Preview Organic Chemistry by Marye Anne Fox James K. Whitesell (1994)

Preview Organic Chemistry by Marye Anne Fox James K. Whitesell (1994) Preview Organic Chemistry by Marye Anne Fox James K. Whitesell (1994) Preview Organic Chemistry by Marye Anne Fox James K. Whitesell (1994) Preview Organic Chemistry by Marye Anne Fox James K. Whitesell (1994) Preview Organic Chemistry by Marye Anne Fox James K. Whitesell (1994)

I

Periodic Table of the Elements

Key

1 0079

2.2

12.011 2.5 [He]2s22p2

electronic configuration

[Ar]4s2

44.9559 1.2 [Ar]3d4s2

47.88 1.3 [Ar]3d24s2

50.9415 1.5 [Ar)3d34s2

51.996 1.6 (Ar]3d54s

54.9380 1.6 [Ar]3d54s2

55.847 1.6

[Ar^s2

58.9332 1.7 [Ar]3d74s2

JX 19 Ca 20 SC 21 Ti 22 V 23 Cr 24 Mn 25 Fe 26 CO 27 Potassium Calcium Scandium Titanium Vanadium Chromium Manganese Iron Cobalt 85.4678

0.9

[Krj5s

87.62 1.0

92.9064 1.2

[Kr]4rf 4

5s

95.94 1.3 [Kr]4d55s

98.906 1.4

[Kr]4c/65s

101.07 1.4 [Kr]4d75s

102.9055 1.5 [Kr]4de5s

[Xe]4f~

,4

5d36s2

183.85 1.4

[Xe]4/ K 5d46s2

186.207 1.5

[Xe]4/'45d56s2

190.2 1.5 [Xe]4f,45d66s2

192.22 1.6

227.0278 1.0 {Rr\$d7s*

(261) [Rn]5f"6d27s2

157.25

1.1 [Xe]4r75d6s2

237.0482 1.2 [Rn]5f6o7s2

(244) 1.2 [RnjSr^s2

(243) 1.2 [RnJSrVs2

(247)

=1.2 [Rn]5r76d7s 2

7 Thorium Protactinium Uranium Neptunium Plutonium Americium Curium

He 2 Helium 10.81

2.0 [He]2s22p

12.011 2.5 [He]2s22p2

14.0067 3.1 [He]2s22p3

15.9994 3.5 [He]2s22p4

18.9984 4.1 [He]2s22p5

20.179 [He]2s22p4

Boron Carbon Nitrogen Oxygen Fluoride Neon

26.9815 1.5 [Ne]3s23p

28.0855 1.7 [Ne]3s23p2

30.97376 2.1 [Ne]3s23p3

32.06 2.4 [Ne]3s23p4

35.453 2.8 [Ne]3s23p5

39.948 [Ne]3s23p6

Argon 1

69.72 1.8 [Ar)3d,04s24p

72.59 2.0 [Ar]3d'°4s24p2

74.9216 2.2 [Ar]3d,04s24p3

78.96 2.5 [Ar]3d'°4s24p4

79.904 2.7 [Ar]3d'°4s24p5

83.80 [Ar]3d,04s24p6

114.82 1.5 [Kr]4d'°5s25p

,18.69 1.7 [Kr]4d'°5s25p2

121.75 1.8 [Kr)4d,05s25p3

127.60 2.0 [Kr]4d105s25p4

126.9045 2.2 [Kr]4d,05s25p5

131.30 [Kr]4d,05s25p6

[Xe]4f ,4

5d'°6s2

204.37 1.4

[Xel4^' 4

5cf' 6s26p

207.2 1.6 [Xe]4r5d'°6s26p2

208.9804 1.7 [Xe]4f45d,06s26p

3

(209) 1.8

[Xe]4/'45d,06sV

(222)

[Xe]4f ,4

5d,06s26p6

Pt 78 AU 79 Hg 80 Tl 8, Pb 82 Bi 83 PO 84 At 85 Rn se Platinum Gold Mercury Thallium Lead Bismuth Polonium Astatine Radon

(257)

=1.2 [Rn]5f,27s2

Berkelium Californium Einsteinium Fermium Mendelevium Nobelium Lawrencium

CHEMISTRY

of a

lection,froma bookpublished in1497in Basel,

Switzer-land, depictinganalchemist (standing at the right)andhistwoassistants,one workingat the"fumehood"and

which the longsnoutserves as the condenser. (Another

retort is in use in thefumehood,anda thirdoneison

the floor.)

and Customer

Jonesand BartlettPublishers

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Copyright©1994byJonesandBartlettPublishers, Inc.

be reproducedorutilized inanyform,electronicor mechanical, including

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Library ofCongressCataloging-in-PublicationData

Fox,MaryeAnne,

1947-Organic chemistry /Marye AnneFox,JamesK Whitesell

Acquisitions: ArthurC.Bartlett,David E.Phanco

ProductionEditor: Judy Songdahl

ManufacturingBuyer: DanaL.Cerrito

Design: NancyBlodget

Illustrations: SarahMittelstadtBean

Typesetting: TheClarindaCompany

PrintingandBinding: RandMcNally

Cover: Opiatedrugs suchasmorphineare effective in relievingpain becausethey

on thecoveris of crystals ofanenkephalin,viewed betweencrossedpolarizersso

astobringout the vividrainbowdisplayof colors.(Photograph©Dr. DennisKunkel/PhototakeNYC)

