bluuebunny/crossref_metadata_2025 huggingface dataset:
Theories and models: scope and limitations
Authors: Norman Nicholas C.
Published: September 2023

This chapter addresses some recent developments in terms of bonding, looking at the involvement of d orbitals in hybridization. Recent work by Matthias Wuttig has introduced the term and idea of metavalent bonding and makes the claim that this should be considered as a new type of bonding distinct from covalent, metallic, or ionic. Wuttig's proposal focuses principally on the properties of compounds such as GeSe, GeTe, SnSe, SnTe, PbSe, and PbTe, although it is by no means restricted to this group. Wuttig refers to these materials as 'metavalent solids' or 'incipient metals', and focuses on their properties which are distinct not just from metals and from covalently bonded solids but also from metalloid materials. The chapter then looks at the application of some of the various theories and models discussed in the previous chapters.
Protein Function
Authors: Lesk Arthur
Published: September 2023

This chapter evaluates the wide variety of ways that proteins support the structures and life processes of viruses, cells, and organisms. It begins by looking at structural proteins, enzymes and enzyme kinetics, and antibodies. The chapter then considers transmembrane transport proteins—including channels, gates, and pumps—and receptors, all embedded in the general phospholipid bilayer membrane structure. Finally, it studies the role of transmembrane proton gradients in the electron transport chain and adenosine triphosphate (ATP) synthesis. Two catalogues of protein function are available. The first is the Enzyme Commission classification, which covers only catalytic functions. It has been extended by the Gene Ontology classification, devised in 2000 in connection with the task of annotating the Drosophila melanogaster genome.
Why low power is undesirable
Authors: Colegrave Nick , Ruxton Graeme D.
Published: September 2023

This chapter addresses the questions why a low-powered study has a high probability of failing to detect genuine effects. It highlights how low power makes drawing useful inferences from failure to reject the null hypothesis more difficult. It shows that the risk that a significant result is a Type I error increases if an experiment is low-powered and analyses why low power inflates the effect sizes associated with statistical significance. The chapter clarifies that the statistical power of an experiment is one minus the probability of making a Type II error based on the outcome of that experiment. It confirms that low power is undesirable because it means an increased risk of a Type II error, emphasizing that the lower the power, the less likely it is that a significant result is actually triggered by a real underlying effect.
Simple factorial designs
Authors: Colegrave Nick , Ruxton Graeme D.
Published: September 2023

