bluuebunny/crossref_metadata_2025 huggingface dataset:
The Marine Environment: United and Divided
Authors: Kent Michael
Published: September 2023

This chapter provides an overview of the marine environment, which generally refers to the abiotic (physical) and biotic (biological) conditions that occur in the global ocean. The marine environment can be divided into polar, temperate, and tropical zones. The polar zones occur in the Arctic and Antarctic; ice algae form the base of polar food webs, with krill playing a central role in the Antarctic. The temperate zones are characterized by seasonal fluctuations in weather and primary production. Meanwhile, the warm sunlit waters of the tropical zones have a very low biodiversity in the open ocean and a very rich biodiversity in coral reefs. Spatially, the marine environment can be divided into two major zones: the pelagic and benthic zones. It can also be divided into a sunlit photic zone and a dark aphotic zone.
The Chemistry Maths Book
Authors: Steiner Erich
Published: September 2023

The Chemistry Maths Book begins with an examination of numbers, variables, and units. The text then moves on to look at algebraic functions, transcendental functions, differentiation, integration, and methods of integration. Other topics covered include methods of integration, sequence and series, complex numbers, functions of several variables, and functions in three dimensions. There are also chapters on first-order differential equations, second-order differential equations, partial-differential equations, and orthogonal expansions and vectors. Finally, there are chapters on determinants, matrices, linear transformations, the matrix eigenvalue problem, numerical methods, and probability.
Algebraic functions
Authors: Steiner Erich
Published: September 2023

This chapter focuses on functions of only one variable. It shows graphical representations of functions and explains the cartesian coordinate system, including the x-coordinate or abscissa and the y-coordinate or ordinate. The chapter then discusses how the structure of an algebraic expression is simplified by the process of factorization. Furthermore, it tackles inverse functions and polynomials. The chapter also discusses rational functions, differentiating proper and improper functions. Lastly, it explains partial fractions, emphasizing that the decomposition into partial fractions is an important tool in the solution of some differential equations in the theory of reaction rates, and in integration in general.
Differentiation
Authors: Steiner Erich
Published: September 2023

This chapter focuses on the process of differentiation, highlighting that the physical sciences are interested in the value of a physical quantity and how it is related to other physical quantities, how the value of the physical quantity changes on going from one state of the system to another, and in the rate of change with respect to time or with respect to some other physical quantity. The chapter reviews concepts such as change or increment, continuous function, infinite discontinuity, and essential discontinuity. It also tackles the differentiation from first principles and differentiation by rule. Then it describes implicit functions, logarithmic differentiation, and successive differentiation. The chapter likewise tackles linear and angular motion, emphasizing that the description of the motion of bodies in space is an important application of differential calculus.
Functions in 3 dimensions
Authors: Steiner Erich
Published: September 2023

This chapter takes a closer look at functions of three variables, in which the variables are the coordinates of a point in ordinary three-dimensional space. This is called a function of position, a point function, or a field that describes a great variety of physical quantities. The chapter first explains the spherical polar coordinates then describes the volume integrals. The discussion dives deeper into the concept of the Laplacian operator in three dimensions. It highlights that the Laplacian operator occurs in the equations of motion concerned with wave motion and potential theory in both classical and quantum mechanics. Furthermore, the chapter tackles other coordinate systems: the orthogonal curvilinear coordinates, cylindrical polar coordinates, and confocal elliptic coordinates.
Exploring proteins: a student’s guide to experimental skills and methods
Authors: Price Nicholas C. , Nairn Jacqueline
Published: September 2023

Exploring Proteins is composed of three sections. The first section looks at the basic concepts and tools. In particular, the key mathematical tools. Section B considers goals and methods and includes an examination of the important properties of proteins and how to explore them. The final section discusses data analysis and looks at data analysis in practice. It considers analytical methods, purification of proteins, the protein structure, enzyme activity, the binding of ligands to proteins, and how to report experimental work.
The key mathematical tools
Authors: Price Nicholas C. , Nairn Jacqueline
Published: September 2023

This chapter examines the basic concepts involved in tackling quantitative problems. It is a very good idea to develop the habit of trying to estimate the result of a calculation in advance. It is also extremely important to quote the results of calculations to the appropriate number of significant figures. The number of significant figures in the quoted value of a quantity is the number of figures ignoring leading or trailing zeroes and ignoring the position of the decimal point; it provides a measure of the confidence with which that value is known. The chapter then looks at logarithms, which are expressions of the power to which a number is raised. The use of logarithms makes it possible to compress what can be a huge numerical range. The chapter also considers reciprocals. It details the process of testing hypotheses, before outlining some important statistical concepts.
The important properties of proteins and how to explore them
Authors: Price Nicholas C. , Nairn Jacqueline
Published: September 2023