Printed in theUnitedStates ofAmerica

Structure and Bonding in Alkanes 1

Alkenes, Arenes, and Alkynes 21 Functional Groups Containing Heteroatoms

Chromatography and Spectroscopy 109

Stereochemistry 155

Understanding Organic Reactions 193

Mechanisms of Organic Reactions 227 Nucleophilic Substitutions at sp -Hybridized Carbon 267

Addition and Substitution by Heteroatomic

Nucleophiles at sp -Hybridized Carbon 401

Addition and Substitution by Carbon Nucleophiles at

sp -Hybridized Carbon 451

Skeletal-Rearrangement Reactions 477 Multistep Syntheses 505

Polymeric Materials 541

Compounds Containing Oxygen Functional

Groups 581

Chapter 18 Structures and Reactions of Naturally Occurring

Compounds Containing Nitrogen Functional

Groups 613

Chapter 19 Noncovalent Interactions and Molecular

Recognition 651

Chapter 20 Catalyzed Reactions 681

Chapter 21 Cofactors for Biological Redox Reactions 713

Chapter 22 Energy Storage in Organic Molecules 745

Chapter 23 Molecular Basis for Drug Action 789

spHybridization 51Higher Alkynes 52

Review Problems 56 Chapter 3

Functional Groups Containing Heteroatoms 59

3-1 Compounds Containing sp -Hybridized Nitrogen 59

Contents ix

Alcohols: R — OH 78

Heterolytic Cleavage ofC-OH Bonds: Formation

of Carbocations 84

Conjugation in Radicals and Cations 86

4-1 The Use of Physical Properties to Establish Structure 109

4-2 Chromatography 111

Liquid Chromatographyon StationaryColumns 112

Paper andThin-LayerChromatography 115

5-1 Geometric Isomerization: Rotation about Pi Bonds 155

5-2 Conformational Analysis: Rotation about Sigma

Multiply Substituted Cyclohexanes 171

FusedSix-membered Rings 112

5-6 Absolute Configuration 177

5-7 Polarimetry 179

5-8 Designating Configuration 181

Multiple Centers ofChirality 182

Meso Compounds 184

Fischer Projections 185

5-9 Optical Activity in Allenes 186

5-10 Stereoisomerism at Heteroatom Centers 187

Review Problems 190

Chapter 6

Understanding Organic Reactions 193

6-1 Reaction Profiles (Energy Diagrams) 193

6-2 Characterizing Transition States: The Hammond

Inductive and Steric Effects 209

Hybridization Effects 2i2

Enolate Anion Stability 214

Aromaticity 215

6-9 Reaction Rates: Understanding Kinetics 219

Oxidation and Reduction Reactions 23

7-2 Bond Making and Bond Breaking: Thermodynamic

Feasibility 232

7-3 How to Study a New Organic Reaction 236

7-4 Mechanism ofa Concerted Reaction: Concerted

Nucleophilic Substitution (SN2) 239

7-5 Mechanism of Two Multistep Heterolytic Reactions:

(SN1) 244

Multistep Nucleophilic Substitution (SN1): Hydrolysis of Alkyl

7-6 Mechanism ofa Multistep Homolytic Cleavage: Free

Radical Halogenation of Alkanes 251

Energetics ofHomolytic Substitution in the Cholorination

of Ethane 252

Steps in aRadical Chain Reaction 253

Relative Reactivity ofHalogens 255

Regiocontrol in Homolytic Substitution 251

8-1 Review of Mechanisms of Nucleophilic Substitution 261

8-2 Functional-Group Transformations through S N2

Reactions 270

Williamson Ether Synthesis 211

Reaction of Alkyl Halideswith Nitrogen Nucleophiles 213

Phosphinesas Nucleophiles 216

8-3 Preparation of Carbon Nucleophiles 277

5/>-Hybridized Carbon Nucleophiles: Cyanide and Acetylide

277

sp2 and 5/)

3-HybridizedCarbon Nucleophiles: OrganometallicReagents 218

Protonation as a Limitation 283

SN2 Reactions by sp-HybridizedCarbonNucleophiles 284

Alkylation ofOtherOrganometallics 285

Alpha-Halogenation ofEnolate Anions 286

Enolate Anion andEnamine Alkylation 288

Alkylation of Beta-DicarbonylCompounds 290

9-1 Mechanistic Options for Eliminations 304

9-3 Elimination of HX from Vinyl Halides 31 6

9-4 Elimination of HX from Aryl Halides 319

9-5 Dehydration of Alcohols 320

9-6 Elimination of X2 3219-7 Oxidations of Alcohols 3229-8 Oxidation of Hydrocarbons 325