This chapter elaborates on the organization of data from experiments in a spreadsheet and uses that as a guide to producing exactly analogous simulated data. It discusses the production of simulated data which is organized in the same way as actual experimental data. This makes the calculation of power for more complicated designs much easier. The chapter also demonstrates the use of power analyses to explore the effects of adverse events which lead to an unplanned loss of some data. The chapter cites hypothetical studies, such as determining the resistance to herbicides and uses two genotypes of Chlamydomonas reinhardtii, a single-celled algae that is a convenient lab system, to explore questions about herbicides.
The kinetic model
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter examines the kinetic model, which assumes that a gas consists of molecules of negligible size in ceaseless random motion and obeying the laws of classical mechanics in their collisions. As well as accounting for the gas laws, this model can be used to predict the average speed at which molecules move in a gas, and its dependence on temperature. The chapter then looks at pressure and molecular speeds, the Maxwell–Boltzmann distribution of speeds, and mean values. The Maxwell–Boltzmann distribution of speeds gives the fraction of molecules that have speeds in a specified range. The chapter also considers the collision frequency and the mean free path. The collision frequency is the average number of collisions made by a molecule in a period of time divided by the length of that period. Meanwhile, the mean free path is the average distance a molecule travels between collisions.
Internal energy
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter examines how heat and work contribute to the exchange of energy between the system and its surroundings. That discussion leads to the definition of the ‘internal energy’ of a system and to the formulation of the ‘First Law’ of thermodynamics. Internal energy, the total energy of a system, is a state function. The First Law states that the internal energy of an isolated system is constant. The chapter then looks at expansion work, which arises from a change in volume. A reversible change is a change that can be reversed by an infinitesimal change in a variable. To achieve reversible expansion, the external pressure is matched at every stage to the pressure of the system. The chapter also considers heat transactions, describing calorimetry, the study of the transfer of energy as heat during a physical or chemical process.
Enthalpy
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter focuses on the concept of enthalpy. This property is used to track the heat output (or requirements) of physical processes and chemical reactions taking place at constant pressure. Changes in internal energy or enthalpy are measured by techniques known collectively as ‘calorimetry’. A calorimeter for studying processes at constant pressure is called an isobaric calorimeter. For a combustion reaction, an adiabatic flame calorimeter may be used. The most sophisticated way to measure enthalpy changes, however, is to use a differential scanning calorimeter (DSC). The chapter then looks at the variation of enthalpy with temperature. The enthalpy of a substance increases as its temperature is raised. The reason is the same as for the internal energy: molecules are excited to states of higher energy so their total energy increases.
State functions and exact differentials
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter addresses the state function, which is a property that depends only on the current state of a system and is independent of its history. It looks at exact and inexact differentials. In general, an exact differential is an infinitesimal quantity that, when integrated, gives a result that is independent of the path between the initial and final states. Meanwhile, an inexact differential is an infinitesimal quantity that, when integrated, gives a result that depends on the path between the initial and final states. The chapter then considers changes in internal energy and enthalpy. It also explains the Joule–Thomson effect, which is the change in temperature of a gas when it undergoes isenthalpic expansion.
Entropy changes accompanying specific processes
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter shows how to use the definition of entropy change to calculate its value for a number of common physical processes, such as the expansion of a gas, a phase transition, and heating a substance. The change in entropy accompanying a process is calculated by identifying a reversible path between the initial and final states. The entropy of a perfect gas increases when it expands isothermally. Meanwhile, the change in entropy of a substance accompanying a change of state at its transition temperature is calculated from its enthalpy of transition. The increase in entropy when a substance is heated is calculated from its heat capacity.
The thermodynamic description of mixtures
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter evaluates the thermodynamic description of mixtures. It develops the concept of chemical potential as an example of a partial molar quantity and explores how the chemical potential of a substance is used to describe the physical properties of mixtures. The key idea is that at equilibrium the chemical potential of a species is the same in every phase. By making use of the experimental observations known as Raoult's and Henry's laws, it is possible to express the chemical potential of a substance in terms of its mole fraction in a mixture. The chapter looks at the Gibbs–Duhem equation, as well as ideal–dilute solutions.
Phase diagrams of ternary systems
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter addresses how the behaviour of a system with three components is represented using a triangular phase diagram and how such diagrams are interpreted. Ternary phase diagrams are widely used in metallurgy and materials science. At a fixed temperature and pressure, the phase diagram of a ternary system is conveniently represented using a triangular graph. In a ternary system, the tie lines in the two-phase region are constructed experimentally by determining the compositions of the two phases that are in equilibrium, marking them on the diagram, and then joining them with a straight line. The chapter then looks at partially miscible liquids and ternary solids.
The origins of quantum mechanics
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter traces the origins of quantum mechanics. The classical mechanics developed by Isaac Newton in the seventeenth century is an extraordinarily successful theory for describing the motion of everyday objects and planets. However, late in the nineteenth century, scientists started to make observations that could not be explained by classical mechanics. They were forced to revise their entire conception of the nature of matter and replace classical mechanics by a theory that became known as quantum mechanics. The chapter begins by looking at energy quantization, considering black-body radiation, heat capacity, and atomic and molecular spectra. It then discusses wave–particle duality, which is the recognition that the concepts of particle and wave blend together.
Operators and observables
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter explains that a central feature of quantum theory is its representation of observables by ‘operators’, which act on the wavefunction and extract the information it contains. It shows how operators are constructed and used. Observables are represented by hermitian operators, which have real eigenvalues and orthogonal eigenfunctions. When the system is not described by a single eigenfunction of an operator, it may be expressed as a superposition of such eigenfunctions. One consequence of the use of operators is the ‘uncertainty principle’, one of the most profound departures of quantum mechanics from classical mechanics. The uncertainty principle restricts the precision with which complementary observables may be specified and measured simultaneously.
Applications of symmetry
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter explores the applications of symmetry while referring to group theory as a significant tool for constructing molecular orbitals and formulating spectroscopic selection rules. It explains how group theory provides simple criteria for deciding whether certain integrals necessarily vanish. Additionally, character tables can be used to determine whether an integral is necessarily zero. The integrand must include a transforming component as the totally symmetric irreducible represent to acknowledge an integral to be non-zero. The chapter also expounds on the concept of symmetry-adapted linear combination (SALC) as a linear combination of atomic orbitals constructed from equivalent atoms and having a specified symmetry.
The canonical ensemble
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