This chapter describes the goals and methods employed to separate, identify, and characterize proteins. It begins by considering how to establish the function and structure of a protein and how its activity may be regulated. The chapter then outlines the range of assays used to monitor the biological activity of proteins; such assays underpin protein characterization and purification. The classical approach to studying proteins requires their purification from their native source using bespoke purification procedures for individual proteins. This task has been simplified greatly with the advent of protein expression in recombinant systems. The chapter then looks at how a protein is regulated within the cellular environment and the types of interactions in which it is involved. Typically, this is achieved by monitoring the effects of a number of physical and chemical variables on protein activity. Finally, the chapter discusses the use of bioinformatics in exploring the properties of proteins.
Determination of protein structure
Authors: Fichte Johann Gottlieb
Published: September 2023

This chapter identifies the various aspects of protein structure, which allow us to gain insights into the size and shapes of proteins, as well as the stability of the folded structure itself. The molecular mass of a protein can be determined using a number of methods, including polyacrylamide gel electrophoresis, gel filtration, analytical ultracentrifugation, and mass spectrometry. Each method differs according to the amount of protein required for analysis; the accuracy (resolution); the extent of retention of non-covalent interactions, which may allow the mass of oligomeric structures to be determined; and the molecular mass range. The chapter then assesses what can be learned about the secondary, tertiary, and quaternary structures of the protein. It also considers the stability of the native folded structure of the protein.
How to report experimental work
Authors: Price Nicholas C. , Nairn Jacqueline
Published: September 2023

This chapter discusses the different ways in which scientific work can be reported. One way is by oral presentations, either in a relatively small-scale setting, such as a group meeting or a departmental seminar, or at a large conference. However, for most scientists the primary means of communication is via the written word, in the form of a report, a thesis, or a scientific paper. Papers are published in journals which can be aimed at a general scientific audience, or show varying degrees of specialization. The chapter then outlines the structure of a scientific report. It is important to give due credit to the work of other scientists and making sure that one does not try to pass off the work of others as one's own - a practice known as plagiarism. The chapter also looks at poster presentations, which are commonly used at scientific conferences.
Sporting talent: the genetic basis of athletic capability
Authors: Maughan Ronald J. , Gleeson Michael
Published: September 2023

This chapter explores the different factors that can determine success in sport. These include motivation, appropriate training, nutrition, and tactics. However, perhaps the most important factor is raw talent in terms of the body's phenotype; in other words, the body's physical, physiological, and metabolic characteristics. These characteristics, which in terms of athletic capability might be taken to include muscle fibre-type composition, the size of the heart and lungs, body height and mass, etc., are all to a large extent determined by the genotype (or genetic endowment) of the individual. The chapter then looks at the structure and composition of the genetic material (DNA) and the principles of heredity. It also considers the possibility of gene doping.
Units; precision and accuracy
Authors: Reed Martin B
Published: September 2023

This chapter explains units, precision, and accuracy, including the conversion of decimal numbers to scientific notation, and vice versa. It explores the Système Internationale
d'unitês or ‘SI units’ and prefixes and demonstrates their calculations to find the units for the result. It also covers the use of non-SI units in calculations and dimensional analysis to find the correct units for a quantity in an equation. The chapter highlights dimensional analysis as a way of checking whether complicated equations involving physical variables make sense and what are the correct units for physical constants and coefficients. It defines the term error in mathematical parlance, which means the difference between an approximate value and the true value.
Exponential and logarithmic functions
Authors: Reed Martin B
Published: September 2023

This chapter deals with exponential and logarithmic functions, which constitute arguably the most important area of mathematics for bioscientists. This is because many nonlinear natural processes involve some form of exponential growth or exponential decay. The chapter talks about the natural process of exponential growth and relates it to the geometric growth model. It also cites an example wherein a cell culture of 100 cells doubles in size each hour, which can be modelled by the function N(t) = 100.2t. The chapter introduces allometry, which is the study of power-law relationships between physical characteristics of an organism; these usually take the mass of the organism as the basic characteristic.
Essential communication skills
Authors: Aysha Divan
Published: September 2023

