bluuebunny/crossref_metadata_2025 huggingface dataset:
Geography and Ecology of the Paleozoic
Authors: Harvey Pough F. , Bemis William E. , Mcguire Betty , Janis Christine M.
Published: September 2023

This chapter explores earth's history and divides it into the Precambrian and the Phanerozoic. No life was present during the first part of the Precambrian, informally known as the Hadean, while the Phanerozoic represents the last 540 million years of Earth's 4-billion-year history. Yet it is from this time that most multicellular life is known. The chapter details the three eras of the Phanerozoic: Paleozoic, Mesozoic, and Cenozoic. The continental blocks move over time, and their positions affect how heat is transferred via oceanic circulation, and also whether there is ice at the poles. The chapter talks about the Paleozoic continents, which were initially widespread, but by the end of the period they came together and formed the supercontinent Pangaea.
Origin of Osteichthyes and Radiation of Actinopterygians
Authors: Harvey Pough F. , Bemis William E. , Mcguire Betty , Janis Christine M.
Published: September 2023

This chapter covers the origin of Osteichthyes and the radiation of actinoptergians. It details the key differences between actinopterygians and sarcopterygians before turning to actinopterygian evolution, diversity, swimming, reproduction, and ecology. After the industrial world brought increasing destruction and pollution of resources, different groups of bony fishes face different anthropogenic threats and require different conservation solutions. The chapter explores the impact and specializations of actinopterygians for life in Earth's waters from small, still freshwater ponds to coral reefs and deep ocean habitats. It cites how scuba, crewed submersibles, and remotely operated vehicles (ROVs) have helped expand the understanding of marine teleosts living in remote and previously inaccessible environments.
Geography and Ecology of the Mesozoic
Authors: Harvey Pough F. , Bemis William E. , Mcguire Betty , Janis Christine M.
Published: September 2023

This chapter details the geography and ecology of the Mesozoic period. It explains that the Mesozoic period was a time of major diversification and radiation, leading to large-scale changes in flora and fauna by the end of the era. In Mesozoic oceans, neoselachians diversified, while the total diversity of tetrapods changed relatively slowly. Meanwhile, lissamphibians evolved and the two major lineages of amniotes diversified into Synapsida and Sauropsida. The chapter highlights how the era's history of extinction events opened the way for a new faunal balance in the Cenozoic period. Most Mesozoic extinction events resulted from intense episodes of volcanic activity accompanying collisions and splitting of continents as Pangaea formed and later ruptured.
Living on Land
Authors: Harvey Pough F. , Bemis William E. , Mcguire Betty , Janis Christine M.
Published: September 2023

This chapter focuses on the demands of terrestrial life. It highlights how the viscosity of water compared to forces in the air and on land resulted in change. Since the most important difference between living in water and on land is the effect of gravity on support and locomotion, the skeletons of terrestrial tetrapods needed to be able to support the body. The chapter discusses the changes to body structures and key organ systems associated with living on land, which include feeding mechanisms, blood circulation, and sensing the world. It also details the sensory systems of terrestrial vertebrates, which looks at how terrestrial vertebrates couple olfaction and respiration.
Lissamphibians
Authors: Harvey Pough F. , Bemis William E. , Mcguire Betty , Janis Christine M.
Published: September 2023

This chapter focuses on lissamphibians. It details the life histories of lissamphibians, which include egg hatching, parental care, vocalization, and fertilization. The distinct lineages of extant animals generally referred to as amphibians range between Gymnophiona (caecilians), Caudata (salamanders), and Anura (frogs). Since lissamphibians are the only tetrapods that metamorphose, they play a critical role in the flow of matter and energy in ecosystems. The chapter shows that despite their importance in the ecosystem, some lissamphibians developed toxins or venoms. It also considers the worldwide crisis of rapidly declining lissamphibian populations, and notes how the disappearance of anurans caused a domino effect of changes in energy and nutrient flow in aquatic and terrestrial communities.
Ectothermy and Endothermy
Authors: Harvey Pough F. , Bemis William E. , Mcguire Betty , Janis Christine M.
Published: September 2023

This chapter looks at the concept of ectothermy and endothermy in relation to regulating body temperature. It highlights the importance of controlling body temperature. Vertebrates employ a variety of behavioral and physiological mechanisms to control body temperature. The evolution of endothermy was a major event in vertebrate evolution, especially within the sauropsid and synapsid lineages. Moreover, the processes of endothermy and ectothermy are not mutually exclusive since many tetrapods combine elements of both modes. The consequences of ectothermy and endothermy shaped the lifestyles of different vertebrates and this informs some important consequences of these lifestyles in the context of ecosystems.
Primate Evolution and the Emergence of Humans
Authors: Harvey Pough F. , Bemis William E. , Mcguire Betty , Janis Christine M.
Published: September 2023

