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Organic ChemistrySecond Edition

The INSTANT NOTES seriesSeries Editor: B.D. Hames School of Biochemistry and Molecular Biology,University of Leeds, Leeds, UKAnimal Biology 2nd editionBiochemistry 2nd editionBioinformaticsChemistry for Biologists 2nd editionDevelopmental BiologyEcology 2nd editionImmunology 2nd editionGenetics 2nd editionMicrobiology 2nd editionMolecular Biology 2nd editionNeurosciencePlant BiologyChemistry seriesConsulting Editor: Howard StanburyAnalytical ChemistryInorganic Chemistry 2nd editionMedicinal ChemistryOrganic Chemistry 2nd editionPhysical ChemistryPsychology seriesSub-series Editor: Hugh Wagner Dept of Psychology, University of CentralLancashire, Preston, UKPsychologyForthcoming titlesCognitive PsychologyPhysiological Psychology

Organic ChemistrySecond EditionG. L. PatrickDepartment of Chemistry and Chemical Engineering,Paisley University, Paisley, Scotland

This edition published in the Taylor & Francis e-Library, 2005."To purchase your own copy of this or any of Taylor & Francis or Routledge'scollection of thousands of eBooks please go to www.eBookstore. tandf.co.uk.” Garland Science/BIOS Scientific Publishers, 2004First published 2000Second edition published 2004All rights reserved. No part of this book may be reproduced or transmitted, in any form or by any means,without permission.A CIP catalogue record for this book is available from the British Library.ISBN 0-203-42761-0 Master e-book ISBNISBN 0-203-44168-0 (Adobe eReader Format)ISBN 1 85996 264 5 (Print Edition)Garland Science/BIOS Scientific Publishers4 Park Square, Milton Park, Abingdon, Oxon OX14 4RN, UK and29 West 35th Street, New York, NY 10001–2299, USAWorld Wide Web home page: www.bios.co.ukGarland Science/BIOS Scientific Publishers is a member of the Taylor & Francis GroupDistributed in the USA byFulfilment CenterTaylor & Francis10650 Toebben DriveIndependence, KY 41051, USAToll Free Tel.: 1 800 634 7064; E-mail: taylorandfrancis@thomsonlearning.comDistributed in Canada byTaylor & Francis74 Rolark DriveScarborough, Ontario M1R 4G2, CanadaToll Free Tel.: 1 877 226 2237; E-mail: tal fran@istar.caDistributed in the rest of the world byThomson Publishing ServicesCheriton HouseNorth WayAndover, Hampshire SP10 5BE, UKTel.: 44 (0)1264 332424; E-mail: brary of Congress Cataloging-in-Publication DataPatrick, Graham L.Organic chemistry / G.L. Patrick.—2nd ed.p. cm. — (Instant notes series)Includes bibliographical references and index.ISBN 1-85996-264-5 (alk. paper)1. Chemistry, Organic—Outlines, syllabi, etc. I. Title: Instant notes organic chemistry.II. Title. III. Series.QD256.5.P37 2003547—dc22Production Editor: Andrew Watts

C ONTENTSPrefaceixSection A – Structure and bondingA1 Atomic structure of carbonA2 Covalent bonding and hybridizationA3 sp3 HybridizationA4 sp2 HybridizationA5 sp HybridizationA6 Bonds and hybridized centers113581417Section B – Alkanes and cycloalkanesB1DefinitionB2Drawing structuresB3Nomenclature19192022Section C – Functional groupsC1 Recognition of functional groupsC2 Aliphatic and aromatic functional groupsC3 Intermolecular bondingC4 Properties and reactionsC5 Nomenclature of compounds with functional groupsC6 Primary, secondary, tertiary and quaternarynomenclature27272930333543Section D – StereochemistryD1 Constitutional isomersD2 Configurational isomers – alkenes and cycloalkanesD3 Configurational isomers – optical isomersD4 Conformational isomers4545464956Section E – Nucleophiles and electrophilesE1DefinitionE2Charged speciesE3Neutral inorganic speciesE4Organic structures6363646669Section F – Reactions and mechanismsF1ReactionsF2Mechanisms737375Section G – Acid–base reactionsG1 Brønsted–Lowry acids and basesG2 Acid strengthG3 Base strengthG4 Lewis acids and basesG5 Enolates797982889495