This chapter discusses the essential skills necessary for effective communication in the sciences. It specifically outlines the basic features associated with scientific communication: accuracy, conciseness, clarity, and source referencing. The chapter argues that the essential features underpinning all forms of scientific communication are that the work should be reported accurately and concisely, and that any source material used in compiling the work is acknowledged appropriately. The chapter also offers guidance on selecting and writing references. It details the main reasons for referencing the sources used in any work and it describes the two parts to referencing completely. Finally, the chapter explains the three stages a piece of work passes through before it is ready for submission or presentation: planning, drafting, and revising. It then presents some guidance on communicating effectively with your supervisor and research group members.
Ethics in communication
Authors: Aysha Divan
Published: September 2023

This chapter considers ethical issues relating to research and the communication of research. By presenting some of the ethical questions relating to communication that research students will encounter, the chapter offers a framework for understanding what is acceptable and what is unacceptable scientific conduct. It specifically outlines key ethical issues relating to data ownership and data sharing, and it explains plagiarism and strategies for avoiding plagiarism. The chapter also looks at the key ethical issues relating to the publication of primary research data including duplicate publication, conflicts of interest, authorship, and acknowledgement. Then, it provides a basic overview of copyright and how to use copyright material in your work appropriately.
Writing a literature review
Authors: Aysha Divan
Published: September 2023

This chapter aims to develop students' ability to write well-structured literature reviews. The chapter argues that the literature review provides a critical overview of recent research in a particular topic area, and that it can be written either as a self-contained report or as an introduction to a larger piece of work. Undertaking a literature review has many benefits, ranging from expanding our knowledge of a specific topic to enhancing our information retrieval and critical review skills. The chapter then identifies the different types and purposes of literature reviews. It also explicates the six-stage process for writing a literature review. Next, the chapter presents an annotated example of a completed literature review, then displays the checklist for reviewing drafts of literature reviews.
Writing a research proposal
Authors: Aysha Divan
Published: September 2023

This chapter outlines the process of writing a well-planned and well-structured research proposal. It stresses that the research proposal puts forward a clear research question or hypothesis and then sets out an experimental strategy for investigating the hypothesis or question within a defined period of time. The chapter asserts that it is a skill that a student will continue to develop as a research scientist, especially in writing a proposal at the beginning of the Master's or PhD research programme. The chapter then reviews the typical content of each component of the research proposal. It describes a strategy for writing the proposal, starting from defining the scope of the project to submitting the completed proposal. Ultimately, the chapter explores how a student can find funding sources for bioscience research. It describes how applications submitted to funding organizations are peer-reviewed and how the decision for allocating funding is reached.
Delivering effective oral presentations
Authors: Aysha Divan
Published: September 2023

This chapter offers some guidelines for the preparation and delivery of effective oral presentations. It notes that it is expected for a scientist to communicate orally in different environments and to different types of audiences, adding that it is also essential that they learn how to communicate their work in an informative and coherent way. The chapter examines how to plan an effective oral presentation and how to organize and structure a talk. It also investigates how to design effective visual aids to support the presentation and the techniques for rehearsing the talk and managing nerves. Next, the chapter explores the use of body language and voice to complement the content of the talk. It also considers how to deal effectively with questions and how to evaluate the success of the presentation.
Preparing and presenting a research poster
Authors: Aysha Divan
Published: September 2023

This chapter examines the process of presenting research findings in the form of a poster display. First, it describes the content and style of a poster. The chapter emphasizes that the objective of a research poster is to communicate research findings in a visual format. Then, the chapter highlights some guidelines on presenting the poster at a scientific conference or symposium. Poster sessions form an integral part of scientific conferences and are used by the researchers to communicate initial research findings which have not yet been published as a full research paper. The chapter further discusses the four steps to designing and presenting a good poster: planning stage, preparing the poster, presenting the poster, and evaluating how successful the poster presentation was. It concludes by showing an example of a well-designed poster.
Physicochemical Aspects of Pharmacokinetics
Authors: Moynihan Humphrey A. , Crean Abina M.
Published: September 2023

This chapter looks at physicochemical aspects of pharmacokinetics. When a quantity of a drug is administered to a patient, only a proportion of the drug will reach the target receptors, not least because only a proportion of the drug administered may be absorbed from the site of administration into the systemic circulation. The chapter begins by defining the terms pharmacodynamics and pharmacokinetics. Pharmacodynamics is the study of the relationship between drug plasma concentration and the pharmacological and toxicological responses, while pharmacokinetics is the study of the time course of drug movement in the body. The chapter then looks at how the processes of absorption, metabolism, distribution, and elimination influence the level of a drug in the body. It considers the pharmacokinetic parameters used to describe drug absorption, metabolism, distribution, and elimination. The chapter also describes the type of metabolism that occurs during phase I and II metabolism.
Sugars and phosphates: an introduction
Authors: Dobson C. M. , Gerrard J.A. , Pratt A.J.
Published: September 2023