This chapter discusses the relationship between primate evolution and the emergence of humans. Molecular techniques show that chimpanzees and bonobos are the closest extant relatives to humans. Humans and their fossil relatives belong to a tribe within Hominidae called Hominini. In comparison to other hominids, humans exhibit three major derived characteristics which are bipedality, a greatly enlarged brain, and the ability for speech and language. The chapter then details the effects of Homo sapiens, the only surviving hominin species, on other vertebrates and the course of life on Earth. It acknowledges humans as superpredators that kill large animals that otherwise have no natural predators as adults.
Conserving Populations and Species
Authors: Sher Anna A.
Published: September 2023

This chapter explores approaches for monitoring, managing, prioritizing, and protecting species and their populations in their natural environments, and how this information is used to establish legal protection for endangered species. Population viability analysis (PVA) can be used to calculate the minimum viable population (MVP) size: the smallest population size that can be predicted to have a high chance of persisting for the foreseeable future. The International Union for Conservation of Nature (IUCN) has developed quantitative criteria for populations and ecosystems to assign species to conservation categories. Priorities for protection can be determined in several ways, including the species approach, the ecosystem approach, the wilderness approach, and the hotspot approach. The chapter then considers the Endangered Species Act (ESA) and the Convention on International Trade in Endangered Species (CITES).
Restoration Ecology
Authors: Sher Anna A.
Published: September 2023

This chapter discusses ecological restoration, which is the practice of re-establishing populations, ecosystems, and landscapes that include degraded, damaged, or even destroyed habitat. The establishment of new communities on degraded or abandoned sites provides an opportunity to enhance biodiversity and can improve the quality of life for the people living in the area. Restoration ecology can also provide opportunities for scientists to learn more about ecological processes and for the public to be involved in conservation efforts. Restoration projects begin by eliminating or neutralizing factors that prevent the system from recovering. Then some combination of site preparation, habitat management, and reintroduction of original species gradually allows the community to regain the species and ecosystem characteristics of designated reference sites. The chapter then considers biological control, bioremediation, and compensatory mitigation or biological offsetting.
An Agenda for the Future
Authors: Sher Anna A.
Published: September 2023

This chapter reflects on the future of conservation biology. Protecting biodiversity presents several challenges. To address these problems, there is a need to change many policies and practices. Recent evaluations suggest that reaching international goals for conservation and sustainability is possible but will require major shifts away from “business as usual” practices in production, management, and valuing biodiversity. Changes must occur at the local, national, and international levels and will require action on the part of individuals, conservation organizations, and governments. Conservation biologists must demonstrate the practical value of the theories and approaches of their discipline and actively work with all components of society to protect biodiversity and restore the degraded elements of the environment. To achieve the long-term goals of conservation biology, practitioners need to become involved in conservation education and the political process.
Specifying Identity
Authors: Barresi Michael J. F. , Gilbert Scott F.
Published: September 2023

This chapter discusses cell differentiation, which is the process by which a cell acquires the structural and functional properties unique to a given cell type. It examines how cells go through a process of maturation as they experience different levels of commitment to their respective end fates. It also highlights three different modes of cell specification: autonomous, conditional, and syncytial. The chapter reviews syncytial specification that occurs when cell fates are determined in a syncytium of unseparated nuclei. It describes the blastoderm, cytoskeletal arrangements in drosophila that maintain the positions of nuclei in the syncytium, which enables specification of nuclei by the opposing morphogen gradients Bicoid and Caudal.
Birds and Mammals
Authors: Barresi Michael J. F. , Gilbert Scott F.
Published: September 2023

This chapter focuses on reptiles and birds which undergo discoidal meroblastic cleavage, wherein the early cell divisions do not cut through the yolk of the egg but form a blastoderm. It discusses the primitive streak which is derived from epiblast cells and the central cells of Koller's sickle. It also describes the prechordal plate which helps induce formation of the forebrain, wherein the chordamesoderm induces the formation of the midbrain, hindbrain, and spinal cord. The chapter examines the two signaling centers of mammalian gastrulation, one in the node and one in the anterior visceral endoderm. It reviews the homology of gene structure and the similarity of expression patterns between drosophila and mammalian Hox genes that suggest that this patterning mechanism is extremely ancient.
Regeneration
Authors: Barresi Michael J. F. , Gilbert Scott F.
Published: September 2023

This chapter focuses on four modes of regeneration: stem cell-mediated regeneration, epimorphosis, morphallaxis, and compensatory regeneration. In stem cell-mediated regeneration, new cells are routinely produced to replace the ones that die, while in epimorphosis, tissues form a regeneration blastema, divide, and redifferentiate into the new structure. In morphallaxis, existing tissue is re-patterned but there is little or no growth, while in compensatory regeneration, cells divide but retain their differentiated state. The chapter describes the mammalian liver, wherein no regenerating blastema is formed but regenerates the same volume it lost and each of its cell generates its own cell type. It cites the research on the African spiny mouse that has revealed the importance of macrophages in promoting a regenerative environment that prevents fibrotic scar formation.
Developmental Mechanisms of Evolutionary Change
Authors: Barresi Michael J. F. , Gilbert Scott F.
Published: September 2023