11-1 Mechanism ofElectrophilic Aromatic Substitution 369

11-2 The Introduction of Groups by Electrophilic Aromatic

ElectronDonors andAcceptors 382

An Exception: Electrophilic Substitution ofHalogen-substituted

Aromatics 386

MultipleSubstituents 389

xiv ( Contents

Chapter 12

Addition and Substitution by Heteroatomic

Nucleophiles at sp -Hybridized Carbon 401

12-1 Nucleophilic Addition to Carbonyl Groups 40212-2 Complex Metal Hydride Reductions 404

Aldehydes and Ketones 404

Relative Reactivityof Carbonyl Compounds

toward Hydride ReducingAgents 408

12-4 Nonhydride Chemical Reductions 410

Dissolving-Metal Reductions 41312-5 Anions as Nucleophiles 41512-6 Addition of Oxygen Nucleophiles 411

Addition ofWater: Hydrate Formation 411

Hydroxide Ion as aNucleophile: The Cannizzaro Reaction 419

Addition ofAlcohols 42012-7 Addition of Nitrogen Nucleophiles 423

12-8 Nucleophilic Acyl Substitution of Carboxylic Acids

HydrolysisofCarboxylicAcid Derivatives 429

Interconversion ofCarboxylic Acidsand Esters 43

AmideHydrolysis 433

Reactions ofAcid Anhydrides 436

Formation ofCarboxylic Acidsfrom Nitriles 43

12-10 Phosphoric Acid Derivatives 440

Contents xv

Conjugate Addition 456

The WittigReaction 459

13-2 Enolates and Enols as Nucleophiles: The Aldol

Condensation 460

Base-catalyzedCondensation of Aldehydes 461

Acid-catalyzed Condensation of Aldehydes 463

Aldol Condensations ofKetones 464

Crossed Aldol Condensations 465

Intramolecular AldolCondensation 461

13-3 The Claisen Condensation 468

Base-induced Claisen Condensation 468

Crossed Claisen Condensations 469

The Beckmann Rearrangement 481

The Hofmann Rearrangement 489

14-3 Carbon-Oxygen Rearrangements 491

The Baeyer-Villiger Oxidation 492

15-1 Grouping Chemical Reactions 506

15-2 Retrosynthetic Analysis: Working Backward 509

15-3 Complications: Reactions Requiring both Functional-Group

Transformation and Skeletal Construction 512

15-4 A Multistep Example 514

xvi ( intents

15-7 "Real World" Examples: Functional-Group

Compatibility 52215-8 Protecting Groups 521

ProtectingGroups for Aldehydes and Ketones 521

ProtectingGroups forAlcohols 529

ProtectingGroups for Carboxylates 529

ProtectingGroups for Amines 530

16-1 Linear and Branched Polymers 54316-2 Types of Polymerization 545

16-3 Addition Polymerization 545

RadicalPolymerization 546

Cross-Linking 551Heteroatom-containing Addition Polymers 55316-4 Condensation Polymers 556

Structures and Reactions of Naturally Occurring

Compounds Containing Oxygen Functional

Structures and Reactions of Naturally Occurring

Acidic andBasicProperties 62

Zwitterionic CharacterofAmino Acids 622

Chapter 19 Noncovalent Interactions and Molecular Recognition 651

19-1 Nonpolar (Hydrophobic) Interactions 651

19-5 Multiple Hydrogen Bonds in Two Dimensions 66419-6 Genetic Coding, Reading, and Misreading 66519-7 Molecular Recognition ofChiral Molecules 611

Three-Point ContactsAre Necessary forChiralRecognition 671Resolution 674

20-2 Avoiding Charge Separation in Multistep Reactions 687

20-8 Enzymes and Chiral Recognition 704

20-9 Artificial Enzymes: Catalytic Antibodies 706

Transformations 716

21-4 Pyridoxamine Phosphate: Reductive Amination of

Alpha-Ketoacids as a Route to Alpha-Amino acids 718

Contents xix

21-6 FADH2 : Electron-Transfer Reduction of an Alpha,

Beta-Unsaturated Thiol Ester 723

21-7 Acetyl CoA: Activation of Carboxylic Acids (as Thiol

21-8 Thiamine Pyrophosphate and Lipoic Acid: Decarboxylation

of Alpha-Ketoacids 726

21-9 Mimicking Biological Activation with Reverse Polarity

Reagents 730

21-10 Tetrahydrofolic Acid: A One-Carbon Transfer Cofactor

for the Methylation of Nucleic Acids 736

22-2 Complex Reaction Cycles 749

22-3 Energy Storage in Anhydrides 750

22-4 Energy Storage in Redox Reactions 752

22-5 Energy Storage in Fatty Acid Biosynthesis 754

Carbon—Carbon Bond Formation 754

Synthesis ofLongerChains 758

22-6 Energy Release in Fatty Acid Degradation 759

22-7 The Krebs Cycle 760

22-8 Controlling Heat Release 767

22-9 Energy Release from Carbohydrates through

Isomerization of Glucose to Fructose 770

Cleavage ofFructose into Three-CarbonFragments 772

Conversion ofthe Three-CarbonFragments into AceticAcid

Molecular Basis for Drug Action 789

23-1 Chemical Basis of Disease States 790

23-3 Beta-Blockers: Modern Antacids 19423-4 Beta-Phenethylamines: Peptide Mimics 19523-5 Blocking Tetrahydrofolic Acid Synthesis 191

