bluuebunny/crossref_metadata_2025 huggingface dataset:
Radical ions, radical pairs, and biradicals
Authors: Perkins John
Published: September 2023

This chapter discusses the single-electron occupancy of an individual spatial orbital, organic photochemistry, and the chemistry of carbenes and nitrenes. It presents examples of oxidation and reduction. It recounts the early days of electron spin resonance (ESR) spectroscopy, wherein dried and oxygen-free solvents were employed for the detection and spectroscopic characterization of radical ions. It also mentions how the naphthalene radical anion may be generated by the reduction of naphthalene in tetrahydrofuran. The chapter talks about the benzophenone ketyl radical anion, which places the negative charge on the electronegative oxygen atom and the unpaired electron on carbonyl carbon. It highlights the presence of low-lying vacant antibonding orbitals in non-conjugated carbonyl compounds which that facilitates one-electron reduction.
Vertebrate development II: Xenopus and zebrafish
Authors: Wolpert Lewis , Tickle Cheryll , Arias Alfonso Martinez , Lawrence Peter , Locke James
Published: September 2023

This chapter discusses the earliest stages of vertebrate development by using Xenopus and zebrafish as model organisms. Moreover, it looks into how the embryo grows from fertilized eggs and develops with body axes and germ layers. The chapter also looks at the embryotic development in line with the relative roles of pre-existing maternal factors in the egg and its developmental program in the formation of body axes. In addition, the chapter explains the Spemann organizer alongside its role in patterning the body plan along the dorso-ventral and antero-posterior axes. The chapter acknowledges the similarity of body plan between Xenopus and zebrafish.
Germ cells, fertilization, and sex determination
Authors: Wolpert Lewis , Tickle Cheryll , Arias Alfonso Martinez , Lawrence Peter , Locke James
Published: September 2023

This chapter explores the development of germline cells and their correlation with fertilization and sex determination. It notes the difference between germ cells and somatic cells. Additionally, germ cells are specified by localised cytoplasmic determinants in the egg. The chapter defines fertilization as the fusion of sperm and egg initiating development. It references sea urchins and mammals as it explores the process of fertilization. The chapter also notes how sex is determined through the chromosomal constitution. It mentions how sex determination mechanisms and compensations for the unequal complement of sex chromosomes between males and females differ considerably in different species.
Organogenesis
Authors: Wolpert Lewis , Tickle Cheryll , Arias Alfonso Martinez , Lawrence Peter , Locke James
Published: September 2023

This chapter focuses on organogenesis. It looks into the process of developing organs such as vertebrate eyes, vertebrate heart, teeth, vertebrate lungs, vertebrate limb, and insect wings. The chapter also highlights the complexity of organogenesis as it involves large numbers of genes and different types of tissues while ensuring integrated development. Moreover, the chapter notes how mechanisms and cell activities like migration and differential adhesion operate similarly as they would in relation to early development. The chapter uses Drosophilia as a model organism. It discusses the possibility of human congenital abnormalities due to mutations in developmentally important genes involved in organogenesis.
Evolution and development
Authors: Wolpert Lewis , Tickle Cheryll , Arias Alfonso Martinez , Lawrence Peter , Locke James
Published: September 2023

The evolution of development

The diversification of body plans

The evolutionary modification of specialized characters

Changes in the timing of developmental processes

The evolution of multicellular organisms is fundamentally linked to embryonic development, for it is through development that genetic changes...
Genetic Analysis
Authors: Meneely Philip
Published: September 2023

Genetic Analysis applies the combined power of molecular biology, genetics, and genomics to explore how the principles of genetics can be used as analytical tools to solve biological problems. Opening with a brief overview of key genetic principles, model organisms, and epigenetics, the book goes on to explore the use of gene mutations and the analysis of gene expression and activity. A discussion of the genetic structure of natural populations follows, before the interaction of genes during suppression and epistasis, how we study gene networks, and personalized genomics are considered.
Obtaining and verifying data
Authors: Blann Andrew D.
Published: September 2023

This chapter clarifies how to obtain data from machines and people, how to ensure the results are correct, and how the results should be interpreted. It analyses sources of potential error and looks at crucial factors in laboratory practice, such as optimizing assay performance, ensuring reliability, and monitoring reliability. It also considers operator performance, the clinical value of data generated in the laboratory, and the formal comparison of different techniques. The chapter explores pre-analytical error, the importance of accuracy and precision, and the differences between intra- and inter-assay coefficients of variation. It outlines the principles of sensitivity and specificity and the methods for comparing a new method with an existing method.
Research 2: The analysis of modest data sets
Authors: Blann Andrew D.
Published: September 2023