This chapter centers on evolution, which is the result of inherited changes in development and contributes to modifications of embryonic or larval development. It discusses the modularity of development that allows parts of the embryo to change without affecting other parts and is caused by the modularity of enhancers. It also considers the recruitment of existing genes and pathways for new functions as a fundamental mechanism for creating new phenotypes. The chapter details how new anatomical structures may result from duplicated genes whose regulation has diverged. It outlines the ways evolutionary change is affected through development at the level of gene expression: change in location (heterotopy), change in timing (heterochrony), change in amount (heterometry), and change in kind (heterotypy).
Cell Walls: Structure, Formation, and Expansion
Authors: Taiz Lincoln , Møller Ian Max , Murphy Angus , Zeiger Eduardo
Published: September 2023

This chapter focuses on the intrinsic organismal functions of the plant cell wall, noting that cell walls provide the raw material for many products important to humans and society. It talks about globally, aggregated cell walls described as cellulosic biomass, which are widely used for energy generation, heat, and fuel. It also considers the plant cell wall as one of the most abundant reservoirs of organic carbon in nature and a major sink for photosynthetically captured carbon, which plays an integral role in carbon flow through ecosystems. The chapter covers some of the general functions of plant cell walls and provides an overview of their composition biosynthesis, and assembly. It examines how secondary cell walls are produced via lignification, including their importance for the physiology of water transport and plant structure.
Respiration and Lipid Metabolism
Authors: Taiz Lincoln , Møller Ian Max , Murphy Angus , Zeiger Eduardo
Published: September 2023

This chapter reviews respiration in its metabolic context, emphasizing connections between the pathways involved and special features that are peculiar to plants. It relates respiration to the understanding of the biochemistry and molecular biology of plant mitochondria and respiratory fluxes in intact plant tissues. It also describes the pathways of lipid synthesis that lead to the accumulation of fats and oils, which plants use both for energy and carbon storage, and as a principal component of cellular membranes. The chapter discusses the catabolic pathways involved in the breakdown of lipids and the conversion of their degradation products into sugars that occurs during the germination of fat-storing seeds. It highlights the four main processes of respiration: glycolysis, toxidative pentose phosphate pathway, tricarboxylic acid (TCA) cycle, and oxidative phosphorylation.
Signals from Sunlight
Authors: Taiz Lincoln , Møller Ian Max , Murphy Angus , Zeiger Eduardo
Published: September 2023

This chapter discusses the primary signaling mechanisms involved in light regulated growth and development, focusing primarily on the red-light (600–700 nm), far-red light (700–750 nm), blue light (400–500 nm), and UV-B radiation (290–320 nm) receptors. It highlights photoreceptors, phytochromes, and cryptochromes, and phototropins that help plants regulate developmental processes over their lifetimes by sensitizing plants to incident light. It also points out how photoreceptors initiate protective processes in response to harmful radiation. The chapter examines the association of phytochrome with changes in lipid composition and membrane potentials. It analyzes phototropins located in the plasma membrane and has two flavin mononucleotide (FMN) chromophores that can induce conformational changes.
Sexual Reproduction: From Gametes to Fruits
Authors: Taiz Lincoln , Møller Ian Max , Murphy Angus , Zeiger Eduardo
Published: September 2023

This chapter analyzes the development of the male and female gametophytes, which produce the gametes. It describes plants as sessile organisms that depend on gravity and vectors, such as wind or insects, to bring about pollination and fertilization. It also investigates how plants have evolved complex mechanisms, both anatomical and biochemical. It also looks at how they ensure outcrossing. The chapter highlights sexual selection in plants that occurs not by visual displays by males as in animals, but by competition between male gametophytes to reach the female gametophyte and fertilize the egg within the ovule. It discusses the development of the seed and fruit, which includes the structure that protect and nourish the embryo and its delivery to a suitable substrate on which to germinate and establish itself as a new seedling.
Embryogenesis: The Origin of Plant Architecture
Authors: Taiz Lincoln , Møller Ian Max , Murphy Angus , Zeiger Eduardo
Published: September 2023

This chapter focuses on the embryogenesis of seed plants, emphasizing the angiosperms. It points out how seed plant embryogenesis, which evolved about 320 million years ago, is derived from a much older process. This has defined land plants since their origin about 450 million years ago. It also describes the embryogenesis in seed plants that transforms the single-celled zygote into a complex, multicellular individual contained within a mature seed. The chapter looks at how embryogenesis provides many examples of developmental processes by which the basic architecture of the plant is established. It covers the elaboration of forms, the associated formation of functionally organized structures, and the differentiation of cells to produce anatomically and functionally distinct tissues.
Inhibitors of angiotensin converting enzyme as effective antihypertensive agents
Authors: Saunders John
Published: September 2023