23-7 Disruption ofBacterial Cell Walls 803

23-8 Drugs Affecting Nucleic Acids Synthesis 809

Each year, most of the thousands of students who finish a first course in

learned.They convey theirdispleasurebothvocally and,even more

advanced science courses Ask a typical group of such students what was

wrong with their course and youwill hearthe same answer that this query

draws from deans of medical schools, from educational psychologists who

specialize in the instruction of mathematics and science, from university

administrators,and even from manyinstructors of the courses: allsaythata

typical organic chemistry text contains too much information, much of

whichis excruciatingly detailed, disconnected from "real life," irrelevant to

even among the strongest students, many emerge from a year of organic

Adopting a "lessis more" philosophyfor an introductory

undergradu-ate course, we have tried in this text to address eachofthesecommon

thousand pages

con-taining only those topics and reactions that are needed to understand

theintellectualroots oforganicchemistryasit iscurrently practiced

> Third, specific examplesareincludedateachstage to illustrate familiar,

». And, fourth, the story that we tell isintended to enhancethe student's

pre-professional courses, in undergraduate research in a modern organic

In attempting to accomplish these objectives, we have had to take asubstantially different approach from that in virtually all other currentlyavailable organic texts. Like most synthetic chemists, we began by "work-

ing backward." We first asked ourselves what topics a well-informed

organicstudent should understand aftera one-year course inorganic

chem-istry. We consulted extensively with health-profession faculty and with

chem-istry, naturally occurring compounds, energy conversion and storage

modes of action of natural and artificial catalysts, and design criteria for

new materials and biologically active molecules are of key importance in

describing the contributions of organic chemistry to civilization. Most

cur-rentlyavailabletexts, iftheytreat these topicsat all,do so only asbriefsidiary applications ratherthanasintrinsic intellectualgoals of the course

would have to go, ifwe were to adhere toour firstobjective ofconcise

pre-sentation

unrelated reactions This approach has required that we move away

since the early sixties as a means of tabulatingreactions, reasoningthat

this organizationhas become unwieldy, owingtothe ongoing

develop-ment oflargenumbersofnew reagents

topics and reactions to include Only those reactions that recur in the

essential reactions We reasoned that good pedagogy should inhibit us from feeling obliged to include every chemical topic and detail known

by either author Rather, we sought to identify those topics absolutelyrequired toreachour objectiveof givingthe studentsufficientinforma-

tion to understand the principles and practice of modern organicchemistry

These goals led to an organizational structure that begins with seven

chaptersthatdealprimarilywiththethree-dimensionalstructures ofvarious

organic functional groups (Chapters 1 through 5) and therelation between

structureand reactivity,both fromathermodynamic point ofview and from

a kineticone (Chapters6and 7). As soonas thestudenthasbeen exposedto

through 14) deal with specific reaction types, each organized by common mechanismratherthanbyfunctional group,and arefollowedby an integra-

togetherwiththespecificreactionscoveredinthesecondpart,canbesources

of insight into the chemical structure and function of important naturally

artificialenzymes Howthese materialsaccomplishspecificchemical

conver-sionsin biologicalsystemsby molecular and

couplingwithcofactorconversionsisshown by example,ultimately

describ-ing thefunctionofpharmaceutical agentsinthelastchapter

attained in a high school course or in the first semester of standard college

chemistry Forcurricula that so require, the self-contained course presented

in this book can be offered in the freshman year, without the prerequisite

quantitative development of a one-year college general chemistry course

The topics covered here afford a solid basis for a description of common

natural organic phenomena, which might effectively instill in students a

greater enthusiasm for the more-abstract topics of introductory physical

chemistry

Apart from organizing the text itself in what we think to be a better

stimu-lants.

to integrate the concepts in the chapter as a whole Both the exercises

and the problems cover a range of difficulty, progressing from those

that provide basic reinforcement of a concept to those that require the

detailed answers for all the exercises and problems, preparing the

Third, each chapter includes a narrative summary (Conclusions) of the

principal ideas of importance in the chapter These summaries,

together witha listof Important Topics in the Study Guideand Solutions

Manualare intended tohelp the studentrecognize, and learn, themain

that are new to the chapter, and Chapters 7 through 18 also include

tables that regroup the reactions considered according to what they

accomplishas synthetic transformations

chapter

means ofreviewingtheconcepts developed

Sixth, the publisher has made it possible to supply a student package

three-dimensional molecules at no added cost when combined with the

use ofsuch plastic models is strongly recommended in the textual

pre-sentation

Finally, a set of fifty full-color transparencies is available to qualified

adopters

We hope that students will enjoy and benefit from the experience oflearning modern organic chemistry as it is presented in this book We will

begrateful indeedtoourreadersfor theirevaluationofourwork

Marye Anne Fox James K.Whitesell

fromthe traditional approach ofthe past three decades has been a

detailed criticismsof a number ofreviewers, whose names aregiven below

We are indeed grateful to each of them Their comments were universally

helpful; any errors or deviations from theiradvice areour own

responsibil-ity. Weare also deeplygratefulforthehighly professional editing ofPatricia