This chapter discusses various aspects of research by considering the verification of the data and its subsequent analysis. It outlines the analysis of categorical data and the importance of distribution, which rely heavily on understanding key words such as mean, standard deviation, median, and inter-quartile range. It also looks at data linked by individuals or over several time periods. The chapter reviews differences in approach when analysing two groups, or three or more groups, the nature of the analysis of paired and serial measurements, and the methods and purpose of correlation. It considers humans to be the most frequent source of error in statistics, which is inevitably caused by the incorrect input of raw data into a spreadsheet.
Nutrition
Authors: Jong Jessica Kiefte-de , Behrens Paul
Published: September 2023

This chapter explores the environmental impacts of diets. It starts by outlining the key components of diets, including macronutrients and micronutrients. Then the chapter examines malnutrition and links it to health impacts and the prevalence of major diseases around the world. Next, it looks at how diets have changed around the world in response to the alleviation of poverty and the global increase of incomes. The chapter also describes the impact of different food types on the environment, and how these may change in the future. It tackles alternative diets such as vegetarianism, veganism, and entomophagy. Lastly, the chapter outlines a case study on nationally recommended diets.
The silent enemy
Authors: Fullick William
Published: September 2023

This chapter traces the evolution of infectious diseases. Infectious diseases have evolved alongside humanity, taking advantage of changes in human society to help them to spread from person to person. Many early theories of disease involved religious or magical constructs. Moreover, in many early models, diseases were described in terms of an imbalance of the four humours. Some historical attempts to treat disease may have had some degree of success, as some of the herbs used in traditional medicines have antimicrobial properties, and people began to understand the principles of quarantine. An understanding of the nature of infectious disease has developed over time, but linking the discovery of microorganisms to the theory of infectious disease (known as the germ theory of disease) was a slow process, taking many different scientists many hundreds of years to develop.
Why thermodynamics?
Authors: Price Gareth
Published: September 2023

This chapter provides a background on predicting and understanding the behaviour of substances, chemical reactions, and processes. It explains thermodynamics as a study that is concerned with macroscopic systems, emphasizing large, measurable amounts of matter rather than individual molecules. It also analyses the chemical context of the name thermodynamics, which is considered a misnomer as it is useful in fundamental studies of understanding what drives chemical reactions and processes. The chapter focuses on chemical reactions and phase equilibria as the two main areas to which chemical thermodynamics can be applied. It cites the combustion of methane as an example of a reaction that goes to completion, as no methane is left after combustion if there is enough oxygen available.
Phase equilibrium and solutions
Authors: Price Gareth
Published: September 2023

This chapter focuses on the concept of matter existing in either the solid, liquid, or gas phase and is dependent on temperature and pressure. It explains that this phase is part of a system that is homogeneous throughout and separated from other phases by a definite boundary. It also describes the factors that determine why compounds exist in a particular phase under a particular set of conditions and what influences the transitions between phases. The chapter talks about the Gibbs energy of the phases in order to derive quantitative information on phase transitions. It considers pressure and temperature as major experimental variables that affect phase behaviour, noting that matter exists in the solid phase at sufficiently low temperatures or high pressures.
Evolution of the land plants
Authors: Murphy Denis , Cardona Tanai
Published: September 2023

This chapter examines the evolution of photosynthetic organisms on land, noting that the vast majority of photosynthetic life was confined to aquatic habitats for the first three billion years of their existance. It discusses genomic novelty, stating that this was common in streptophyte algae, which developed increasingly complex multicellular forms with a wider range of tissue and organ types. It also looks at bryophytes, noting how these dominated land flora from 450 to 360 Ma, which is a relatively warm, wet period favouring the rise of pteridophytes. The chapter reviews how high photosynthetic productivity led to atmospheric O2 levels rising to over 30% and the formation of the Carboniferous coal deposits from huge amount of plant remains. It explains that 1% of all flowering plants have partially or completely lost the ability to photosynthesize and have instead become parasites.
Investigation of urine samples
Authors: Graham Clive
Published: September 2023

This chapter assesses the investigation of urine samples. It begins by describing the anatomy of the urinary tract: urine is produced in the kidneys and passes through the ureter (a small tube) by a process known as peristalsis into the bladder. Urine collects in the bladder and is intermittently emptied via the urethra. The chapter then looks at the different urinary tract pathogens; E. coli is by far the most common cause of urinary tract infection. It also outlines the common specimen types used to diagnose urinary tract infection, including midstream urine (MSU), clean catch urine, ‘pad’ urine, ‘bag’ urine, ‘in-out catheter’ urine, catheter stream urine (CSU), and suprapubic aspirate. Finally, the chapter explains the routine tests performed on urine, such as urine microscopy, as well as urinary antibiotics.
Bacterial pathogenesis
Authors: Dover Lynn G.
Published: September 2023