This chapter discusses the role of angiotensin converting enzyme (ACE) in reducing the blood pressure of hypertensive patients. The ACE is vital in the cascade of proteolytic reactions which ultimately control the levels of angiotensin II, a potent vasoconstrictor. The chapter provides a brief background of the treatment of hypertension in the 1970s, highlighting the impact of the discovery of captopril, a landmark in rational drug design. It explains the synthesis of captopril, as well as the syntheses of enalaprilat and lisinopril. The chapter also discusses the synthesis of quinapril, which involves direct N-alkylation and is characterized by a re-ordering of the coupling sequence. It then tackles benazepril, which evolved from thiol-based inhibitors. The chapter also describes ramipril which is rapidly converted by hepatic cleavage of the ethyl ester entity to ramiprilat. It ends with a discussion on fosinopril.
Modulation of central serotonin in the treatment of depression
Authors: Saunders John
Published: September 2023

This chapter discusses different selective serotonin uptake inhibitors which are used in the treatment of depression. It explains the synthesis of fluoxetine which, unlike earlier anti-depressants, exerts little direct activity at other receptors resulting in a lower occurrence of sedative and cardiovascular side effects. The chapter highlights that a Mannich reaction on acetophenone provided the key starting material for the first reported synthesis of fluoxetine. It also discusses the synthesis of sertraline which includes a Stobbe reaction between benzophenone and diethyl succinate, as well as hydrolysis and decarboxylation of mono acid under strongly acidic conditions, among others. The chapter likewise tackles the synthesis of paroxetine, another selective serotonin uptake inhibitor.
The metals: occurrence, physical properties and uses
Authors: Housecroft Catherine E.
Published: September 2023

This chapter provides a background on representative inorganic and coordination chemistry of the heavier metals of the d-block. It collectively refers to ruthenium, osmium, rhodium, iridium, palladium, and platinum as the platinum-group metals. These occur together naturally. It also surveys the properties and uses of the second- and third-row d-block elements, such as gold, mercury, and zirconium. The chapter talks about yttrium. This occurs in the form of ores monazite and bastnãsite, while niobium occurs in the ore pyrochlore NaCaNb2O6F and in columbite, which has varying compositions of the general formula (Fe,Mn)(Nb,Ta)2O6. The chapter mentions molybdenite MoS2 as the main ore from which molybdenum is extracted.
Coordination complexes: magnetic properties and electronic spectra
Authors: Housecroft Catherine E.
Published: September 2023

This chapter deals with the role that the metal d-orbitals play in governing the properties of transition metal complexes. It introduces the magnetic properties and electronic spectra of the heavier d-block metal coordination complexes and focuses on comparisons of properties between the metals of the first and later rows. It also mentions octahedral complexes which may be low- or high-spin, and tetrahedral complexes which are high-spin. The chapter analyses the importance of a splitting diagram for square planar complexes in the later metals of the d-block, particularly for group 10 metal(II) ions. It looks at how the character of the metal d-orbitals changes in progressing from the first to third rows of the d-block.
Multiply bonded dinuclear complexes
Authors: Housecroft Catherine E.
Published: September 2023

This chapter examines a multiple bond often associated with double and triple bonds. It discusses the effects of combining Albert Einstein's theory of relativity with quantum theory. This results in an understanding of why d-orbitals are subject to a relativistic expansion that is more significant for 5d than 4d. It also talks about an equation which shows a general preparative method and the incorporation of axial ligands, which has the potential for the synthesis of polymeric materials, such as the two-dimensional polymer. The chapter refers to a group of quadruply bonded dimolybdenum species that contain four carboxylate bridges and that are considered a valuable precursor to many compounds with dimolybdenum cores. It cites an example of axial ligand coordination where terminal oxygen atoms from the sulfate bridges of one anion enter into axial coordination interactions with Mo centres on adjacent anions.
Optimization
Authors: Green N. J. B.
Published: September 2023

This chapter points to the fact that certain quantum-mechanical problems cannot be solved, even with the aid of symmetry. It cites two basic types of approximations, which include the simplification to a form that permits explicit solution and building an accurate computational solution by superposing large numbers of simple wavefunctions. It also explains that approximation must be optimised as it is necessary to have a foolproof way to find the best possible approximation of the assumed form. The chapter talks about expectation energy as the basis of the variation method, which is calculated from an approximate wavefunction that must be greater than the true ground state energy. It attempts to describe a system in its ground state that has an approximate wavefunction which contains a variable parameter.
Silyl protecting groups
Authors: Robertson Jeremy
Published: September 2023

This chapter evaluates silyl protecting groups. To categorise silicon protecting groups as either acid or base-labile is impractical because both types of cleavage are possible and find routine use. Organosilicon chemistry is characterised by a high affinity for oxygen, which has led to the widespread use of silyl ethers for the protection of alcohols, and higher affinity for fluorine, which provides a very selective deprotection pathway. The chapter then looks at alcohols, diols, aldehydes and ketones, and amines. Deprotection of silyl protecting groups with F-ion is normally highly selective but the basic properties of the hydrated ion in solution can interfere with functionality not containing silicon and can lead to unexpected reactions.
The aquatic environment
Authors: Howard Alan G.
Published: September 2023

