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Chapter

Cover Chemical Structure and Reactivity

Organic chemistry 1: functional groups  

This chapter studies functional groups, which can be classified according to the number of bonds a given carbon has to elements of greater electronegativity. The functional group level is the number of these bonds. Reactions can be classified according to the change in functional group level. The outcome of a reaction can be rationalized by considering where the highest energy electrons are to be found, and what low energy vacant molecular orbitals are available. Within a particular functional group level, there is often a general order of reactivity for different functional groups. Ultimately, transformations from one functional group to another may take place via different mechanisms depending on the particular reagents and reaction conditions.

Chapter

Cover Protecting Group Chemistry

Introduction  

This introductory chapter provides an overview of the strategy of protecting group chemistry. In general, a protecting group is introduced onto a functional group to block its reactivity under the experimental conditions needed to make modifications elsewhere. The conditions under which a particular protecting group is either removed or left unaffected must be known; therefore, this book is organised around the mechanistic principles that influence protecting group reactivity. The choice of protecting group is heavily influenced by the type of reactivity that must be blocked, which requires a knowledge of the characteristic reactivity of each functional group. The chapter then looks at protecting group devices and temporary protecting group. Identification of a device within a given protecting group allows one to predict whether the protecting group will be labile (or stable) under specified reaction conditions.

Chapter

Cover Organic Synthesis

Selectivity I: Chemoselectivity and protecting groups  

This chapter evaluates chemoselectivity and protecting groups. In a chemoselective reaction, one functional group within the molecule reacts, leaving further potentially reactive functionality unaffected. Many of the principal transformations involved in functional group interconversions (FGIs) were introduced in the third chapter of this text. The reactions may involve addition, substitution, elimination, reduction, and oxidation. There are now a plethora of mild and selective reagents available to effect specific transformations. As a general rule, when there are two functional groups of unequal reactivity within a molecule, the more reactive can be made to react alone. However, it may not be possible to react the less reactive functional group selectively.

Chapter

Cover Oxidation and Reduction in Organic Synthesis

Reduction of heteroatoms attached to carbon  

This chapter assesses the reduction of heteroatoms attached to carbon. It begins by looking at the reduction of nitrogen-containing functional groups. Aromatic nitro compounds (such as nitrobenzene) play a vital role in the synthesis of substituted arenes partly because they direct electrophilic aromatic substitution so powerfully. In general terms, both aromatic and aliphatic nitro groups are easy to reduce, often without affecting other functionality. The chapter then considers the reduction of phosphorus–oxygen bonds. Reduction of a phosphorus–oxygen double bond is not a particularly common reaction, and there is not a great deal of work in this area. As such, the chapter turns to reduction of sulfur- and selenium-containing functional groups.

Chapter

Cover An Introduction to Drug Synthesis

Retrosynthesis  

This chapter discusses retrosynthesis. It also refers to retrosynthesis as the strategy wherein synthetic routes arecan be designed by considering the structure of the product and identifying what this target product could be synthesized from. The chapter looks intoconsiders the process of disconnection and functional group interconversions to achieve retrosynthesis. Additionally, umpolung, is the reversal of polarity, is considered. The chapter explores the examples of synthons, corresponding reagents, protecting groups, and latent groups. It highlights the importance of identifying molecular signatures to indicate which disconnections are the most sensible ones to make. Moreover, organic synthesis involves the creation of a target molecule from simpler structures serving as the building blocks for the synthesis.

Chapter

Cover Protecting Group Chemistry

Nucleophile/base-labile protecting groups  

This chapter examines nucleophile/base-labile protecting groups. The majority of the functional groups described in this book are based on heteroatoms that, by virtue of higher electronegativity or more diffuse orbitals, can support a negative charge more effectively than carbon. Consequently, some protecting groups can be cleaved by expulsion of the functional group as an anion either by elimination or by nucleophilic substitution. Whether or not activation is necessary depends upon the leaving group ability of the protected functional group, the nucleophilicity of the attacking species, the solvent, and the steric availability at the electrophilic site. The chapter then looks at protecting group cleavage by SN2 chemistry and by nucleophilic addition, as well as deprotection by β-elimination. It also considers allylic protecting groups.

