Organic chemistry with biological applications

Organic chemistry with biological applications Organic chemistry with biological applications Organic chemistry with biological applications Organic chemistry with biological applications Organic chemistry with biological applications Organic chemistry with biological applications Organic chemistry with biological applications Organic chemistry with biological applications

Structures of Common Coenzymes The reactive parts of the molecules are darkened, while nonreactive parts are ghosted Adenosine triphosphate—ATP (phosphorylation) NH2 N O O –O P O– O P N O O P O– OCH2 N O O– N OH OH Coenzyme A (acyl transfer) NH2 N O O CH3 N O O HSCH2CH2NHCCH2CH2NHCCHCCH2OPOPOCH2 O O– O– HO CH3 2–O PO N N OH Nicotinamide adenine dinucleotide—NAD+ (oxidation/reduction) (NADP+) NH2 CONH2 N N O O + CH2OPOPOCH2 N O– O– OH HO O N O OH N OH (OPO32–) Flavin adenine dinucleotide—FAD (oxidation/reduction) NH2 N HO OH HO CHCHCHCH2OPOPOCH2 O– O– CH2 H3C N H3C N N O O N O N O OH N N OH H O Unless otherwise noted, all content on this page is © Cengage Learning Copyright 2015 Cengage Learning All Rights Reserved May not be copied, scanned, or duplicated, in whole or in part Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s) Editorial review has deemed that any suppressed content does not materially affect the overall learning experience Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it Tetrahydrofolate (transfer of C1 units) H H 2N H N N N N O H H N CO2– H O NHCHCH2CH2C O– 1–5 O S-Adenosylmethionine (methyl transfer) NH2 N N CH3 O –OCCHCH CH 2 +NH S + CH2 N O N OH OH Pyridoxal phosphate (amino acid metabolism) Lipoic acid (acyl transfer) S CH2OPO32– S CHO CH2CH2CH2CH2CO2– + H N OH CH3 Thiamin diphosphate (decarboxylation) Biotin (carboxylation) H S O NH2 + N H N O O –OPOPOCH CH 2 O– O– CH3 N CH3 N N H H H H S CH2CH2CH2CH2CO2– Unless otherwise noted, all content on this page is © Cengage Learning Copyright 2015 Cengage Learning All Rights Reserved May not be copied, scanned, or duplicated, in whole or in part Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s) Editorial review has deemed that any suppressed content does not materially affect the overall learning experience Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it in our courses, Dear Colleague: of the students t os m at th ow kn er than in pure fe sciences rath ganic chemistry li or e h th ac in te y il ho ar w prim d doctors All of us biochemists, an s, are interested , or ts aj is m og y ol tr bi is re em we tu even the ch hing so many fu questioning why e ac te ar e us ar e of w e or se m ng the details of ves, more and chemistry Becau h time discussi rsions of oursel uc ve r m ge so un d yo en sp an ogy? Why e rather th nnection to biol e Why w co w le ay tt li w e ve th h t ac bu sms? continue to te search chemists of living organi re y to tr is st re em te ch in c of ni e sing the orga reactions that ar ore time discus m d en sp ional way, but it d ea st try in the tradit don’t we in is em ch c ni ga s who want or id for teaching those instructor r sa fo be e iv to at h rn uc te m al l logical al There is stil mistry with Bio e has been no re he er C th ic w an no rg l ti O te un more is also true that that is why I wro , I suspect that nd ce A en y in tl en om er pr ff di in hat inues to gain to teach somew ical biology cont em ch s A 3e accordingly s Application ng their teaching gi an ciple ch be l il w y my guiding prin ut B y tr is and more facult em ch on organic exclusively to focus almost is still a textbook is en th be : s ke ta t is ou m e av space saved Make no e and what to le chemistry The ud al cl ic in og to ol t bi in w t action ar in deciding direct counterp r almost every re a fo ve e, us at od th go s to s been put e book is on those reaction gical reactions ately 25% of th lo im io ox nb pr no ap t d ou an g e ations In pl by leavin eir biotransform biological exam th a of by y tr ed is ow em ll fo ch c orter discussed is es and the organi arly 200 pages sh ul ne ec is ol 3e om s bi on to ti a typical twogical Applica devoted entirely istry with Biolo e entire book in m th r he C ve ic co an to y rg lt O addition, ssible for facu xts, making it po te rd da an st an th xt; I believe om any other te fr t en er ff semester course di is pplications 3e ith Biological A w y tr is m he C Organic ts r today’s studen fo l ea id is it at th Sincerely, John McMurry All royalties from Organic Chemistry with Biological Applications will be donated to the Cystic Fibrosis (CF) Foundation This book and donation are dedicated to the author’s eldest son and to the thousands of others who daily fight this disease To learn more about CF and the programs and services provided by the CF Foundation, please visit http://www.cff.org Copyright 2015 Cengage Learning All Rights Reserved May not be copied, scanned, or duplicated, in whole or in part Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s) Editorial review has deemed that any suppressed content does not materially affect the overall learning experience Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it Organic Chemistry w i t h B i o l o g i c a l a p p l i c at i o n s Copyright 2015 Cengage Learning All Rights Reserved May not be copied, scanned, or duplicated, in whole or in part Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s) Editorial review has deemed that any suppressed content does not materially affect the overall learning experience Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it Copyright 2015 Cengage Learning All Rights Reserved May not be copied, scanned, or duplicated, in whole or in part Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s) Editorial review has deemed that any suppressed content does not materially affect the overall learning experience Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it 3rd Edition Organic Chemistry w i t h B i o l o g i c a l a p p l i c at i o n s John McMurry COrnEll UnivErsity Australia • Brazil • Mexico • Singapore • United Kingdom • United States Copyright 2015 Cengage Learning All Rights Reserved May not be copied, scanned, or duplicated, in whole or in part Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s) Editorial review has deemed that any suppressed content does not materially affect the overall learning experience Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it This is an electronic version of the print textbook Due to electronic rights restrictions, some third party content may be suppressed Editorial review has deemed that any suppressed content does not materially affect the overall learning experience The publisher reserves the right to remove content from this title at any time if subsequent rights restrictions require it For valuable information on pricing, previous editions, changes to current editions, and alternate formats, please visit www.cengage.com/highered to search by ISBN#, author, title, or keyword for materials in your areas of interest Copyright 2015 Cengage Learning All Rights Reserved May not be copied, scanned, or duplicated, in whole or in part Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s) Editorial review has deemed that any suppressed content does not materially affect the overall learning experience Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it Organic Chemistry with Biological Applications, 3e John McMurry Product Director: Mary Finch Product Manager: Maureen Rosener Content Developer: Sandra Kiselica Content Coordinator: Elizabeth Woods Product Assistant: Karolina Kiwak © 2015, 2011 Cengage Learning WCN: 02-200-203 ALL RIGHTS RESERVED No part of this work covered by the copyright herein may be reproduced, transmitted, stored, or used in any form or by any means graphic, electronic, or mechanical, including but not limited to photocopying, recording, scanning, digitizing, taping, Web distribution, information networks, or information storage and retrieval systems, except as permitted under Section 107 or 108 of the 1976 United States Copyright Act, without the prior written permission of the publisher Media Developer: Lisa Weber Marketing Manager: Julie Schuster Content Project Manager: Teresa L Trego Art Director: Maria Epes Manufacturing Planner: Judy Inouye Rights Acquisitions Specialist: Dean Dauphinais Production Service: Graphic World Inc Photo Researcher: PreMedia Global Text Researcher: PreMedia Global Copy Editor: Graphic World Inc Illustrator: Graphic World Inc Text Designer: Parallelogram Graphics Cover Designer: Cheryl Carrington Cover Image: Vickie Lewis/National Geographic Creative Compositor: Graphic World Inc We gratefully acknowledge SDBS for providing data for figures on the following pages: 331, 335, 339, 341, 475, 476, 523, 524, 549, 672; and data for the spectra in problems on pages 349d, 349g, 482i, and 598g (http://riodb01.ibase.aist go.jp/sdbs/, National Institute of Advanced Industrial Science and Technology, 8/26/05, 2/7/09, 2/13/09, 3/10/09) For product information and technology assistance, contact us at Cengage Learning Customer & Sales Support, 1-800-354-9706 For permission to use material from this text or product, submit all requests online at