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Chapter

Cover Organic Chemistry

Isomerism  

This chapter discusses isomerism, which describes the different ways in which we can arrange the atoms in a molecule with a fixed formula. This arrangement of atoms can take the form of constitutional (structural) isomerism, where the atoms are joined in a different order, or stereoisomerism, where the atoms are arranged differently in space. Stereoisomerism is subdivided into conformational isomerism and configurational isomerism. Two conformational isomers can be converted into each other (interconverted) by rotation around single bonds, whereas configurational isomers cannot be interconverted without breaking a bond. The chapter also discusses cis/trans isomerism and optical isomerism (chirality). Cis/trans isomers arise when rotation is restricted at a particular point in a molecule, most commonly due to a carbon–carbon double bond. This restricted rotation allows groups positioned on either side of the double bond to either sit adjacent to each other (cis), or opposite each other (trans).

Chapter

Cover Chemistry3

Isomerism and stereochemistry  

This chapter explores different types of isomerism in organic compounds and shows how the spatial arrangements of atoms in molecules determine their stereochemistry, and hence their shape. An understanding of stereochemistry will prove invaluable in the study of the reactions of functional groups — and it is crucial to the molecular machinery of life itself. The chapter discusses the conformational isomers and the factors that influence the conformation of organic molecules, such as ethane, butane, cyclohexane, and substituted cyclohexanes. It shows how to recognize enantiomers and assign the configuration of chiral centres as R or S using the Cahn–Ingold–Prelog sequence rules and how to convert a hashed–wedged line structure into a Fischer projection. The difference between diastereomers and enantiomers is also covered.

Chapter

Cover Chemistry for the Biosciences

Isomerism: generating chemical variety  

This chapter explores the concept of isomerism—the joining together of identical groups of atoms to form different molecules. Structural isomers are molecules that have the same chemical composition but whose atoms are joined together in different ways. Stereoisomers possess the same atoms, which exhibit the same connectivities. However, stereoisomers exhibit different configurations. Stereoisomers fall into two groups: cis–trans isomers, and enantiomers. Cis–trans isomers are stereoisomers that possess groups of atoms locked in specific configurations, while enantiomers are non-superimposable mirror images of one another. Cis–trans isomerism is most common in molecules that possess one or more double bonds. The chapter describes the nomenclature used to differentiate isomers, including E/Z nomenclature and the use of Fischer projections. The chapter then looks at chirality in biological systems and why it is important, before considering the chemistry of isomers.

Chapter

Cover Chemical Structure and Reactivity

Organic chemistry 2: three-dimensional shapes  

This chapter examines three-dimensional shapes adopted by organic molecules. It begins by looking at the phenomenon of isomerism, which is where a compound with a given molecular formula can exist as various isomers in which the constituent atoms are joined up or arranged in space in different ways. Sometimes there are large differences between isomers. They might, for example, contain different functional groups, but the distinction can be much more subtle than this. The chapter then considers how different shapes or conformations of molecules may be obtained by rotating about single bonds. Different conformations which are energy minima for that compound are called conformational isomers, or conformers. The chapter also covers enantiomers, chirality, and cyclic molecules.

Chapter

Cover Organic Chemistry

Molecular Structure and Shapes of Organic Molecules  

This chapter examines the shapes of organic molecules. It investigates what molecules look like and why molecules have a particular shape. The chapter reveals that three-dimensional shapes of simple molecules are the result of electrostatic repulsion between electron pairs and can be explained in terms of shapes of molecular orbitals involved in chemical bonding. The s and p atomic orbitals may be transformed into hybrid atomic orbitals with different shapes which lead to two types of covalent bonds, σ and π, and account for the various shapes of molecules. Next, the chapter elaborates on the meaning of isomers. Isomers are different compounds with the same molecular formulas. The chapter then displays the two principal kinds of isomers: constitutional isomers and stereoisomers.

Chapter

Cover How to Succeed in Organic Chemistry

Bonds Can Rotate  

This chapter highlights molecular models that can be twisted and turned. This provides insight into what might happen in a real molecule. It considers how some compounds prefer to react in specific orientations and how the ease of adopting a particular orientation often determines the reactivity of the compound. It also discusses conformational isomers or conformers which regard a special type of stereoisomer related simply by rotation around single bonds. The chapter reviews the applications of conformational isomerism in substitution reactions and the energy difference between conformers fundamental to E2 elimination reactions. It outlines the fundamental principles of conformational analysis in cyclohexanes to substitution and elimination reactions.

