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Chapter

Cover Inorganic Chemistry

Hydrogen  

This chapter looks at hydrogen, the most abundant element in the universe and the tenth most abundant by mass on Earth. It discusses reactions of hydrogen species that are particularly interesting in terms of fundamental chemistry as well as important applications, including energy. The chapter describes how hydrogen is produced in the laboratory, on an industrial scale from fossil fuels, and on its possible production through increasing use of renewable resources in the future. It also tackles how hydrogen bonding stabilizes the structures of water and DNA. It then summarizes the synthesis and properties of binary compounds that range from volatile, molecular compounds to salt-like and metallic solids. Furthermore, the chapter considers how the hydrogen molecule is activated by binding to catalysts, the processes that can produce hydrogen from water using solar energy.

Chapter

Cover Human Physiology

The chemical constitution of the body  

This chapter describes the human body as consisting largely of four elements: oxygen, carbon, hydrogen, and nitrogen. It shows that about 70 percent of the lean body tissues is water, while the remaining 30 percent made up of organic material (i.e. molecules and minerals). The principal organic constituents of mammalian cells are the carbohydrates, fats, proteins, and nucleic acids, which are built from smaller molecules belonging to four classes of chemical compounds: sugars, fatty acids, amino acids, and nucleotides respectively. The chapter outlines the principal minerals found in tissues: calcium, phosphorus, potassium, and sodium. It gives an approximate indication of the chemical composition of the body for a young adult male, noting that there is individual variation and that the proportions of the various constituents vary between tissues and change during development.

Chapter

Cover Chemistry3

Hydrogen  

This chapter considers hydrogen to have the simplest atoms of all the elements, which means that the hydrogen atom is the only one for which the Schrödinger equation can be solved exactly. Hydrogen is the most abundant element in the Universe, and the tenth most abundant element on Earth by mass, but it does not occur naturally on Earth in the elemental form. The chapter confirms why binary hydrides can be protic or hydridic and describes the character of a particular hydride. It illustrates how to predict whether the bonding in a binary hydride is covalent or ionic, and whether a covalent hydride is likely to contain bridging hydrogen atoms. Calculating the effects of replacing hydrogen by deuterium on infrared stretching frequencies is also covered.

Chapter

Cover Foundations of Inorganic Chemistry

Hydrogen  

This chapter evaluates hydrogen, which is by far the most abundant element in the universe and all the other chemical elements are made from it. Without hydrogen there would be no water to drink, and DNA molecules would not form the double-helix structure that allows our genetic code to be copied and passed on to future generations. Hydrogen can form a positive ion like the metals of Group 1 but, since it is one electron short of a noble gas configuration, it can also form a negative ion and a single covalent bond, like the halogens of Group 17. Hydrogen forms compounds with many other elements but the properties of these hydrides vary considerably. The chapter then considers the self-ionization behaviour of water, which may be regarded as an acid—base reaction. It also looks at sulphuric acid and nitric acid.

Chapter

Cover Organic Chemistry

1H NMR: Proton nuclear magnetic resonance  

This chapter highlights proton (1H) nuclear magnetic resonance (NMR). Proton NMR differs from 13C NMR in a number of ways. 1H is the major isotope of hydrogen, while 13C is only a minor isotope. 1H NMR is quantitative: the area under the peak shows the number of hydrogen nuclei, while 13C NMR may give strong or weak peaks from the same number of 13C nuclei. Moreover, protons interact magnetically (couple) to reveal the connectivity of the structure, while 13C is too rare for coupling between 13C nuclei to be seen. Finally, 1H NMR shifts give a more reliable indication of the local chemistry than that given by 13C spectra. Nevertheless, proton NMR spectra are recorded in the same way as 13C NMR spectra: radio waves are used to study the energy level differences of nuclei in a magnetic field, but this time they are 1H and not 13C nuclei.

Chapter

Cover Introduction to Quantum Theory and Atomic Structure

The hydrogen atom  

This chapter focuses on the hydrogen atom, which is the most important chemical application of the quantum theory. The hydrogen atom was Erwin Schrödinger's immediate goal when he developed his equation, and the solution obtained in 1926 persuaded him and indeed most interested physicists that his theory was successful. Indeed, the solutions of Schrödinger's equation — known as atomic orbitals — form the basis of our understanding, not only of atomic structure, but also of chemical bonding in molecules and solids. The chapter begins by considering the Rutherford–Bohr atom. It then looks at hydrogenic ions. The solutions described in the chapter are 'exact', in the mathematical sense that they can be obtained from the Schrödinger's equation without approximation. However, they are not quite 'correct', because this equation does not truly describe a real hydrogen atom.