The chapter illustrates ensemble as the crucial concept needed in the treatment of systems of interacting particles. It notes the requirements to set up an ensemble: a closed system of specified volume, composition, and temperature. Thus, an imaginary collection of replications of the actual system with a common temperature is called the canonical ensemble. While the canonical distribution provides the most probable number of members of the ensemble with a specified total energy, the mean energy of the members of the ensemble can be calculated from the canonical partition function. The chapter notes the variation of the energy with volume.
Self-assembly
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter talks about aggregates of small and large molecules form the basis of many established and emerging technologies, including their structures and properties. It cites colloids and micelles, which form spontaneously by self-assembly of molecules or macromolecules and are held together by molecular interactions. It also defines self-assembly as the spontaneous formation of complex structures of molecules or macromolecules, which are held together by molecular interactions, such as Coulombic, dispersion, hydrogen bonding, and hydrophobic interactions. The chapter cites examples of self-assembly, which include the formation of liquid crystals and of protein quaternary structures from two or more polypeptide chains. It analyses the dissolution process in more detail by illustrating a hypothetical initial state in which the alcohol is present in water as individual molecules.
The mechanical properties of solids
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter looks at the characteristic mechanical properties of a solid that include various aspects of its rigidity. It explains that the mechanical properties are reported in terms of several parameters that can be related to the structure of the solid, which is crucial to the development of modern materials. It also talks about how mechanical properties of solids are expressed in terms of various ‘moduli’ that are related to the intermolecular potential energy of the constituents. The chapter shows that the fundamental concepts needed for the discussion of the mechanical properties of solids are stress and strain, noting that the stress on an object is the applied force divided by the area to which the force is applied. It describes a sample subjected to a low stress that typically undergoes elastic deformation in the sense that it recovers its original shape when the stress is removed.
Transport properties of a perfect gas
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter discusses the transport of matter and physical properties that can be described by a set of closely related empirical equations. For a gas, it is possible to understand the form of these equations by building a model based on the kinetic theory of gases. The chapter reviews the rate of diffusion, the rate of thermal conduction, viscosity, and effusion, which can all be related to quantities arising from kinetic theory. The chapter analyses physical processes that take place by the transfer of a property from one region to another and gas-phase chemical reactions that depend on the rate at which molecules collide. It shows how a molecule carries properties through space in steps of about the distance of its mean free path.
Motion in liquids
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter shows how molecular motion in liquids from is different to that that in gases on account of the presence of significant intermolecular interactions and the much higher density typical of a liquid. It explores the electrical resistance of electrolyte solutions and analyses it in terms of the response of the ions to an applied electric field. It discusses how solute molecules and ions move through liquid environments. The chapter demonstrates how ions reach a terminal velocity when the electrical force on them is balanced by the drag due to the viscosity of the solvent. It mentions inelastic neutron scattering, in which the energy neutrons collect or discard as they pass through a sample is interpreted in terms of the motion of its molecules.
Examples of reaction mechanisms
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter cites examples of reaction mechanisms. It provides a description of a special class of reactions in the gas phase that depend on the collisions between reactants and the formation of polymers. It shows how the kinetics of their formation affects their properties and examines the general mechanism of action of enzymes, which are biological catalysts. It also analyses some important reactions that have complex mechanisms and need special treatment in order to demonstrate how to make and implement assumptions about the relative rates of the steps in a mechanism. The chapter assesses the steady-state approximation that can often be used to derive rate laws for proposed mechanisms. It highlights the setting up and testing of a rate law by proposing a mechanism and applying the steady-state approximation.
Photochemistry
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter focuses on photochemistry, which is the study of reactions that are initiated by light. It explores the fate of the electronically excited molecules formed by the absorption of photons, such as energy transfer to another molecule that estimate the distance between certain groups in large molecules. It also reviews the initiation of chemical and biological processes, including photosynthesis and vision, by the absorption of electromagnetic radiation. The chapter discusses the mechanisms of many photochemical reactions that lead to relatively simple rate laws which are used to assess the efficiency with which radiant energy induces reactions. It looks at photochemical processes that are initiated by the absorption of electromagnetic radiation, noting processes that capture the radiant energy of the Sun.
Transition-state theory
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter focuses on transition-state theory, in which it is assumed that the reactant molecules form a complex that can be discussed in terms of the population of its energy levels. The transition-state theory inspires an approach to reaction rates in which the rate constant is expressed in terms of thermodynamic parameters, which is useful for parametrizing the rates of reactions in solution. It shows how the transition-state theory provides a way to relate the rate constant of reactions to models of the cluster of atoms supposed to form when reactants come together. The chapter provides a link between information about the structures of reactants and the rate constant for their reaction. It makes use of two strands: one is the relation between equilibrium constants and partition functions; the other is the relation between equilibrium constants and thermodynamic functions.
Electron transfer in homogeneous systems
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter uses transition-state theory to examine the transfer of electrons in homogeneous systems, which include oxidation–reduction reactions in solution. It introduces Marcus theory, which establishes a relation between the activation parameters and the rate constant of electron transfer and can be expressed in terms of structural parameters of the species involved. It also explores how electron transfer reactions between protein-bound cofactors or between proteins play an important role in a variety of biological processes. The chapter discusses the rate constant of electron transfer in a donor–acceptor complex that depends on the distance between electron donor and acceptor, the standard reaction Gibbs energy, and the energy needed to reach a particular arrangement of atoms. It makes use of transition-state theory and the concept of tunnelling, steady-state approximation, and the Franck–Condon principle.
Rare Diseases: A Genomics Perspective
Authors: Chappell Lia , Lindsay Sarah J , Jones Phil , Parkhill Julian , Roberts Jonathan , Holroyd Nancy , Szpak Michal , Gale Francesca
Published: September 2023

