bluuebunny/crossref_metadata_2025 huggingface dataset:
Chemical disaccharide formation
Authors: Davis Benjamin G. , Fairbanks Antony J.
Published: September 2023

This chapter considers a crucial step in the synthesis of any oligosaccharide, namely the linking of two monosaccharide precursors by the construction of the glycosidic linkage. It talks about how glycosidic bond formation is achieved by the operation of the displacement of a leaving group at the anomeric position of one sugar, termed the glycosyl donor. It also defines the terms glycosylation reaction, glycosyl donor, and glycosyl acceptor. The chapter highlights the problems of regio- and stereochemistry inherent in the synthesis of di- and oligosaccharides. It explains how to synthesise and activate the most commonly used classes of glycosyl donors.
Resetting the clock: oscillations
Authors: Scott Stephen K.
Published: September 2023

This chapter focuses on class reactions and single travelling wavefronts that arise from taking the initial reactants through to final products. It explores ways of resetting the clock for repetitive events, such as an oscillatory reaction in a well-stirred system. It also describes the BZ system as the most familiar example of an oscillatory chemical reaction. This reaction involves the oxidation of malonic acid by an acidified bromate solution in the presence of a metal ion catalyst. The chapter notes the concentrations of bromate and malonic acid that decrease slowly but continuously during the reaction process, although there are oscillatory variations in the concentrations of certain intermediate species. It elaborates how the BZ system has been developed in terms of the Field–Körös–Noyes (FKN) mechanism.
Targets, spirals, and scrolls
Authors: Scott Stephen K.
Published: September 2023

This chapter focuses on reactions that show oscillations in closed systems which give rise to a range of interesting wave behaviour in unstirred systems. It looks at clock reactions that give rise to the one-off diffusion fronts as reactants are consumed as the front passes. It also cites BZ-type systems wherein the front corresponds to a wave reaction involving intermediates that have little consumption of the major reactants. The chapter explains the meaning of resetting mechanism, which covers a wave back that follow a front and return the system to its original and prefront state. It highlights the ability of BZ-type systems to lead to a series of pulses or a wave train, which can organize the reaction mixture in two or three dimensions into a variety of intricate, evolving patterns.
Bistability and oscillations in flow reactors
Authors: Scott Stephen K.
Published: September 2023

This chapter reviews the disadvantages of studying reactions in thermodynamically closed vessels in which anything other than equilibrium state is strictly transient. It discusses the use of open reactors that have a continuous inflow of fresh reactants matching the outflow of products. It also describes well-stirred flow reactors that are widely exploited in practical situations in the chemical industry and are considered an important part of chemical engineering. The chapter explains how a reaction proceeds to a true steady state wherein the net rate of inflow of each reactant species balances its net rate of chemical removal by reaction. It highlights iodate-arsenite and iodate-bisulphate reactions, which have been studied in flow reactors.
Nomenclature of inorganic compounds to non-aqueous solvents
Authors: Mingos D.M.P.
Published: September 2023

This chapter begins by discussing the nomenclature of inorganic compounds. Inorganic chemistry deals with very different types of compounds and therefore different naming schemes have evolved. Increasingly systematic names based on well-defined rules are replacing trivial names which have a long history but do not have the flexibility to be adapted for naming the wide range of compounds that currently exist. The chapter then looks at non-aqueous solvents. Ammonia is particularly useful for solvating electrons; the use of ammonia leads to the isolation of salts which are not generally accessible in water. Meanwhile, non-protic solvents such as liquid SO2 are particularly useful for dissolving iodide salts.
Periodic table to polyhedral cage geometries
Authors: Mingos D.M.P.
Published: September 2023

This chapter evaluates the periodic table before looking at periodic trends. Although historically the periodic table can be traced back to Mendeleev in 1871, its modern interpretation depends on the quantum mechanical solution of the wavefunctions of the hydrogen atom and its extension to polyelectronic atoms. The arrangement of elements in order of increasing atomic number with the elements showing similarities placed in vertical columns formed the basis of the original periodic table. We now realize that the fundamental basis of this periodicity is the repeating character of electron configurations of atoms resulting from the Aufbau filling of quantized energy levels for polyelectronic atoms. The chapter then looks at platinum metals, polarizability, and polyhedral cage geometries.
Hydride ligands
Authors: Housecraft Catherine E.
Published: September 2023

This chapter introduces aspects of the chemistry of transition metal carbonyl dimers and clusters and illustrates classes of compound with hydride ligands, phosphine and phosphite ligands, organic ligands, interstitial atoms, and other groups involving elements from the p-block. It considers selected methods in preparing heterometallic clusters. It also discusses dimers and clusters containing hydrogen atoms attached directly to one or more metal centres, which are generally termed as hydrides. The chapter explores the electron withdrawing properties of some ligands in the molecule that meant that the metal-bound hydrogen atom can be removed by treatment with base or introduced by reaction of an anionic dimer or cluster with acid. It analyses the general modes of attachment of a hydride ligand to a metal dimer or cluster.
Clusters containing p-block atoms other than carbon
Authors: Housecraft Catherine E.
Published: September 2023