This chapter deals with sugars and their derivatives, which are considered important molecules in biochemistry as they are manipulated to provide building blocks for the synthesis of other organic compounds. It explains how sugars are used as a fuel for the generation of cellular energy, as structural materials, and as components of the molecules of genetic information. It also refers to phosphate esters, which are the most important derivatives of sugars in cells, such as triose phosphates. The chapter scrutinizes the structural and chemical properties and biological importance of sugars and their phosphate esters. It talks about the trioses glyceraldehyde and dihydroxyacetone and this illustrates the principles of how isomeric sugars arise by variation in the position of a carbonyl group along the chain and in the configuration of chiral centres.
Epilogue: where to from here?
Authors: Dobson C. M. , Gerrard J.A. , Pratt A.J.
Published: September 2023

This chapter reviews some of the intrinsic chemical properties of important types of biological molecules, particularly amino acids, sugar phosphate derivatives, and related macromolecules. It explains that a small number of fundamental chemical properties can be used to understand many of the biological functions of molecules. The chapter also discusses the chemical potential of the functional groups found in biological molecules, highlighting the way in which amphiphilic molecules can adopt ordered, functionalized structures in an aqueous environment. The chapter analyses the availability of ordered structures with diverse chemical functional groups which provide the foundations for the molecular basis of life. It refers to macromolecules that adopt extended structures that are used by biology as fibres and for information storage.
What makes a reaction go?
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter looks into the process of a reaction. It explains the equations used to derive changes to chemical reactions. The chapter explores energy changes by referencing how temperature plays a big role in line with endothermic, exothermic, entropy, and the Second Law of Thermodynamics. It discusses the chemical process of generating ice. Energy change is due to the making and breaking of chemical bonds alongside their links to a reaction. In addition, the chapter uses Gibbs energy to compute the entropy change of systems in terms of quantity. It highlights the significance of achieving equilibrium in terms of reactions.
Electrons in larger molecules
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter discusses electrons in larger molecules. It notes how computer programs have been developed for calculating both the shapes and energies of molecular orbital through the process of specifying types and positions of atoms. The chapter mentions a process called energy minimization. Here, computers are used to determine the minimum energy arrangement required. The chapter also discusses the two–centre, two–electron bond, in addition to its analysis of hybrid atomic orbitals by referencing water, ammonia, and the inversion of ammonia. It then explores the usage of hybrid atomic orbitals to describe diatomics. The chapter ends with a discussion about reconciling the delocalised and hybrid atomic orbital approaches.
Equilibrium
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter covers equilibrium. It starts with the concept of the Second Law of Thermodynamics and Gibbs energy impacting entropy. It notes the general chemical equilibrium in terms of gas, solid, liquid, and solution. The chapter uses diagrams and equations to show how equilibrium is achieved in relation to Gibbs energy and equilibrium constants. It investigates how temperature, dimerization, extraction of metals, concentration, the Haber process, and coupling reactions influence the position of equilibrium. Additionally the chapter explores the rates of reaction in terms of equilibrium.
Bonding in extended systems – conjugation
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter discusses bonding in extended systems and relates this to conjugation. It uses the reaction of benzene bonding with all of the carbons as a reference. The chapter also refers to the structure of butadiene and propenal as examples showing the case of four p orbitals in a row. Amides, allyl anion and carboxylate anion are used to show cases where three p orbitals are in a row. In addition, the chapter discusses the chemical consequences of carbonyl compound reactions. It concludes by examining the stabilization of negative charges following the conjugation of bonds.
Competing reactions
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter explores the possible outcomes for a given set of reactions. It examines the reactions of carbonyls with hydroxide which would result in the formation of enolates, isotopic labelling, and energy profiles for alternative reactions. The chapter notes how reactions can be manipulated by changing the alkylating agent and changing the solvent. It explains how unsymmetrical enolates will be formed following the removal of hydrogen from unsymmetrical ketones. Thermodynamic and kinetic products also impact the formation of enolates. In addition, the chapter looks at how substitution and elimination could incite various reactions. It concludes by examining the importance of chemists understanding why and how reactions occur.
Structure of molecules
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter investigates the structure of molecules. Molecules are not simply a jumble of atoms: they are atoms held together in a defined three-dimensional shape. A compound’s properties are determined not only by the atoms it contains, but also by the spatial arrangement of these atoms. We know what shapes molecules have because we can see them using methods such as atomic force microscopy (AFM). Molecules hold together because positively charged atomic nuclei are attracted to negatively charged electrons, and this fact allows electrons to act as ‘glue’ between the nuclei. The chapter then looks at atomic orbitals, molecular orbitals, and the bonds between different atoms.
Nucleophilic addition to the carbonyl group
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter details the simplest of all organic reactions: the addition of a nucleophile to a carbonyl group. Nucleophilic additions to carbonyl groups generally consist of two mechanistic steps: nucleophilic attack on the carbonyl group and protonation of the anion that results. Why does cyanide, in common with many other nucleophiles, attack the carbonyl group? And why does it attack the carbon atom of the carbonyl group? To answer these questions, the chapter looks in detail at the structure of carbonyl compounds in general and the orbitals of the C=O group in particular. The chapter then considers the attack of cyanide on aldehydes and ketones; the acid and base catalysis of hemiacetal and hydrate formation; and bisulfite addition compounds.