This chapter focuses on bacterial pathogenesis. Most of the bacteria that colonize our bodies do so without causing us any harm. However, some bacteria are inherently more damaging than others. Their degree of pathogenicity is described in the term ‘virulence’, which can be quantified by establishing experimental metrics such as median lethal dose and median time to death. Virulence and pathogenicity are dependent upon the composition of the bacterial genome; pathogen genomes encode many virulence factors which operate in a concerted fashion to express pathogenicity. The chapter then describes the characteristics of pathogenic bacteria that allow them to adhere to epithelial surfaces (adhesins), evade the immune system (evasins and impedins), invade tissues (invasins), and damage underlying tissues (toxins). It looks at toxinogenesis and considers pan-genomes, mobile genetic elements, and the acquisition virulence factors.
Molecular diagnostics
Authors: Harwood Jayne
Published: September 2023

This chapter assesses molecular diagnostics. Molecular methods are now well-established as the ‘gold standard’ in non-clinical diagnosis of infectious disease. However, in practice, although the use of molecular methods is widespread, the number of molecular tests performed is still low compared to serological tests. The reason for this is that molecular methods are generally more complex and therefore costlier than the simple detection of an antigen or antibody. The polymerase chain reaction (PCR) provides an extremely sensitive method of amplifying small quantities of DNA. Despite the development of alternative amplification technologies, PCR remains the most widely used method in diagnostic laboratories for pathogen detection. The chapter then looks at DNA sequencing, DNA microarrays, and nucleic acid hybridization.
Whole genome sequencing in microbiology
Authors: Ford Michael
Published: September 2023

This chapter addresses how genomics is now one of the most rapidly developing areas in microbiology, mainly due to the rapid progression of whole genome sequencing (WGS) techniques such as Sanger sequencing. As the cost per test has decreased, the more useful WGS has become as a routine diagnostic tool across diagnostic microbiology. These uses include epidemiology, detection of virulence markers, detection of drug resistance, and in vaccine development. In the early 2000s, DNA sequencing changed rapidly with the introduction of ‘non-Sanger’ technologies — so-called next generation sequencing (NGS). As rapid developments in sequencing technologies are occurring every year, they will rapidly change microbiology and enhance its ability to better diagnose and monitor causes of infectious disease throughout the world.
Writing assignments
Authors: Overton Tina , Johnson Stuart , Scott Jon
Published: September 2023

This chapter talks about written assignments and reports and states that these are a common form of assessment in most degree courses in chemistry. It emphasizes that producing extended pieces of written work represents a real challenge for many students at university as it is a skill that is only developed to a limited extent in pre-university science courses. It also deals with writing extended pieces of work on a topic. Such writing includes assignments, reports, or essays. The chapter demonstrates the easiest approach to writing, which is the typical written assignment or essay in chemistry. Such a written piece is usually 1000 to 3000 words in length and answers a specific question or responds to a specific title. The chapter discusses how students are expected to be able to display knowledge and understanding of the subject material in their writing.
Communicating with a non-scientific audience
Authors: Overton Tina , Johnson Stuart , Scott Jon
Published: September 2023

This chapter emphasizes how to improve communication about chemistry with a range of different people by making chemical content more accessible for people without advanced scientific training. It emphasizes the importance of communicating a subject to an audience, whatever their background, in a way that they can understand. It also notes the language used and the assumptions made when communicating to a non-scientific audience, which are the key factors to consider when writing as well. The chapter explains that the names for elements and compounds and names for processes, theories, and models turn chemistry into a foreign language impenetrable for the uninitiated. It highlights the process of selecting the appropriate language when writing for a non-expert audience, such as removing all the scientific detail and presenting the basic information much more simply.
Preparing scientific presentations
Authors: Overton Tina , Johnson Stuart , Scott Jon
Published: September 2023

This chapter considers a student’s ability to present information verbally to a group of people. This is an increasingly important skill for students undertaking chemical science degrees. The chapter explores the public nature of a presentation, as compared to the privacy and anonymity of a report or exam, which makes getting presentations right all the more important. It also highlights that giving good presentations is a crucial skill to learn because presenting is something most graduates must do during the interview process for a job. The chapter covers presentations as a form of assessment and identifies some of the characteristics of effective presentations, particularly scientific presentations. It highlights the significance of preparing effective and appropriate notes.
Delivering scientific presentations
Authors: Overton Tina , Johnson Stuart , Scott Jon
Published: September 2023