www.cengage.com/permissions Further permissions questions can be e-mailed to permissionrequest@cengage.com Library of Congress Control Number: 2013956751 ISBN-13: 978-1-285-84291-2 ISBN-10: 1-285-84291-X Cengage Learning 200 First Stamford Place, 4th Floor Stamford, CT 06902 USA Cengage Learning is a leading provider of customized learning solutions with office locations around the globe, including Singapore, the United Kingdom, Australia, Mexico, Brazil, and Japan Locate your local office at www.cengage.com/global Cengage Learning products are represented in Canada by Nelson Education, Ltd To learn more about Cengage Learning Solutions, visit www.cengage.com Purchase any of our products at your local college store or at our preferred online store www.cengagebrain.com Printed in the United States of America 18 17 16 15 14 Copyright 2015 Cengage Learning All Rights Reserved May not be copied, scanned, or duplicated, in whole or in part Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s) Editorial review has deemed that any suppressed content does not materially affect the overall learning experience Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it Brief Contents structure and Bonding polar covalent Bonds; acids and Bases 28 organic compounds: alkanes and their stereochemistry 59 organic compounds: cycloalkanes and their stereochemistry 87 stereochemistry at tetrahedral centers 113 an overview of organic Reactions 146 alkenes and alkynes 179 Reactions of alkenes and alkynes 212 aromatic compounds 265 10 structure Determination: Mass spectrometry, infrared spectroscopy, and Ultraviolet spectroscopy 319 11 structure Determination: nuclear Magnetic Resonance spectroscopy 350 12 organohalides: nucleophilic substitutions and Eliminations 382 13 alcohols, phenols, and thiols; Ethers and sulfides 435 ** a preview of carbonyl chemistry 483 14 aldehydes and Ketones: nucleophilic addition Reactions 492 15 carboxylic acids and nitriles 530 16 carboxylic acid Derivatives: nucleophilic acyl substitution Reactions 555 17 carbonyl alpha-substitution and condensation Reactions 599 18 amines and heterocycles 644 19 Biomolecules: amino acids, peptides, and proteins 678 20 amino acid Metabolism 714 21 Biomolecules: carbohydrates 738 22 carbohydrate Metabolism 773 23 Biomolecules: lipids and their Metabolism 805 24 Biomolecules: nucleic acids and their Metabolism 852 To access the following online-only chapters, enter ISBN: 978-1-285-84291-2 at www.cengagebrain.com and visit this book’s companion website e25 secondary Metabolites: an introduction to natural products chemistry 877 e26 orbitals and organic chemistry: pericyclic Reactions 905 e27 synthetic polymers 925 v Copyright 2015 Cengage Learning All Rights Reserved May not be copied, scanned, or duplicated, in whole or in part Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s) Editorial review has deemed that any suppressed content does not materially affect the overall learning experience Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it Meperidine, structure of, 885 Mepivacaine, structure of, 57 Mercapto group, 438 Mercurinium ion, 219 Merrifield, R Bruce, 698 Merrifield solid-phase synthesis, 698–700 Fmoc protecting group in, 699 PAM resin in, 699 steps in, 698–699 Wang resin in, 699 Meso compound, 131 plane of symmetry in, 131 Messenger RNA, 860 codons in, 861–862 translation of, 861–863 Mestranol, structure of, 264g Meta (m), 267 Meta-directing group, 296 Metabolic pathways, cyclic, 792–793 linear, 792 Metabolism, 715 overview of, 715–716 Methadone, structure of, 885 Methandrostenolone, structure and function of, 841 Methane, bond angles in, 13 bond lengths in, 12 bond strengths in, 12 molecular model of, 13, 67 pKa of, 257 reaction with Cl2, 149–150 sp3 hybrid orbitals in, 12–13 structure of, 13 Methanethiol, bond angle in, 19 dipole moment of, 32 electrostatic potential map of, 178a molecular model of, 19 pKa of, 440 sp3 hybrid orbitals in, 19 structure of, 19 Methanol, annual worldwide production of, 435 bond angle in, 19 dipole moment of, 32 electrostatic potential map of, 30, 48, 49, 153, 439 industrial synthesis of, 435–436 molecular model of, 19, 436 pKa of, 440 polar covalent bond in, 29–30 sp3 hybrid orbitals in, 19 structure of, 19 toxicity of, 436 uses of, 436 Methionine, biosynthesis of, 529g molecular model of, 127 reaction with ATP, 474 S-adenosylmethionine from, 474 structure and properties of, 680 Methoxide ion, electrostatic potential map of, 49, 442 p-Methoxybenzoic acid, pKa of, 539 p-Methoxypropiophenone, 1H NMR spectrum of, 373 index Methyl acetate, electrostatic potential map of, 561 13C NMR spectrum of, 353 1H NMR spectrum of, 353 pKa of, 608 Methyl anion, electrostatic potential map of, 257 Methyl a-cyanoacrylate, polymerization of, 927 Methyl 2,2-dimethylpropanoate, 1H NMR spectrum of, 370 Methyl group, 70 directing effect of, 297–298 inductive effect of, 297 orienting effect of, 299–300 Methyl phosphate, bond angle in, 19 molecular model of, 19 sp3 hybrid orbitals in, 19 structure of, 19 Methyl propanoate, 13C NMR spectrum of, 361 Methyl thioacetate, electrostatic potential map of, 561 pKa of, 608 9-Methyladenine, electrostatic potential map of, 876a Methylamine, bond angles in, 18 dipole moment of, 32 electrostatic potential map of, 18, 31, 49, 651 sp3 hybrid orbitals in, 18 structure of, 18 2-Methylbutane, molecular model of, 67 Methylcyclohexane, 1,3-diaxial interactions in, 103–104 conformations of, 103–104 mass spectrum of, 324 molecular model of, 117 Methylcyclohex-1-ene, 13C NMR spectrum of, 364 1-Methylcyclohexanol, 1H NMR spectrum of, 379 2-Methylcyclohexanone, chirality of, 117 molecular model of, 117 N-Methylcyclohexylamine, 13C NMR spectrum of, 673 1H NMR spectrum of, 673 Methylene group, 184 9-Methylguanine, electrostatic potential map of, 876a 6-Methylhept-5-en-2-ol, DEPT-NMR spectra of, 362 5-Methylhexan-2-one, mass spectrum of, 525 Methyllithium, electrostatic potential map of, 30, 152 polar covalent bond in, 29–30 Methylmagnesium iodide, electrostatic potential map of, 392 N-Methylmorpholine N-oxide, alkene hydroxylation with OsO4 and, 230 2-Methylpentane, mass spectrum of, 349c 2-Methylpentan-3-ol, mass spectrum of, 327 2-Methylpent-2-ene, mass spectrum of, 325 I-21 p-Methylphenol, pKa of, 440 2-Methylpropane, molecular model of, 67 2-Methylpropene, heat of hydrogenation of, 193 Metoprolol, synthesis of, 470 Mevacor, mechanism of action of, 2, 849–850 Mevaldehyde, biosynthesis of, 588–589 Mevalonate, biosynthesis of, 830–833 decarboxylation of, 832–833 isopentenyl diphosphate from, 830–833 phosphorylation of, 832–833 Micelle (soap), 810 Michael reaction, 632–633 acceptors in, 633 donors in, 633 mechanism of, 632 Stork enamine reaction and, 635–636 Microwaves, electromagnetic spectrum and, 330 Mineralocorticoid, 841 Minor groove (DNA), 856–857 Mitomycin C, structure of, 677j Molar absorptivity, 344 Molecular ion (M1), 321 Molecular mechanics, 111 Molecular model, acetaminophen, 27a acetyl CoA carboxylase, 530 acetylene, 17 acyl CoA dehydrogenase, 179 adenine, 58b N6-adenine methyltransferase, 382 adrenaline, 145a alanine, 27, 678 alanylserine, 689 a helix (protein), 701 d-amino-acid aminotransferase 714 p-aminobenzoic acid, 24 anisole, 437 anti periplanar geometry, 424 arecoline, 65 aspartame, 27a aspirin, 16 bacteriorhodopsin, 319 p-bromoacetophenone, 360 bromocyclohexane, 101 butane, 67 tert-butyl carbocation, 201 cis-but-2-ene, 187, 192 trans-but-2-ene, 187, 192 C-terminal domain of spider dragline silk protein, 925 camphor, 110 cellulose, 763 chair cyclohexane, 98 chlorotrimethylsilane, 462 cholesterol, 839 cholic acid, 531 chorismate mutase, 905 citrate synthase, 678, 708 citric acid, 27 coniine, 27 cyclobutane, 96 cyclodecapentaene, 273 Unless otherwise noted, all content on this page is © Cengage Learning Copyright 2015 Cengage Learning All Rights Reserved May not be copied, scanned, or duplicated, in whole or in part Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s) Editorial review has deemed that any suppressed content does not materially affect the overall learning experience Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it I-22 index Molecular model (continued) cyclohexane ring flip, 101 cyclopentane, 96 cyclopropane, 91, 95 cytosine, 58b cis-decalin, 109, 838 trans-decalin, 109, 838 decane, 84 diethyl ether, 437 dimethyl sulfide, 19 cis-1,2-dimethylcyclopropane, 91 trans-1,2-dimethylcyclopropane, 91 2,2-dimethylpropane, 67 DNA, 857 dopamine, 656 eclipsed ethane conformation, 80 enflurane, 118 enoyl CoA hydratase, 212 ethane, 10, 13, 67 ethanol, 436 ethylene, 15 (S)-fluoxetine, 142 fructose-1,6-bisphosphate aldolase, 348 a-d-glucopyranose, 750 b-d-glucopyranose, 750 glucose, 99, 107 glutamine synthase, 644 glycogen synthase, 113 halomon, 431 hemoglobin, 265 hexane, 14 hexokinase, 174, 738 HIV protease, 28 HMG-CoA reductase, hydroxyacyl-CoA dehydrogenase, 805 (S)-ibuprofen, 144 isobutane, 67 isoleucine, 130 b-ketoacyl-CoA thiolase, 599 lactic acid, 116 lactose, 764 lidocaine, 86a (2)-limonene, 141 (1)-limonene, 141 linolenic acid, 808 liver alcohol dehydrogenase, 435 maltose, 763 mannose, 107 membrane channel protein, 59, 87 menthol, 97 meso-tartaric acid, 