Chapter

Cover Pharmaceutical Chemistry

Stereochemistry and Drug Action  

Rosaleen J. Anderson, Adam Todd, Mark Ashton, and Lauren Molyneux

This chapter mentions the forms of common analgesic ibuprofen, which have mostly identical physical properties but have three-dimensional shapes that are different. The three-dimensional shape of biological molecules and drugs is profoundly important for their action. The chapter introduces the concepts of isomerism, structure, and shape, particularly with reference to the activity of drugs and relates strongly to hybridization and bonding. The chapter defines the term ‘isomerism’, which is used to describe the ways in which molecules can have identical compositions in terms of carbon, hydrogen, and nitrogen. However, differences in their patterns of bonding or conformation may lead to dramatically different three-dimensional shapes. There are many drugs used in medicine which exhibit isomerism and it is essential to have a good understanding of this.

Book

Cover How to Succeed in Organic Chemistry
How to Succeed in Organic Chemistry first lays out the foundations for the topic and looks at the basics. It talks about isomers, chemical names, how to name organic compounds, double bond equivalents, bond polarization, and electronegativity. The second section is about building on the foundations. It looks at breaking bonds, enthalpy, carbocations, carbanions, and reactivity. The third section looks at shape. The section that follows looks at types of selectivity. Section 5 is about rotating bonds and looks at cyclohexanes. The sixth section is about elimination. The seventh section is all about building skills.

Chapter

Cover Alicyclic Chemistry

The conformational analysis of alicyclic rings  

This chapter reviews several aspects of molecular stereochemistry, which is important in the discussion about the behavior of alicyclic compounds. It analyses various types of isomerism in a given molecular formula, such as the assembly of atoms in a variety of different ways that lead to a number of alternative chemical structures and different atom-atom connectivity patterns. It also describes structural arrangements that form additional isomers and have the same connectivity but are different in the spatial arrangement of the atoms within the molecule. The chapter analyzes enantiomers and diastereoisomers as the two classes of stereoisomers. Enantiomers occur in pairs and are defined as structures that are non-superimposable mirror images of each other, while diastereoisomers are derived from a particular structural formula.

Chapter

Cover Workbook in Inorganic Chemistry

Coordination complexes of the d-block metals  

Matthew Almond, Mark Spillman, and Elizabeth Page

Edited by Elizabeth Page

This chapter assesses the coordination complexes of the d-block metals. The d-block elements are distinguished by having electrons in d orbitals. There are five d orbitals and it is important to be able to draw these orbitals and be able to label them according to their shape and orientation. The chapter begins by looking at electronic configurations of the d-block metals and their ions, before explaining the determination of oxidation states of d-block metal complexes and their electronic configurations. It then considers the coordination number and the coordination geometry in coordination complexes. The chapter also studies isomerism in coordination complexes, studying structural isomerism and stereoisomerism. Finally, it explores crystal-field theory, which is an electrostatic bonding model that assumes that metal ions in coordination complexes are surrounded by ligands that act as negative point charges.

Chapter

Cover Organic Stereochemistry

Stereoisomerism in molecules and compounds  

This chapter emphasizes the classification of isomerism and then goes on to an account of stereoisomerism in molecules and compounds. It argues that classification requires nomenclature–adding that stereochemistry has seen many changes in nomenclature and these are still developing. The chapter seeks to give an adequate but not pedantic account of current nomenclature. It begins with the definition of stereochemical nomenclature, then proceeds to review the relationships between the enantiomeric/diastereomeric and enantiomer/diastereomer. Ultimately, the chapter shifts to examine molecules and compounds, especially in terms of molecular structure. It analyzes the detection of chirality in compounds and presents the stereogenic units in molecules.

Chapter

Cover Making the Transition to University Chemistry

Introduction to Organic Chemistry  

This chapter introduces organic chemistry. This type of chemistry involves the study of compounds formed by carbon. The chapter highlights how living organisms are mainly composed of carbon compounds. Structural formula shows exactly which atoms are bonded together. A homologous series is a collection of molecules with the same functional group differing only in the number of carbon atoms present. The chapter discusses the IUPAC nomenclature for the alkane molecules. It also examines the major classes of isomers: structural isomers and stereoisomers. Organic reactions are classified as either radicals, nucleophiles, or electrophiles. The functional group level of a particular carbon atom establishes the number of bonds to the atom that is more electronegative than carbon.

Book

Cover Organic Chemistry

Michael Cook and Philippa Cranwell

Edited by Elizabeth Page

Workbook in Organic Chemistry begins with a look at the foundations of this subject. It then looks in more detail at isomerism, nucleophilic substitution, elimination reactions, and the reactions of unsaturated compounds. The text then moves on to focus on aromatic chemistry before examining carbonyl chemistry.