This chapter explains that communicating content involves a very different set of skills to preparing content and focuses on how a student can communicate content to the best effect. It highlights common concerns people have about presentations and how to address them. It determines how to use visual aids effectively and provides some key techniques for smooth presentations. The chapter shows that there are important differences between written and spoken presentations, although both forms require the presentation and analysis of evidence, the structure of an argument, and referencing sources. It teaches how presenters can make sure their listeners stay with them, both in terms of their understanding and their attention, during a presentation.
Binary compounds: oxides and halides
Authors: Aspinall Helen C.
Published: September 2023

This chapter examines binary compounds, looking at lanthanoid and actinoid oxides and halides. Binary oxides and halides of the f-elements are important as starting materials for manufacture of the elements, as starting materials for synthesis of other compounds and complexes, and as materials in their own right. For example, CeO2 has a very rich chemistry and this is a result of the accessibility of both +3 and +4 oxidation states for Ce, and this results in practical applications. The oxide chemistry for the actinoid elements from Pa to Pu is also very rich as a result of the accessibility of a range of oxidation states. Structures and stoichiometries of oxides and halides reflect trends in ionic radii and in relative stabilities of oxidation states.
Major haematology parameters and basic techniques
Authors: Blann Andrew , Moore Gary , Knight Gavin
Published: September 2023

This chapter explores certain aspects of haematology, detailing principal haematology tests, such as the full blood count, and basic techniques that are used to define particular indices, such as haemoglobin. It highlights the importance of different anticoagulants and glass or plastic tubes for the different blood tests requested. It also covers major haematology techniques such as spectrometry, microscopy, light scatter, impedance technology, and calibration. The chapter emphasizes the major components of the full blood count, which include the red blood cell indices, the white blood cell indices, and platelets. It describes the differences in the values of the erythrocyte sedimentation rate and plasma viscosity, including the important aspects of the micronutrients iron, vitamin B12, folate, and plasma proteins such as transferrin and ferritin.
Anaemia 1: The bone marrow, micronutrients, and disease in other organs
Authors: Blann Andrew , Marwah Sukhjinder
Published: September 2023

This chapter describes anaemia as the major and clinically significant disease of red cells, causing a great deal of morbidity and mortality. It examines how problems with the bone marrow, micronutrients such as iron and vitamins, and disease in other organs can lead to anaemia. It also describes the pathological consequences of low and high levels of iron. The chapter talks about the effects of the poor supply of vitamins B12 and B6 and folate to the bone marrow. It outlines how diseases in different body organs can lead to anaemia and suggests how the laboratory can diagnose these conditions.
Blood-borne parasites
Authors: Moore Gary
Published: September 2023

This chapter introduces the major blood-borne parasites that cause disease in humans and looks at their parasitic life cycles. It talks about how morphological characteristics are important for accurate diagnosis, and it covers laboratory tests that are available to biomedical scientists for the detection of blood parasites. It also describes the appearances of parasites in Romanowsky-stained blood films. The chapter elaborates that blood-borne parasites target specific organs and species for different stages of their life cycles, noting that the nature of each life cycle and the target organs involved dictate the clinical symptoms of each infection. It mentions eosinophilia, which is a likely haematological effect of arthropods such as head lice and scabies mites.
White blood cells in health and disease
Authors: Knight Gavin
Published: September 2023

This chapter outlines the main types of white blood cell (WBC) encountered in the peripheral blood, their development, structure, and function. It describes the particular function of neutrophils, lymphocytes, monocytes, eosinophils, and basophils as WBC species, and it highlights their precursors. It also demonstrates how to suggest a differential diagnosis for a patient based on the way in which the WBCs are represented in the full blood count and their appearance using microscopy. The chapter clarifies that WBCs are responsible for immunity through phagocytic means, through the production of antibodies that help in the destruction of foreign bodies entering the human system, or through cytotoxic mechanisms. It talks about lymphocyte species that are involved in adaptive immunity as they adapt to the specific antigens encountered.
An introduction to haematological malignancies
Authors: Knight Gavin
Published: September 2023

This chapter introduces haemato-oncology, which is the study of cancers of the haemopoietic system. It refers to the term ‘haematological malignancy’, which is used to describe a range of cancerous conditions of the haemopoietic system and differentiate cancers of this system with cancers of other tissues. It also considers haemato-oncology as a subject that provides scientists with the opportunity to work at the cellular, molecular, or genetic level, and enables clinicians to piece together a wide variety of data for accurate diagnosis. The chapter looks at some of the cellular, molecular, and genetic mechanisms responsible for the development of haematological malignancies. It discusses the role of the cancer stem cell in leukaemogenesis and lymphomagenesis.
Surveillance
Authors: McCann Derek
Published: September 2023