This chapter discusses the aquatic environment. Water is the most important liquid on the Earth and has a major impact on the chemical, physical, and biological processes which take place. There are many ways by which natural waters can be classified and it must be recognized that the movement of water through the environment does not limit it to any single category. It is often convenient however to consider the Earth's surface as a suitable cut-off point. Groundwater is the water below the Earth's surface. Meanwhile, surface waters can be divided into two broad categories: freshwater and seawater. The chapter then looks at the hydrologic cycle, before considering the dissolved inorganic compounds and organic material in natural waters.
Oxidation and reduction
Authors: Howard Alan G.
Published: September 2023

This chapter focuses on oxidation and reduction. When the muddy sediments at the bottom of a river or lake are disturbed, two things are often noticed. First, there is a smell of rotten eggs, indicative of the generation of hydrogen sulfide. Secondly, the colour of the sediment may change from a red-brown at the surface to a dark brown-black below. Both of these observations are linked to a lack of oxygen. In purely chemical terms, the absence of oxygen in these sediments has resulted in the reduction of sulfur(VI) to sulfur(-II); that the reduction has been carried out by bacteria does not necessarily alter the chemical result. It is not only the sediments which can become devoid of oxygen. The water in lakes, and even the bottom waters of fjords, can reach this state if the oxygen is consumed by organisms and if the chemical processes faster than it can be replaced.
Dissolution and deposition processes
Authors: Howard Alan G.
Published: September 2023

This chapter assesses dissolution and deposition processes. Some of the solid matter which is suspended in a natural water, or deposited to make up the top layers of the bottom sediments, is material which has been recently deposited from solution. This may arise from a purely chemical process such as precipitation or colloidal aggregation, or may result from the production of solid biomass, such as that which results from the photosynthetic activity of algae. Some of this solid material will be rapidly returned to the dissolved phase by changes in solution chemistry or bacterially-assisted decomposition; the remainder will eventually be incorporated into the sediments. The chapter then considers chemical weathering, looking at hydrolysis and oxidation.
Surface Chemistry
Authors: McCash Elaine M.
Published: September 2023

Surface Chemistry conveys the fundamental concepts of surface chemistry. It describes solid surfaces, their properties at macroscopic and microscopic levels and their interrelation, and reflects the striking advances made in recent years through the study of well-defined single crystal surfaces. It begins with a discussion of the clean surface, its electronic and structural properties and goes on to describe adsorption, desorption, reactions, and reactivity at the surface. In the final section, the growth and properties of ultrathin films is introduced. Starting with the established concepts in terms of kinetics and thermodynamics, the book develops to look at phenomena such as surface dynamics and photochemistry. Important techniques which are applied to surfaces are also covered; this is a concept-driven rather than technique-driven approach.
Surface reactions and reactivity
Authors: McCash Elaine M.
Published: September 2023

This chapter focuses on surface reactions and reactivity, starting with an explanation of transition state theory. One of the major motivations for studying surface reactions has been to apply the knowledge to the field of catalysis. However, studies of surface reactions are also highly important in fields other than catalysis. In particular, two of the most important are the semiconductor industry and environmental chemistry, where the study of heterogeneous processes in the atmosphere has proved enormously valuable. The chapter details the mechanisms of surface reactions, discussing single molecular species and reactions involving more than one. It also looks at surface photochemistry.
Electromagnetism
Authors: Ritchie G.A.D. , Sivia D.S.
Published: September 2023

This chapter considers the magnetic effects arising from moving charged particles, noting the experimental observation that two current carrying wires exert force on one another. It recounts how Jean-Baptiste Biot and Félix Savart derived a mathematical formula that allows the magnetic flux density to be determined for an arbitrary arrangement of conductors. It also cites examples wherein current loops behave like magnetic dipoles in the far field and show many properties that are analogous to electric dipoles. The chapter demonstrates the classical calculation for an atomic magnetic dipole moment, which is introduced and related to the angular momentum of the electron. It uses microscopic magnetic moments to explain the macroscopic properties of magnetic materials.
The ultrasonic cleaning bath
Authors: Mason Timothy J.
Published: September 2023

This chapter discusses the ultrasonic cleaning bath, which is by far the most widely available and cheapest source of ultrasonic irradiation for the chemical laboratory. The construction of an ultrasonic cleaning bath is very simple—a laboratory model generally consists of a stainless steel tank of rectangular cross-section with either one or several transducers firmly attached underneath the flat base. The frequency and power of an ultrasonic bath depends upon the type and number of transducers used in its construction. The chapter then details the process of choosing the correct type of ultrasonic bath, as well as setting up an ultrasonic cleaning bath for sonochemistry. It also looks at the design of the reaction vessel; laboratory demonstrations of the physical effects of ultrasound; the advantages and disadvantages of using an ultrasonic bath for sonochemistry; and other types of equipment related to cleaning baths.
Pre-reaction equilibria
Authors: Atherton John H. , Carpenter Keith J.
Published: September 2023