This chapter considers clusters that incorporate p-block atoms, other than carbon, into the skeletal framework and looks at compounds in which PR groups or P atoms are part of the cluster, including nitrogen- and boron-containing clusters. It refers to the use of phosphine or PH3. This permits the successive activation of three P-H bonds and the eventual formation of an interstitial phosphorus atom. The chapter also analyses the transformation which involves the metal-bound NO group. This has some relevance to studies of atmospheric pollution by nitric oxide. The chapter illustrates a stabilizing effect in which an interstitial atom causes the metal skeleton to reorganize itself with the p-block that holds the metal fragments in place. It describes the structure of a tetrairon cluster that is similar to the butterfly carbides and nitrides.
Organic halides
Authors: G. Denis Meakins
Published: September 2023

This chapter refers to the general tendencies, methods of preparation, and characteristic reactions of alkyl halides and halides containing a double bond. It talks about chlorides, bromides, and iodides, which fall into a graded series, while fluorides are described to be of a different nature. It also points out the importance of the halides and their reactions with nucleophiles, including the general reaction of the attack of a base on halides. The chapter considers factors that influence the substitution/elimination ratio that show the marked differences between primary, secondary, and tertiary halides. It describes primary bromides as the most effective halides while primary iodides give side-reactions that lower the yield of the required product.
Photochemistry
Authors: Wayne Carol E. , Wayne Richard P.
Published: September 2023

Photochemistry studies this subject which sits in the broad filed of chemistry. The text describes the 'new' chemistry that follows the absorption of light, and explains how light has this extraordinary influence on chemical behaviour. Examples of established principles are presented examining the way in which life and the other natural processes depend on photochemistry, and also how photochemistry can be used in a variety of applications. Chapters focus on chemical change, photophysics, photochemical kinetics, photochemistry in nature, and applied photochemistry.
State-specific cross-sections
Authors: Brouard M.
Published: September 2023

This chapter evaluates state-specific cross-sections. It begins by looking at experimental considerations, examining molecular beam experiments and spectroscopic based experiments. The chapter then explores the models of energy utilization and disposal, considering the role of collision energy. A qualitative appreciation of how the reaction cross-section varies with collision energy is provided by the line-of-centres model, which forms the basis of simple collision theory. In this model, the reactants are treated as two structureless spherical particles which react provided the radial kinetic energy is greater than zero at the reaction barrier. Finally, the chapter studies kinematic constraints. A kinematic constraint is a constraint imposed purely on account of the reactant and product mass combination and the operation of the laws of conservation of (linear and angular) momentum and total energy.
Microcanonical rate coefficients
Authors: Brouard M.
Published: September 2023

This chapter focuses on microcanonical rate coefficients. It begins by looking at the cumulative reaction probability. The chapter then considers transition state theory. The transition state may be thought of as a bottleneck somewhere on the potential energy surface through which reactants must pass if they are to form products. More precisely, it is a dividing surface, which separates reactants from products. The key dynamical assumption of transition state theory is that of 'direct dynamics', which is often referred to as the no-recrossing rule. Trajectories which cross the transition state dividing surface from the reactant side are assumed to go on to form products and cannot be reflected back into the reactant valley. Finally, the chapter studies the measurement of microcanonical rate coefficients.
Introduction to Molecular Symmetry
Authors: Ogden J.S
Published: September 2023

Introduction to Molecular Symmetry first looks at symmetry elements, symmetry operations, and point groups. The next chapter examines matrices, multiplication tables, and representations. The text then covers the reduction formula, matrices and representations in higher order point groups, and molecular vibrations. The next chapter is about vibrational spectroscopy. The last chapter covers symmetry aspects of chemical bonding.
Symmetry aspects of chemical bonding
Authors: Ogden J.S
Published: September 2023

This chapter provides an introduction to symmetry aspects of molecular bonding, particularly to the sets of orbitals that can combine to form a molecular orbital diagram. It focuses on the use of symmetry in describing and depicting the chemical bonding and electronic energy levels within molecules. It also mentions the molecular orbital description of chemical bonding, wherein the molecular wave function establishes energy levels and acquire symmetry properties that relate to the point group of the molecule. The chapter emphasizes how each wave function must have a symmetry corresponding to one of the irreducible representations. It explains that wave functions are constructed from linear combinations of the constituent atomic orbitals.
Further reading
Authors: Cox P. A.
Published: September 2023

Books marked * are more advanced, and not recommended for beginners.