This chapter looks at why the National Plant Protection Organizations (NPPOs) around the world spend considerable time and money to track down widespread plant diseases. It talks about how NPPOs seek to prevent the damage that plant pathogens can do to crop plants, garden plants, and the wider natural environment. It also reviews the collecting and recording of information on plant disease, known as surveillance. The chapter discusses the need to prevent phytosanitary controls from being used in order to put restrictive trade barriers in place, and the importance of ensuring that international standards are upheld. It investigates how surveillance is carried out and the elaborates the necessity of getting it right.
Disease Management in Crops
Authors: Little Julian
Published: September 2023

This chapter focuses on the ways people manage and treat diseases which affect the crops everyone relies on. It mentions farmers who carefully use a whole range of techniques which ensure their crops are healthy, reduce the risk of infections occurring, and treat diseases or pests. It also highlights measures in planting seeds, ploughing, crop rotations, and break crops which have an enormous effect on the health of crop plants and yield quality produce. The chapter describes crop rotation as the most basic method of cultural control, which is done by growing a series of very different crops from different plant families in a particular field over a series of years. It analyses the break in cultivation that both helps to maintain field fertility and reduce plant disease, which has less obvious benefits in areas such as weed management.
The Gibbs energy
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter explores the procedure developed by American theoretician J. W. Gibbs, who laid the foundations of chemical thermodynamics towards the end of the nineteenth century. Gibbs discovered how to combine the two contributions needed in entropy calculations into one. Indeed, almost the whole of biochemical thermodynamics is now discussed in terms of the Gibbs energy. As this chapter shows, at constant temperature and pressure, the direction of spontaneous change is towards lower Gibbs energy. It also relates the Gibbs energy to work — particularly non-expansion work, which includes muscle contraction (for movement) and causing neurotransmitters to move across synapses to give rise to thought, or at least, neuronal response. Finally, the chapter examines the action of adenosine triphosphate in a case study.
Buffer solutions
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter considers buffer solutions, or solutions which show ‘buffer action’ — the ability to oppose changes in pH when small amounts of strong acids and bases are added. An acid buffer solution, one that stabilizes the solution at a pH of less than seven, is typically prepared by making a solution of a weak acid and a salt that supplies its conjugate base. A base buffer, one that stabilizes a solution at a pH of greater than seven, is prepared by making a solution of a weak base and a salt that supplies its conjugate acid. The chapter also studies two buffer systems that help maintain the pH of blood: one arising from a carbonic acid/hydrogencarbonate (bicarbonate) ion equilibrium and another, within red blood cells, involving protonated and deprotonated forms of hemoglobin. It also considers pH regulation by ion transport. The chapter concludes by discussing other buffer systems.
The values of rate constants
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter considers the properties of rate constants. First, it distinguishes between the rate at which reactants encounter each other from the rate at which they undergo change once they have met. The very important feature of the latter step is the dependence of the relevant rate constant on temperature, which is found in most cases to obey an expression in terms of two parameters. These considerations inspire an expression for the rate at which reactants pass over an energy barrier and become products and clarifies one of the roles of enzymes acting as catalysts. The expression also inspires the introduction of parameters that resemble those used in thermodynamics. With those parameters established it is possible to see how factors other than temperature, specifically isotopic substitution and ionic strength, affect the rates of reactions.
Conformational stability and molecular aggregation
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter addresses conformational stability and molecular aggregation. It contends that not all macromolecules are rigid, and indeed many of them need to be flexible to carry out their function. The ability of a macromolecule to adjust its shape gives rise to the concept of a melting temperature and suggests how thermodynamic arguments developed for phase transitions of bulk matter can be adapted to describe macromolecules, including their representation using phase diagrams. Here, the chapter discusses the stability of nucleic acids and proteins, before providing case studies on the polymerase chain reaction and protein crystallisation. Additionally, the chapter looks into micelles and biological membranes, as well as the mobility transitions of membranes.
Vibrational spectroscopy
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter concerns vibrational spectroscopy. All molecules are capable of vibrating, and complicated molecules may do so in many different ways. The spectroscopic observation of the vibrations of molecules is used in this chapter to explore the stiffness of bonds and the rigidity of macromolecular structure. The core principles are explored by considering the single mode of vibration of a diatomic molecule, and then the principles are extended to the numerous modes of vibration of biochemically significant macromolecules. The chapter introduces techniques which have been developed specifically for the study of proteins and, by incorporating microscopes into the spectrometer, of sampling regions containing only a few molecules.
Biomedical science and biomedical scientists
Authors: Glencross Hedley
Published: September 2023