131 methane, 13, 67 methanethiol, 19 methanol, 19, 436 methionine, 127 methyl phosphate, 19 methylamine, 18 2-methylbutane, 67 methylcyclohexane, 117 2-methylcyclohexanone, 117 2-methylpropane, 67 naphthalene, 58a Newman projections, 80 norbornane, 110 norcoclaurine synthase, 877 oseltamivir, 111 pancreatic lipase, 555 pentane, 67 phenylalanine, 86a phosphoglucoisomerase, 492 phosphoribosyl-diphosphate synthetase, 852 piperidine, 662 b-pleated sheet (protein), 702 propane, 67, 81 protein kinase A, 146 pseudoephedrine, 145a R-glyceraldehyde, 741–742 serine, 145a serylalanine, 690 S-malate, 368 staggered ethane conformation, 80 stearic acid, 808 steroid, 838 sucrose, 765 syn periplanar geometry, 424 tamiflu, 111 testosterone, 109 tetrahydrofuran, 437 threose, 118 trimethylamine, 647 triose-phosphate isomerase, 773 tRNA, 863 twist-boat cyclohexane, 99 ubiquinone–cytochrome c reductase, 350 urocanase, 735 vitamin C, 551 Molecular orbital (MO) theory, 20–21 Molecular orbital, 20 algebraic signs of lobes in, 20–21, 186 antibonding, 20–21 benzene and, 271 bonding, 20–21 buta-1,3-diene, 243–244, 906 conjugated dienes and, 243–244 ethylene, 906 1,3,5-hexatriene, 907 Hückel 4n rule and, 273 Molecular weight, determination of, 322 Molecule, electron-dot structures of, 8–9 lone-pair electrons in, Molozonide, 231 Monomer, 235 Monosaccharide(s), 739 aldaric acids from, 758 alditols from, 756–757 aldonic acids from, 758 anomers of, 750–751 configurations of, 746–747 cyclic forms of, 750–751 essential, 761–762 esters from, 754 ethers from, 754 glycosides of, 755 hemiacetal forms of, 750–751 osazones from, 772f oxidation of, 757–759 phosphorylation of, 756 reaction with acetic anhydride, 754 reaction with NaBH4, 756–757 reduction of, 756–757 see also Aldose uronic acids from, 758–759 Monoterpene, 210 Monoterpenoid, 829 Morphine, biosynthesis of, 884–892 from opium, 884 from thebaine, 892–893 mechanism of action of, 885 specific rotation of, 120 structure of, 57 Morphine rule, 885 MRI, see Magnetic resonance imaging, 380 mRNA, see Messenger RNA MS, see Mass spectrometry Mullis, Kary, 869 Multiplet (NMR), 371–373 table of, 373 Mutarotation, 751 glucose and, 751–752 mechanism of, 752 l-Mycarose, structure of, 901 3-O-Mycarosylerythronolide B, structure of, 901 Mycomycin, structure of, 145h Mylar, structure of, 591 Myoglobin, a helix in, 701 ribbon model of, 701 Myrcene, structure of, 209 Myristic acid, catabolism of, 819–820 structure of, 807 n (normal), 67 n 1 rule (NMR), 372 N-terminal amino acid, 690 N6-Adenine methyltransferase, function of, 382 molecular model of, 382 NAD1, see Nicotinamide adenine dinucleotide NADH, see Nicotinamide adenine dinucleotide (reduced) NADPH, see Nicotinamide adenine dinucleotide phosphate (reduced) Naming, acid anhydrides, 556 acid chlorides, 556 acid halides, 556 acyl groups, 532 acyl phosphates, 557 alcohols, 437–438 aldehydes, 493 aldoses, 747–748 alkanes, 68–69, 72–76 alkenes, 183–184 alkyl groups, 70–71, 75–76 alkyl halides, 383–384 alkynes, 185 alphabetization and, 75–76 amides, 557 amines, 645–646 aromatic compounds, 266–268 carboxylic acid derivatives, 556–558 Unless otherwise noted, all content on this page is © Cengage Learning Copyright 2015 Cengage Learning All Rights Reserved May not be copied, scanned, or duplicated, in whole or in part Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s) Editorial review has deemed that any suppressed content does not materially affect the overall learning experience Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it carboxylic acids, 531–532 crown ethers, 472 cycloalkanes, 88–90 cycloalkenes, 184 eicosanoids, 827 enzymes, 704 esters, 556 ethers, 464–465 heterocyclic amines, 646 ketones, 494 nitriles, 533 phenols, 438 prostaglandins, 827 sulfides, 465 thioesters, 557 thiols, 438 Naphthalene, aromaticity of, 279–280 electrostatic potential map of, 280 Hückel 4n rule and, 279 molecular model of, 58a reaction with Br2, 279 resonance in, 279 Naproxen, structure of, 315 Natural gas, composition of, 85 thiols in, 463 Natural product, 877 alkaloids, 879 bioprospecting for, 903 classification of, 878–879 drugs from, 176 enzyme cofactors, 879 fatty-acid derived substances, 879 nonribosomal polypeptides, 879 polyketides, 879 terpenoids and steroids, 878 Natural rubber, structure of, 258 NBS, see N-Bromosuccinimide NDA, see New drug application, 176–177 Neopentyl group, 76 SN2 reaction and, 402 Neuraminic acid, biosynthesis of, 762 influenza virus and, 762 Neuraminidase, influenza virus and, 802 New drug application (NDA), 176–177 New molecular entity (NME), number of, 176 Newman projection, 80 molecular model of, 80 Nicotinamide adenine dinucleotide, biological oxidations and, 458, 706 biological reductions with, 517 mechanism of, 517 oxidative deamination and, 723 structure and function of, 706 yeast alcohol dehydrogenase and, 139–140 Nicotinamide adenine dinucleotide (reduced), mechanism of reduction with, 446–447 structure of, 175 Nicotinamide adenine dinucleotide phosphate (reduced), biological reductions with, 226 mechanism of reduction with, 446–447 index Nicotine, structure of, 27b, 644 Ninhydrin, reaction with amino acids, 692 Nitration (aromatic), 286 Nitric acid, pKa of, 45 Nitrile(s), 532 alkylation of, 618 amides from, 545–546 amines from, 547 carboxylic acids from, 541, 545–546 from alkyl halides, 541 from amides, 544–545 Grignard reaction of, 547 hydrolysis of, 541, 545–546 IR spectroscopy of, 549 ketones from, 547 mechanism of hydrolysis of, 545–546 naming, 533 naturally occurring, 544 NMR spectroscopy of, 549 nucleophilic additions to, 545 pKa of, 608 reaction summary of, 553–554 reaction with LDA, 618 reaction with LiAlH4, 547 reduction of, 547 synthesis of, 544–545 Nitrile group, directing effect of, 297–298 inductive effect of, 297 orienting effect of, 300 resonance effect of, 298 Nitrile rubber polymer, structure and uses of, 931 Nitro group, directing effect of, 297–298 inductive effect of, 297 orienting effect of, 300 resonance effect of, 298 Nitroarene, arylamines from, 655 reaction with iron, 655 reaction with tin, 655 reduction of, 655 Nitrobenzene, aniline from, 287 reduction of, 287 synthesis of, 286 p-Nitrobenzoic acid, pKa of, 539 Nitrogen rule (mass spectrometry), 673 Nitronium ion, 286 electrostatic potential map of, 286 p-Nitrophenol, pKa of, 440 p-Nitrophenoxide ion, resonance in, 442 NME, see New molecular entity, 176 NMR, see Nuclear magnetic resonance Nomenclature, see Naming Nomex, structure of, 942a Nonbonding electrons, Noncoding strand (DNA), 861 Noncovalent interaction(s), 54 kinds of, 54–55 dipole–dipole forces and, 54 dispersion forces and, 54 hydrogen bonds and, 54–55 van der Waals forces and, 54 Nonequivalent protons, spin–spin splitting and, 377–378 tree diagram in NMR of, 378 I-23 Nonessential amino acid, 683, 731–732 biological precursors of, 732 Nonribosomal polypeptide, 879 Norbornane, molecular model of, 110 structure of, 110 (S)-Norcoclaurine, biosynthesis of, 888–889 Norcoclaurine synthase, function of, 877 molecular model of, 877 Norepinephrine, biosynthesis of, 306 Norethindrone, structure and function of, 841 Normal (n) alkane, 67 Norsorex, synthesis of, 936 Novocain, structure of, 57 Noyori, Ryoji, 526 NSAID, 314–315 Nuclear magnetic resonance spectrometer, operation of, 354 Nuclear magnetic resonance spectroscopy (NMR), 350 acid anhydrides, 593–594 acid chlorides, 593–594 alcohols, 476–477 aldehydes, 523–524 amides, 593–594 amines, 672–673 13C chemical shifts in, 358–359 calibration peak for, 355–356 carboxylic acid derivatives, 593–594 carboxylic acids, 549 chart for, 355 coupling constants in, 373 delta scale for, 356 DEPT-NMR and, 361–363 diastereotopic protons and, 367 enantiotopic protons and, 366 energy levels in, 352 esters, 593–594 ethers, 477 field strength and, 351–352 FT-NMR and, 357–358 1H chemical shifts in, 368–369 homotopic protons and, 366 integration of 1H spectra, 370 ketones, 524 multiplets in, 373 n 1 rule and, 372 nitriles, 549 overlapping signals in, 376–377 peak assigning in 13C spectra, 359, 361–362 peak size in 13C spectra, 360 peak size in 1H spectra, 370 phenols, 477 principle of, 350–352 proton equivalence and, 365–367 radiofrequency energy and, 351–352 shielding in, 352–353 signal averaging in, 357–358 spin-flips in, 351 spin–spin splitting in, 371–373 time scale of, 354 uses of 13C spectra in, 363–364 uses of 1H spectra in, 379 Unless otherwise noted, all content on this page is © Cengage Learning Copyright 2015 Cengage Learning All Rights Reserved May not be copied, scanned, or duplicated, in whole or in part Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s) Editorial review has deemed that any suppressed content does not materially affect the overall learning experience Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it I-24 13C index Nuclear magnetic resonance spectrum, acetaldehyde, 524 acetophenone, 524 benzaldehyde, 524 benzoic acid, 549 p-bromoacetophenone, 359 butan-2-one, 359e, 524 crotonic acid, 549 cyclohexanol, 476 cyclohexanone, 524 ethyl benzoate, 381f methyl acetate, 353 methyl propanoate, 361 1-methylcyclohexene, 364 N-methylcyclohexylamine, 673 pentan-1-ol, 358 propanenitrile, 549 propanoic acid, 549 