This chapter provides an overview of genomics, which is the study of the structure and function of genomes. A genome is the complete set of genetic instructions for an organism. Genomics is a huge area of study that encompasses many different (and sometimes controversial) scientific techniques, which together can help us understand ourselves and the world around us. The chapter then looks at the impact of genomics, starting with how they have changed the way we view some of the most unusual human diseases. Our understanding of rare diseases is rapidly improving, having been accelerated by next-generation sequencing (NGS) technologies and pioneering bioinformatics and statistical techniques. However, new knowledge brings new challenges around the sharing and analysis of data, and new ethical questions around how and when we diagnose and treat rare disease.
Genomes And Ethics
Authors: Chappell Lia , Lindsay Sarah J , Jones Phil , Parkhill Julian , Roberts Jonathan , Holroyd Nancy , Szpak Michal , Gale Francesca
Published: September 2023

This chapter examines some of the ethical implications of genomics, looking at how advances in genetics are likely to be experienced by people, as patients, consumers, and citizens. Our ability to sequence genomes is getting faster and cheaper all the time. Indeed, genomic technology is now being utilized in more settings across society than ever before, from medicine, population health screening, and recreational consumerism (ancestry testing, nutritional testing), through to policing and crime prevention. Given that genomic information links us to our relatives, the decisions that we make about it will all have an impact on those we are related to and the knowledge that they too can gain. It is this fact that makes genetic information quite different from other sorts of medical information. Thus, we all have a stake in how we as a society use genomic data.
Carbohydrates: Why Life is Sweet
Authors: Bowater Richard , Bowater Laura , Husband Tom
Published: September 2023

This chapter describes the chemistry that underpins biomolecules, before considering the variety and flexibility of carbohydrates and their roles in living organisms. All biological cells are made up of common building blocks, or biomolecules, which carry out similar types of biochemical reactions. There are four types of these fundamental biomolecules: carbohydrates, proteins, lipids, and nucleic acids. Carbohydrates are the most abundant biomolecules on Earth and are characterized by great chemical and structural diversity. They are classified by size as monosaccharides, disaccharides, oligosaccharides, or polysaccharides. Carbohydrates are found in plant cell walls, the connective tissues of animals, and exoskeletons, and they are essential to the function of some proteins and cell-to-cell communication. They are also important fuels and energy stores, underpinning energy-yielding pathways in non-photosynthetic organisms.
Lipids and Proteins: The Building Blocks of a Cell
Authors: Bowater Richard , Bowater Laura , Husband Tom
Published: September 2023

This chapter discusses lipids and proteins, which are two of the key components of cellular life in every environment. Lipids are essential components of cell membranes. They can be used to store energy, they are able to provide a waterproof coating to animals, and they are the basic building blocks of essential molecules that include hormones, vitamins, and pigments. They are classified in different ways and they include fatty acids, phospholipids, and triglycerides. Proteins are essential to all cells since almost all tasks that cells perform at some point involve proteins. The versatility of proteins is due to the great variety of shapes that they can adopt. Overall structures are dictated by their primary structure and the sequence of amino acids, but these take on different secondary structural conformations, patterns, and shapes. These come together to form three-dimensional conformations, or tertiary structures, that are unique to each protein.
Drawing Structures from Chemical Names
Authors: Elliott Mark C.
Published: September 2023

The Purpose of The Exercise

The point of this section is not really about drawing the correct structure from a chemical name. This is only one aspect of it. The main focus is to practise drawing good skeletal structures of organic compounds.

If you need...
Ignore What Doesn’t Change
Authors: Elliott Mark C.
Published: September 2023

This is an important idea, but one that is almost impossible to teach in a formal way.

In any reaction of an organic molecule, there will be a change to one functional group (or sometimes more), while the rest of the molecule is untouched. The...
Introduction to Curly Arrows
Authors: Elliott Mark C.
Published: September 2023

There are few ideas more important in organic chemistry than curly arrows. We use them to represent ‘electron flow’ in reactions.