This chapter provides an overview of biomedical science and the role of biomedical scientists. Biomedical science is often described as the application of the basic sciences, but especially the biological sciences, to the study of medicine, in particular, the causes, consequences, diagnosis, and treatment of human diseases. The title of biomedical scientist is a protected one and biomedical scientists are registered practitioners of the subject. They normally work in departments of clinical pathology. Thus, they are vital healthcare, scientifically qualified professionals who, for example, perform diagnostic tests on clinical samples of blood and urine. Given their role(s), biomedical scientists are typically active in laboratory-based work and tend to have a relatively limited contact with patients compared with other healthcare professionals.
Personal development
Authors: Glencross Hedley , Lavender Georgina
Published: September 2023

This chapter looks at the personal and professional development of biomedical scientists. We are all aware that science is constantly evolving, and that today's innovations and discoveries are often old news and outdated by tomorrow. Anybody listed on a professional register is required to reaffirm and review continually their knowledge base within their chosen profession; biomedical scientists are no exception. Indeed, biomedical scientists are expected to be able to demonstrate a designated level of continuing professional development (CPD) to remain on the Health and Care Professions Council (HCPC) register. Moreover, every two years at the renewal of their registration, they must declare that they have been undertaking CPD to a predefined standard and, crucially, must be able to provide evidence to support this claim, if required.
Hormones
Authors: Hinson Joy , Raven Peter
Published: September 2023

Hormones begins by presenting an introduction to the broad topic of hormones. It then turns to an examination of hormones and disease, looking at what happens when things go wrong. Chapters that follow discuss hormones and development, hormones and reproduction, and hormones and behaviour. Finally, the text ends with a brief assessment of the use and abuse of hormones.
Binding of charged guests
Authors: Beer Paul D. , Barendt Timothy A. , Lim Jason Y. C.
Published: September 2023

This chapter discusses the supramolecular chemistry of binding charged guests. The ubiquity of ions in the natural environment impact many biological and chemical processes. As a result, numerous naturally occurring receptors capable of selectively binding a wide variety of cations and anions have evolved. Before considering the common design strategies for cation and anion receptors, the chapter identifies the fundamental differences between cations and anions, and how these factors make anion binding significantly more challenging than for cations. An alternative strategy for binding charged guests is to bind both the cation and anion together using the same receptor—a concept known as heteroditopic ion pair recognition. Often, the resulting complex is charge neutral, and this can help with extraction, solubilization, and sensing applications. The chapter then looks at three fundamentally different approaches to binding ion pairs: the cascade approach, heteroditopic ion-pair binding, and zwitterion binding.
Mammalian Synthetic Biology
Authors: Davies Jamie A.
Published: September 2023

Mammalian Synthetic Biology starts by introducing the biology of mammals and providing a broad overview of how synthetic biology is applied to mammals. It then presents some special features of mammalian systems that distinguish mammals from other organisms before introducing methods used in mammalian synthetic biology. After that, the text moves on to look at mammalian synthetic biology as a research tool. It also examines teaching mammalian cells to make new, useful things, i.e. their role in bioproduction. Towards the end of the text there is an examination of synthetic biology, stem cells, and regenerative medicine. Finally, the text ends by looking at ethical concerns and responsibilities related to synthetic biology.
Dealing with multiple hypotheses
Authors: Colegrave Nick , Ruxton Graeme D.
Published: September 2023