Nucleophilic substitution at the carbonyl group
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter describes nucleophilic substitution at the carbonyl group. Most of the starting materials for, and products of, these substitutions will be carboxylic acid derivatives. Acetyl chloride will react with an alcohol in the presence of a base to give an acetate ester. The first step of the reaction is addition of the nucleophilic alcohol to the electrophilic carbonyl group. The base is important because it removes the proton from the alcohol once it attacks the carbonyl group. A base commonly used for this is pyridine. If the electrophile had been an aldehyde or a ketone, we would get an unstable hemiacetal, which would collapse back to starting materials by eliminating the alcohol. With an acyl chloride, the alkoxide intermediate we get is also unstable. It collapses again by an elimination reaction, this time losing chloride ion, to form the ester.
Electrophilic addition to alkenes
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter evaluates electrophilic addition to alkenes. Electrophilic addition to double bonds gives three-membered ring intermediates with bromine (Br2), with Hg2+, and with peroxy-acids (in which case the three-membered rings are stable and are called epoxides). Alkenes decolourize bromine water: alkenes react with bromine. The product of the reaction is a dibromoalkane. All three classes of three-membered rings react with nucleophiles to give 1,2-difunctionalized products with control over regioselectivity and stereoselectivity. Meanwhile, protonation of a double bond gives a cation, which also traps nucleophiles, and this reaction can be used to make alkyl halides. The chapter also looks at dihydroxylation, periodate cleavage, and ozonolysis.
Chemoselectivity and protecting groups
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter describes chemoselectivity and protecting groups. Most organic molecules contain more than one functional group, and most functional groups can react in more than one way, so organic chemists often have to predict which functional group will react, where it will react, and how it will react. These questions are what can be called selectivity. Selectivity comes in three sorts: chemoselectivity, regioselectivity, and stereoselectivity. The chapter focuses on chemoselectivity (which group reacts). It begins by looking at reductions of carbonyl compounds, introducing a few more specialized reducing agents. The chapter then considers the other type of reduction in the salmefamol synthesis: catalytic hydrogenation.
Regioselectivity
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter explores regioselectivity. Chemoselectivity means that there are two separate functional groups and that a reagent must choose between them. By contrast, regioselectivity implies that there is one functional group that can react in two different places and a reagent must choose where to react. Simple examples include addition of HX to an alkene and nucleophilic attack on the epoxide derived from that alkene. It might also mean that two functional groups are combined in a single conjugated system that can again react in two (or more) places. The choice between ortho/para and meta substitution when an electrophile attacks a benzene ring is also a matter of regioselectivity. The chapter considers regioselectivity in electrophilic aromatic substitution and in radical reactions.
Reactions of enolates with carbonyl compounds: the aldol and Claisen reactions
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter highlights reactions of enolates with carbonyl compounds: the aldol and Claisen reactions. The simplest enolizable aldehyde is acetaldehyde. What happens if we add a small amount of base, say NaOH, to this aldehyde? Some of it will form the enolate ion. Each molecule of enolate is surrounded by molecules of the aldehyde that are not enolized and so still have the electrophilic carbonyl group intact. The enolate ion will attack one of these aldehydes to form an alkoxide ion, which will be protonated by the water molecule formed in the first step. The product is an aldehyde with a hydroxy (ol) group and it has the trivial name aldol. This reaction is so important because of the carbon–carbon bond formed when the nucleophilic enolate attacks the electrophilic aldehyde.
Sulfur, silicon, and phosphorus in organic chemistry
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter discusses three of the most important elements in the periodic table: sulfur, phosphorus, and silicon. They all form stable organic compounds and play nearly as important roles in organic chemistry as oxygen, nitrogen, and the halogens. Silicon forms tetrahedral silanes, rather like alkanes, but also forms stable five-valent anions. Phosphorus forms phosphines, rather like amines, but also tetrahedral phosphine oxides. Meanwhile, sulfur can have any coordination number from zero to seven, forming sulfides, like ethers, and tetrahedral sulfones with six bonds to sulfur. The chapter then looks at sulfur-stabilized anions, sulfur salts, and sulfonium ylids. It also considers allyl silanes as nucleophiles, before studying the selective synthesis of alkenes.
Saturated heterocycles and stereoelectronics
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter focuses on saturated heterocycles and stereoelectronics. What are the ‘special chemical features’ of saturated heterocycles? Putting a heteroatom into a ring does two important things. Firstly, the heteroatom makes the ring easy to make by a ring-closing reaction, or (in some cases) easy to break by a ring-opening reaction. Secondly, the ring fixes the orientation of the heteroatom—and, in particular, the orientation of its lone pairs—relative to the atoms around it. This has consequences for the reactivity and conformation of the heterocycle which can be explained using the concept of stereoelectronics. The chapter then considers the reactions and conformation of saturated heterocycles.
Stereoselectivity in cyclic molecules
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter assesses stereoselectivity in cyclic molecules. Not only is stereochemistry easier to understand in cyclic compounds, it is also better behaved in cyclic compounds. The chapter looks at reactions happening to cyclic compounds, reactions with cyclic intermediates, and reactions with cyclic transition states. Diastereoselectivity in rings generally follows a few simple principles. Diastereoselectivity in compounds without rings is different: it is less well controlled because there are many more conformations available to the molecule. But even in acyclic compounds rings can still be important, and some of the best diastereoselectivities arise when there is a ring formed temporarily in the transition state of the reaction.