Book

Cover d-Block Chemistry
d-Block Chemistry begins with a chapter which introduces the topic as a whole. The next chapter covers complexes. The chapter that follows considers shape and isomerism. The fourth chapter looks into metal classification and electron counting. The next chapter covers an ionic model of metal complexes. There follows chapters on covalent models of metal complexes and the consequences of d-orbital splitting. The final chapter looks at formulae and nomenclature.

Chapter

Cover Functional Groups

Alcohols 10 Ethers  

This chapter describes a reaction concerned with sodium periodate and lead tetraacetate, which are useful reagents that have similar oxidizing properties. It demonstrates how salt NaIO4 is dissolved using an aqueous medium and how a covalent compound Pb(OAc)4 is soluble in some organic solvents and is decomposed by water. It highlights that the choice of reagent is determined by the solubility of the substrate. The chapter explains the difference in rates between cis cyclopentane-1,2-diol, which is the easy ring formation, and the trans isomer, which is the difficult ring formation. It covers reagents that cause fission of several other systems that have 1,2-oxygen-containing groups.

Chapter

Cover Aromatic Heterocyclic Chemistry

Answers to problems  

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.

Chapter

Cover Inorganic Chemistry

An introduction to coordination compounds  

This chapter introduces the common structural arrangements for ligands around a single metal atom and the isomeric forms that are possible. It starts with an explanation of coordination chemistry, discussing representative ligands, coordination numbers, and polymetallic complexes, among others. The chapter also tackles isomerism and chirality. It illustrates square-planar, trigonal-bipyramidal, square-pyramidal, and octahedral complexes. Then it explains the thermodynamics of complex formation, describing the formation constants, as well as the chelate and macrocyclic effects, which are of great practical importance in analytical chemistry. It describes trends in successive formation constants. The chapter closes with a discussion on steric effects and electron delocalization.

Chapter

Cover Organic Chemistry

Conformation and Strain in Molecules  

This chapter explores how internal rotations about single bonds cause some molecules to be flexible rather than to have single fixed shapes. It recalls that four single bonds radiate in tetrahedral directions from a saturated (sp3-hybridized) carbon atom, which leads to organic molecules having three-dimensional structures. The chapter then argues that molecules are not rigid because molecular vibrations cause bond lengths and bond angles to be oscillating constantly about their average values. The chapter then shifts to examine what causes strain in a molecule, and how molecular strain affects the three-dimensional shape of a molecule. It employs several methods to represent the three-dimensional structures of organic molecules in two dimensions, which help us to generate mental images of three-dimensional shapes of organic molecules, and hence better understand stereochemical aspects of organic chemistry. The chapter concludes by discussing conformations of alkanes and cycloalkanes, as well as cis-trans Isomerism in cycloalkanes.

Book

Cover Chemistry for the Biosciences
Chemistry for the Biosciences explores all of the essential chemical concepts that students of biology need to know and understand. It starts by looking at atoms as the foundations for life, and how chemical bonding brings together atoms to form molecules and compounds. It also considers the interactions that operate between molecules, and what the chemical and biological implications of these interactions are. After considering a range of quantitative concepts relevant to the study of biology – moles, concentrations, and dilutions – it discusses the molecular basis of organic chemistry by considering hydrocarbons and functional groups. The text moves on to consider isomerism, molecular shape and structure, and the structure and function of key biological macromolecules. After explaining why metals have an important role in biological systems, it goes on to explore what happens during chemical reactions, and introduces oxidation, and reduction. It then explores concepts from the field of physical chemistry that are vital our understanding of life: energy, equilibria, and kinetics. After exploring acids, bases and buffers and their importance to biological systems, it concludes with a review of how we can use chemical analysis to better understand biological molecules.

Chapter

Cover Essentials of Inorganic Chemistry 1

Inertness and lability to isomerism  

This chapter explores inertness and lability. The ability to isolate molecules depends not only on their thermodynamic stability, but also on the activation energies for decomposition pathways. Inert (kinetically stable) compounds have high activation energies associated with their possible decomposition pathways, while labile compounds have low energy pathways and react rapidly to form the thermodynamically favoured products. These qualitative ideas may be placed on a more quantitative basis using half-lives derived from kinetic data. The chapter then looks at inert gases and the inert pair effect, inorganic reactions, intermolecular forces, ionic bonds, ionization energy, isoelectronic molecules, and isomerism. Structural isomerism arises from a different bonding arrangement of atoms.