A good organic chemist will draw a curly arrow mechanism with an understanding of the meaning, but a great deal of what they do...
Bond Dissociation Energy
Authors: Elliott Mark C.
Published: September 2023

In order to better understand bond dissociation energy, and the energetics of bond breaking, we need to look at three reactions, all of which simply involve the breaking of a C–H bond.

Make sure you follow the curly arrows in each case, and you understand...
Calculating Enthalpy of Reaction from Bond Dissociation Energies
Authors: Elliott Mark C.
Published: September 2023

Introduction

If we know how strong each chemical bond in a molecule is, we can calculate the enthalpy change for a reaction.

Here is a table of average bond dissociation energies, all in kJ mol−1. These are representative values for the...
Reactivity of Conjugated Systems
Authors: Elliott Mark C.
Published: September 2023

Let’s join up some dots. We have seen that conjugated systems are more stable than nonconjugated systems. We have seen the evidence for this. We have also seen that conjugation leads to stabilization of carbocations and carbanions that are intermediates in a lot of organic...
Nucleophilic Substitution at Saturated Carbon
Authors: Elliott Mark C.
Published: September 2023

Introduction

Now, we need to look at more detailed aspects of reactions. Inevitably, these chapters will be longer and include more factual information. However, the style stays the same. You will be guided to apply the basic principles to show you that you already know...
Assignment of Stereochemistry—The Cahn–Ingold–Prelog Rules
Authors: Elliott Mark C.
Published: September 2023

It takes a little time to get used to assigning stereogenic centres. After a while, you will be able to do it without thinking. As with so many other aspects of organic chemistry, the route to competence is practice. Don’t learn this once, think it...
Stereoisomers with Symmetry
Authors: Elliott Mark C.
Published: September 2023

This one is another habit. It is relatively easy to look at a structure, count the number of stereogenic centres, and state the number of possible stereoisomers as 2n (2 to the power n). Most of the time you will be correct—but not...
Selectivity in Organic Chemistry—Stereoselectivity
Authors: Elliott Mark C.
Published: September 2023

Introduction

Before we start, let’s establish one thing. There is nothing special about stereoselectivity. It follows the same ‘rules’ as the other types of selectivity.

We are going to do a lot more work in this chapter, because stereoselectivity often causes problems. In the early...
Conformational Isomers 2
Authors: Elliott Mark C.
Published: September 2023

This is an applications chapter. There won’t really be any additional information. It just looks like there is. We will be taking what we learned in Basics 30 and adding some information from Basics 5, plus the occasional hydrogen bond, and...
Stereospecificity
Authors: Elliott Mark C.
Published: September 2023

Stereospecificity

This is a convenient point to formalize the idea of stereospecificity.

A stereospecific reaction can only produce one stereoisomer.

We have encountered several stereospecific reactions so far. An SN2 substitution reaction proceeds by attack of the nucleophile opposite to the leaving group,...
Curly Arrows and Reaction Profiles
Authors: Elliott Mark C.
Published: September 2023

Introduction

Let’s start with a statement.

Substitution reactions are often accompanied by elimination reactions as competing pathways.

This is standard textbook material, but we are going to do this as a series of worked problems so that you apply basic knowledge to predict the outcomes...
Is cis-Cyclohexane-1,2-diol Really Achiral?
Authors: Elliott Mark C.
Published: September 2023

This chapter is somewhere between a worked problem and a more detailed insight.

In
Habit 7
we discussed the cis isomer of cyclohexane-1,2-diol, and recognized that it has a plane of symmetry.

In
Practice 12
we reinforced the point, and we considered that sometimes...
Complex Substitution Stereochemistry
Authors: Elliott Mark C.
Published: September 2023

Introduction

There is a classic experiment that illustrates many points about stereochemistry in substitution reactions. It is covered at some point in almost every textbook, and with good reason.

In this chapter, we are going to describe the results, but the key point will be...
Cyclization Reactions
Authors: Elliott Mark C.
Published: September 2023

Advance Warning!

This is a problem without many clear answers. That doesn’t mean we cannot use it to practise the basics.

In this case, the basics are correct curly arrows and consideration of the shape of a compound when it reacts. Let’s have a look...
Curly Arrows and Reaction Profiles
Authors: Elliott Mark C.
Published: September 2023

Answer 1

Assuming a given substrate has the option of either a substitution reaction (purple) or an elimination reaction (blue), the two possible mechanisms are as shown below.

We aren’t balancing charges—assume the nucleophile has a proton it can lose!