Zimmerman, for the financial and moral support of Art Bartlett and Dave

Phanco, and for the technical assistance of Susie Pruett, Michael Fox,

MatthewFox, andCharlotteHicks

JohnL Kice

Mathematics, and Engineering, UniversityofDenver

XXV

Chapter 1

in Alkanes

Organic chemistry— what is it and why do we have a full year course

de-voted to the subject? Chemistry itself is the study of the properties ?nd

disci-pline, concentrating on compounds that contain the element carbon As we

will learn during this course, the chemistry ofcarbon is far richer thanthat

of different types of strong bonds that carbon readily forms and in part

from the ease with which many carbon atoms join together to form long

chains This diversityis apparent even in the forms ofcarbon itself, such as

diamond and graphite Diamond is hard and colorless, but graphite is softand black However, above all else is the fascination that goes with the

study of organic chemistry, which is, indeed, the chemistry of life. The life

forms on this planet— from algae to fish and ultimately to mammals,

amaz-ingly diverse in form and structure, but all of it is based on organic

chem-istry. Indeed, though distinct in detail, the fundamental chemistry that

twenti-eth century But howdid we get to this point in organic chemistry? We can

trace the origins of organic chemistry to the period before Christ, with the

prepared fromcharcoaland used as animportantarticleoftrade Sucrose, a

crystalline sugar obtained from sugarcane, and plantextracts to be used asflavorings and perfumes also figured prominently as valued items in an-

cient civilization Among pure compounds of interest to elite members ofthe Egyptian and Roman empiresaretwo other classes: dyes with which to

color their clothes and poisons with which to kill their enemies Organic

compounds wereobtainedfromnatural sourcesto addressbothneeds:

pur-ple dyes from plants and a red dye from an insect; and extracts from the

politicalintrigues thatarose amongthe nonworking upperclasses

The struggles of the alchemists (like the fellows in the frontispiece of

compounds of carbon until the sixteenth century when scientists began to

turn their attention to practical (and less greedy) endeavors In particular,

University of Basel, became convinced that drugs could be found thatwould relieve the suffering of the masses Indeed, he was thefirst torecog-nize that opium, an extractof the poppy plant, could be used as a pain re-

com-pounds could be useful, organic chemistry did not flourish The structures

ad-vanced his atomic theory in 1803 At that time, many chemists began to

focus theirattentiononorganiccompounds obtained fromnature, and

mor-phine, the active constituent of opium, was isolated in 1804 by a French

chemist Nonetheless, it was not until 1847 that the empirical formula of

HO OH morphine was determined and another three-quarters of a century lapsed

Morphine before thecorrectstructure (showninthemargin) was proposed in1925

that it was realized that the molecules found in nature are composed of

atoms and can be described and handled in thesame way as minerals and

metals What an astounding generalization: that the hand holding this

andores Itwas fromthisdiscoverythat organicchemistrywasborn

The lack of detailed structures for organic compounds did not prevent

knowledge that they had to the preparation of new and much less costly

dyes and to the isolation of compounds from plants for medical purposes

structural features of naturally occurring large molecules such as those incotton, silk, and wool were recognized As the number of useful com- pounds fromnature increased,so did interest inorganicchemistry

Thanks to the curiosity and tireless drive of chemists in the twentieth

century, we now have a detailed understanding of the inner workings of

behind the complex operations essential for multicell animals With this

knowledge, chemists have synthesized sophisticated compounds with

properties that enhance the quality of life. The variety of uses for organic

compounds is truly amazing, ranging from the natural and synthetic

poly-mers that are the basis of many of the materials for clothing, housing,

such asthe penicillins,forthetreatment ofmany humandiseases

The objective ofthis course, then, is todevelop sufficient knowledgeoforganic chemistry that the structures and reactions of seemingly compli-

cated systems such as organic polymers and penicillin antibiotics become

unique bonding states available to carbon demands that we begin slowly,

Like the early chemists, we must proceed step by step, learning thestructures of various kinds of organic molecules and how they are deter-

mined before studying a variety of typical reactions that take place with

these classes ofcompounds When we have a good grasp of organic

will learn how syntheses of new compounds and materials are planned,

about the properties of synthetic and naturally occurring polymers, and

about the structureand function of natural products containing oxygen and

nitrogen We will then be ready to understand how organic chemistry

works in nature through theuse of cofactors as biological reagents, various

substituent groups to help two reactants to recognize each other, and

en-zymes to control reaction rates. When these concepts have been mastered,

wewillbe able tounderstand how organisms use theorganic reactions

sugars, to transfer information in replication and reproduction, and to

may seem long, and sometimes tedious, it leads to a fascinating goal and

Organic chemistry,then, is thechemistryofcarbon compounds. All

are composed of atoms, as are the metals and salts used bythe alchemists

especially rich in carbon and hydrogen, and many also contain small

amounts of oxygen, nitrogen, sulfur, phosphorus, and the halogens The

central roleofcarbon inorganic chemistry follows directlyfromits position

nu-merous types of molecules found in living matterare possibleonly because

many different compounds can be formulated from a small number of

ele-ments by the joining of the component atoms into chains and rings to

pro-duce many different structures This is most easily achieved with elementsnearthe center ofa rowof the periodic tablebecause such atoms require the