Chapter

Cover Biochemistry and Molecular Biology

The structure of proteins  

This chapter focuses on proteins, which are made up of one or more polypeptide chains constructed from 20 species of amino acids. The length and sequence of each polypeptide is specified by its gene. The chapter describes 20 different amino acids which are of differing sizes and degrees of hydrophobicity, hydrophilicity, and electrical charge. These present the possibility of a vast variety of different proteins. The primary structure is the linear amino acid sequence, while the secondary structure involves folding of the polypeptide backbone. The chapter explains that the main secondary structure motifs are the α helix and the β-pleated sheet, which are stabilized by hydrogen bonding. The tertiary structure involves the further folding of the secondary structure motifs into the three-dimensional form of the protein.

Chapter

Cover Elements of Physical Chemistry

Hydrogenic atoms  

This chapter examines the hydrogenic atom, which is a one-electron atom or ion of general atomic number Z. It provides a set of concepts which are used to describe the structures of atoms and of molecules. It analyzes the experimental information from a study of the spectrum of atomic hydrogen and describes the results of solving the Schrödinger equation. It also considers the importance of wavefunctions to the atomic orbitals of hydrogenic atoms. The chapter talks about the atomic orbitals which are labelled by quantum numbers that specify the energy and angular momentum of an electron in a hydrogenic atom. It shows the production of energetically excited atoms when an electric discharge is passed through a gas or vapour or when an element is exposed to a hot flame.

Chapter

Cover Thrive in Human Physiology

Introduction  

This chapter considers underlying molecular and cellular elements and the link between structure and function in physiology to provide an understanding of the structures within the body. It discusses the body in terms of the hierarchical nature of organization from the molecular level through to the organismal level. It also highlights the elemental composition of the vast majority of the body which is formed from carbon, oxygen, hydrogen, oxygenydrogen, carbon, and nitrogen. The chapter analyzes an individual's body weight in terms of body composition, which is accounted for by water and is found in a variety of compartments. Given that water accounts for most of an individual’s body weight, the chapter looks in depth at the forms this water takes. It explains that the water within the body has a variety of solutes dissolved in it that. These form extracellular fluid and intracellular fluid, each of which has a unique composition.

Chapter

Cover An Introduction to Medicinal Chemistry

Drug design: optimizing target interactions  

This chapter discusses interactions that involve dipole moments or induced dipole moments. These play a role in binding a lead compound to a binding site. The chapter demonstrates how reactive functional groups, such as alkyl halides, may lead to irreversible covalent bonds being formed between a lead compound and its target. It also examines the relevance of a functional group to binding, which can be determined by preparing analogues where the functional group is modified or removed. The chapter outlines functional groups, such as alcohols, amines, esters, amides, carboxylic acids, phenols, and ketones, and looks at how these can interact with binding sites by means of hydrogen bonding. It reviews alkyl substituents and carbon skeleton of the lead compound which can interact with hydrophobic regions of binding sites by means of van der Waals interactions.

Chapter

Cover Pharmaceutical Chemistry

Properties of Aliphatic Hydrocarbons  

Andrew J. Hall

This chapter details how molecules that have short or long chains or more complicated arrangements of carbon atoms can be produced. Hydrocarbons are compounds made solely of carbon and hydrogen atoms, in which each carbon forms four covalent bonds. The chapter highlights the importance of hydrocarbons in everyday lives as they are a source of energy used to heat and light homes, power vehicles, and provide many of the plastic items being used. The chapter talks about the abundance of hydrocarbons in nature, such as flavours or fragrances produced by plants, insect pheromones, and natural rubber and lipids. It explores the properties of the aliphatic hydrocarbons: the alkanes, alkenes, and alkynes.

Chapter

Cover Organonitrogen Chemistry

N-Oxides  

This chapter focuses on oximes. It regards oximes as a simple way to make N-O-containing functional groups that undergo numerous important reactions. The chapter looks into the synthesis of oximes with the analogy of hydrazones. It considers the reactions of oximes such as hydrolysis, dehydration, the Beckmann rearrangement, and reduction. In terms of hydrolysis, oximes are referred to as relatively inert. Hydrogenation over highly active catalysts, on the other hand, leads to a reduction of α-bond and the N-O α-bond. The most important commercial use of the Beckmann rearrangement is the formation of α-caprolactam.

Chapter

Cover Functional Groups

Alkynes  

This chapter focuses on the differences between alkynes and alkenes, particularly those that affect synthetic work. It explains that one difference concerns the CC double bond, which is usually created from saturated intermediates by elimination but is formed in a different way in alkynes. In these, ethene is widely used in building up the higher members and other compounds containing the triple bond. The chapter observes that alkynes are less reactive than alkenes, but with nucleophiles, the relative reactivity is reversed as simple alkenes do not undergo nucleophilic addition while simple alkynes undergo few additions. It discusses the hydrogenation of an alkyne with a poisoned catalyst that stops at the alkene stage.