Diastereoselectivity
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter addresses diastereoselectivity. It explains how to make compounds as single diastereoisomers. The chapter begins by differentiating between stereospecific and stereoselective reactions. In stereospecific reactions, the mechanism means that the stereochemistry of the starting material determines the stereochemistry of the product and there is no choice involved. In stereoselective reactions, one stereoisomer of product is formed predominantly because the reaction has a choice of pathways, and one pathway is more favourable than the other. The reactions that give single diastereoisomers—in other words, those that are diastereoselective—all involve the creation of a new, tetrahedral stereogenic centre at a carbon that was planar and trigonal. Trigonal carbons that are not stereogenic (or chiral) centres but can be made into them are called prochiral. The chapter then considers stereoselective reactions of acyclic alkenes.
Participation, rearrangement, and fragmentation
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter studies two other types of ionic reactions: rearrangements and fragmentations. In rearrangements the molecule changes its carbon skeleton and in fragmentations the carbon skeleton splits into pieces. The chapter begins by looking at the phenomenon known as participation. How do we know that neighbouring group participation is taking place? The first piece of evidence is the increase in rate. The neighbouring groups become involved only if they can increase the rate of the substitution reaction, otherwise the mechanism will just follow the ordinary SN2 pathway. But more important information comes from reactions where stereochemistry is involved. The chapter then considers how rearrangements occur when a participating group ends up bonded to a different atom, before looking at the Favorskii rearrangement, the Baeyer–Villiger reaction, and the Beckman rearrangement.
Synthesis and reactions of carbenes
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter reviews the synthesis and reactions of carbenes. The best evidence for the existence of carbenes comes from a group of structures which contain a carbene but are stable compounds. The most important of these are known as the ‘N-heterocyclic carbenes’—the carbene is incorporated into a five-membered ring and stabilized by the presence of two adjacent electron-donating nitrogen atoms and the bulky N-substituents. These stable carbenes are very much the exception: most carbenes are too reactive to be isolated. Ultimately, carbenes can be formed from many other reactive intermediates, such as carbocations, carbanions, and diazoalkanes. The chapter then looks at how they can react to give yet further reactive intermediates such as ylids.
Determining reaction mechanisms
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter discusses the determination of reaction mechanisms. Organic chemists have to face situations where the structure of a compound is initially thought to be one thing but later corrected to be something different. The same is true of mechanisms. When a new reaction is discovered, one or more mechanisms are proposed; evidence is then sought for and against these mechanisms until one emerges as the best choice. That one then remains the accepted mechanism for the reaction until fresh evidence comes along that does not fit the mechanism. The chapter looks at one reaction, the Cannizzaro reaction, and uses this to introduce the different techniques used in elucidating mechanisms. It considers systematic structural variation, the Hammett relationship, acid and base catalysis, and stereochemistry.
Asymmetric synthesis
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter focuses on asymmetric synthesis. It begins by discussing chirality. A laboratory synthesis of a chiral compound from achiral or racemic starting materials alone always gives a racemic mixture of enantiomers. If we want to make just one enantiomer, we have to use a starting material or reagent which is also just one enantiomer. Nature provides a collection of ‘off the shelf’ enantiomerically pure compounds that we can exploit in various ways. This collection of natural, enantiomerically pure compounds is called the chiral pool. The chapter then looks at chiral auxiliaries and reagents, before studying asymmetric catalysis, asymmetric formation of carbon–carbon bonds, and asymmetric aldol reactions. It also considers enzymes as catalysts.
Organic chemistry of life
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter assesses the organic chemistry of life. Life runs on chemistry, and the chemical side of biology is fascinating for that reason alone. Nucleic acids contain the genetic information of every organism, and they control the synthesis of proteins. Proteins are partly structural, as in connective tissue, and partly functional, as in enzymes, the catalysts for biological reactions. Meanwhile, sugars and lipids used to be thought of as the poor relations of the other two, storing energy and building membranes, but it is now clear that they also have a vital part to play in recognition and transport. The chemistry common to all living things is known as primary metabolism. The chapter also looks at mechanisms in biological chemistry.
Organic chemistry today
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter explores organic chemistry today and in the future. The most dramatic scientific developments involving organic chemistry at the beginning of the 21st century are new methods in medicine from collaborations between organic chemists and biologists. Progress is slow but secure across a whole range of diseases long thought impregnable to treatment. The chapter looks at two medical developments, both battles pitting chemists against viruses: the synthesis of indinavir and oseltamivir. Not all organic chemists can be involved in such exciting projects as the launching of a lifesaving antiviral drug. Some most certainly have to be: resistant bacteria are fast catching up with the current range of antibiotics, and it is teams of organic chemists, in conjunction with biologists, who will be able to erect the next line of defence against these infections.
Earliest forms of plant life
Authors: Willis K. J. , McElwain J. C.
Published: September 2023