This chapter evaluates pre-reaction equilibria. Equilibria involving either organic or inorganic species can play an important part in influencing both the reaction and workup stage of organic syntheses. In the reaction stage, these equilibria can determine the proportion of reactive species present, which may not be the same as the total or stoichiometric concentration, and can thus influence both the rate and selectivity of the reaction. During workup, the same principles can determine the actual concentration of species involved in crystallisation or extraction processes. The chapter then looks at examples of the influence of pre-equilibria, as well as multiple ionisation in aqueous systems. It also considers homoconjugation, the situation where a product of an equilibrium reacts with the starting material. Finally, the chapter explains the more complex systems of nitrosation and diazotisation.
Dispersion and mass transfer in multi - phase systems aqueous alkali
Authors: Atherton John H. , Carpenter Keith J.
Published: September 2023

This chapter explores dispersion and mass transfer in multi-phase systems. Many reactions involve more than one phase, usually two, commonly three and even four or more. In order for the reaction to proceed, mass must transfer between these phases, and it is easy to overlook the fact that considerable effort may be required to distribute them well enough and promote mass transfer to a sufficient extent that the reaction can proceed at a reasonable rate. A gas bubbled through a liquid will not react at any meaningful rate unless well dispersed as small bubbles, and immiscible liquids will not react unless one is dispersed as fine droplets within the other. It is most common for fine chemical reactions to be carried out in a continuous liquid phase. The chapter then looks at phase boundary diagrams and phase inversion.
Product isolation and work-up
Authors: Atherton John H. , Carpenter Keith J.
Published: September 2023

This chapter discusses product isolation and work-up. A laboratory multi-stage synthesis will often start from purified materials and include isolation and purification of intermediates at each stage. In contrast, in order to reduce waste for treatment and to contain equipment costs within reasonable limits, an industrial process will have fewer isolation stages and operate with crude intermediates as far as possible. The most popular isolation technique in a laboratory process is multiple crystallisation. At full scale, crystallisation is still a very common technique, but by no means always the best. The chapter then looks at the most common isolation technologies, distillation, liquid extraction, precipitation, and crystallisation. It does not describe them in detail, but the basic principles are explained in order to highlight the important issues and provide guidance for process development.
Interfacing computers to experiments
Authors: Pete Biggs
Published: September 2023

This chapter introduces techniques on getting experimental information into a computer and causing a computer to control the experiment. It explains that an analogue to digital converter (ADC) is a device that is used to measure voltage, while the digital to analogue converter (DAC) is a device used to generate a specific voltage. It also describes the output of an ADC in a computer system. This is designed to reflect one or more memory locations on the microprocessor bus. The chapter discusses the parallel input and output (PIO) device, which allows a single bit or group of bits to be output or input. It also senses whether a signal is on or off. It highlights the principle of DAC, wherein the device produces a voltage proportional to binary data.
Periodic table of the elements and element atomic weights (adapted from IUPAC 1991
Authors: Kaltsoyannis Nikolas , Scott Peter
Published: September 2023

Notes: Elements for which the atomic weight is contained within parentheses have no stable nuclides and the weight of the longest-lived known isotope is quoted. The three elements Th, Pa, and II do have characteristic terrestrial abundances and these are the values quoted. In...
Polymorphism
Authors: Davey Roger J. , Garside John
Published: September 2023

This chapter assesses polymorphism, which is the ability of some molecules to adopt more than one crystal structure. When preparing materials by crystallization, it is important to recognize and to be able to control this phenomenon, because each polymorph has its own unique combination of mechanical, thermal, and physical properties. The production of specific and well-defined polymorphs is therefore crucial in chemical manufacture. In the chemical and pharmaceutical industry, the demand for high yields and high production rates has forced chemists and engineers to operate processes far from equilibrium, so exacerbating the tendency to form polymorphic structures that, for a given temperature, pressure, and composition, are not the most stable. Such unstable structures will eventually undergo phase transitions to more stable phases. This transformation process and its structural and thermodynamic basis are the subjects of the chapter.
The canonical ensemble
Authors: Bowley Roger , Sánchez Mariana
Published: September 2023

This chapter describes the canonical ensemble, which is an ensemble of systems that are all prepared in the same way with the same number of particles, volume, shape, magnetic field, and electric field. However, the energy of each system fluctuates. The chapter details experiments that involve condensed matter wherein a system is placed in contact with a heat bath that eventually reaches thermal equilibrium. It also clarifies how the system being studied together with the heat bath or combined system is thermally isolated so that its total energy is constant. The chapter illustrates a Boltzmann probability distribution, wherein probabilities are drawn along the horizontal axis and the energies along the vertical. It highlights the use of the Boltzmann probability distribution on systems that are in contact with a heat bath, granted the number of particles in the system is constant.
Systems with variable numbers of particles
Authors: Bowley Roger , Sánchez Mariana
Published: September 2023