neighboring atoms

For biological efficiency, naturally occurring compounds must also be

as light as possible and mustderive from common,easily accessible atoms

The lightest atom near the center of the periodic table is carbon, and the

earth's atmosphere is a rich source ofthis element (now, from carbon diox

ide and, in prebiotic times, from methane) Even silicon, fromthe same

col-umn of the periodic table as carbon, is much less versatile and has a much

com-pounds are largely composed of carbon — bound to hydrogen, other carbon

chemi-calsense

If we are to understand the chemistry of the molecules of nature, we

mustfirstunderstand thechemistryofsimple carbon compounds. In

Hydrocarbons are familiar to us in our everyday life: the natural gas

thatwe burn to cook our food, the liquid gasoline used to power our

gases,liquids,or solids Theirstructures atthemolecular level,about which

wewilllearnin this chapter,are similarly diverse Wearequiteawareof the

extremely soft, leaving a trail of carbon particles as it is drawn across thesurface of a sheet of paper These physical differences are due to the con-

trasting three-dimensional cross-linked net of chemical bonds in diamond

and the less highlyinterconnected array ofplanesofatoms in graphite

An-other form ofcarbon has recently been discovered: isolated from soot, this

structural resemblancetothegeodesicdomes firstdesignedby Buckminster

with the structures ofcarbonindiamond and graphiteinFigure 1-1.

can dramatically alter the shapes of hydrocarbons We will learn about thehybridization of carbon and its consequences for the structure of organic

molecules We will learn how atomic and molecular orbitals combine to

formdifferentkinds ofchemical bonds: covalent and ionic,sigma(a) and pi

dimensions and tocalculatesitesofformalcharge Wewilllearn howto

correlate physical properties with the functionality We will also learn how

particularly stable molecules from their structures and chemical formulas,

andtounambiguously name specificmolecules

Before we consider bonding in hydrocarbons in detail, it is essentialthat we understand two very important principles The first is thata mole-

cule exists because of chemical bonds; that is, because the favorable tion ofits negatively charged electrons for its positively charged nuclei ex-

Sheets of graphite

A FIGURE 1-1

Three-dimensional

with nucleus and electron with electron The balance of these forces

pro-ducesa chemical bond and determinesthedistancebetweenadjacent

bond-ed nuclei ina molecule In a chemical bond,a pair of electrons mutually

at-tracted tobothnuclei isfoundnearthe "line" connecting theatomicnuclei.The second principle concerns the repulsive forces (electrons versus

electrons) that dominate the interactions between nonbonded atoms in a

ofanother.Thenucleus-electron(+/-)attractiveinteractionsareweakerthan

the electron-electron (-/-) repulsive interactions when atoms are separated

by distances longer than those of typical chemical bonds These repulsions

fixtherelativepositions of nuclei that arenotconnected byachemicalbond.

To minimizerepulsion, thebonds emanating froma singleatomare directed

asfaras possiblefrom eachother

These principles lead to specific molecular shapes For example, when

a carbon atom is bound to four other atoms (as in methane, CH4/ a

hydro-carbon composed of carbon surrounded by four hydrogens), the molecule adopts an arrangement inwhich thefour hydrogen nuclei (each located at afixed distancefrom the carbon atom) are as far from each otheras possible

This produces a tetrahedron-shaped molecule (Figure 1-2) with an HCH

mini-mal electrostatic repulsionagain places the threeneighborsas far from each

These simple principles have become progressively more quantitative

through theyears Theoretical chemistshavegiven not onlynumerical

justi-fication for their use,butalso a description thatpermitsa more-detailed

deal with their quantitative aspects in this book, these simple principles of

bonds in organic compounds Because the bonds in molecules arebetween

molec-ular orbitalsused inbonding areconstructed

1-1 Atomic Structure

Atomic orbitals describe probability surfaces within which an electron is

likely to be found Precise calculations have been made to describe the

only a single proton need be accommodated in that atom's nucleus and asingle electron located in its possible atomic orbitals. These shapes, calcu-

lated for hydrogen, are assumed to apply equally in describing the atomic

orbitalsof heavier elements Thesecalculations producethedifferent shapes

for the hydrogen atomic orbitals shown inFigure 1-3: we will be most

directed along the x, y, and z axes ofa molecule The electrons in elements

in the first row of the periodic table (hydrogen and helium) can be

accom-modated by s orbitals (Is), but those in the second row also require p

tablebutneednot be considered indescribing first- orsecond-rowatoms

orthogonalporbitals.Thepx

axis;the pyalongtheyaxis;

andthe alongthe z axis.