This chapter outlines the patterns of environmental change and biological evolution in the first four billion years of the history of Earth. It describes the processes that led to the development of the first forms of multicellular plant life. It also talks about the continental crust that started to form on Earth from approximately 4200 Ma, and by 1,100 million years ago, when a large landmass called Rodinia developed. The chapter describes the oceans that formed early in the history of Earth as a result of condensation of atmospheric water vapour. Estimates suggest that the earliest oceans were warm and fairly acidic. It reviews the evidence from both the geological and molecular records that suggests that both prokaryotic and eukaryotic evolution occurred in relatively rapid bursts.
The colonization of land
Authors: Willis K. J. , McElwain J. C.
Published: September 2023

This chapter examines the environmental changes leading up to and during terrestrialization and the fossil evidence for changes in plant morphology that enabled land dwelling. It reviews possible evolutionary pathways from the earliest aquatic plants to land plants. It also considers the global biogeographical distribution of the earliest land plants and provides an assessment of how they changed the system on Earth. The chapter analyses geological, morphological, and molecular evidence that suggests that the earliest vascular plants occurred as a result of a lineage split from the hornworts. It discusses the terrestrialization of land surfaces by plants which had significant impacts on the system on Earth, including altering river drainage patterns, rates of erosion, atmospheric concentrations of CO2 and O2, and ultimately biogeochemical cycles.
Major emergence of the seed plants
Authors: Willis K. J. , McElwain J. C.
Published: September 2023

This chapter outlines the emergence and radiation of seed plants and the environmental and climatic conditions that existed prior to and during their radiation. It highlights a major transformation that occurred in global vegetation, with the emergence and widespread radiation of seed plants during the period spanning the Permian. It also details the major floral evolution that occurred against a backdrop of increasing global warmth, widespread aridity within continental interiors, high seasonal temperature fluctuations, equatorial aridity, and monsoonal conditions in the southern hemisphere. The chapter reviews the formation of the supercontinent Pangea by 300 Ma, which is thought to be one of the main reasons accounting for the global climate change. It discusses the evolution and radiation of the conifers that occurred between ~248–206 Ma.
Flowering plant origins
Authors: Willis K. J. , McElwain J. C.
Published: September 2023