This chapter explains how to evaluate the powers for study designs with multiple hypotheses, emphasizing that no single design will offer exactly the same power for all the hypotheses. It points out that ranking hypotheses in terms of their importance can help with the process of finding a design that offers sufficient power for all the hypotheses of prime importance. It also discusses how to evaluate whether the power available for testing ancillary hypotheses is sufficient to continue to include them in the study after one has settled on a design with sufficient power for the most important hypotheses. The chapter explores how to select a single experiment offering good power to address all hypotheses and involve further simulations after carrying out power analyses for each of the hypotheses in isolation. It examines power analyses that flag up situations where bonus investigations are of little value. This is because an experiment optimized to address questions of primary interest means there is low power to address bonus hypotheses.
Concentrating on the system
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter highlights the Helmholtz and Gibbs energies to develop the Clausius inequality. The Clausius inequality implies a number of criteria for spontaneous change under a variety of conditions which may be expressed in terms of the properties of the system alone. A spontaneous process at constant temperature and volume is accompanied by a decrease in the Helmholtz energy. The change in the Helmholtz energy is equal to the maximum work obtainable from a system at constant temperature. Meanwhile, a spontaneous process at constant temperature and pressure is accompanied by a decrease in the Gibbs energy. The change in the Gibbs energy is equal to the maximum non-expansion work obtainable from a system at constant temperature and pressure. The chapter then looks at the standard Gibbs energies of formation and the Born equation.
Combining the First and Second Laws
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter presents a combination of the First and Second Laws, which leads to a very powerful way of applying thermodynamics to the properties of matter. The fundamental equation is an expression for the change in internal energy that accompanies changes in the volume and entropy of a system. Relations between thermodynamic properties are generated by combining thermodynamic and mathematical expressions for changes in their values. The chapter then considers the Maxwell relations, which are a series of relations between partial derivatives of thermodynamic properties based on criteria for changes in the properties being exact differentials. The Maxwell relations are used to derive the thermodynamic equation of state and to determine how the internal energy of a substance varies with volume. The chapter also looks at the variation of the Gibbs energy of a system, which suggests that it is best regarded as a function of pressure and temperature.
The response of equilibria to the conditions
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter studies how the thermodynamic formulation of the equilibrium constant is used to establish the quantitative effects of changes in the conditions. One very important aspect of equilibrium is the control that can be exercised by varying the conditions, such as the pressure or temperature. The thermodynamic equilibrium constant is independent of the presence of a catalyst and independent of pressure. The response of composition to changes in the conditions is summarized by Le Chatelier's principle. Meanwhile, the dependence of the equilibrium constant on the temperature is expressed by the van 't Hoff equation and can be explained in terms of the distribution of molecules over the available states.
Electrochemical cells
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter examines electrochemical cells, which consist of two electrodes, or metallic conductors, each in contact with an electrolyte, an ionic conductor. Because many reactions involve the transfer of electrons, they can be studied (and used) by allowing them to take place in a cell equipped with electrodes, with the spontaneous reaction forcing electrons through an external circuit. The electric potential of the cell is easily measured and is related to the reaction of Gibbs energy, thus providing a convenient method for the determination of some thermodynamic quantities. The chapter looks at galvanic cells, the liquid junction potential, and the Nernst equation. It also considers how the standard cell potential may be used to calculate the standard Gibbs energy of the cell reaction and hence its equilibrium constant.
Electrode potentials
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter discusses electrode potentials. Each electrode can be considered to make a characteristic contribution to the overall cell potential. The standard potential of a couple is the potential of a cell in which the couple forms the right-hand electrode and the left-hand electrode is a standard hydrogen electrode, all species being present at unit activity. The electrochemical series lists the metallic elements in the order of their reducing power as measured by their standard potentials in aqueous solution: low reduces high. The chapter then explains how the difference of the cell potential from its standard value is used to measure the activity coefficient of ions in solution. Meanwhile, standard potentials are used to calculate the standard cell potential and then to calculate the equilibrium constant of the cell reaction.
Translational motion
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter evaluates translational motion, motion through space, which is one of the fundamental types of motion treated by quantum mechanics. According to quantum theory, a particle constrained to move in a finite region of space is described by only certain wavefunctions and can possess only certain energies. That is, quantization emerges as a natural consequence of solving the Schrödinger equation and the conditions imposed on it. The solutions also expose a number of non-classical features of particles, especially their ability to tunnel into and through regions where classical physics would forbid them to be found. Light particles are more able to tunnel through barriers than heavy ones. The chapter also considers the occurrence of degeneracy, which is a consequence of the symmetry of the system.
Molecular orbital theory: homonuclear diatomic molecules
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter looks into molecular orbital theory (MO theory) with respect to homonuclear diatomic molecules and ions. Molecular orbitals are constructed as linear combinations of all valence orbitals of the appropriate symmetry. Meanwhile, σ orbitals are constructed separately from valence s and p orbitals and π orbitals are constructed from the sideways overlap of p orbitals. The chapter notes overlap integral as a measure of the extent of orbital overlap. It considers the building-up principle as electrons occupy the available molecular orbitals to achieve the lowest total energy subject to the Pauli exclusion principle. Moreover, a technique like a photoelectron spectroscopy (PES) can probe the energies of molecular orbitals.