Book

Cover Atomic Spectra
Atomic Spectra starts off by looking at quantum mechanics and the relationship of quantum mechanics with light. The next chapter considers the structure and spectrum of the hydrogen atoms. The text also covers the spectrum of the helium atom. Finally, the text examines the spectra of many-electron atoms.

Chapter

Cover Foundations of Physical Chemistry: Worked Examples

Taking it further  

This chapter reviews examples that show the four base pairs involved in hydrogen bonding of stranded DNA, wherein the pairs thymine (T) and adenine (A), and cytosine (c) and guanine (G) are complementary. It addresses the question of whether there is any difference in the stability to heat of DNA sequences that contain a higher proportion of GC base pairs. It also shows the translation of RNA message into a protein and the DNA code contains four letters G, C, A, and T, wherein the DNA codes for proteins that are made up of chains of amino acids. The chapter explains how ethanol is removed from blood through the action of the enzyme alcohol dehydrogenase in the liver. It discusses the alcohol dehydrogenase that contains two zinc atoms one of which provides an active site for the reaction.

Chapter

Cover Physical Chemistry for the Life Sciences

The thermodynamic properties of water  

This chapter discusses how hydrogen bonding influences many physical properties of water. Water has unusually high melting and boiling points, reflecting the extensive array of intermolecular hydrogen bonds that form in its solid and liquid phases. The origin of hydrogen bonding in water reflects in part the underlying polarity of the water molecule. That polarity has a major biological consequence because the resulting high relative permittivity (dielectric constant) of water makes liquid water an excellent solvent for the substances that participate in the chemical reactions that occur in cells. To explain this, the chapter first delves into the phases of water. Next, it discusses characteristic points in the thermodynamics of water. Surface tension is also addressed.

Chapter

Cover Physical Chemistry for the Life Sciences

Atomic orbitals  

This chapter takes a look at the atomic orbital, which is a one-electron wavefunction describing the spatial distribution of an electron in an atom. Atomic orbitals are used throughout chemistry in discussions of the electronic structure of atoms in general and in discussions of molecular electronic structure. This chapter extends the discussion of atomic structure to include the effect of nuclear charge by considering one-electron ions with higher atomic numbers. It shows how hydrogenic atoms are important because the Schrödinger equation can be solved for them. Furthermore, the concepts learned from a study of hydrogenic atoms can be used to describe the structures of many-electron atoms and of molecules too. To that end the chapter takes a look at the energy levels of hydrogenic atoms as well as the wavefunctions of hydrogenic atoms.

Chapter

Cover Oxidation and Reduction in Organic Synthesis

Oxidation of activated carbon–hydrogen bonds  

This chapter evaluates the oxidation of activated carbon–hydrogen bonds. During the course of an oxidation, hydrogen can be removed in three ways, as either H+, H*, or H-. Normally, it is beneficial to have a functional group which stabilises the carbon left behind by such removal of hydrogen. As such, the chapter considers the hydrogen atom that is lost, activated by the functional group. It begins by looking at oxidation adjacent to oxygen. This is the most useful and widespread area of oxidation, as it encompasses the alcohol-aldehyde-carboxylic acid sequence which is used so often in synthesis. The chapter then studies oxidation adjacent to a carbon–carbon multiple bond, a carbonyl group, and nitrogen, as well as the oxidation of phenols and the formation of quinones.

Chapter

Cover Physical Chemistry for the Life Sciences

Many-electron atoms  

This chapter focuses on many-electron atoms. The atomic orbitals developed for hydrogenic atoms are used to describe the electronic structure of many-electron atoms by using the building-up principle, a set of rules for predicting the order in which electrons occupy the available energy states, allowing for the repulsion between electrons and the Pauli exclusion principle. The building-up principle accounts for the structure of the periodic table and the variation through it of atomic radii, ionization energies, and electron affinities. One application of this material is to the discussion of an important inorganic contributor to life: zinc. The chapter also looks into the orbital approximation and the role of electron repulsion.

Chapter

Cover Physical Chemistry for the Life Sciences

Molecular interactions  

This chapter explores molecular interactions, showing how these can be expressed in terms of the electrostatic interactions between arrays of point charges. It begins by recognizing that molecules may have partial charges on their atoms which interact electrostatically. There are some advantages in recognizing that partial charges exist as dipoles, and to use the electrostatic interactions as dipolar. Those dipoles need not be permanent, but might be induced by nearby charges or result from transient fluctuations in electron density. The chapter also takes a look at hydrogen bonding and steric repulsion. Finally, it provides a case study on molecular recognition in biology and pharmacology.