This chapter analyszes the evidence for the first flowering plants, and considers various theories as to why their appearance was so late in the geological record. It discusses the proposed evolutionary pathways leading to angiosperm evolution. It also looks at various hypotheses that have been suggested to account for the relatively late appearance of angiosperms in the fossil record, including a bias in the fossil evidence. The chapter highlights two biotic interactions, which include the co-evolution of flowering plants with low-browsing dinosaurs and with pollinating insect groups. It reviews the cladistic analyses based on morphological and molecular traits of both extant and fossil material, which. This indicates that angiosperms were derived from a single common ancestor.
The foundations of quantum mechanics
Authors: Atkins Peter , Friedman Ronald
Published: September 2023

Operators in quantum mechanics

Linear operators

Eigenfunctions and eigenvalues

Representations

Commutation and non-commutation

The construction of operators

Integrals over operators

Dirac bracket and matrix notation

Hermitian operators

The postulates of quantum mechanics

States and wavefunctions
Angular momentum
Authors: Atkins Peter , Friedman Ronald
Published: September 2023

This chapter considers rotational motion as the second class of motion of an object around a fixed point and angular momentum, which is one of the most important topics in quantum mechanics. It discusses the rotational motion and angular momentum in terms of solutions of the Schrödinger equation and see how its properties emerge from the operators for angular momentum and their commutation relations. It also examines the quantum mechanical description of a particle travelling on a circular ring, which applies to the motion of a bead on a circle of wire and any body rotating in a plane. The chapter describes the moment of inertia the property, which determines the characteristics of the rotational motion of a body. It cites a particle of mass m travelling on a circle of radius r in the xy-plane and its potential energy that is constant and taken to be zero.
An introduction to molecular structure
Authors: Atkins Peter , Friedman Ronald
Published: September 2023

This chapter looks at a great deal of chemically interesting information that can be obtained by interpreting the line spectra of atoms, the frequencies of the electromagnetic radiation that atoms emit when they are excited. It explains how to use the information to establish the electronic structures of the atoms and how to use that information as a basis for discussing the periodicity of the elements and the structures of the bonds they form. Atomic spectra were also of considerable historical importance because their study led to the formulation of the Pauli principle, without which it would be impossible to understand atomic structure, chemical periodicity, and molecular structure. The chapter cites information provided by atoms that is of considerable importance for the discussion of molecular structure. The values of ionization energies and spin–orbit coupling parameters help understand the structures of molecules and their properties, particularly their photochemical reactions.
Computational chemistry
Authors: Atkins Peter , Friedman Ronald
Published: September 2023

This chapter explores the forces that hold atoms together in molecules and discusses why initial arrangements of atoms change into new ones in the course of the events called chemical reactions. It introduces some of the features of valence theory, the theory of the formation of chemical bonds. The description of bonding has been greatly enriched by numerical techniques. The chapter reviews two principal models of molecular structure: molecular orbital theory and valence bond theory, which contribute concepts to the everyday language of chemistry. Born–Oppenheimer approximation takes note of the great difference in masses of electrons and nuclei and the electrons can respond almost instantaneously to displacement of the nuclei.
Molecular electronic transitions
Authors: Atkins Peter , Friedman Ronald
Published: September 2023

This chapter discusses molecular spectra, which are more complex than atomic spectra and convey richer information. It explains how greater complexity arises from the more complicated structures of molecules, for whereas the spectra of atoms are due only to their electronic transitions, the spectra of molecules arise from electronic, vibrational, and rotational transitions. These modes are not independent of one another, and the complexity of the spectra is enriched by the interactions between them. The chapter confirms that an interpretation of molecular spectra yields a great deal of information about the shapes and sizes of molecules, the strengths and stiffnesses of their bonds, and other information that is needed to account for chemical reactions. The energy associated with rotational transitions is usually less than for vibrational transitions, and the energy of vibrational transitions is usually less than for electronic transitions.
Scattering theory
Authors: Atkins Peter , Friedman Ronald
Published: September 2023

This chapter reviews the difference between electric and magnetic perturbations, noting that the former stretch a molecule, while the latter twist it. It looks at the effect of a twisting perturbation, which is to induce electronic currents that circulate through the framework of the molecule. These currents give rise to their own magnetic fields, noting that one effect is to modify the magnetic flux density in the material. The chapter highlights how the substance is classified as paramagnetic if the flux density is increased beyond that due to the applied field alone. If the flux density is reduced, then the substance is classified as diamagnetic.