Molecular orbital theory: heteronuclear diatomic molecules
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter tackles the molecular orbital theory of heteronuclear diatomic molecules. It explains how heteronuclear diatomic molecules introduced the possibility that atomic orbitals on the two atoms contribute unequally to the molecular orbital. The electrons in a covalent bond in a heteronuclear diatomic species are not distributed equally over the atoms. Thus, the imbalance results in a polar bond, which can be regarded as arising from a molecular orbital that is concentrated more on one atom than its partner. The chapter then provides an overview into the practical application of the variation principle, which provides a criterion for optimizing a trial wavefunction.
Group theory
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter focuses on the application of group theory in the systematic treatment of symmetry. It explains that since group theory is systematic, its rules can be applied in a straightforward, mechanical way. Moreover, the theory represents the result of symmetry operations through the form of matrices. The matrices of a representation multiply together in the same way as the operations they represent. The chapter looks into the concept of character tables, which is significant to the application of group theory to chemical problems. It also looks into the symmetry species of atomic orbitals and a linear combination of orbitals.
General principles
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter provides an overview of the general principles of magnetic resonance. Since electrons and nuclei have the spin property, their motion gives rise to a magnetic moment and behaviour similar to small bar magnets. The chapter considers the notion of the nuclear spin quantum number wherein a nucleus is either a non-negative integer or a half-integer. It also discusses the features of nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR). NMR refers to the observation of the absorption of radiofrequency electromagnetic radiation by nuclei in a magnetic field. EPR is the observation of the resonant absorption of microwave electromagnetic radiation by unpaired electrons in a magnetic field.
Features of NMR spectra
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter details the features of nuclear magnetic resonance (NMR) spectra. It starts with the chemical shift of a nucleus carrying the difference between its resonance frequency and that of a reference standard. The resonance frequency of a magnetic nucleus is affected by its electronic environment and the presence of nearby magnetic nuclei. The appearance of an NMR spectrum is changed if magnetic nuclei can jump rapidly between different environments. The chapter also discusses the origin of spin-spin coupling involving the polarization mechanism and the Fermi contact interaction. It cites how the coalescence of two NMR lines occurs when nuclei are exchanged rapidly between environments by conformational or chemical processes.
Interactions between molecules
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter reviews different types of molecular interactions that are responsible for the formation of condensed phases and large molecular assemblies. It explains how attractive interactions result in cohesion, while repulsive interactions prevent the complete collapse of matter to nuclear densities. It also mentions the van der Waals interaction, which is an attractive interaction between closed-shell molecules that depends on the separation of the molecules as the inverse sixth power. The chapter explains how the precise criterion of a van der Waals interaction is often relaxed to include all nonbonding interactions. It talks about how attractive interaction between closed-shell molecules occur in various guises and can be traced to the interaction of partial charges.
The magnetic properties of solids
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter focuses on the magnetic properties of solids, which are reported in terms of their ‘susceptibility’. It points out that the magnetic property can be traced to individual atoms or molecules if the magnetic centres are independent, and that ferromagnetism emerge if the centres interact. It also analyses the electrical conductivity of common materials that arises from the motion of electrons and some ionic solids that display ionic conductivity in which whole ions migrate through the lattice. The chapter describes different types of solid that are distinguished by the temperature dependence of their electrical conductivity. It explains how a semiconductor generally has a lower conductivity than that typical of metallic conductors and that the magnitude of the conductivity is not the criterion for distinguishing between them.
The rates of chemical reactions
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter discusses the definition of reaction rate and outlines the techniques for its measurement, which shows that reaction rates depend on the concentration of reactants. It points out how ‘rate constants’ are characteristic of the reaction, which can be expressed in terms of differential equations known as ‘rate laws’. It also highlights the rates of consumption of reactants and formation of products that make it possible to predict how quickly a reaction mixture approaches equilibrium and lead to detailed descriptions of the molecular events that transform reactants into products. The chapter looks at experiments that show that reaction rates depend on the concentration of reactants in characteristic ways that can be expressed in terms of differential equations. It considers the establishment of the stoichiometry of the reaction and identification of any side reactions as the first step in the kinetic analysis of reactions.
Reactions approaching equilibrium
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

The chapter discusses how rate laws must take into account both the forward and reverse reactions and describe the approach to equilibrium in order to be complete. It notes that the results of the analysis are relations between the equilibrium constant of the overall process and the rate constants of the forward and reverse reactions. It also looks at how the analysis of the time dependence reveals the connection between rate constants and equilibrium constants. The chapter emphasizes that both forward and reverse reactions must be incorporated into a reaction scheme in order to account for the approach to equilibrium. It reviews kinetic studies that are made on reactions that are far from equilibrium and if the concentration of the products is low and the reverse reactions are unimportant.