viContentsSection H – Alkenes and alkynesH1 Preparation of alkenes and alkynesH2 Properties of alkenes and alkynesH3 Electrophilic addition to symmetrical alkenesH4 Electrophilic addition to unsymmetrical alkenesH5 Carbocation stabilizationH6 Reduction and oxidation of alkenesH7 Hydroboration of alkenesH8 Electrophilic additions to alkynesH9 Reduction of alkynesH10 Alkylation of terminal alkynesH11 Conjugated dienes9999101105112115117121124127129131Section I – Aromatic chemistryI1AromaticityI2Preparation and propertiesI3Electrophilic substitutions of benzeneI4Synthesis of mono-substituted benzenesI5Electrophilic substitutions of mono-substitutedaromatic ringsI6Synthesis of di- and tri-substituted benzenesI7Oxidation and reduction135135137139147Section J – Aldehydes and ketonesJ1PreparationJ2PropertiesJ3Nucleophilic additionJ4Nucleophilic addition – charged nucleophilesJ5Electronic and steric effectsJ6Nucleophilic addition – nitrogen nucleophilesJ7Nucleophilic addition – oxygen and sulfurnucleophilesJ8Reactions of enolate ionsJ9α-HalogenationJ10 Reduction and oxidationJ11 α,β-Unsaturated aldehydes and ketones167167169173175181184Section K – Carboxylic acids and carboxylic acid derivativesK1 Structure and propertiesK2 Nucleophilic substitutionK3 ReactivityK4 Preparations of carboxylic acidsK5 Preparations of carboxylic acid derivativesK6 ReactionsK7 Enolate reactions205205209213217219224234Section L – Alkyl halidesL1Preparation and physical properties of alkyl halidesL2Nucleophilic substitutionL3Factors affecting SN2 versus SN1 reactionsL4EliminationL5Elimination versus substitutionL6Reactions of alkyl halidesL7Organometallic 8200202

ContentsviiSection M – Alcohols, phenols, and thiolsM1 Preparation of alcoholsM2 Preparation of phenolsM3 Properties of alcohols and phenolsM4 Reactions of alcoholsM5 Reactions of phenolsM6 Chemistry of thiols263263264266270277281Section N – Ethers, epoxides, and thioethersN1 Preparation of ethers, epoxides, and thioethersN2 Properties of ethers, epoxides, and thioethersN3 Reactions of ethers, epoxides, and thioethers283283286289Section O – Amines and nitrilesO1 Preparation of aminesO2 Properties of aminesO3 Reactions of aminesO4 Chemistry of nitriles295295299305311Section P – Organic spectroscopy and analysisP1SpectroscopyP2Visible and ultra violet spectroscopyP3Infra-red spectroscopyP4Proton nuclear magnetic resonance spectroscopy13P5C nuclear magnetic resonance spectroscopyP6Mass spectroscopy315315317322324339342Further readingIndex347349

P REFACEThis textbook aims to provide a comprehensive set of basic notes in organicchemistry, which will be suitable for undergraduate students taking chemistry,chemistry-related courses, or courses which involve organic chemistry as anancillary subject. The book concentrates on core topics which are most likelyto be common to those organic chemistry courses which follow on from a foundation or introductory general chemistry course.Organic chemistry is a subject which can lead some students to the heightsof ecstasy, yet drive others up the wall. Some students ‘switch on’ to it immediately, while others can make neither head nor tail of it, no matter how hardthey try. Certainly, one of the major problems in studying the subject is thevast amount of material which often has to be covered. Many students blancheat the prospect of having to learn a seemingly endless number of reactions,and when it comes to drawing mechanisms and curly arrows, they see onlya confusing maze of squiggly lines going everywhere yet nowhere. Theconcepts of organic reaction mechanisms are often the most difficult to master.These difficulties are often compounded by the fact that current textbooks inorganic chemistry are typically over 1200 pages long and can be quite expensive to buy.This book attempts to condense the essentials of organic chemistry into amanageable text of 310 pages which is student friendly and which does notcost an arm and a leg. It does this by concentrating purely on the basics of thesubject without going into exhaustive detail or repetitive examples.Furthermore, key notes at the start of each topic summarize the essential factscovered and help focus the mind on the essentials.Organic chemistry is a peculiar subject in that it becomes easier as you goalong! This might seem an outrageous statement to make, especially to a firstyear student who is struggling to come to terms with the rules of nomenclature,trying to memorize a couple of dozen reactions and making sense of mechanisms at the same time. However, these topics are the basics of the subject andonce they have been grasped, the overall picture becomes clear.Understanding the mechanism of how a reaction takes place is particularlycrucial in this. It brings a logic to the reactions of the different functional groups.This in turn transforms a list of apparently unrelated facts into a sensible themewhich makes remembering the reactions a ‘piece of cake’ (well, nearly).Once this happy state of affairs has been reached, the relevance of organicchemistry to other subjects such as genetics and biochemistry suddenly leapsoff the page. Understanding organic chemistry leads to a better understandingof life chemistry and how the body works at the molecular level. It also helpsin the understanding of the molecular mechanisms involved in disease andbodily malfunction, leading in turn to an understanding of how drugs can bedesigned to cure these disease states – the science of medicinal chemistry.And that’s not all. An understanding of organic chemistry will help the industrial chemist or chemical engineer faced with unexpected side-reactions in achemical process, and the agro-scientist trying to understand the molecularprocesses taking place within plants and crops; and it will assist in the designand synthesis of new herbicides and fungicides which will be eco-friendly. It