Historical and philosophical background

J. C. Polkinghorne, The quantum world, Penguin Books, Harmondsworth (1986).

*J. Baggott, The meaning of the quantum theory, Oxford University Press (1992).

Applications in atomic and molecular spectroscopy

T. P....
Mechanistic organometallic chemistry
Authors: Whyman Robin
Published: September 2023

This chapter recognizes the vital role played by organometallic chemistry in the understanding of industrial process applications and looks at developments in organometallic chemistry which occurred in parallel to industrial applications. It refers to the successful commercial application of homogeneous catalysis. This is based on a good understanding of the underlying organometallic chemistry. It also illustrates a framework of transformations upon which the construction of catalytic cycles can be based. The chapter discusses the rules of organometallic complexes and their reactions. This emphasizes that diamagnetic organometallic complexes of transition metals may exist in significant concentration at moderate temperatures. It describes organometallic reactions that proceed by a series of elementary steps involving intermediates with 16 or 18 valence electrons.
Redox reactions
Authors: Mingos D.M.P.
Published: September 2023

This chapter analyses redox reactions. It explains that the oxidation–reduction reactions of transition metal complexes proceed via two primary mechanistic pathways: outer and inner sphere reactions. An outer sphere mechanism occurs when an electron is transferred between two coordination complexes in solution, both of the coordination spheres remain intact, and no ligand is transferred between them. The chapter notes that it is only possible to establish such a mechanism unambiguously when both of the coordination complexes are substitutionally inert. Finally, the chapter describes the inner sphere mechanism: the electron transfer is mediated by an ambidentate ligand which is capable of bridging the two metal centres in the transition state and is transferred from one complex to the second in the course of the reaction.
The important elements in biology
Authors: Wilkins Patricia C. , Wilkins Ralph G.
Published: September 2023

This chapter talks about essential elements which are derived from the s-, p-, and d-blocks and analyses the different general functions of each block. It discusses the vital role played by elements other than carbon for specific functions and emphasizes a fine balance between a deficiency, an excess intake, and a short range of daily intake that is essential and optimal. It also outlines the importance of organic compounds in the functioning of the human body. It mentions elements that have become of marked clinical value. The chapter analyses highly toxic elements, such as soft cations that bind sulfur ligands and S-containing amino acids. It points out that all toxic elements are chemically similar to an essential element.
The examination of the properties of metalloproteins
Authors: Wilkins Patricia C. , Wilkins Ralph G.
Published: September 2023

This chapter examines the physical and chemical properties of most metalloproteins that yield information on their overall structure and provides insight into details of the active site. It focuses on the metal ion and its immediate environs, noting the presence of a metal ion in a biomolecule that has not been easy to detect. It also analyses the iron content of a number of metalloproteins which can been wrongly assessed at first, and which results in serious misjudgments of the number of irons present in the protein. The chapter discusses methods for the determination of the basic characteristics of a metalloprotein that are applicable to all proteins. It recounts exciting developments in mass spectrometry techniques in relation to the assessment molecular weights since the 1980s.
Structures and functions
Authors: Wilkins Patricia C. , Wilkins Ralph G.
Published: September 2023

This chapter reviews the spectroscopic properties of metalloproteins that are vital for their monitoring and for their illuminating of the details of the metal site. The chapter mentions properties that are directly related to the function of the metalloprotein, which are distributed between those that originate from polypeptide from those arising from the metal ion. It also analyses the artificial division of metalloprotein that act synergistically, which results in a unique entity. The chapter talks about protein, which imposes a rigid and often unusual arrangement of ligands around the metal ion. It explains how protein provides a pathway for the protected or guided entry of substrates to the metal site.
The s-block
Authors: Wilkins Patricia C. , Wilkins Ralph G.
Published: September 2023

This chapter cites elements of groups one and two that have one s- and two s-outer electrons, which can be lost in giving the predominant +1 and +2 oxidation states. It discusses ionic bonds that predominate compounds in the elements and radii of the ions of biological relevance. It also reviews the aquated ion that includes inner shell coordination and outer shell attraction of solvent molecules. The chapter describes s-cations as generally poor complexers that require strong binding and chelating or macrocyclic ligands or proteins to form stable entities. It analyses group one and group two in terms of providing the background electrolytes for living systems.
The d-block - redox chemistry
Authors: Wilkins Patricia C. , Wilkins Ralph G.
Published: September 2023

This chapter explains the d-block of elements as a family of metals with similar characteristics that represent the transition between the highly electropositive s-block metals and the electronegative p-block non-metals. It discusses the behaviour of d-block elements as ions in solution and relates this to coordination and redox chemistry. It also examines transition elements that exhibit variable oxidation states, such iron that exist in oxidation states of II, III, IV, and VI. The chapter describes the octahedral arrangement of the six d electrons that can be in two dispositions and the possible dichotomy that plays an important role in iron-protein chemistry. It mentions a pair of Fe(II) and Fe(III) ions that behave like an isolated metal centre.
The d-block – nonredox chemistry
Authors: Wilkins Patricia C. , Wilkins Ralph G.
Published: September 2023