1H Nuclear magnetic resonance spectrum, acetaldehyde, 524 anethole, 482g bromoethane, 371 2-bromopropane, 373 trans-cinnamaldehyde, 377 cyclohexylmethanol, 379 ethyl acetate, 593 p-methoxypropiophenone, 373 methyl acetate, 353 1-methylcyclohexanol, 379 N-methylcyclohexylamine, 673 phenacetin, 677f phenylacetic acid, 550 propan-1-ol, 477 toluene, 377 Nuclear spin, common nuclei and, 352 NMR and, 350–351 Nuclease, function of, 871 Nucleic acid, 852–855 biosynthesis of, 873–874 catabolism of, 871–873 hydrolysis of, 871 phosphodiester bonds in, 855 see also Deoxyribonucleic acid, Ribonucleic acid structure of, 855 synthesis of, 866–869 Nucleophile, 154–155 characteristics of, 159–160 curved arrows and, 154, 159–161 electrostatic potential maps of, 155 examples of, 155 SN1 reaction and, 415 SN2 reaction and, 403–404 Nucleophilic acyl substitution reaction, 488, 559–562 abbreviated mechanism for, 733 acid anhydrides, 576–578 acid chlorides, 570–576 acid halides, 570–576 amides, 584–586 biological example of, 570–571 carboxylic acids and, 564–570 esters, 579–583 kinds of, 561–562 mechanism of, 559–560 reactivity in, 560–561 Nucleophilic addition reaction, 486–487, 497–500 acid catalysis of, 501–502 base catalysis of, 501–502 kinds of, 499 mechanism of, 497–498 steric hindrance in, 499 trajectory of, 497–499 Nucleophilic aromatic substitution reaction, 303–305 characteristics of, 304–305 mechanism of, 304 Nucleophilic substitution reaction, 396 biological examples of, 418–419 see also SN1 reaction, SN2 reaction Nucleophilicity, 403 basicity and, 403–404 table of, 404 trends in, 403–404 Nucleosidase, function of, 871 Nucleoside, 852–855 Nucleotidase, function of, 871 Nucleotide, 852–855 biosynthesis of, 873–874 catabolism of, 871–873 3′ end of, 855 5′ end of, 855 Nucleus, size of, Nylon, 590 naming, 590 uses of, 591 Nylon 6, synthesis of, 932 Nylon 66, structure of, 591 synthesis of, 932 o, see Ortho, 267 Octane number (fuel), 86 -oic acid, name ending for carboxylic acids, 531 Okazaki fragment, DNA replication and, 859 -ol, alcohol name ending, 437 Olefin, 179 Olefin metathesis polymerization, 934–936 Grubbs catalyst for, 934–935 kinds of, 935–936 mechanism of, 934–935 Oleic acid, structure of, 807 Oligonucleotide, 866 synthesis of, 866–869 Olive oil, composition of, 807 Omega-3 fatty acid, 808 -one, ketone name ending, 494 -onitrile, nitrile name ending, 533 Opium, 884 Optical activity, measurement of, 119–120 Optical isomers, 121 Orbital, hybridization of, 12–19 Organic acids, 48–49 Organic bases, 49–50 Organic chemicals, elements found in, number of, 59 risk evaluation of, 25 toxicity of, 25 Organic chemistry, Organic reactions, conventions for writing, 196 kinds of, 147 Organic synthesis, enantioselective, 526–527 strategy for, 308–313 Organoborane, from alkenes, 220 reaction with H2O2, 220 Organodiphosphate, biological SN1 reactions and, 418–419 Friedel-Crafts reactions and, 292–293 Organohalide, biological uses of, 431 naturally occurring, 430–431 number of, 430 reaction with Gilman reagents, 393–394 Organomagnesium halide, see Grignard reagent Organometallic compound, 391 polarity of, 152 Organometallic coupling reaction, 393–395 mechanism of, 394 Organopalladium compound, Suzuki–Miyaura reaction of, 394 Organophosphate, electrostatic potential map of, 61 polarity of, 61 sp3 hybrid orbitals in, 19 structure of, 19 Ornithine biosynthesis of, 734 citrulline from, 725–726 from arginine, 727 reaction with carbamoyl phosphate, 725–726 urea cycle and, 725–726 Ortho (o), 267 Ortho- and para-directing group, 296 Osazone, 772f -ose, carbohydrate name ending, 740 Oseltamivir, molecular model of, 111 mechanism of, 802–803 -oside, glycoside name ending, 755 Osmium tetroxide, reaction with alkenes, 230 toxicity of, 230 Oxalic acid, structure of, 532 Oxaloacetate, aspartate from, 724, 731 decarboxylation of, 797–798 from malate, 792 from pyruvate, 796–797 phosphoenolpyruvate from, 797–798 reaction with acetyl CoA, 789 Oxaloacetic acid, structure of, 532 Oxalosuccinate, decarboxylation of, 790 from isocitrate, 790 Oxaphosphetane, 513 Oxidation, alcohols and, 456–458 aldehydes, 497 Dess–Martin periodinane and, 457–458 Unless otherwise noted, all content on this page is © Cengage Learning Copyright 2015 Cengage Learning All Rights Reserved May not be copied, scanned, or duplicated, in whole or in part Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s) Editorial review has deemed that any suppressed content does not materially affect the overall learning experience Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it FAD and, 817–818 NAD1 and, 458 organic, 227 phenols, 459 Oxidative deamination, 723 mechanism of, 723 Oxidative decarboxylation, 783 a-ketoglutarate and, 790 mechanism of, 784–787 pyruvate and, 783–787 thiamin diphosphate and, 785–786 Oxidoreductase, 704–705 Oxime, 760 Oxirane, 227 see also Epoxide Oxo group, 494 Oxyfluorfen, synthesis of, 305 Oxymercuration, mechanism of, 219–220 Oxymercuration–demercuration, 219 regiochemistry of, 219–220 -oyl, name ending for acyl groups, 532 Ozone, laboratory preparation of, 231 reaction with alkenes, 231–232 Ozonide, 231 dangers of, 231 reduction of with zinc, 231 p-, see Para, 267 p Orbital, algebraic signs of lobes in, 20–21, 186 Paclitaxel, origin of, 903 structure and function of, 903 Palmitic acid, fatty acid biosynthesis and, 825 structure of, 807 Palmitoleic acid, structure of, 807 PAM resin, peptide synthesis and, 699 Pancreatic lipase, function of, 555 molecular model of, 555 Papaver somniferum, morphine from, 884 Para (p), 267 Paraffin, 78 Parent (nomenclature), 73 Parent peak (mass spectrum), 321 Partial charge, 29–30 Pasteur, Louis, 121 Pasteur, enantiomers and, 121 Patchouli alcohol, structure of, 829 Pauling, Linus, 12 PCR, see Polymerase chain reaction, 869–870 PDB, see Protein Data Bank Peanut oil, composition of, 807 Penicillin, discovery of, 594 mechanism of action of, 595 Penicillin G, structure of, 584 Penicillin V, specific rotation of, 120 stereochemistry of, 143 Penta-1,4-diene, electrostatic potential map of, 244 Pentadienyl radical, resonance forms of, 41 Pentane, molecular model of, 67 index Pentane-2,4-dione anion, resonance forms of, 40 enol content of, 601 pKa of, 609 Pentan-1-ol, 13C NMR spectrum of, 358 Pentobarbital, synthesis of 640 Pentose phosphate pathway, 804c, 804d PEP, see Phosphoenolpyruvate Pepsin, isoelectric point of, 686 Peptide, 679 amino acid analysis of, 691–692 backbone of, 690 covalent bonding in, 690 disulfide bonds in, 691 Edman degradation of, 693–695 hydrolysis of, 691 partial hydrolysis of, 695 reaction with phenylisothiocyanate, 693–694 sequencing of, 693–695 solid-phase synthesis of, 698–700 synthesis of, 696–700 Peptide bond, 689 DCC formation of, 696 restricted rotation in, 690 Pericyclic reaction, 247, 905 Claisen rearrangement and, 471–472 cycloaddition reactions and, 913–916 Diels–Alder reaction and, 247–251 electrocyclic reactions and, 908–912 frontier orbitals and, 907 kinds of, 905 sigmatropic reactions and, 917–921 stereochemical rules for, 922 Woodward–Hoffmann rules for, 906–907 Periodic acid, diol cleavage with, 232 Periplanar geometry 423 E2 reactions and, 423–424 Peroxyacid, 227 reaction with alkenes, 227 Petroleum, catalytic cracking of, 86 composition of, 85 gasoline from, 85–86 refining of, 85–86 Pfu DNA polymerase, 870 Pharmaceuticals, approval procedure for, 176–177 fluorine-containing, 284–285 origin of, 176 Phenacetin, 1H NMR spectrum of, 677f Phenol, 435 acidity of, 439–442 Bakelite from, 939–940 electrophilic aromatic substitution of, 300–301 electrostatic potential map of, 297 hydrogen bonds in, 439 IR spectroscopy of, 476 IR spectrum of, 476 naming, 438 NMR spectroscopy of, 477 oxidation of, 459 phenoxide ions from, 440–441 I-25 pKa of, 440 properties of, 439–442 quinones from, 459 reaction summary of, 482 uses of, 436 Phenolic resin, 939–940 Phenoxide ion, 440 electrostatic potential map of, 442 resonance in, 441 Phenyl group, 267 Phenylacetaldehyde, aldol reaction of, 621 IR spectrum of, 341 Phenylacetylene, IR spectrum of, 342 1H NMR spectrum of, 550 Phenylalanine, from chorismate, 472 molecular model of, 86a structure and properties of, 680 Phenylisothiocyanate, Edman degradation and, 693–694 Phenylthiohydantoin, Edman degradation and, 693–694 Phosphatidic acid, structure of, 812 Phosphatidylcholine, structure of, 812 Phosphatidylethanolamine, structure of, 812 Phosphatidylserine, structure of, 812 Phosphine(s), chirality of, 137, 689 Phosphite, 868 oxidation of, 868 Phosphodiester, nucleic acid and, 855 Phosphoenolpyruvate, from oxaloacetate, 797–798 from 2-phosphoglycerate, 782 2-phosphoglycerate from, 798 pyruvate from, 782 function of, 492 Phosphoglucoisomerase, molecular model of, 492 2-Phosphoglycerate, from phosphoenolpyruvate, 798 from 3-phosphoglycerate, 781 3-Phosphoglycerate, from 1,3-bisphosphoglycerate, 781 isomerization of, 781 Phospholipid, 811–812 abundance of, 812 classification of, 811 function of, 812 Phosphopantetheine, structure of, 588, 716 Phosphoramidite, 868 Phosphorane, 513 Phosphoribosyl-diphosphate synthetase, function of, 852 molecular model of, 852 Phosphoric acid, pKa of, 45 Phosphoric acid anhydride, 716 Phosphorus