xPrefacewill aid the forensic scientist wishing to analyze a nondescript white powder– is it heroin or flour?The list of scientific subject areas involving organic chemistry is endless –designing spacesuits, developing new photographic dyes, inventing new molecular technology in microelectronics – one could go on and on. Organicchemistry is an exciting subject since it leads to an essential understanding ofmolecules and their properties.The order in which the early topics of this book are presented is important.The first two sections cover structure and bonding, which are crucial to latersections. Just why does carbon form four bonds? What is hybridization?The third section on functional groups is equally crucial if students are to becapable of categorizing the apparent maze of reactions which organiccompounds can undergo. It is followed by section D on stereochemistry, thensections E and F, in which the basic theory of reactions and mechanisms iscovered. What are nucleophiles and electrophiles? What does a mechanismrepresent? What does a curly arrow mean?The remaining sections can be used in any order. These look at the reactionsand mechanisms of the common functional groups which are important inchemistry and biochemistry.It is hoped that students will find this textbook useful in their studies andthat once they have grasped what organic chemistry is all about they will readmore widely and enter a truly exciting world of molecular science.

Section A – Structure and bondingA1 ATOMIC STRUCTURE OF CARBONKey NotesAtomic orbitalsThe atomic orbitals available for the six electrons of carbon are the s orbitalin the first shell, the s orbital in the second shell and the three p orbitals inthe second shell. The 1s and 2s orbitals are spherical in shape. The 2porbitals are dumbbell in shape and can be assigned 2px, 2py or 2pz depending on the axis along which they are aligned.Energy levelsThe 1s orbital has a lower energy than the 2s orbital which has a lowerenergy than the 2p orbitals. The 2p orbitals have equal energy (i.e. theyare degenerate).ElectronicconfigurationCarbon is in the second row of the periodic table and has six electrons whichwill fill up lower energy atomic orbitals before entering higher energyorbitals (aufbau principle). Each orbital is allowed a maximum of two electrons of opposite spin (Pauli exclusion principle). When orbitals of equalenergy are available, electrons will occupy separate orbitals before pairing2up (Hund’s rule). Thus, the electronic configuration of a carbon atom is 1s2112s 2px 2py .Related topicAtomic orbitalsCovalent bonding andhybridization (A2)Carbon has six electrons and is in row 2 of the periodic table. This means that thereare two shells of atomic orbitals available for these electrons. The first shell closestto the nucleus has a single s orbital – the 1s orbital. The second shell has a single sorbital (the 2s orbital) and three p orbitals (3 2p). Therefore, there are a total offive atomic orbitals into which these six electrons can fit. The s orbitals are sphericalin shape with the 2s orbital being much larger then the 1s orbital. The p orbitalsare dumbbell-shaped and are aligned along the x, y and z axes. Therefore, they areassigned the 2px, 2py and 2pz atomic orbitals (Fig. 1).yyxz1sFig. 1.Atomic orbitals.xz2syyxz2pxyxz2pyxz2pz

2Energy levelsSection A – Structure and bondingThe atomic orbitals described above are not of equal energy (Fig. 2). The 1s orbitalhas the lowest energy. The 2s orbital is next in energy and the 2p orbitals have thehighest energies. The three 2p orbitals have the same energy, meaning that theyare degenerate.Energy2px2py2pz2s1sFig. 2.ElectronicconfigurationEnergy levels of atomic orbitals.Carbon is in the second row of the periodic table and has six electrons which willfill up the lower energy atomic orbitals first. This is known as the aufbau principle. The 1s orbital is filled up before the 2s orbital, which is filled up before the 2porbitals. The Pauli exclusion principle states that each orbital is allowed a maximum of two electrons and that these electrons must have opposite spins. Therefore, the first four electrons fill up the 1s and 2s orbitals. The electrons in eachorbital have opposite spins and this is represented in Fig. 3 by drawing the arrowspointing up or down. There are two electrons left to fit into the remaining 2porbitals. These go into separate orbitals such that there are two half-filled orbitalsand one empty orbital. Whenever there are orbitals of equal energy, electrons willonly start to pair up once all the degenerate orbitals are half filled. This is knownas Hund’s rule.Energy2px2py2pz2s1sFig. 3.Electronic configuration for carbon.2211The electronic configuration for carbon is 1s 2s 2px 2py . The numbers insuperscript refer to the numbers of electrons in each orbital. The letters refer to thetypes of atomic orbital involved and the numbers in front refer to which shell theorbital belongs.