This chapter explains that a system can have a variable number of particles when particles can enter or leave or because a reaction takes place inside the system. It cites a sealed vessel containing a pure substance with both liquid and gas phases present as an example that demonstrates the presence of a meniscus separating the gas from the liquid. This meniscus allows for determining which atoms to exist in the gas phase and in the liquid phase. The chapter also discusses how gas atoms can condense into liquid or how liquid can evaporate into gas. The chapter highlights the application of mathematical language to reactions of elementary particles or reactions that occurred in the early stages of the universe. It outlines the subject of reactions that occur frequently in science, such as solid-state physics, chemistry, and phase equilibrium.
Mechanisms
Authors: Michael Hornby , Josephine Peach
Published: September 2023

This chapter outlines the classification of reactions, reagents, and bond-making/breaking and covers substitution, addition, elimination, nucleophilic, electrophilic, radical, homolytic, and heterolytic. It reviews mechanisms that use curly arrows, energy profiles, intermediates, transition states, equilibria, and kinetics. It also describes the nucleophile which include four nonbonded pairs of electrons and donate an electron pair to make a new bond. The chapter discusses electrophiles that can accept a pair of electrons, radicals that has an unpaired electron, and polarized molecules. It mentions how the loss of one electron from a bromine atom brings aboutthe six-electron, positively charged Br+ ion.
Taking it further
Authors: Michael Hornby , Josephine Peach
Published: September 2023

This chapter cites examples that include the indicator phenolphthalein, which has different structures in acid and in alkaline solution at pH > 10. It explains a compound that is coloured because it absorbs some wavelengths of visible light, noting that the energy of the light absorbed corresponds to an energy gap between two electronic energy states of the molecule. It also discusses how boiling points go up as intermolecular forces in the liquid get stronger, making it more difficult for molecules to escape from each other into the gas phase. The chapter shows how the rate of an enzyme-catalysed decomposition of hydrogen peroxide varies with changing peroxide concentration. It presents a diagram that shows some interactions of the side-chains in two sections of a protein, which might be involved in maintaining its tertiary structure at about pH7.
Electronic energy levels and chemical bonding
Authors: Cox P. A.
Published: September 2023

This chapter examines a number of important features of the electronic structure of the solid, which include energies and widths of the various bands, the energy gaps between them, and the number of electrons that occupy them. It details how the electronic energy levels of simple solids are related to chemical models of bonding. It also highlights the ionic model, wherein bonding is accompanied by an electron transfer between one atom to another. The chapter highlights the use of the ionic model in predicting the heats of formation and the chemical and physical properties of compounds, such as halides and oxides. It considers the solids formed by non-metallic elements and looks at compounds where covalent bonding is combined with some degree of ionic character.
The Fermi-Dirac distribution function
Authors: Cox P. A.
Published: September 2023

The normal derivation of the Boltzmann distribution needs to be modified to take account of two properties of electrons:

that they are indistinguishable;

that they obey the exclusion principle, so that when the spin quantum number is included, only one electron can occupy...
Pyrroles, thiophenes, and furans
Authors: Davies David T.
Published: September 2023

This chapter discusses pyrroles, thiophenes, and furans. Pyrrole, thiophene, and furan are five-membered ring heteroaromatic compounds containing one heteroatom. They derive their aromaticity from delocalization of a lone pair of electrons from the heteroatom. Consequently, the lone pair is not available for protonation and hence these heterocycles are not basic. Furan is the least aromatic of the trio because oxygen has the greatest electronegativity. The chapter then considers how this variation in aromaticity affects the reactivities of these three related heterocycles. It also looks at the synthesis of pyrroles, thiophenes, and furans, using the Paal–Knorr synthesis. Finally, the chapter reviews the electrophilic substitution and anion chemistry of pyrroles, thiophenes, and furans.
Five-membered ring heterocycles with three or four heteroatoms
Authors: Davies David T.
Published: September 2023

This chapter addresses the broad category of five-membered ring heterocycles containing three or four heteroatoms, which encompasses many heterocyclic systems. Obviously, there is considerable variation in the physical and chemical properties of such a large group of heterocycles. For instance, with regard to aromaticity, oxadiazole is considered to be less aromatic than triazole or tetrazole. Nevertheless, this collection of heterocycles does share certain characteristics. The trend of decreasing tendency towards electrophilic substitution on going from furan, pyrrole, and thiophene to the azoles is continued into these series. The presence of additional ‘pyridine-like’ nitrogen atoms renders these systems particularly ‘electron-deficient’, and electrophilic substitution is of little importance. Conversely, nucleophilic substitution does occur in these systems. The chapter then considers the synthesis of 1,2,4-ozadiazoles; 1,2,3-triazoles; and tetrazoles.
Answers to problems
Authors: Davies David T.
Published: September 2023