oxychloride, alcohol dehydration with, 454 Phosphorus tribromide, reaction with alcohols, 390–391, 405, 452 Phosphorylation, ATP and, 717 mechanism of, 717 Photochemical reaction, 908 Unless otherwise noted, all content on this page is © Cengage Learning Copyright 2015 Cengage Learning All Rights Reserved May not be copied, scanned, or duplicated, in whole or in part Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s) Editorial review has deemed that any suppressed content does not materially affect the overall learning experience Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it I-26 index Photon, 329, 331 energy of, 331 Photosynthesis, 739 Phthalic acid, structure of, 532 Phylloquinone, biosynthesis of, 293 Physiological pH, 537 Phytyl diphosphate, vitamin K1 biosynthesis and, 293 Pi (p) bond, 15 acetylene and, 17 ethylene and, 14–15 molecular orbitals in, 21 Picometer, Pinacol rearrangement, 482j Pineapple, esters in, 578 Piperidine, molecular model of, 662 structure of, 646 PITC, see Phenylisothiocyanate, 693–694 pKa, 44 table of, 45 PKS, see Polyketide synthase Planck equation, 331 Plane of symmetry, 115–116 meso compounds and, 131 Plane-polarized light, 119 Plasmalogen, structure of, 851a Plastic, recyclable, 940–941 see also Polymer Plasticizer, 579, 938 structure and function of, 938 toxicity of, 938 Plavix, structure of, 27f b-Pleated sheet (protein), 701–702 PLP, see Pyridoxal phosphate PMP, see Pyridoxamine phosphate Poison ivy, urushiols in, 436 Polar aprotic solvent, 406 SN1 reaction and, 416 SN2 reaction and, 406–407 Polar covalent bond, 28–29 dipole moments and, 31–32 electronegativity and, 29–30 electrostatic potential maps and, 30 polar reactions and, 152–155 Polar reaction, 149, 152–155 characteristics of, 152–155 curved arrows in, 154, 159–161 electrophiles in, 154–155 nucleophiles in, 154–155 Polarimeter, 119 Polarizability, 153 Polyamide, 589 Polycarbonate, 933 Polycyclic aromatic compound, 279 Polycyclic compound, 108 conformations of, 108–110 Polyester, 589 uses of, 591 annual worldwide production of, 237 Polyethylene, crystallites in, 937 high-density, 929 high-molecular-weight, 929 kinds of, 929 low-density, 929 synthesis of, 237–238 ultrahigh-molecular-weight, 929 Ziegler–Natta catalysts and, 929 Polyimide, structure of, 598e Poly(ethylene terephthalate), structure of, 938 Poly(glycolic acid), biodegradability of, 941 Poly(hydroxybutyrate), biodegradability of, 941 Poly(lactic acid), biodegradability of, 941 Polyketide(s), 879 number of, 879, 895 biosynthesis of, 894–895 examples of, 894 Polyketide synthase (PKS), 895 domains in, 895 modules in, 895 size of, 895 Polymer(s), 235 atactic, 928 biodegradable, 940–941 biological, 235–236 chain-growth, 237, 926–927 classification of, 926 crystallites in, 937 elastomer, 939 fiber, 938 glass transition temperature of, 937 isotactic, 928 kinds of, 937–940 melt transition temperature of, 937 plasticizers in, 938 recycling codes for, 941 step-growth, 589, 932–934 syndiotactic, 928 thermoplastic, 937–938 thermosetting resin, 939–940 van der Waals forces in, 937 Polymerase chain reaction (PCR), 869–870 amplification factor in, 869 steps in, 870 taq DNA polymerase in, 870 Polymerization, anionic, 927 cationic, 926 mechanism of, 237–238 radical, 237–238 Ziegler–Natta catalysts for, 929 Polypeptide, nonribosomal, 879 Polypropylene, polymerization of, 928–929 stereochemical forms of, 928 Polysaccharide, 765–768 synthesis of, 767–768 Polyunsaturated fatty acid, 807 Polyurethane, 933 foam, 934 kinds of, 933–934 stretchable, 933–934 Poly(vinyl butyral), uses of, 942b Poly(vinyl chloride), plasticizers in, 938 Porphobilinogen, biosynthesis of, 677h Potassium permanganate, reaction with alkenes, 232 Pravachol, mechanism of action of, 2, 849–850 structure of, 86f Pravastatin, mechanism of action of, 2, 849–850 structure of, 86f Prefix (nomenclature), 73 Priestley, Joseph, 258 Prilocaine, structure of, 57 Primary alcohol, 437 Primary amine, 645 Primary carbon, 70–71 Primary hydrogen, 71 Primary protein structure, 700 Priming reaction, fatty acid biosynthesis and, 821 pro-R prochirality center, 139 pro-S prochirality center, 139 Problems, how to work, 26–27 Procaine, structure of, 27d, 57 Prochirality, 138–140 assignment of, 138–139 biological reactions and, 139–140 Re, 138 Si, 138 Prochirality center, 139 pro-R, 139 pro-S, 139 Progesterone, structure and function of, 841 Progestin, 840 function of, 840–841 Proline, biosynthesis of, 658, 734 catabolism of, 737a from glutamate, 734 structure and properties of, 680 Promotor sequence (DNA), 860 Propagation step (radical reaction), 150 Propane, bond rotation in, 81 conformations of, 81 mass spectrum of, 321 molecular model of, 67 Propane conformation, molecular model of, 81 Propanenitrile, 13C NMR absorptions in, 549 Propanoic acid, 13C NMR absorptions in, 549 Propan-1-ol, 1H NMR spectrum of, 477 Propenal, electrostatic potential maps of, 249 Propenenitrile, electrostatic potential maps of, 249 Propionyl CoA, catabolism of, 819–820 Propyl group, 71 Propylene, annual worldwide production of, 180 heat of hydrogenation of, 193 industrial uses of, 180 Prostaglandin(s), 826–828 biosynthesis of, 827–828 functions of, 150–151, 826 naming, 827 occurrence of, 826 Prostaglandin E1, structure of, 826 structure of, 87 Unless otherwise noted, all content on this page is © Cengage Learning Copyright 2015 Cengage Learning All Rights Reserved May not be copied, scanned, or duplicated, in whole or in part Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s) Editorial review has deemed that any suppressed content does not materially affect the overall learning experience Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it Prostaglandin E2, biosynthesis of, 827–828 Prostaglandin F2a, structure of, 93 Prostaglandin H2, biosynthesis of, 151, 240–241, 827–828 Prostaglandin I2, structure of, 826 Protease, mechanism of action of, 585 Protecting group, 461 alcohols and, 460–462 aldehydes and, 511 amino acids, 696–697 DNA synthesis and, 867 ketones and, 511 Protein, 679 a helix in, 700–701 backbone of, 690 biological hydrolysis of, 585 biosynthesis of, 861–863 classification of, 700 denaturing, 702 electrophoresis of, 687 fibrous, 700 globular, 700 isoelectric point of, 686 number of in humans, 866 b-pleated sheet in, 701–702 posttranslational modifications of, 866 primary structure of, 700 purification of, 687 quaternary structure of, 700 reaction with Sanger’s reagent, 303 secondary structure of, 700–702 see also Peptide structure of, 700–703 tertiary structure of, 700–702 X-ray crystallography of, 348 Protein Data Bank, 710–711 uses of, 710–711 visualizing enzyme structures and, 735–736 X-ray crystallographic structures in, 348 Protein kinase A, function of, 146 molecular model of, 146 Protic solvent, SN1 reaction and, 416 SN2 reaction and, 406 Proton equivalence, 1H NMR spectroscopy and, 365–367 Protonated methanol, electrostatic potential map of, 153 Protosteryl cation, steroid biosynthesis and, 846–847 Prozac, see Fluoxetine Pseudoephedrine, molecular model of, 145a PTH, see Phenylthiohydantoin, 693–694 Purine, aromaticity of, 280 basicity of, 671 catabolism of, 871–873 electrostatic potential map of, 671 Pyramidal inversion, amines and, 647–648 energy barrier to, 648 Pyran, structure of, 750 Pyranose, 750 Pyridine, aromaticity of, 276, 668 basicity of, 650 bond lengths in, 668 index dipole moment of, 669 electrophilic substitution reactions of, 668 electrostatic potential map of, 276 Hückel 4n rule and, 276 pKa of, 668 Pyridoxal phosphate, alanine catabolism and, 728 amino acid deamination and, 719–721 amino acid transamination and, 719–721 asparagine catabolism and, 730–731 biosynthesis of, 879–884 from pyridoxamine phosphate, 721–722 imines of, 505, 721 serine catabolism and, 729–730 structure and function of, 707 Pyridoxamine phosphate, structure of, 722 transamination of, 721–722 Pyridoxine, structure of, 719 Pyridoxine 5′ phosphate, from 1-deoxyxylulose 5-phosphate, 883 oxidation of, 884 Pyrimidine, aromaticity of, 276 basicity of, 650, 669 electrostatic potential map of, 276 Hückel 4n rule and, 276 Pyrrole, aromaticity of, 276–277, 666 basicity of, 650, 666 electrophilic substitution reactions of, 667 electrostatic potential map of, 276–277, 666 Hückel 4n rule and, 276–277 industrial synthesis of, 666 Pyrrolidine, electrostatic potential map of, 666 enamines from, 635 structure of, 646 Pyrrolysine, structure of, 682 Pyruvate, acetyl CoA from, 783–787 alanine from, 731 carboxylation of, 796–797 catabolism of, 783–787 decarboxylation of, 783–787 from alanine, 728 from phosphoenolpyruvate, 782 from serine, 729–730 oxaloacetate from, 796–797 reaction with thiamine diphosphate, 785 Pyruvic acid, hydrate of, 501 Qiana, structure of, 598d Quartet (NMR), 373 Quaternary ammonium salt, 645 Hofmann elimination and, 660–661 Quaternary carbon, 70–71 Quaternary protein structure, 700 Quetiapine, structure of, 27e Quinine, structure of, 280, 670 Quinoline, aromaticity of, 280 electrophilic substitution reaction of, 670 Quinone, 459 from phenols, 459 hydroquinones from, 459 reduction of, 459 I-27 R configuration, 123 assignment of, 123–124 R group, 71 Racemate, 133 Racemic mixture, 133 Radical, 