Chapter

Cover Biological Science

Building Blocks  

Molecules and Macromolecules

This chapter discusses the building blocks of molecules and macromolecules. It cites the importance of understanding chemical compounds and chemical reactions in biology. Key properties of molecules, including their size, shape and reactions, are determined by the atoms that make them up and the ways these are bonded together into functional groups. The chapter examines the structure and function of biological macromolecules, referencing the four main classes: carbohydrates, lipids, nucleic acids, and proteins. It also discusses the function and structure of water, which holds a key role in supporting life.

Chapter

Cover Biological Science

Building Blocks  

Molecules and Macromolecules

This chapter discusses the building blocks of molecules and macromolecules. It cites the importance of understanding chemical compounds and chemical reactions in biology. Key properties of molecules, including their size, shape and reactions, are determined by the atoms that make them up and the ways these are bonded together into functional groups. The chapter examines the structure and function of biological macromolecules, referencing the four main classes: carbohydrates, lipids, nucleic acids, and proteins. It also discusses the function and structure of water, which holds a key role in supporting life.

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

Alcohols, Phenols, Ethers, Organic Halogen Compounds, and Amines  

Chris Rostron

This chapter considers a number of functional groups, such as oxygen in the air and oxygen as a component of water. It is also found in many molecules. Functional groups are made, changed, and destroyed in chemical reactions. The chapter highlights oxygen's value as a component of functional groups that stems from its high electronegativity, which means that it strongly attracts electrons. The chapter describes the hydroxyl group as the most biologically significant functional group as it is one of the most widely occurring in nature, being present in carbohydrates, proteins, and nucleic acids. The properties of carbohydrates, for example, are essentially a combination of hydroxyl chemistry and the chemistry of aldehydes and ketones.

Chapter

Cover Bifunctional Compounds

Preparation of bifunctional compounds  

This chapter describes methods used to prepare bifunctional compounds, which are usually specific to the particular combination of functional groups. It explains the retro-synthetic analysis, which is an approach to the synthesis of 1,2-bifunctional compounds that considers as a possible precursor the alkene that would result from eliminating the two functional groups. The chapter also considers an alternative approach that involves imagining cleaving the bond which links the two functionalized carbon atoms. The chapter emphasizes that working backwards is a logical way to tackle the synthesis of a given target molecule as it leads to a selection of appropriate methods for bringing about forward transformation. It details the preparation of 1,2-diols by preparing hydroxylation of alkenes, reductive dimerization of ketones, or nucleophilic addition to α-hydroxycarbonyl compounds.

Chapter

Cover Organic Chemistry

Chemoselectivity and protecting groups  

This chapter describes chemoselectivity and protecting groups. Most organic molecules contain more than one functional group, and most functional groups can react in more than one way, so organic chemists often have to predict which functional group will react, where it will react, and how it will react. These questions are what can be called selectivity. Selectivity comes in three sorts: chemoselectivity, regioselectivity, and stereoselectivity. The chapter focuses on chemoselectivity (which group reacts). It begins by looking at reductions of carbonyl compounds, introducing a few more specialized reducing agents. The chapter then considers the other type of reduction in the salmefamol synthesis: catalytic hydrogenation.

Chapter

Cover Organic Chemistry

Alkylation of enolates  

This chapter studies the alkylation of enolates. The alkylations in the chapter each consists of two steps. The first is the formation of a stabilized anion—usually (but not always) an enolate—by deprotonation with base. The second is a substitution reaction: attack of the nucleophilic anion on an electrophilic alkyl halide. All the factors controlling SN1 and SN2 reactions are applicable here. Problems that arise from the electrophilicity of the carbonyl group can be avoided by replacing C=O by functional groups that are much less electrophilic but are still able to stabilize an adjacent anion. The chapter then looks at the alkylation of nitriles and nitroalkanes.