This chapter discusses transition elements with a propensity for facile one or two electron changes that feature heavily in the oxidoreductases. It analyses the H2O liability that is essential for the metal ions to operate in metalloenzymes wherein the substitution of H2O by substrate is often a necessary step and is rarely rate limiting in the overall mechanism. It also explains how a substrate is added to the existing coordinated ligands, which is possible because the metal ions have variable coordination numbers. The chapter talks about the loss of liability when the metal ion is strongly chelated, which is required when the purpose of the ligand is to help transport the metal ion. It describes first row transition elements that are represented in the hydrolase, lyase, and isomerase classes.
Introduction
Authors: Brisdon Alan K.
Published: September 2023

This introductory chapter provides an overview of spectroscopy, which can be defined as the study of the interaction between radiation and matter. Since the spectroscopic techniques described in this book, with the exception of mass spectrometry, involve such an interaction, it begins by considering electromagnetic radiation and some of its properties. To observe a spectrum, the compound must interact either with the electric or magnetic component of the applied radiation. The chapter then explains molecular energy levels, population distributions, selection rules, and time-scales. It also details the basic components of a scanning spectrometer. It is more common these days for an alternative method to be used which essentially allows all the data for the complete spectrum to be recorded very rapidly. Such techniques use Fourier transform methods to mathematically de-convolute individual absorptions at particular energies (or frequencies) from data containing all such energies which are recorded as an interference pattern.
Introduction
Authors: Procter Garry
Published: September 2023

This introductory chapter provides an overview of stereoselectivity in organic synthesis. Given the importance of the three-dimensional structure of organic compounds, and the fact that all organic compounds arise as a result of a previous reaction or reaction sequence, it is not surprising that an area of chemistry which encompasses organic reactions and stereochemistry is central to organic chemistry. This book focuses on the area of stereoselective organic reactions, highlighting their usefulness in organic synthesis where appropriate. For the most part, it is concerned with reactions which involve the formation of tetrahedral carbon atoms within a molecular framework. The chapter then looks at diastereoselective reactions, enantioselective reactions, and stereospecific and stereoselective reactions.
Rearrangements
Authors: Procter Garry
Published: September 2023

This chapter explores rearrangements. The most important types of rearrangement reactions which find use in stereoselective organic synthesis are 2,3- and 3,3-sigmatropic rearrangements, and the isomerization of alkenes. The sigmatropic rearrangements which the chapter discusses are the Claisen rearrangement and its variants, and the 2,3-Wittig rearrangement. These rearrangements have been used for some time in organic synthesis, unlike the isomerization of alkenes. In this context, the latter has become important relatively recently owing to the discovery of very effective enantioselective catalysts. The Claisen rearrangement of allyl vinyl ethers is probably the most widely used 3,3-sigmatropic rearrangement in stereoselective organic synthesis. The transition state for this type of reaction is closely analogous to that of the aldol reaction.
Catlytic materials and their preparation
Authors: Bowker Michael
Published: September 2023

This chapter evaluates catalytic materials and their preparation. Catalysts can take a broad range of forms and this is reflected in the range of materials produced, and used, by the chemical industry and by nature. Thus, they can range from solid materials to biological enzymes, from gas phase molecules to liquid coatings on surfaces. The chapter highlights the important types of applied industrial catalysts, including metals and oxides. There is a wide range of properties of a catalyst that are required in order for it to be an efficient one for any particular reaction. The foundations of catalyst production are the correct kinetic reaction parameters, that is, high product yield per unit time, and so the correct active phase is the basis of catalyst preparation. The chapter then looks at catalyst design methods, as well as the making of catalysts.
Enolate alkylations with alkyl halides
Authors: Jones John
Published: September 2023

This chapter addresses enolate alkylations with alkyl halides. Simple enolates react irreversibly with soft (polarized) electrophiles such as methyl iodide. A new carbon–carbon bond is formed in an SN2, which is of considerable synthetic importance. The chapter then looks at enolates derived from simple ketones, simple esters, and β dicarbonyl compounds. If cyclohexanone is treated with ethanolic sodium ethoxide in the presence of methyl iodide, most of the latter reacts with ethoxide ion. However, if the considerably more hindered and slightly more basic t-butoxide is used as base, little reaction of it with the methyl iodide occurs. The difficulty arises from the fact that substantial concentrations of bases derived from alcohols are necessary to obtain even small concentrations of enolates from simple ketones.
Radiation Heat Transfer
Authors: Jones H. R. N.
Published: September 2023