149 reactivity of, 149–151 Radical reaction, 149–151 addition to alkenes, 237–238 biological examples of, 150–151, 240–241 characteristics of, 149–150 fishhook arrows and, 148 initiation steps in, 150 polymerization, 237–238 propagation steps in, 150 prostaglandin biosynthesis and, 240–241 termination steps in, 150 Radio waves, electromagnetic spectrum and, 330 Radiofrequency energy, NMR spectroscopy and, 351–352 Rapa Nui, rapamycin from, 903 Rapamycin, immunosuppressant activity of, 903 structure and function of, 894 Rate equation, 399 Rate-determining step, 409 Rate-limiting step, 409 Rayon, synthesis of, 765 Re prochirality, 138 Reaction (polar), 149, 152–155 Reaction (radical), 149–151 Reaction coordinate, 168 Reaction energy diagram, 168–170 biological reactions and, 171–172 electrophilic addition reactions and, 168–169 endergonic reactions and, 169–170 exergonic reactions and, 169–170 intermediates and, 171 Reaction intermediate, 170–171 Reaction mechanism, 148 Reaction rate, activation energy and, 169 Rearrangement reaction, 147 Red fox, scent marker in, 482g Reducing sugar, 758 Reduction, acid chlorides, 575 aldehyde, 445–446, 504 alkene, 223–226 alkyne, 253 amides, 586 aromatic compounds and, 307 biological with NADH and NADPH, 226 carboxylic acids, 447 ester, 447, 582–583 ketone, 445–446, 504 lactam, 586 nitrile, 547 organic, 223 quinone, 459 Reductive amination, 657–658 biological example of, 658 mechanism of, 657 Refining (petroleum), 85–86 Unless otherwise noted, all content on this page is © Cengage Learning Copyright 2015 Cengage Learning All Rights Reserved May not be copied, scanned, or duplicated, in whole or in part Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s) Editorial review has deemed that any suppressed content does not materially affect the overall learning experience Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it I-28 index Regiospecific, 197 Replication (DNA), 858–859 error rate during, 859 Replication fork (DNA), 858 Residue (protein), 689 Resolution (enantiomers), 133–134 Resonance, acetate ion and, 36–37 acetyl CoA anion and, 39 acyl cations and, 292 allylic carbocations and, 245–246 allylic radicals and, 387 amides and, 651 arylamines and, 652 benzene and, 37, 270 benzylic carbocation and, 413 benzylic radical and, 306 carboxylate ions and, 535–536 enolate ions and, 607 naphthalene and, 279 p-nitrophenoxide ion and, 442 pentadienyl radical and, 41 pentane-2,4-dione anion and, 40 phenoxide ion and, 441 Resonance effect (electrophilic aromatic substitution), 298 Resonance form, 36–37 drawing, 39–40 electron movement and, 38–39 rules for, 37–39 three-atom groupings in, 39–40 stability of, 39 Resonance hybrid, 37 Restriction endonuclease, 864 (S)-Reticuline, biosynthesis of, 889–890 epimerization of, 890–891 Retinal, vision and, 347 Reye’s syndrome, aspirin and, 315 Rhodopsin, isomerization of, 347 vision and, 347 Ribavirin, structure of, 318g Ribonucleic acid (RNA), 852–855 bases in, 853 biosynthesis of, 859–861 3′ end of, 855 5′ end of, 855 functional, 860 kinds of, 860 messenger, 860 ribosomal, 860 size of, 854 small, 860 structure of, 855 transfer, 860 translation of, 861–863 Ribonucleotide, biosynthesis of, 873–874 catabolism of, 871–873 structures of, 854 Ribose, configuration of, 747 Ribosomal RNA, 860 function of, 861 Ring-flip (cyclohexane), 101 energy barrier to, 101 molecular model of, 101 Ring-opening metathesis polymerization (ROMP), 935 Risk, chemicals and, 24–25 RNA, see Ribonucleic acid Robinson, Robert, 885 Rod cells, vision and, 347 Rofecoxib, structure of, 315 ROMP (ring-opening metathesis polymerization), 935 Rosuvastatin, mechanism of action of, 2, 849–850 rRNA, see Ribosomal RNA Rubber, history of, 258–259 vulcanization of, 259 S configuration, 123 assignment of, 123–124 s-Cis conformation, 249 Diels–Alder dienes and, 249–250 Saccharin, structure of, 770 sweetness of, 770 SAH, see S-Adenosylhomocysteine Salt bridge (protein), 701 Salutaridine, biosynthesis of, 890–891 SAM, see S-Adenosylmethionine Sanger, Frederick, 865 Sanger dideoxy DNA sequencing, 865–866 Sanger’s reagent, 303 uses of, 303 Saponification, 579, 809 mechanism of, 579–580 Saran, structure and uses of, 930 Saturated, 66 Sawhorse representation, 80 SBR polymer, structure and uses of, 931 Schiff base, 505, 779 see also Imine Scurvy, vitamin C and, 551 sec-Butyl group, 71 Secobarbital, synthesis of 640 Second-order reaction, 399 Secondary alcohol, 437 Secondary amine, 645 Secondary carbon, 70–71 Secondary hydrogen, 71 Secondary metabolite, 877 examples of, 877–878 function of, 877 number of, 877 Secondary protein structure, 700–702 a helix in, 700–701 b sheet in, 701–702 Sedoheptulose, structure of, 740 Selectfluor, aromatic fluorination with, 284 Selenocysteine, structure of, 682 Semiconservative replication (DNA), 858 Sense strand (DNA), 861 Sequence rules (Cahn–Ingold–Prelog), 122–125 alkenes and, 188–189 enantiomers and, 122–125 Serine, catabolism of, 729–730 molecular model of, 145a pyruvate from, 729–730 structure and properties of, 681 Seroquel, structure of, 27e Serylalanine, molecular model of, 690 Sesquiterpene, 210 Sesquiterpenoid, 829 Sex hormone, 840–841 Sharpless, K Barry, 526 Sharpless epoxidation, 527 Shielding (NMR), 352 Si prochirality, 138 Sialic acid, 762 Side chain (amino acid), 682 Sigma (s) bond, 11 cylindrical symmetry of, 11 Sigmatropic rearrangement, 917–918 antarafacial geometry of, 918 biological example of, 922–923 examples of, 919–921 [1,5] hydrogen shift and, 919 notation for, 917–918 stereochemical rules for, 918 suprafacial geometry of, 918 vitamin D and, 922–923 Signal averaging, FT-NMR spectroscopy and, 357–358 Sildenafil, structure of, 665 Silver oxide, Hofmann elimination reaction and, 660 Silyl ether, alcohol protecting group, 461–462 Simple sugar, 739 Simvastatin, mechanism of action of, 2, 849–850 structure of, 86f Single bond, electronic structure of, 13 Sitagliptin, structure of, 285 Skeletal structure, 22–23 rules for drawing, 22–23 Skunk scent, cause of, 463 Small RNAs, 860 sn-, naming prefix, 815 SN1 reaction, 409 allylic halides in, 413 benzylic halides in, 413 biological example of, 418–419 carbocation in, 410–411 carbocation stability and, 413–414 characteristics of, 412–416 energy diagram for, 410 Hammond postulate and, 412–413 ion pairs in, 411 kinetics of, 409–410 leaving groups in, 414 mechanism of, 409–410, 414–415 nucleophiles and, 415 racemization in, 411 rate law for, 409 rate-limiting step in, 409–410 solvent effects on, 415–416 stereochemistry of, 410–411 substrate structure and, 413–414 summary of, 416–417 SN2 reaction, 399 allylic halides in, 414 amines and, 656 benzylic halides in, 414 biological example of, 418–419 characteristics of, 401–408 Unless otherwise noted, all content on this page is © Cengage Learning Copyright 2015 Cengage Learning All Rights Reserved May not be copied, scanned, or duplicated, in whole or in part Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s) Editorial review has deemed that any suppressed content does not materially affect the overall learning experience Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it crown ethers and, 473 electrostatic potential maps of, 400 epoxide cleavage and, 469 inversion of configuration in, 399–400 kinetics of, 398–399 leaving groups and, 404–406 mechanism of, 399–400 nucleophiles in, 403–404 rate law for, 399 solvent effects and, 406–407 stereochemistry of, 399–400 steric hindrance in, 401–402 substrate structure and, 401–403 summary of, 407 table of, 404 Williamson ether synthesis and, 467 Soap, 809–810 history of, 809 manufacture of, 809–810 mechanism of action of, 810 micelles of, 810 Sodium amide, reaction with alcohols, 441 Sodium ammonium tartrate, optical activity of, 121 Sodium bisulfite, osmate reduction with, 230 Sodium borohydride, reaction with aldehydes, 445 reaction with ketones, 445 reaction with organomercury compounds, 219–220 reductive amination with, 657–658 Sodium chloride, dipole moment of, 32 Sodium cyclamate, LD50 of, 25 Sodium hydride, reaction with alcohols, 441 Solid-phase DNA synthesis, 866–869 Solid-phase peptide synthesis, 698–700 see also Merrifield, 698–700 Solvation, 406 carbocations and, 416 SN2 reaction and, 406 Solvent, polar aprotic, 406 SN1 reaction and, 415–416 SN2 reaction and, 406–407 Soot, carcinogenic compounds in, 230 Sorbitol, structure of, 757 Spandex, synthesis of, 933–934 Specific rotation, 119–120 table of, 120 Sphingomyelin, 812 function of, 812 structure of, 812 Spin-flip, NMR spectroscopy and, 351 Spin–spin splitting (NMR), 371–373 alcohols and, 477 bromoethane and, 371–372 2-bromopropane and, 372–373 n 1 rule and, 372 13C NMR spectroscopy and, 374–375 1H NMR spectroscopy and, 371–373 nonequivalent protons and, 377–378 origin of, 371–372 rules for, 373–374 tree diagrams and, 377–378 index Squalene, biological epoxidation of, 228, 842–843 from farnesyl diphosphate, 835, 842 steroid biosynthesis and, 842–843 Staggered conformation, 80 molecular model of, 80 Standard state, biological, 164 thermodynamic, 164 Starch, digestion of, 766–767, 774 glucose from, 774 hydrolysis of, 774 limit dextrin from, 774 maltotriose from, 774 structure of, 766 Statins, heart disease and, 