We...
Epoxide Opening Reactions
Authors: Elliott Mark C.
Published: September 2023

Answer 1

We haven’t really covered this before, but we know that an alkyne hydrogen is moderately acidic (pK
a 25).

We saw this in
Basics 18.

Yes, it’s diﬃcult to keep track of all the things you have to ‘remember’. That’s why...
Is cis-Cyclohexane-1,2-diol Really Achiral?
Authors: Elliott Mark C.
Published: September 2023

Answer

As usual, it’s all about the method—making systematic adjustments to how you think about organic chemistry so that you see all aspects of a problem. In this case, we are asking about chirality, so we need to think about shape. These are cyclohexanes, so...
SN2′ Stereochemistry and Conformations
Authors: Elliott Mark C.
Published: September 2023

Answer 1

Here it is, without any stereochemistry. We don’t yet know which double bond isomer or OH stereoisomer will be formed, so I have used wiggly bonds to indicate ambiguity.
Cyclization Reactions
Authors: Elliott Mark C.
Published: September 2023

Answer 1

Here is the mechanism. I’m not going to talk you through each curly arrow at this stage of the book. Make sure you can see why each arrow is going in the direction it is, and why it leads to formation of the...
Intracellular Signals
Authors: Hancock John T.
Published: September 2023

This chapter discusses the need for intracellular signalling and talks about signalling pathways that involve cAMP. It clarifies how G proteins are involved in signalling and can mediate disease. It also shows how cGMP is involved in signalling. It then highlights the use of inositol compounds in signalling and points out the importance of calcium ions in signalling events. The chapter focuses on the modulation of the concentration of molecules that are involved in relaying the message into and across the inner structures of the cell. It specifically explains how cyclic nucleotides, lipid-derived compounds, inositol-based compounds, calcium ions, and proteins are involved in mediating some of the signalling pathways.
Stress Responses and The Changing Cell Environment
Authors: Hancock John T.
Published: September 2023

This chapter analyses the importance of perceiving the environment and describes what happens when cells undergo a pathogen challenge, in both animals and plants. It discusses how organisms adapt to changing environments and talks about the impact of human activity and how organisms respond. It also mentions the necessity for organisms to sense their environment, noting how humans have easily evolved to be able to see the surroundings, to hear what is around, and to sense the presence of chemicals. The chapter reviews the ability of cells to survive, sense aspects of their environment, and mount the appropriate response when required. It cites climate change as one of the biggest challenges facing the world in present times and notes that the unprecedented rise in global temperature forces organisms to adapt to the changing environment to survive.
The Seat of Self and Neurosurgery
Authors: Fullick William , Fullick James
Published: September 2023

This chapter examines the inner workings of the nervous system and some ways to repair any damage to it. The nervous system is composed of the central and peripheral systems that provide control and communication to the body. The nervous system is as susceptible as any other organ to damage through trauma and its risk goes higher due to the inability of the nervous system to repair damaged neurones. Even though neurosurgery offers ways to manage acute and subacute damage to the brain and spinal cord, it is still a high-risk procedure. The chapter considers the extensive field of reconstructive neurology and bionics to improve the outcomes of brain and nerve damage.
Evolution
Authors: Ingram Neil , Andrews Sylvia Hixson , Still Jane
Published: September 2023

Evolution provides an introduction to evolution. It traces the history of the emergence of life, by contextualizing the development of evolutionary thought and discussing the implications of evolutionary processes on modern-day genomics, biochemistry, and ecology. The text explores topics that are familiar and also introduces new ideas. Chapters include an introduction to evolution, the birth and death of species, and an examination of the evidence. The latter half of the book looks at the evolution of a theory, human evolution, and the human story so far.
Human Evolution: Where Do We Come From and How Did We Get Here?
Authors: Ingram Neil , Andrews Sylvia Hixson , Still Jane
Published: September 2023

This chapter examines the theory of human evolution. The forces of evolution (such as gene flow and natural selection) serve as a mould for the human species through time, thus research on human evolution is constrained by ancestral animals. The chapter examines animals such as primates and argues that they are the possible evolution ancestor of humans. The chapter also looks at human characteristics such as bipedalism, facial morphology, dentition, and brain expansion. It notes that Hominini, whose fossils were found in Africa, are the earliest members of the human family on record. DNA has helped determine the genetic relationships and similarities among modern animals.
Getting the drug to market
Authors: Patrick Graham L.
Published: September 2023