Radiation Heat Transfer is an introductory text on radiation heat transfer. It starts from the basic physical principles of thermal radiation, and then goes on to develop methods for the calculation of view factors, rates of heat transfer between surfaces, effects of intervening gases, and the treatment of combined modes of heat transfer. It applies these methods to a number of practical engineering examples, including heat transfer in furnaces, techniques for the measurement of temperature, and radiation from particles in combustion gases.
Combined modes of heat transfer
Authors: Jones H. R. N.
Published: September 2023

This chapter analyses systems where two or more mechanisms of heat transfer modes are occurring simultaneously. It talks about the general importance of conduction for heat transfer through solids, noting that radiation is needed in transparent or porous solids. It also points out that radiation is only possible through a vacuum and is dominant in many low-pressure systems. The chapter introduces the idea of incorporating convective heat transfer into a radiative problem by including a convection term in the heat balance. It considers approaches that deal with combined modes of heat transfer, which covers the use of heat transfer coefficients in the context of radiative heat transfer and analytical methods for combining heat transfer modes.
Material balances for chemical reactors
Authors: Metcalfe Ian S.
Published: September 2023

This chapter discusses how material balances should be performed for the three fundamental reactor types used in reaction engineering. These include the plug flow reactor (PFR), the continuous stirred tank reactor (CSTR), and the perfectly mixed batch reactor. In a batch reactor, all of the reactants are supplied to the reactor at the outset; there is no addition of reactants or removal of products during the reaction. Meanwhile, a PFR is a special type of tubular reactor. Feed is continuously supplied to the reactor and products are continually removed. The CSTR, like the PFR, has a continuous supply of feed while products are continually removed. However, in this case, perfect mixing is achieved, i.e. there are no concentration or temperature gradients within the reactor.
Non-ideal reactors
Authors: Metcalfe Ian S.
Published: September 2023

This chapter focuses on non-ideal reactors. In practice, plug flow and perfect mixing are never achieved. This is because of effects such as stagnant regions and ‘short circuiting’. In a tubular reactor, these stagnant regions will have a longer residence time than the rest of the process stream and mixing will occur within the stagnant regions. In stirred tank reactors, some elements might ‘short circuit’ or bypass the well-mixed bulk of the reactor. This will result in a larger fraction of the process stream having short residence times and there will be incomplete mixing of all the elements in the reactor. The chapter then looks at the concept of residence time distributions (RTDs). We can model a continuous reactor as a collection of small elements. The RTD is a distribution plot of the fraction of these elements exiting the reactor with different residence times.
Fundamentals of X-ray crystallography
Authors: Clegg William
Published: September 2023

This chapter provides a background on the technique of structure determination through X-ray crystallography and discusses its importance in the context of modern chemistry. It explains the basis of X-ray crystallography through an optical analogy that outlines the main relevant properties of crystalline materials and aspects of symmetry. It also examines the properties of the diffraction pattern of a single-crystal in relation to features of interest in the crystal structure. The chapter covers the geometry of diffraction, symmetry observed in the pattern, and the variation of intensity in the discrete diffraction measurements. It cites available sources of X-rays for crystallography.
X-ray crystallography case studies
Authors: Clegg William
Published: September 2023

This chapter illustrates the process of X-ray crystal structure determination through a series of examples drawn from a wide range of structural chemistry research. It analyzes the complex [Et4N] [Hg(SR)3], which is an empirical formula corresponding to a monomeric structure. It also addresses the key questions that are answered by crystal structure determination regarding the anion that can be a dimer with bridging thiolate ligands, a higher oligomer, or a polymer. The chapter talks about the equivalence of different isotopes of an element in X-ray diffraction and the determination of the absolute structure of a chiral molecule by resonant scattering effects. It outlines the occurrence of disorder that can be modelled by the use of atoms with partial occupancy in alternative positions.
Related topics
Authors: Clegg William
Published: September 2023

This chapter covers the core subject of X-ray single-crystal diffraction for the determination of chemical compounds. It analyses the use of neutrons instead of X-rays and of powder diffraction. It also discusses the applications to biological macromolecules and crystal structure prediction. The chapter explains how X-rays are used for crystal structure determination, in that they have wavelengths comparable to the separations between atoms in molecules and give measurable diffraction effects from crystals. It refers to neutrons generated by a nuclear reactor or a neutron spallation source in which the associated wavelengths lie in the same range as X-rays, which causes a beam of neutrons to be diffracted as a particulate radiation by crystalline material.
Chemical shifts
Authors: Hore P.J
Published: September 2023

This chapter discusses chemical shifts. These give information on molecular identity and structure. The nuclear magnetic resonance (NMR) frequency of a nucleus in a molecule is determined principally by its magnetogyric ratio and the strength of the magnetic field it experiences. Chemical shifts arise because the field actually experienced by a nucleus in an atom or molecule differs slightly from the external field produced by the magnet. A magnetic field can induce two kinds of electronic current in a molecule: diamagnetic and paramagnetic. Diamagnetic and paramagnetic currents flow in opposite directions and give rise to nuclear shielding and deshielding, respectively. Chemical shifts can often be understood by considering the effects of electron donating and withdrawing groups, induced currents in neighbouring groups, charged or polar groups, hydrogen bonds, and unpaired electrons.
The vector model
Authors: Hore P. J. , Jones J. A. , Wimperis S.
Published: September 2023