2, 849–850 mechanism of action of, 2, 849–850 Stearic acid, molecular model of, 808 structure of, 807 Step-growth polymer, 589, 932–934 table of, 590 Stereochemistry, 79, 92 absolute configuration and, 124 cis–trans alkene isomers and, 187 cis–trans cycloalkane isomers and, 91–92 diastereomers and, 127–128 Diels–Alder reaction and, 249 E,Z alkene isomers and, 188–189 E1 reaction and, 428 E2 reactions and, 424–425 enantiomers and, 114–115 epimers and, 129 R,S configuration and, 123–124 SN1 reaction and, 410–411 SN2 reactions and, 399–400 Stereogenic center, 116 Stereoisomers, 91 cis–trans isomers and, 91–92, 187 diastereomers and, 127–128 enantiomers and, 121 epimers and, 129 kinds of, 135–136 Stereospecific, 235 Stereospecific numbering (sn-), 815 Steric hindrance, SN2 reaction and, 401–402 Steric strain, 82 cis alkenes and, 191–192 substituted cyclohexanes and, 103–104 Steroid(s), 837–841 adrenocortical, 841 anabolic, 841 biosynthesis of, 842–847 carbocation rearrangements in biosynthesis of, 843–847 classification of, 840 conformations of, 109, 838–839 molecular model of, 838 numbering of, 838 synthetic, 841 Steroid hormones, 840–841 Stork enamine reaction, 635–636 mechanism of, 635–636 STR loci, DNA fingerprinting and, 875–876 Straight-chain alkane, 67 I-29 Structure, condensed, 21–22 electron-dot, Kekulé, Lewis, line-bond, skeletal, 22–23 Strychnine, LD50 of, 25 Styrene, anionic polymerization of, 927 Substituent effect, electrophilic aromatic substitution and, 295–302, 308–313 Substitution reaction, 147 Substrate (enzyme), 704–705 Succinate, dehydrogenation of, 791 from succinyl CoA, 790–791 fumarate from, 791 Succinic acid, structure of, 532 Succinyl CoA, from a-ketoglutarate, 790 succinate from, 790–791 Sucralose, structure of, 770 sweetness of, 770 Sucrose, molecular model of, 765 sources of, 764 specific rotation of, 120 structure of, 765 sweetness of, 770 Suffix (nomenclature), 73 Sugar, see also Aldose, Carbohydrate, Monosaccharide simple, 739 d Sugar, 745 Fischer projections of, 745 l Sugar, 745 Fischer projections of, 745 Sulfa drugs, 664 synthesis of, 287 Sulfanilamide, structure of, 287 synthesis of, 664 Sulfathiazole, structure of, 665 Sulfide(s), 435 electrostatic potential map of, 64 from thiols, 474 naming, 465 occurrence of, 437 oxidation of, 475 polarity of, 61 reaction with alkyl halides, 474 sp3 hybrid orbitals in, 19 structure of, 19 sulfoxides from, 475 Sulfonamides, synthesis of, 287 Sulfonation (aromatic), 287 Sulfone(s), 475 from sulfoxides, 475 Sulfonium ion, 137 chirality of, 137–138 Sulfoxide(s), 475 from sulfides, 475 oxidation of, 475 Sunshine vitamin, 922 Superglue, structure of, 927 Suprafacial geometry, 914 Suzuki–Miyaura reaction, 394 mechanism of, 395 Sweeteners, synthetic, 770 Swine flu, 802 Unless otherwise noted, all content on this page is © Cengage Learning Copyright 2015 Cengage Learning All Rights Reserved May not be copied, scanned, or duplicated, in whole or in part Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s) Editorial review has deemed that any suppressed content does not materially affect the overall learning experience Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it I-30 index Swine H1N1 virus, 802 Symmetry plane, 115–116 Symmetry-allowed reaction, 906 Symmetry-disallowed reaction, 906 Syn periplanar geometry, 423 molecular model of, 424 Syn stereochemistry, 220 Syndiotactic polymer, 928 Synthase, 821 Synthesis, trisubstituted aromatic compounds, 308–313 Table sugar, see Sucrose Talose, configuration of, 747 Tamiflu, influenza virus and, 802–803 mechanism of, 802–803 molecular model of, 111 Tamoxifen, structure of, 211e synthesis of, 529h Taq DNA polymerase, PCR and, 869–870 Tartaric acid, stereoisomers of, 130–131 meso-Tartaric acid, molecular model of, 131 Tautomer, 254, 600 Tazobactam, structure of, 598k Termination step (radical reaction), 150 Terpene, 209, 829 number of, 209 Terpenoid, 209, 829–836 biosynthesis of, 829–836 classification of, 829 number of, 878 occurrence of, 829 tert-Amyl group, 76 tert-Butyl group, 71 Tertiary alcohol, 437 Tertiary amine, 645 Tertiary carbon, 70–71 Tertiary hydrogen, 71 Tertiary protein structure, 700–702 hydrophilic interactions in, 701 hydrophobic interactions in, 701 noncovalent interactions in, 701 salt bridges in, 701 Testosterone, conformation of, 109 molecular model of, 109 structure and function of, 840 Tetracycline, structure and function of, 894 Tetrahydrobiopterin, monooxygenase activity and, 886 Tetrahydrofolate, structure and function of, 707 Tetrahydrofuran, as reaction solvent, 213 molecular model of, 437 Tetramethylsilane, NMR spectroscopy and, 355–356 Tetrapyrroles, biosynthesis of, 904a Tetraterpenoid, 829 Tetrazole, DNA synthesis and, 868 Thebaine, biosynthesis of, 892 morphine from 892–893 Thermodynamic quantities, 164–165 Thermodynamic standard state, 164 Thermoplastic polymer, 937–938 characteristics of, 937–938 Tg of, 937 uses of, 938 Thermosetting resin, 939 cross-linking in, 939–940 uses of, 939 Thiamin, aromaticity of, 278 basicity of, 667 Thiamin diphosphate, decarboxylations with, 785–786 pKa of, 785 reaction with pyruvate, 785 structure and function of, 707, 785 ylide from, 785 Thiazole, basicity of, 667 Thiazolium ring, aromaticity of, 278 pKa of, 785 Thioanisole, electrostatic potential map of, 554a -thioate, thioester name ending, 557 Thioester(s), 555 biological hydrolysis of, 598j biological partial reduction of, 588–589 biological reactivity of, 587–589 electrostatic potential map of, 561 naming, 557 pKa of, 608 polarity of, 64 Thioesterase domain (TE), polyketide synthase and, 895 Thioglycolic acid, pKa of, 554c Thiol(s), 435 acidity of, 441 disulfides from, 463 electrostatic potential map of, 64 from alkyl halides, 463 hydrogen bonds in, 439 naming, 438 occurrence of, 437 odor of, 463 oxidation of, 463 polarity of, 61 polarizability of, 154 reaction summary of, 482 reaction with alkyl halides, 474 reaction with Br2, 463 reaction with NaH, 474 sp3 hybrid orbitals in, 19 structure of, 19 sulfides from, 474 thiolate ions from, 474 -thiol, thiol name ending, 438 Thionyl chloride, reaction with alcohols, 390–391, 405, 452 reaction with amides, 544–545 reaction with carboxylic acids, 564 Thiophene, aromaticity of, 278 Thiophenol, 435 Thiourea, reaction with alkyl halides, 463 Threonine, catabolism of, 737e–737f stereoisomers of, 127–128 structure and properties of, 681 Threose, configuration of, 747 molecular model of, 118 Thromboxane B2, structure of, 826 Thymine, electrostatic potential map of, 856 structure of, 853 Thyroxine, biosynthesis of, 286 structure of, 682 Time-of-flight (TOF) mass spectrometry, 328–329 sensitivity of, 329 Tin, reaction with nitroarenes, 655 Titration curve, amino acids and, 684–685 TMS, see Tetramethylsilane, 355 Tollens test, 758 Toluene, electrostatic potential map of, 299 IR spectrum of, 339 1H NMR spectrum of, 377 Toluene-2,4-diisocyanate, polyurethanes from, 933 Torsional strain, 81 Tosylate, 396–397 from alcohols, 405 SN2 reactivity of, 405 Toxicity, chemicals and, 25 TPP, see Thiamin diphosphate Trans fatty acid, formation of, 225–226 from hydrogenation of fats, 808–809 Transamination, 719 amino acids and, 719–722 mechanism of, 719–720 pyridoxamine phosphate and, 721–722 Transcription (DNA), 859–861 Transesterification, 581–582 Transfer RNA, 860 anticodons in, 862–863 function of, 861–863 molecular model of, 863 shape of, 862–863 Transferase, 704–705 Transimination, 721 amino acids and, 721 mechanism of, 721 Transition state, 169 Hammond postulate and, 204–206 Translation (RNA), 861–863 Tree diagram (NMR), 378 Triacylglycerol, 806 catabolism of, 813–820 Trialkylsulfonium ion, alkylations with, 475 from sulfides, 474 Tricarboxylic acid cycle, see Citric acid cycle Trifluoroacetic acid, ether cleavage with, 468 pKa of, 535 (Trifluoromethyl)benzene, electrostatic potential map of, 299 Triglyceride, see Triacylglycerol, 806 Trimethylamine, bond angles in, 647 electrostatic potential map of, 649 molecular model of, 647 Trimetozine, synthesis of, 574 2,4,6-Trinitrochlorobenzene, electrostatic potential map of, 303 Triose-phosphate isomerase, function of, 773 molecular model of, 773 Unless otherwise noted, all content on this page is © Cengage Learning Copyright 2015 Cengage Learning All Rights Reserved May not be copied, scanned, or duplicated, in whole or in part Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s) Editorial review has deemed that any suppressed content does not materially affect the overall learning experience Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it Triphenylphosphine, reaction with alkyl halides, 513–514 Triple bond, electronic structure of, 17 length of, 17 see also Alkyne strength of, 17 Triplet (NMR), 373 Trisubstituted aromatic compound, synthesis of, 308–313 Triterpenoid, 829 tRNA, see Transfer RNA Trypsin, peptide cleavage with, 695 Tryptophan, structure and properties of, 681 Turnover number (enzyme), 704 Twist-boat conformation, cyclohexane, 98–99 molecular model of, 99 Tyrosine, aromatic hydroxylation of, 886–887 biological iodination of, 286 biosynthesis of, 454–455 catabolism of, 737b structure and properties of, 681 Ubiquinones, function of, 460 redox