Chapter

Cover An Introduction to Drug Synthesis

Drug Synthesis  

This chapter looks intofocuses on the process of drug synthesis. It notes the role of organic synthesis in the drug design and development process alongside the structure structural features affecting the ease of synthesis. Additionally, the chapter explores the significance of coupling reactions and functional groups in the process of synthesis. It also explains how protection groups are needed as some functional groups tend to be more reactive than others before listing the ideal features of a protecting group. Moreover, the chapter discusses case studies focusing on the synthesis of dofetilide and salbutamol. It uses diagrams to showcase the process of synthesis for multiple examples as well.

Chapter

Cover Protecting Group Chemistry

Redox deprotection  

This chapter focuses on redox deprotection. Oxidation-labile protecting groups offer a means of releasing functional groups under essentially neutral conditions which is useful when hydrolytic deprotection is not tolerated and silyl protecting groups are unsuitable. In particular, a CH2 group that links a functional group to an electron-rich aromatic ring is prone to oxidation giving a hemiacetal, which is unstable with respect to aldehyde formation, and release of the functional group. Some oxidising agents activate the CH2 towards nucleophilic attack by water in a process equivalent overall to abstraction of hydride ion. The chapter then looks at internal redox processes, including free-radical deprotection, protecting group interchange, and photochemical deprotection. It also considers reductive methods, including hydrogenolysis.

Chapter

Cover Organic Chemistry

Nucleophilic Addition to the Carbonyl Group in Aldehydes and Ketones  

This chapter discusses the polarity of the carbonyl bond and the catalysis of nucleophilic addition to carbonyl groups by acids and bases. It considers in detail the reactions of a functional group, and looks at nucleophilic additions to the carbonyl group of aldehydes and ketones. The chapter argues that these reactions provide clear examples of several fundamental principles of organic reaction mechanisms, and they also include some of the most useful reactions for organic synthesis. The carbonyl (>C=O) group is a functional group found in aldehydes and ketones as well as carboxylic acids and their derivatives, and is one of the most important in organic and biological chemistry. The chapter ends by explicating the acetal and dithioacetal formation as well as the Wittig reaction. It also investigates the formation of imines and enamines.

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 Protecting Group Chemistry

Acid-labile protecting groups  

This chapter discusses acid-labile protecting groups. In the protected forms of potentially nucleophilic functional groups—alcohols, amines, and thiols—the original heteroatom is usually present and capable of reacting with electrophiles unless steric encumbrance or conjugation is completely effective. Whether or not this leads to deprotection depends on the groups attached to the heteroatom. Reversible protonation or activation with a Lewis acid polarises the electrons in the attached bonds leading to electron deficiency at adjacent centres. If one of the attached groups is capable of supporting a full positive charge then rapid cleavage is likely to follow. This behaviour forms the basis of a large range of acid-labile protecting groups that cleave by forming a stabilised cationic intermediate on addition of either a protic or Lewis acid reagent. The chapter then considers SN1-like deprotection, nucleophile-assisted deprotection, and deprotection following activation by alkylation.

Chapter

Cover Organic Chemistry

Reactions of Carbonyl Compounds with Hydride Donors and Organometallic Reagents  

Tadashi Okusecyama and Howard Maskill

This chapter examines the nucleophilicity of metal–hydrogen and metal–carbon reagents. It states that carbonyl compounds are electrophilic and react with nucleophiles. The nucleophiles involved in the reactions discussed in the previous chapter all had lone pairs and, in each case, the lone pair was the nucleophilic centre. Metal hydrides and organometallic compounds are a different type of nucleophile in which the nucleophilic site is the σ bonding pair of electrons of the M–H or M–C bond (M = metal). The chapter highlights that they are important reagents for reducing carbonyl compounds to alcohols, and synthesizing alcohols with new C–C bonds from carbonyl compounds. The chapter focuses on these reactions of the carbonyl group. It then considers the aspects of designing an organic synthesis, and functional group protection.

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.