This chapter looks at the various issues that need to be tackled before a promising-looking drug candidate reaches the clinic and goes into full-scale production. It discusses toxicity tests that are carried out in vitro and in vivo on drug candidates to assess acute and chronic toxicity. It also examines drug metabolism studies which are carried out on animals and humans to identify drug metabolites, noting how a drug candidate is labelled with an isotope to aid the detection of metabolites. The chapter explores pharmacology tests whcih are carried out to determine a drug's mechanism of action and to determine whether it acts at targets other than the intended ones. The chapter reviews formulation studies that aim to develop a preparation of the drug that can be administered during clinical trials and beyond.
Enzymes: structure and function
Authors: Patrick Graham L.
Published: September 2023

This chapter discusses the structure and function of enzymes, which are proteins that act as the body's catalysts by binding substrates and participating in the reaction mechanism. It examines the active site of an enzyme. This is usually a hollow or cleft in the protein. Here, important amino acids are present and these either bind substrates or participate in the reaction mechanism. The chapter also explains substrate binding, showing how this involves an induced fit where the shape of the active site alters to maximize binding interactions. The chapter reviews the Michaelis constant, which is equal to the substrate concentration at which the rate of the enzyme-catalysed reaction is half of its maximum value. The chapter finally mentions the Lineweaver–Burk plot and illustrates that this provides more accurate values for the maximum rate and K
M.
Miscellaneous drug targets
Authors: Patrick Graham L.
Published: September 2023

This chapter looks at other important common drug targets in medicinal chemistry which illustrate the variety of ways in which drugs can act. It discusses transport proteins which carry polar molecules across the hydrophobic cell membrane. It also explores how drugs can be designed to take advantage of the transport system in order to gain access to cells or to block transport protein. The chapter also describes tubulin as a structural protein and show that this is crucial to cell division and cell mobility and is the target for several anticancer drugs. The chapter examines the vinca alkaloids that bind to tubulin and inhibit the polymerization process. It emphasizes how carbohydrates are more difficult to synthesize than peptides as they offer a greater variety of potential novel structures.
Drug design: optimizing access to the target
Authors: Patrick Graham L.
Published: September 2023

This chapter studies design strategies which can be used to counter barriers. This involves modification of the drug itself. The chapter looks at methods of aiding a drug in reaching its target, which include linking the drug to polymers or antibodies or encapsulating it within a polymeric carrier. It also describes the design of drugs that are absorbed into the blood supply, reach their target efficiently, are stable enough to survive the journey, and are eliminated in a reasonable period of time. The chapter shows how drugs can be made more resistant to metabolism by introducing steric shields to protect susceptible functional groups. It highlights groups susceptible to metabolism which may be modified or removed to prolong activity, as long as the group is not required for drug–target interactions.
The design of ACE inhibitors
Authors: Patrick Graham L.
Published: September 2023

This chapter introduces angiotensin-converting enzyme (ACE) inhibitors, which are important pharmaceutical agents that are used in the treatment of hypertension. It describes ACE as a key component of the renin angiotensin-aldosterone system or the RAAS cascade. This produces a potent vasoconstricting hormone called angiotensin II. The chapter also points out how ACE catalyses the formation of angiotensin II from the biosynthetic precursor angiotensin I, making drugs that inhibit ACE as potent antihypertensives. The chapter focuses on the design of ACE inhibitors, which demonstrates how it is possible to design drugs for a protein target in a rational manner. It considers ACE as a membrane-bound enzyme that is difficult to isolate and study.
Quantitative structure–activity relationships (QSAR)
Authors: Patrick Graham L.
Published: September 2023

This chapter analyzes quantitative structure-activity relationships (QSARs), which is considered a well-established tool in medicinal chemistry. It details how QSAR attempts to relate the physicochemical properties of compounds to their biological activity in a quantitative fashion by using equations. It also describes traditional QSAR and shows that this typically involves synthesizing a series of analogues with different substituents and studying how the physicochemical properties of the substituents affect the biological activities of the analogues. The chapter covers the hydrophobic, steric, and electronic properties and looks at how these are considered when setting up a QSAR equation. It emphasizes how traditional QSAR studies have been largely superseded by three dimensional QSARs (3D QSAR) where the physicochemical properties of the complete molecule are calculated and then related to biological activity.
Cholinergics, anticholinergics, and anticholinesterases
Authors: Patrick Graham L.
Published: September 2023

This chapter describes drugs that have an effect on the cholinergic nervous system, citing several clinically important drugs that act on the peripheral and the central nervous system (CNS). It examines the involvement of CNS with nerves through the use of the neurotransmitter acetylcholine as a chemical messenger. It also covers drugs that influence the activity of motor nerves, which take messages from the CNS to various parts of the body, such as skeletal muscle, smooth muscle, cardiac muscle, and glands. The chapter details how motor nerves innervate skeletal muscle, nerves that synapse with other nerves in the peripheral nervous system, and the parasympathetic nerves innervating cardiac and smooth muscle. It reviews two types of cholinergic receptor: muscarinic receptors that are present in smooth and cardiac muscle and nicotinic receptors that are present in skeletal muscle and in synapses between neurons.
Steroidal anti-inflammatory agents
Authors: Patrick Graham L.
Published: September 2023