Section A – Structure and bondingA2 COVALENT BONDING ANDHYBRIDIZATIONKey NotesCovalentbondingWhen two hydrogen atoms approach each other, their 1s atomic orbitalsinteract to form a bonding and an antibonding molecular orbital (MO). Astable covalent bond is formed when the bonding MO is filled with a pairof electrons and the antibonding MO is empty.Sigma bondsSigma (σ) bonds are strong bonds with a circular cross-section formed bythe head-on overlap of two atomic orbitals.HybridizationThe electronic configuration of atomic carbon implies that carbon shouldform two bonds. However, it is known that carbon forms four bonds. Whencarbon is part of an organic structure, it can ‘mix’ the 2s and 2p orbitals ofthe valence shell in a process known as hybridization. There are three32possible types of hybridization – sp , sp and sp hybridization.Covalent bonding2Atomic structure of carbon (A1)3sp Hybridization (A3)Related topicssp Hybridization (A4)sp Hybridization (A5)A covalent bond binds two atoms together in a molecular structure and is formedwhen atomic orbitals overlap to produce a molecular orbital – so called becausethe orbital belongs to the molecule as a whole rather than to one specific atom. Asimple example is the formation of a hydrogen molecule (H2) from two hydrogenatoms. Each hydrogen atom has a half-filled 1s atomic orbital and when the atomsapproach each other, the atomic orbitals interact to produce two MOs (the numberof resulting MOs must equal the number of original atomic orbitals, Fig. 1).HHAntibonding molecular orbital(empty)EnergyH 1s atomicorbitalFig. 1.H1s atomicorbitalHH HHBonding molecular orbital(full)Molecular orbitals for hydrogen (H2 ).The MOs are of different energies. One is more stable than the original atomicorbitals and is called the bonding MO. The other is less stable and is called theantibonding MO. The bonding MO is shaped like a rugby ball and results from

4Section A – Structure and bondingthe combination of the 1s atomic orbitals. Since this is the more stable MO, thevalence electrons (one from each hydrogen) enter this orbital and pair up. Theantibonding MO is of higher energy and consists of two deformed spheres. Thisremains empty. Since the electrons end up in a bonding MO which is more stablethan the original atomic orbitals, energy is released and bond formation isfavored. In the subsequent discussions, we shall concentrate solely on the bonding MOs to describe bonding and molecular shape, but it is important to realizethat antibonding molecular orbitals also exist.Sigma bondsThe bonding molecular orbital of hydrogen is an example of a sigma (σ) bond: σbonds have a circular cross-section and are formed by the head-on overlap of twoatomic orbitals. This is a strong interaction and so sigma bonds are strong bonds.In future discussions, we shall see other examples of σ bonds formed by theinteraction of atomic orbitals other than the 1s orbital.HybridizationAtoms can form bonds with each other by sharing unpaired electrons such thateach bond contains two electrons. In Topic A1, we identified that a carbon atomhas two unpaired electrons and so we would expect carbon to form two bonds.However, carbon forms four bonds! How does a carbon atom form four bondswith only two unpaired electrons?So far, we have described the electronic configuration of an isolated carbonatom. However, when a carbon atom forms bonds and is part of a molecular structure, it can ‘mix’ the s and p orbitals of its second shell (the valence shell). This isknown as hybridization and it allows carbon to form the four bonds which weobserve in reality.There are three ways in which this mixing process can take place. 3the 2s orbital is mixed with all three 2p orbitals. This is known as sp hybridization;2the 2s orbital is mixed with two of the 2p orbitals. This is known as sphybridization;the 2s orbital is mixed with one of the 2p orbitals. This is known as sphybridization.

Section A – Structure and bonding3A3SPHYBRIDIZATIONKey Notes3DefinitionIn sp hybridization, the s and the p orbitals of the second shell are ‘mixed’3to form four hybridized sp orbitals of equal energy.ElectronicconfigurationEach hybridized orbital contains a single unpaired electron and so fourbonds are possible.GeometryEach sp orbital is shaped like a deformed dumbbell with one lobe muchlarger than the other. The hybridized orbitals arrange themselves as farapart from each other as possible such that the major lobes point to the cor3ners of a tetrahedron. sp Hybridization explains the tetrahedral carbon insaturated hydrocarbon structures.Sigma bondsSigma (σ) bonds are strong bonds formed between two sp hybridized car3bons or between an sp hybridized carbon and a hydrogen atom. A σ bond3formed between two sp hybridized carbon atoms involves the overlap of3half filled sp hybridized orbitals from each carbon atom. A σ bond formed3between an sp hybridized carbon and a hydrogen atom involves a half3filled sp orbital from carbon and a half-filled 1s orbital from hydrogen.Nitrogen, oxygenand chlorineNitrogen, oxygen, and chlorine atoms can also be sp hybridized in organic3molecules. This means that nitrogen has three half-filled sp orbitals and canform three bonds which are pyramidal in

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