Introduction

The so-called vector model of NMR spectroscopy is an essential weapon in the armoury of every practising NMR spectroscopist because it provides the sort of simple, intuitive, non-mathematical picture that every human brain eventually requires. Although it is an excellent way of...
Two-dimensional NMR
Authors: Hore P. J. , Jones J. A. , Wimperis S.
Published: September 2023

Introduction

The workings of a few of the more commonly used two-dimensional NMR experiments will now be described using product operators. Our aim will be to see how they work and to explain their chief features with respect to phase and multiplet structure.
Strong coupling and equivalence
Authors: Hore P. J. , Jones J. A. , Wimperis S.
Published: September 2023

Introduction

Spin systems comprising weakly coupled spins are straightforward to describe quantum mechanically, as we saw in Chapter 9, because the evolution induced by the various interactions can be calculated sequentially, and in any order. This is no longer true for strong coupling...
Retrosynthesis
Authors: Patrick Graham L.
Published: September 2023

This chapter discusses retrosynthesis. It also refers to retrosynthesis as the strategy wherein synthetic routes arecan be designed by considering the structure of the product and identifying what this target product could be synthesized from. The chapter looks intoconsiders the process of disconnection and functional group interconversions to achieve retrosynthesis. Additionally, umpolung, is the reversal of polarity, is considered. The chapter explores the examples of synthons, corresponding reagents, protecting groups, and latent groups. It highlights the importance of identifying molecular signatures to indicate which disconnections are the most sensible ones to make. Moreover, organic synthesis involves the creation of a target molecule from simpler structures serving as the building blocks for the synthesis.
Analogue synthesis in drug design
Authors: Patrick Graham L.
Published: September 2023

This chapter discusses analogue synthesis in drug design. It looks into at how active compounds can be found from the natural world or synthesized in a chemistry laboratory can be used as the starting point for developing a new drug. The chapter notes thediscusses analogues for SAR studies and pharmacophore identification. It explains that the synthesis of simpler structures that retain the pharmacophore of the lead compound may result in active compounds that are more easily synthesisedsynthesized. The chapter, additionally, looks intoIn addition, the chapter considers the process of drug optimisation optimization, which may aim atsuch as improving pharmacodynamic or pharmacokinetic properties or minimizing side effects or toxicity. It explores how the analogues can be synthesised synthesized from a lead compound or through a full synthesis depending on the synthetic steps and reagents involved. Reagents It is highlighted that the required reagents and building blockss should also be either commercially available or easily synthesizedsynthesised.
Hypothesis testing
Authors: Currell Graham
Published: September 2023

This chapter examines hypothesis testing, a key element in scientific methodology, in which a proposed hypothesis is tested experimentally by measuring the value of a test statistic and then using statistical analysis to calculate the probability that the observed value could have occurred by chance. It introduces different forms of hypothesis testing and analysis. The chapter begins by developing the 't' and 'z' statistics for testing differences in mean values, including the family of standard t-tests, before looking at the F-statistic that is at the heart of the 'analysis of the variance' approach to testing and introducing the basic ANOVA. The chapter then extends the ANOVA concept to include simultaneous testing for the effects of multiple factors. The chapter also considers the general linear model; nonparametric analyses; repeated measurements; chi-squared analyses; frequency and proportions; and resampling techniques.
Comparing data
Authors: Graham Currell
Published: September 2023

This chapter brings together a range of different techniques which provide measures of association and agreement between theoretical models and experimental data, and also between different experimental measurements of the same quantities. It begins by developing the statistics of parametric correlation and introducing methods of nonparametric correlation. The chapter then looks at statistics used for testing association, and discusses Fisher's exact test and the ability to test for progression in factors. It also considers the strength of the association between factors, and reviews a range of possible methods of measurement. Finally, the chapter assesses the concept of agreement in various contexts, including the 'goodness of fit' of analytical models, and agreements between variables and within contingency tables.
The Evidence for Evolution
Authors: Bell Graham
Published: September 2023

This chapter provides an overview of the science of evolution, which explains how the vast diversity of living things is governed by a few simple natural principles. The outward diversity of animals and plants is based on a very restricted range of materials, body plans, power sources, and instructions, relative to those we use in everyday life. Evolution is modification through descent. All organisms are similar, not because they have been perfectly engineered, but rather because they all descend from the same common ancestor. The chapter is concerned mainly with descent—how we know that the diversity of living forms springs from a single root. The chapter then introduces the concepts of extinction, adaptation, development, sex, and diversity.
The Tree of Life
Authors: Bell Graham
Published: September 2023