Complete occupancyofany setof theseorbitals (forexample, theIs

distribution aboutthe central atom This is easy to grasp inconsidering the

pro-peller axes disposed along three orthogonal directions (Figure 1-4) and for

probability of encountering an electron is negligible The nucleus of the

ptom istherefore said tobeat a node ofeach pord suborbital, a position atwhich electron density is zero Although the atomic orbitals ofelements in

each row of the periodic table have approximately these same shapes, the

pro-gression down thetable.

According to the Pauli Exclusion Principle, each electron must have a

distinct set ofprincipal, secondary, azimuthal, and spin quantum numbers:

thatis, each electron must be unique The firstthree quantum numbers

electron in the orbital: sometimes this isindicated by an arrow orby a plus

or a minus sign, but, because the absolute spin is arbitrary, these labels areoften omitted Because there are only two possible spin quantum numbersfor an electron, an orbital (or suborbital) is completely filled by two elec-

trons ofoppositespin Thus, ansorbital canaccommodateexactlytwotrons, and each of the three p suborbitals can accommodate two electrons

elec-for a total of six. The periodic table describes, in each row, the number of

electrons needed to completely fill each of the orbital types encountered in

that row: two electrons fill the valence shell of a first-row element; eight

moreareneeded fora second-rowelement; eighteenmorearerequiredfora

As mentionedearlier,first-row elementsaccommodateelectronswithin

these electrons, which is identical with thenumber of the row in which the

spherical atomic orbitals Hydrogen has one electron in this Is orbital, and

so we describe hydrogen's atomic electron configuration as Is1, in which

the superscript specifies the number of electrons in the Is orbital. Similarly,

one orbital (Is), the two electrons of helium completely fill its Is valence

shell.

Second-rowelements haveelectrons in Is, 2s, and 2p orbitals As inthe

first-row elements, each s orbital can hold two electrons Similarly, each of

the p suborbitals (directed respectively along the x, y, and z axes) can hold

two electrons A filled second-row valence shell is therefore attained when

an atom hasten electrons, two in the Is orbital ofthefirst shelland eightin

thesecond shell(twoin the2s andsix inthe three2porbitals).

Because carbonis soimportantto organic chemistry, our primary focus

is the atomic structure of carbon Its atomic number (6) tells us that a

neu-tralcarbon atomhas sixelectrons.Using hydrogenlikeatomicorbitalsin the

these six electrons in the energetically lowest lying orbitals These are the

spherical Isand 2s orbitalsandthepropeller-shaped 2p orbitals

To clearly see how these electrons are accommodated in carbon, let us

compare carbon's atomic structure with those of other elements in the first

and second rows of the periodic table. Valence electrons are those present

in the last, incomplete valence shell. Hydrogen and helium contain only s

electrons Thus, the hydrogen atom can bedescribed as having a single

va-lence electron in a Is orbital. The helium atom has the sameorbital doubly

for accessto additional electronsfora completedvalence configuration For

helium to take on additional electrons would require the use of orbitals of

configura-tionofaninertgas—is particularlystable

electrons in the 2s and 2p orbitals For example, lithium has the electronic

orbitalanda third electronis inits2s orbital. A2s orbitalhas spherical

sym-metry,but ithasa larger radius than the Is orbital.The electronin the2s

Lithiummetalis neutralbecause thenumberofelectrons (3) isexactlyequal

to the number of protons in its nucleus (3). An uncharged atom is

re-moved, a positively charged ion (Li+) results. Because Li+ has a completely

The next element (beryllium, atomic number 4) can accommodate a

second electroninthe 2s orbital,butboron, atomic number 5,mustplaceits

A FIGURE 1-5

Electronic configurations of

first-and second-rowelements

The numberpreceding eachletter isthe principalquantum numberthatdefines the

valenceshell,theletter

designates theorbitalshape,

andthe superscriptspecifies

thenumberof electronsinthe

se-quentially added to these orthogonal 2porbitals. Carbon's atomic structure

canthusbewritten: Is

2

,2s2,2p2.

EXERCISE 1-A

Specify theatomic orbitals (usingIs, 2s,2p,3s,3p, 3d,etc.,orbitals) andtheir

occupancy to define the electronic configuration of each of the following

atomsorions:

(b) metallicmagnesium (e) S2_

carbon.Four atomicorbitals are

sp3-hybridorbitals.

carbon As mentioned in Section 1-1, carbon has six electrons: two in the

outershell, which canbe partly orcompletely filled, isthevalenceshell;

ac-cordingly, the electrons in that shell are valence electrons You probably

va-lence electrons are distributed among thes and porbitals. Forexample, we

Principle) in its filled 2s orbital, and with the remaining two valence

elec-trons singly distributed in two of the three 2p orbitals in accordance with

Hund's Rule This rule states that, when possible, electrons tend to singly

occupy orbitals ofidenticalenergy Alternatively,the four valence electrons

available to second-row elements (2s, 2px , 2py and 2pz ), as in Figure 1-6. In

either arrangement, carbon's electronic configuration is far from a

A hydrogen atom has one electron (in a Is orbital). By thepaired

asso-ciation of the four electrons of four hydrogen atoms with one carbon, the

electronic configurationrequirements ofeachatom can bemet In CH4, bon isassociated not only with its own four electrons,but alsowitheach ofthe single valence electronscontributedby eachofthe fourhydrogens, giv-

elec-trons, providing the two electrons needed to fill its valence requirement

Thedriving force forthis favorable association ofhydrogen atoms withbon isthe electrostatic attractionof the electrons ofeach atom forthe nucle-

car-us ofits partner in the chemical bond Carbon is almost always limited to

fourbondingpartners because the addition of a fifth partnerwouldrequire

anelectronat themuch higherenergy levelof a3sorbital.

