 82.1: Reaction rates from balanced chemical...
Reactions approaching equilibrium
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

First-order reactions close to equilibrium 812

Brief illustration 84.1: The equilibrium constant from rate constants 813

Relaxation methods 813

Example 84.1: Analysing a temperature jump experiment 814

Checklist of concepts 815

Checklist of equations 815

Why do you need to know...
Electron transfer in homogeneous systems
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The rate law 898

The rate constant 899

The role of electron tunnelling 899

The distance dependence of the coupling 900

The reorganization energy 901

The determination of the reorganization energy 903

Checklist of...
Diffusion, osmosis, viscosity, and friction
Authors: Campbell Iain D.
Published: September 2023

Introduction

The cell contains large numbers of ions, metabolites, and macromolecules. The various macromolecules have unique properties, including mass, size, shape, and charge, that influence the way they move in response to flow and an applied driving force. Variation in movement is the basis of...
Mass spectrometry
Authors: Campbell Iain D.
Published: September 2023

Introduction

Mass spectrometry (MS) is a technique that measures the mass/charge ratio of particles (this simply means that a protein with mass 25 kDa (m) and charge +5 (z) will be defined by [math]). Mass...
Electrophysiology
Authors: Campbell Iain D.
Published: September 2023

Introduction

Electrophysiology is the study of the electrical properties of biological cells and tissues. Valuable information can be obtained by measuring voltages and currents in a wide range of systems, ranging from single ion channels to beating hearts. Measurement of the electrical activity of neurons...
Scattering of radiation
Authors: Campbell Iain D.
Published: September 2023

Introduction

Electromagnetic radiation can be considered as a stream of photons moving at the speed of light. These photons have no mass and can be treated as waves. There is a spectrum of electromagnetic radiation, ranging from low-energy radiowaves to high energy γ-rays; this spectrum...
Refraction, evanescent waves, and plasmons
Authors: Campbell Iain D.
Published: September 2023

Introduction

When light goes from one transparent medium to another, for example from air to water, the light beam appears to deviate from a straight line (Figure 4.2.1), a phenomenon known as refraction. Ptolemy made a list of angles observed in...
Optical activity
Authors: Campbell Iain D.
Published: September 2023

Introduction

A molecule is optically active if it interacts differently with left- and right-circularly polarized light. This differential interaction gives rise to two related phenomena known as optical rotatory dispersion (ORD) and circular dichroism (CD). Optical activity measure­ments in the 180–350 nm wavelength...
Motion and energy of particles in different force fields
Authors: Campbell Iain D.
Published: September 2023

The aim of this tutorial is to introduce some basic concepts about how various applied forces (gravity, electric and magnetic fields, and a spring) affect the motion and energy of a particle. These ideas are important for understanding many topics, including the transport phenomena discussed...
Introduction to Immune Responses, Cells, Mediators, and Structures
Authors: Cunningham Anne C.
Published: September 2023

This introductory chapter provides an overview of immune responses, outlining the cells, mediators, and structures of the immune response. The immune system recognizes and destroys things that are dangerous. These are agents or conditions that cause harm to the body. Usually, pathogens first bind body cells to gain entry, and then cause damage in tissue which leads to the activation of signals and the generation of inflammation. In a well-functioning immune system, the signals from the tissues instruct the quantity and the quality of the specific immune responses required to eradicate any danger that is present. The chapter then looks at two integrated systems which work together to eradicate pathogens and limit the development of tumours: innate immunity and adaptive immunity. The key difference between the innate and adaptive immune responses is the way they recognize pathogens (different types of receptors).
Thrive in Biochemistry and Molecular Biology
Authors: Cox Lynne S. , Harris David A. , Pears Catherine J.
Published: September 2023

Thrive in Biochemistry and Molecular Biology starts off by looking at molecules. It then considers cellular components and enzymes. Next, it moves on to genome stability and gene expression. The next chapter after that is about mammalian metabolic pathways. Integration in mammalian metabolism is considered next. Finally, the text looks in detail at microbial and plant metabolism. It ends with an examination of biochemical techniques.
Cardiorespiratory Bases for Performance
Authors: MacDougall Duncan , Sale Digby
Published: September 2023

This chapter provides a background on cardiovascular and respiratory systems from the perspective of the athlete. Their most important function is to deliver oxygen to the exercising muscles and to remove carbon dioxide, while maintaining blood flow to vital organs. The chapter explains how the cardiovascular system matches the blood flow to skeletal muscle to its metabolic rate. It also analyszes two circuits of the cardiovascular system that are arranged both in parallel and in series: pulmonary circuit and systemic circuit. The chapter explains that the pulmonary circuit conducts blood from the right side of the heart to the lungs and back to the left side of the heart. It clarifies how the systemic circuit conducts blood from the left side of the heart to all the tissues in the body and back to the right side of the heart.