This chapter examines how all living organisms are related to one another and describes how these relationships can be worked out. Evolution is the process by which organisms become modified over time. New organisms do not appear spontaneously, of course: they are produced by old organisms. The basic unit that undergoes modification is thus the lineage—the long succession of parents and offspring, extended over time. Three fundamental aspects of organisms are the following: individuals, populations, and lineages. Lineages vary between strictly tree-like and entirely web-like, with any intermediate state being possible according to the degree of mingling of lineages during descent. With the advent of evolutionary biology in the mid-nineteenth century, classification was revolutionized by the use of relatedness, rather than similarity, as the basis for grouping species together. The fact of evolution makes it possible to construct a natural classification that expresses the genealogical relationships among all kinds of organisms.
The Diversity of Life
Authors: Bell Graham
Published: September 2023

This chapter evaluates biodiversity by tracing our own lineage backwards in time. Each clade comprises a group of lineages that have diverged from their common ancestor by adapting to different ways of life. This process of adaptive radiation may occur at any scale, from a small group such as ‘apes’ to a much larger one such as ‘vertebrates’. An innovation is a shared ancestral character that facilitates the adaptive radiation of a clade. The chapter then differentiates between potentiating innovations and implementing innovations. The separate phylogenetic trees of the clades can be fitted together so as to make a tree for the whole of life—although some branches will be much more detailed than others. The chapter describes Homo sapiens, Hominoidea, Primates, Eutheria, Mammalia, Amniota, Tetrapoda, Sarcopterygii, Osteichthyes (bony fishes), Gnathostomata, Chordata, Deuterostomia, Bilateria, Metazoa, Unikonta, and Eukaryota.
Adaptation and Evolved Design
Authors: Bell Graham
Published: September 2023

This chapter describes how both functional utility and ancestry contribute to adaptation and the evolved design of organisms. Evolved structures, unlike fabricated structures, are constrained by their origin as modifications of an ancestral state. Hence, structures in two species may be similar in form not because they operate in a similar fashion, but because their common ancestor had the corresponding structure. Characters that are similar among species because they are inherited from the common ancestor of the group are said to be homologous. The central principle of independent evolution leads to the recognition of homology at different phylogenetic levels. The chapter then looks at how evolutionary engineering combines utility and ancestry.
Selection in Natural Populations
Authors: Bell Graham
Published: September 2023

This chapter discusses natural selection. Each species may be in one of two situations: it is well-adapted to its conditions of life, or it is poorly adapted to its conditions of life. In practice, of course, most species will fall between these two extremes: they are neither poorly adapted nor perfectly adapted. Nevertheless, the distinction between purifying selection, which maintains adaptedness by removing deleterious mutations, and directional selection, which extends adaptedness by favouring beneficial mutations, is clear and useful. The chapter then looks at how local selection leads to divergent specialization, how diversifying selection maintains extensive variation, and how fluctuating selection changes in magnitude and direction over time.
Symbiosis and Struggle
Authors: Bell Graham
Published: September 2023

This chapter assesses how evolutionary processes are likely to be dominated not by physical factors, but rather by the multifarious interactions among species. The basic principle that governs how species interact is the same principle that governs how individuals of the same species behave towards one another. If the physical relation between two individuals of different species is close and cannot easily be changed or dissolved, each will tend to evolve to promote the other's wellbeing. They will evolve as mutualists. If they readily separate, on the other hand, one will evolve to exploit the other as ruthlessly as possible. They will evolve as parasite and host. The evolution of social relations between two species depends on the extent to which the interests of a couple are entrained.
Virology: how it all began and where it will go next
Authors: Oxford John , Kellam Paul , Collier Leslie
Published: September 2023

This chapter introduces viruses, which are remnants of retrovirus genes that remain in animal genomes. Our understanding of the origin of viruses is based on the most slender of clues that are mostly derived from our knowledge of the behaviour of today’s viruses, bacteria, and cells, but influenced sometimes by individual ideas of religion and even cosmology. However, most people would probably take the intuitive approach that simple organisms preceded more complicated ones, and that bacteria evolved from what were once free-living, self-replicating molecules that resemble today’s viruses. The chapter talks about evolutionary scientists that have pin-pointed RNA as being the first biomolecule to be synthesized on the planet, which places RNA viruses in early evolution.
General properties of viruses
Authors: Oxford John , Kellam Paul , Collier Leslie
Published: September 2023