Each C-H bond in methane is equivalentto theothers This canbe

hydrogen atom Is orbitals can overlap effectively with the carbon orbitals.

In particular, would be harder for a hvdrogen atom approach the

smaller-radius 2s orbital than to approach the more-elongated 2p orbitals.

each side of the nucleus; thus, at best, only half of this electron density

This problem can be solved, however, if the carbon orbitals are mixed

toform hybrid orbitals Forexample, the2s and the three2p orbitalscan be

mixed to form a new type of orbital referred to as an sp3-hybrid The

-hybrid orbitals: ls2(2sp3)

4

symmetry ofthe atomicorbitals from which they were composed Because

these hybrid orbitals must occupy separate regions in space, they are

di-rected as far as possible from eachother Simple geometry tells us that this

is best accomplished if the hybrid orbitals point toward the corners of a

pyramid, creating the tetrahedral geometry illustrated in the margin The

directionality problem is then solved, because each hybrid orbital points in

Because these hybrid orbitals are composed substantially (three parts

out of four) of p orbitals, they are elongated, but the fractional s

contribu-tion (1/4) fattens them The s character of the hybrid orbital gives it finite

electron density at the nucleus The larger the fraction of s character, the

more electronegative is the hybrid orbital. Thus, the shape of these sp3

6 1

1-3 Covalent Bonding

hydrogen Is electron toform a chemical bond Because bonding consists of

carbon (Figure 1-7). The four electrons available from the four hydrogen

atoms satisfy the electronic requirement of carbon and give the resulting

molecule (CH4) anelectronicstability comparabletothat ofaninert gas

a limitation For more electrons to be associated with carbon, they would

ener-geticallyfavorable for electronsto beassociated with the positivelycharged

nucleus,accommodating them inanorbitalbeyond thevalenceshellwould

placethem fartherfromthenucleus,which isthermodynamicallycostly.

Inan alternative depiction of the structure ofCH4 , two dots placed

be-tween two atoms represent theshared electrons in the overlappingorbitals

The resulting picture, called a Lewis dot structure, is shown in Figure 1-8

(on page 10). Inthe Lewisdot structure ofmethane, each pair ofdots

repre-sents one of thevalence electrons of carbon and the valence electron of

If either atom in a covalent bond has a greater tendency to attract the

polarized) toward the more-electronegative atom Electronegativity

mea-sures the tendency of a particular atom to attract electrons The

most-electronegative atoms areat thetop and atthe right of the periodictable. In

A FIGURE 1-7

Athree-dimensional

methane FourequivalentC-H

overlapofacarbonsp3-hybrid

orbital.Thebondsaredirected

asfarfromeachother aspossibletominimizeelectronrepulsion

10 ( Chapter I Structure and Bonding in Alkanes

H

H-C-.H

H

FIGURE 1-8

Lewis dot structure of

methane Fouroftheelectrons

areshownincolorto

emphasizetheconceptthatthe

covalentbondsofmethaneare

formed bythe sharing of four

electronegativity of second-row elements is carbon < nitrogen < oxygen

< fluorine Electronegativity also increases in the progression from the

bot-tom to the top of a column. For example, among the halogens, fluorine is

most electronegative; that is, in orderofelectronegativity, iodine < bromine

<chlorine < fluorine These trends result from the greaternuclear (positive)

table and fromthe greater distance of thevalenceelectronsfromthenucleus

Carbon and hydrogen have very similarelectronegativities, and so the

electroneg-ative atom such as fluorine is attached tocarbon, however, the electrons in

theC-Fcovalentbond arenot shared equally Instead, a partial shiftof

elec-trons occurs, placing a partial negative charge on fluorine and leaving bon partially positively charged The periodic table can be used to predicttrends in electronegativity and hence when polar covalent bonding —that

car-is, unequal sharing of the electrons in a covalentbond connecting two

dif-ferent atoms —is likely. The chemical and physical consequences of bond

polarizationwillbeconsidered inmoredetailinChapter3.

EXERCISF 1-B Based on the relative electronegativities of the relevant atoms, choose the

equally share the electronsina covalentbondconnectingthem The

shared,mustthereforebeincorrect

The ions shown at the right-hand side of the reaction are those that would

be formed if the valence requirement of carbon were satisfied by the

addi-tion of four electrons taken from four hydrogen atoms, thus forming fourprotons This carbon would bear four negative charges, having acquired

four extraelectrons Itsformal charge isobtained by comparing thenumber

bytheion

number ofvalence electrons in the neutral atom with the sum ofthe

num-ber of unshared electrons plus half the number ofshared This