This chapter presents the answers to the problems included in the previous chapters. Reaction of diketone with aminoketone produces enamine, which is not isolated, but cyclinizes directly to give pyrrole. Meanwhile, the application of generalised oxazole retrosynthesis leads to a simple glycine derivative. The mechanism of the oxazole formation is identical to that of the Hantzch thiazole synthesis. However, because of the reduced nucleophilicity of a carbonyl group as compared to a thiocarbonyl, this synthesis only proceeds under vigorous conditions. The alternative sequence would give a positional isomer oxazole. Finally, the overall electronic distribution of 2-pyrimidone has a considerable contribution from mesomer. The chapter also shows the mechanism of nitration.
Reductive cleavage reactions
Authors: Donohoe Timothy J.
Published: September 2023

This chapter studies reactions which completely cleave the bonds between carbon and electronegative elements, replacing them with bonds to hydrogen. It presents examples of reductions which cleave purely σ-bonds and also reactions which cleave both σ- and π-bonds. The chapter begins by looking at the reduction of carbon–nitrogen σ-bonds. Amines that are substituted with a benzyl group may be broken by reduction with hydrogen and a transition metal catalyst. Reductive cleavage using hydrogen and a catalyst is known as hydrogenolysis. The chapter then considers the reduction cleavage of carbon–oxygen bonds; reductive dehalogenation; reduction cleavage of carbon–sulfur bonds; and reductive cleavage of cyclopropane rings.
Introduction
Authors: Jenkins Paul R.
Published: September 2023

This chapter provides a background on the reagents of the general structure RM, where R is an organic fragment and M is a metal that had a profound effect on organic synthesis. It explains the chemistry of the organometallic reagents of sodium, potassium, lithium, and magnesium by regarding the reagents as equivalent to a carbanion R- with a metal cation M+. It also discusses the use of carbanion R- for reacting with various organic electrophiles to make carbon-carbon bonds. The chapter covers various structural types and methods of preparation and uses in synthesis of the dual reactivity of the organometallic reagent. It cites examples on the most important uses of reagents, such as the alkoxide salt that is produced when the reaction mixture is poured into water during the work-up procedure.
Carbocation induced alkyl and hydride shifts
Authors: Harwood Laurence M.
Published: September 2023

This chapter recounts the accumulation of structural information by early investigations in the nineteenth century of components of essential oils of plants to establish basic family likeness. It analyses the volatile and fragrant compounds that were found to be unsaturated hydrocarbons and their oxygenated derivatives contain carbon atoms. It also talks about Hans Meerwein, who generalised the carbocationic mechanism to account for some terpenic rearrangements. The chapter examines the fate of the rearranged carbocation which depends on the structure of the molecule and involves quenching by elimination or addition of a nucleophile. It talks about a rearrangement that may occur to give a more stabilized carbocation and become a basis of the biological construction of complex terpene molecules.
Miscellaneous rearrangements
Authors: Harwood Laurence M.
Published: September 2023

This chapter considers cationic processes in allylic rearrangements, sigmatropic migrations which rely upon total or partial charge separation, and radical rearrangements in which the radical species are charged. It describes allylic substrates as being prone to rearrangement during nucleophilic substitution reactions. It also details major reaction pathways by which rearrangement can occur and which are directly analogous to the commonly encountered nucleophilic substitution mechanisms. The chapter highlights reactions under conditions that favour order substitution, which leads to mixtures of isomeric products. It discusses the site of nucleophilic attacks under kinetic conditions that is directed by the degree of positive character at each of the two carbons of the allylic resonance hybrid.
Radical reactions in synthesis
Authors: Moody Christopher J. , Whitham Gordon H.
Published: September 2023

This chapter uses the term “radical”, which is an atom or molecule that possesses one or more unpaired electrons and focuses on reactions where useful yields are obtained using radical processes in a solution. It analyzes radical reactions that proceed by a chain mechanism and a crucial initiation step that requires the generation of radicals from an appropriate precursor. It also deals with the main types of reaction which lead to the production of radicals, such as the thermal and photochemical cleavages of compounds with weak bonds and electron transfer processes. The chapter discusses compounds that contain relatively weak bonds with bond dissociation energies (BDE) that undergo homolysis at a convenient rate. It describes the diacylperoxides as an important group of compounds wherein the already weak bond of a simple peroxide is further weakened by resonance stabilization of the acyloxy radical.
Nitrenes
Authors: Moody Christopher J. , Whitham Gordon H.
Published: September 2023

This chapter focuses on nitrenes, which are six-electron neutral, monovalent, highly reactive nitrogen intermediates wherein the nitrogen atom has four non-bonded electrons. It describes nitrenes as monovalent short-lived species. These were first suggested as intermediates in 1891: the Lossen rearrangement. It also points out that the chemistry of nitrenes closely parallels that of carbenes in all aspects. The chapter examines the possibility of two spins states for nitrenes. These depended on whether two non-bonding electrons have their spins paired or paralleled. It explains how nitrenes obey Hund's Rule and are ground state triplets with two degenerate sp-orbitals containing a single electron. It highlights the energy difference between the singlet and triplet states. This is usually much larger for nitrenes than for carbenes.