This chapter describes viruses as small organisms that retain infectivity after passage through filters small enough to hold back bacteria. Bacteria are measured in terms of the micrometre (μm), which is 10-6 of a metre. For viruses, the nanometre (nm) is used as the unit, which is a thousand times smaller. The chapter points out that viruses are totally dependent on living cells, either eukaryotic or prokaryotic, for their replication and existence, and possess and carry enzymes of their own. Viruses cannot reproduce and amplify and translate into proteins the information in their genomes without the assistance of the cellular architecture and protein translation machinery, namely ribosomes. The chapter discusses viruses that possess only one species of nucleic acid, either DNA or RNA, and have a component for attaching or ‘docking’ to cells so that they can commandeer the cells as virus production factories.
Resistance of the human body to virus infections
Authors: Oxford John , Kellam Paul , Collier Leslie
Published: September 2023

This chapter recounts the scientific investigation of immunology that started about a century ago with Élie Metchnikof’s studies of phagocytosis of foreign particles, including micro-organisms. This early interest in cell-mediated immunity (CMI) was soon overtaken by research on antibody-mediated (humoral) immunity, which was for long regarded as the primary defence against microbial disease. The chapter highlights the presence of antibody as this is important in preventing virus infections and cellular immunity. This plays a major role in the immune response once infection has been established. The relationship between viruses and the immune system is much more intimate than it is for most bacteria as viruses often modify the cells within which they replicate, rendering the cells essentially foreign and susceptible to attack by sensitized lymphocytes. The chapter describes viruses that can multiply within the very lymphocytes and mononuclear phagocytes. These are important components of the immunological defences.
Picornaviruses: polio, hepatitis A, enterovirus, and common cold
Authors: Oxford John , Kellam Paul , Collier Leslie
Published: September 2023

This chapter describes the family of picornaviridae, which is one of the largest families in numerical terms. From a purely molecular viewpoint, the picornavirus was the first animal virus to be cloned and sequenced and then reconstructed from chemical synthesis of the nucleotide sequence. The chapter considers the picornavirus as the first human virus to have its three-dimensional structure analysed using X-ray crystallography, while poliomyelitis is one of the first virus diseases to be recorded. A world polio eradication campaign, spearheaded by WHO, was the largest public health project the world has ever known and should result in this virus becoming eradicated. The chapter also talks about hepatitis A, formerly enterovirus type 72, which is another globally important virus in the family that is controlled by vaccinations.
Flaviviruses: yellow fever, dengue fever, and hepatitis C
Authors: Oxford John , Kellam Paul , Collier Leslie
Published: September 2023

This chapter focuses on flaviviruses and notes that there are at least 70 serotypes of flavivirus. The molecular clock analysis dates the sojourn of these viruses from 10 to 100,000 years. The prototype virus of this family causes yellow fever (YF), which is a classic disease of antiquity, and the application of the term white man’s grave to West Africa resulted from its impact on colonizers. The chapter refers to Carlos Finlay, who viewed the mosquito as the source and scourge of YF, but this was not proven until the volunteer experiments coordinated by Walter Reed in 1900. Other medically important flaviviruses are tick-borne encephalitis virus (TBE), dengue virus and West Nile virus, Japanese encephalitis, Murray Valley encephalitis virus, and Zika virus. The chapter highlights the hepatitis C virus, a well-researched member of the family that does not have the typical mosquito transmission of the other flaviviruses.
Herpesviruses: herpetic lesions, zoster, cancer, and encephalitis
Authors: Oxford John , Kellam Paul , Collier Leslie
Published: September 2023

This chapter focuses on the herpesviruses, which form a large and important group of infective agents that affect many species both of warm- and cold-blooded animals. In humans they cause a wide range of syndromes, varying from trivial mucocutaneous lesions to life-threatening infections including certain cancers. The chapter highlights the extent of the problem by stating that 8090% of the population are infected with human herpesvirus 4 (HHV-4), otherwise known as the EpsteinBarr virus. An important property of all herpesviruses is their ability to cause latent infections where the virus can persist in an infected cell without expressing many of the protein-encoding genes of the virus. The chapter points out that these large genome viruses have a correspondingly large budget that allows a more timely regulated virushost interaction, establishing more often a long-term relationship, fatal infections being the exception rather than the rule.
Antiviral chemotherapy
Authors: Oxford John , Kellam Paul , Collier Leslie
Published: September 2023

This chapter talks about a number of important virus diseases–such as measles, poliomyelitis, yellow fever, and rubella–which can be kept under very good control with live virus vaccines. However, it is difficult to imagine the development of successful vaccines for many other viruses due to the multiplicity of serotypes, or variability or complexity of their antigenic structure. Other viruses such as hepatitis B and C have chronically infected millions, and vaccines cannot break these established infections: they are only able to prevent new infections in the case of hepatitis B. Finally, some viruses such as SARS, MERS, Ebola, and Zika emerge and resurge very quickly, posing serious difficulties in timely vaccine formulation. The chapter mentions antiviral compounds licensed for use against herpesviruses, hepatitis B, hepatitis C, HIV-1, RSV, and influenza A virus.