This chapter focuses on adrenocorticoids, which are steroids released from the adrenal cortex of the adrenal gland. It analyzes the two types of adrenocorticoids, the glucocorticoids and the mineralocorticoids, that have an important anti-inflammatory effect which is separate from their metabolic effects. It also talks about corticosterone, cortisone, and cortisol as the major endogenous glucocorticoids, while aldosterone is the major endogenous mineralocorticoid. The chapter points out how an excess of glucocorticoids causes Cushing's syndrome, whereas a deficit results in Addison's disease and an excess of mineralocorticoids leads to Conn's syndrome. It covers the use of glucocorticoids as anti-inflammatories and immunosuppressants in the treatment of several conditions, such as asthma, and the pregnane skeleton of adrenocorticoids, which contains two-carbon side chain at position 17 of the tetracyclic steroid skeleton.
Comparing multiple samples: boxplots and histograms
Authors: Humphreys Rosalind K. , Ruxton Graeme D.
Published: September 2023

This chapter discusses using boxplots and histograms when comparing multiple samples. It explains how multiple samples can be graphed for comparison through boxplots, histograms, and bar charts. Bar charts are generally less informative than boxplots, giving the reader less detail about each sample. The chapter mentions how boxplots are better than histograms when you need to explore several samples together. Even though histograms are great for showing the distribution of each sample, there can be issues when trying to compare multiple histograms or when interpreting overlapping ones. Thus, boxplots are the best option when you are looking at grouped multiple-sample data. This refers to logically different samples grouped in a figure.
Partial differential equations
Authors: Steiner Erich
Published: September 2023

This chapter focuses on partial differential equations, which are equations that contains partial derivatives. It shows different examples that demonstrate a number of important principles in the solution of partial differential equations. The chapter describes the general solutions as well as the method of separation of variables. It particularly looks at the time-independent Schrödinger equation for the particle in a rectangular box, and in a circular box, and for the hydrogen atom. Furthermore, it discusses how the one-dimensional wave equation is applied to the vibrations of an elastic string, such as a guitar string. The chapter also introduces the phenomenon of degeneracy.
Vectors
Authors: Steiner Erich
Published: September 2023

This chapter focuses on vectors, or physical quantities that require both magnitude and direction for their specification, such as velocity, force, electric field, magnetic field, and displacement. It underscores that vector notation and vector algebra are important for the formulation and solution of physical problems in three dimensions, specifically in mechanics, fluid dynamics, electromagnetic theory, and engineering design. The chapter discusses in examples some of the uses of vectors that are important in molecular dynamics, spectroscopy, and theoretical chemistry. It shows how a vector is graphically represented by a directed line segment. It also gives an overview of vector algebra. Furthermore, it discusses the components of vectors. The chapter progresses to explain the scalar differentiation of a vector, scalar product, and vector product. It also tackles the scalar and vector fields, the gradient of a scalar field, divergence and curl of a vector field, and vector spaces.
Determinants
Authors: Steiner Erich
Published: September 2023

This chapter takes a closer look at the theory of determinants, preparing the reader for the topic of matrix algebra. Determinants have certain symmetry properties that have made them an important tool in quantum mechanics. The chapter starts by explaining how the system of three linear equations in three unknowns can be solved. It also shows the solution of linear equations—introducing the Cramer's rule. The chapter also tackles the general properties of determinants such as transposition, multiplication by a constant, additional rule, interchange of rows or columns, equal two rows or columns, proportional rows or columns, among others. Furthermore, it explains the reduction of determinants to triangular form and describes alternating functions.
Molarity and dilutions
Authors: Reed Martin B
Published: September 2023

This chapter sets out the calculations required to work effectively with materials in solutions. It explains that a solution consists of a certain amount of solid or liquid chemical, called solutes, dissolved in a volume of liquid, called the solvent, which for biological purposes is usually water. It also defines the molar mass of a substance as the mass (in grams) of one mole of the substance, noting that the mass of a substance can help determine the number of moles and molecules present. The chapter points out that, as each molecule is made up of atoms, the mass required for one mole can easily be determined by addition of the masses of the individual atoms that make up the molecule. It discusses the concept of moles, which determines the concentration of solutions in terms of how many moles of a substance are contained in a solution; this is called molarity of the solution.