properties of, 460 structure of, 460 Ubiquinone–cytochrome c reductase, function of, 350 molecular model of, 350 Ultrahigh-molecular-weight polyethylene, uses of, 929 Ultraviolet light, electromagnetic spectrum and, 330 wavelength of, 342 Ultraviolet spectroscopy, 342–344 absorbance and, 343 conjugation and, 345 explanation of, 342–343 HOMO–LUMO transition in, 343 interpretation of, 345 molar absorptivity and, 344 Ultraviolet spectrum, benzene, 345 buta-1,3-diene, 344 but-3-en-2-one, 345 b-carotene, 346 cyclohexa-1,3-diene, 345 ergosterol, 349f hexa-1,3,5-triene, 345 Unimolecular, 409 Unsaturated, 180 Unsaturated ketone, conjugate addition reactions of, 518–521 Unsaturation, degree of, 181 Upfield (NMR), 355 Uracil, structure of, 853 Urea, from ammonia, 724–727 Urea cycle, 724–727 steps in, 725 Urethane, 933 Uric acid, from xanthine, 873 pKa of, 554c structure of, 723 Uridine triphosphate, glycoconjugate biosynthesis and, 756 index Urocanase, active site of, 736 ribbon model of, 735 Uronic acid, 758 from aldoses, 758–759 Urushiols, structure of, 436 UV, see Ultraviolet Valdecoxib, structure of, 318g Valence bond theory, 10–19 orbital hybridization and, 12–19 orbital overlap in, 10–11 Valganciclovir, structure of, 876d Valine, structure and properties of, 681 Valinomycin, structure of, 473 Valsartan, synthesis of, 394 Van der Waals forces, 54 alkanes and, 79 polymers and, 937 Vasopressin, structure of, 691 Vegetable oil, 806 hydrogenation of, 225–226, 808 table of, 807 Vent DNA polymerase, 870 Vestenamer, synthesis of, 936 Viagra, structure of, 665 Vinyl group, 184 Vinyl monomer, 238 Vinylcyclopropane, rearrangement of, 924c Vinylic, 290 Vinylic anion, electrostatic potential map of, 257 Vinylic carbocation, 290 Vinylic halide, SN2 reaction and, 402–403 Vioxx, see Rofecoxib Virion, 802 Visible light, electromagnetic spectrum and, 330 Vision, chemistry of, 346–347 retinal and, 347 Vitamin, 550, 705 Vitamin A acetate, industrial synthesis of, 515 Vitamin B6, structure of, 719 Vitamin B12, structure of, 848 Vitamin C, from glucose, 551 history of, 550–551 industrial synthesis of, 551 molecular model of, 551 scurvy and, 551 uses of, 550 Vitamin, coenzymes from, 705–707 Vitamin D, sigmatropic rearrangements and, 922–923 Vitamin K1, biosynthesis of, 293 Viton polymer, structure and uses of, 931 Vulcanization, 259 rubber and, 259 Walden, Paul, 396 Walden inversion, 396–398 Wang resin, peptide synthesis and, 699 Water, acid–base behavior of, 43 conjugate addition reactions to enones, 520 dipole moment of, 32 electrophilicity of, 155 electrostatic potential map of, 46, 155 hydrogen bond in, 54–55 nucleophilicity of, 155 pKa of, 45 reaction with enones, 520 Watson, James, 855 Watson–Crick DNA model, 855–856 Wave equation, Wave function, molecular orbitals and, 20–21 Wavelength (l), 329 Wavenumber, 333 Wax, 806 Whale blubber, composition of, 807 Williamson ether synthesis, 466–467 Ag2O in, 466 carbohydrates and, 754 mechanism of, 466 Wittig reaction, 513–514 mechanism of, 513 uses of, 514–515 ylides in 513–514 Wohl degradation, 760 Wood alcohol, 435 Woodward, Robert Burns, 906 Woodward–Hoffmann rules, pericyclic reactions and, 906–907 X rays, electromagnetic spectrum and, 330 X-Ray crystallography, 348 X-Ray diffractometer, 348 Xanthine, from guanine, 872 oxidation of, 872–873 Xylocaine, structure of, 57 Xylose, configuration of, 747 Yeast alcohol dehydrogenase, stereochemistry of, 139–140 -yl, alkyl group name ending, 69–70 Ylide, 513 synthesis of, 514 Wittig reaction and, 513–514 -yne, alkyne name ending, 185 Z configuration, 189 assignment of, 188–189 Zaitsev, Alexander, 420 Zaitsev’s rule, 420 alcohol dehydration and, 452–453 Hofmann elimination and, 661 NMR proof for, 363–364 Ziegler–Natta catalyst, 929 Zocor mechanism of action of, 2, 849–850 structure of, 86f Zusammen (Z configuration), 189 Zwitterion, 50, 679 amino acids and, 679 electrostatic potential map of, 679 Unless otherwise noted, all content on this page is © Cengage Learning Copyright 2015 Cengage Learning All Rights Reserved May not be copied, scanned, or duplicated, in whole or in part Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s) Editorial review has deemed that any suppressed content does not materially affect the overall learning experience Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it I-31 Copyright 2015 Cengage Learning All Rights Reserved May not be copied, scanned, or duplicated, in whole or in part Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s) Editorial review has deemed that any suppressed content does not materially affect the overall learning experience Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it Periodic Table of the Elements 79 Au Gold 196.9665 Group number, U.S system IUPAC system Period number An element 8A H Hydrogen 1.0079 4A (14) 5A (15) 6A (16) 7A (17) C N O F Ne Lithium 6.941 Beryllium 9.0122 Boron 10.811 Carbon 12.011 Nitrogen 14.0067 Oxygen 15.9994 Fluorine 18.9984 Neon 20.1797 12 Na Mg Sodium 22.9898 Magnesium 24.3050 20 Al Si 14 15 16 S Cl Ar Aluminum 26.9815 Silicon 28.0855 Phosphorus 30.9738 Sulfur 32.066 Chlorine 35.4527 Argon 39.948 13 3B 4B 5B 6B 7B 8B 8B 8B 1B 2B (3) (4) (5) (6) (7) (8) (9) (10) (11) (12) 21 Sc Ti 22 23 V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr Potassium 39.0983 Calcium 40.078 Scandium 44.9559 Titanium 47.88 Vanadium 50.9415 Chromium 51.9961 Manganese 54.9380 Iron 55.847 Cobalt 58.9332 Nickel 58.693 Copper 63.546 Zinc 65.39 Gallium 69.723 Germanium 72.61 Arsenic 74.9216 Selenium 78.96 Bromine 79.904 Kyrpton 83.80 38 39 Y Zr Nb Rubidium 85.4678 Strontium 87.62 Yttrium 88.9059 Zirconium 91.224 Niobium 92.9064 56 40 42 Mo 43 Tc Molybdenum Technetium 95.94 (98) 46 29 47 30 35 Cd In Sn Sb Te 52 53 I Xe Ruthenium 101.07 Rhodium 102.9055 Palladium 106.42 Silver 107.8682 Cadmium 112.411 Indium 114.82 Tin 118.710 Antimony 121.757 Tellurium 127.60 Iodine 126.9045 Xenon 131.29 La Hf Ta W Re Os 76 77 Ir Pt Au Hg Tl Pb Bi Po At Rn Lanthanum 138.9055 Hafnium 178.49 Tantalum 180.9479 Tungsten 183.85 Rhenium 186.207 Osmium 190.2 Iridium 192.22 Platinum 195.08 Gold 196.9665 Mercury 200.59 Thallium 204.3833 Lead 207.2 Bismuth 208.9804 Polonium (209) Astatine (210) Radon (222) 89 104 88 Ra Francium (223) Radium (226) Ac Actinium (227) 105 107 108 Db Sg Bh Hs Rutherfordium Dubnium (268) Seaborgium (271) Bohrium (270) Hassium (277) (265) 58 Lanthanides Numbers in parentheses are mass numbers of radioactive isotopes 106 Rf Ce Cerium 140.115 60 Nd 61 Pm Praseodymium Neodymium Promethium 140.9076 144.24 (145) 110 Ds 111 Rg 112 Cn 62 63 64 65 114 116 Flerovium Livermorium (289) (293) Fl Meitnerium Darmstadtium Roentgenium Copernicium (281) (280) (285) (276) 66 84 67 85 Lv 68 69 70 71 Sm Eu Gd Tb Dy Ho Er Tm Yb Lu Samarium 150.36 Europium 151.965 Gadolium 157.25 Terbium 158.9253 Dysprosium 162.50 Holmium 164.9303 Erbium 167.26 Thulium 168.9342 Ytterbium 173.04 Lutetium 174.967 U Np Pu Am Cm Bk Cf Es Fm Md No 102 103 Thorium Protactinium Uranium Neptunium Plutonium Americium Curium Berkelium Californium Einsteinium Fermium Mendelevium Nobelium Lawrencium 232.0381 231.0359 238.00289 (237) (244) (243) (247) (247) (251) (252) (257) (258) (259) (262) 92 93 94 95 96 97 98 99 100 101 Pa 91 86 Th 90 Actinides 59 Pr 109 Mt 83 54 Ba 78 36 Ag 82 51 34 Pd 81 50 33 Rh 80 49 32 Ru 79 48 31 Barium 137.327 73 75 45 28 Cs 72 74 44 27 Cesium 132.9054 Fr 57 41 26 18 Ca Sr 25 17 K Rb 24 P 10 B 87 3A (13) 2A (2) Be 55 He Helium 4.0026 Li 37 Nonmetals (18) 19 Semimetals 11 Metals Atomic number Symbol Name Atomic weight 1A (1) Unless otherwise noted, all content on this page is © Cengage Learning Copyright 2015 Cengage Learning All Rights Reserved May not be copied, scanned, or duplicated, in whole or in part Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s) Editorial review has deemed that any suppressed content does not materially affect the overall learning experience Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it Key Lr Structures of Some Common Functional Groups Name Alkene (double bond) Alkyne (triple bond) Structure C Name ending Name -ene Sulfide -yne Disulfide C OCqCO Structure C Sulfoxide C None X Aldehyde C C -ol OH Ketone ether C Carboxylic acid O P O– Ester O– Amine -one C C -oic acid C OH -oate O C N Thioester C O C Imine (Schiff base) C Amide S C C OCqN C N -nitrile Acid chloride SH -amide O C C C None N C -thioate O C Thiol H -amine C Nitrile -al phosphate O C C O C Monophosphate S+ O C O sulfoxide O C Ether S C O– (X 5 F, Cl, Br, I) Alcohol S None C Halide sulfide C disulfide C Arene (aromatic ring) S Name ending -thiol -oyl chloride O C C Cl Unless otherwise noted, all content on this page is © Cengage Learning Copyright 2015 Cengage Learning All Rights Reserved May not be copied, scanned, or duplicated, in whole or in part Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s) Editorial review has deemed that any suppressed content does not materially affect the overall learning experience Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it ... pplications 3e ith Biological A w y tr is m he C Organic ts r today’s studen fo l ea id is it at th Sincerely, John McMurry All royalties from Organic Chemistry with Biological Applications will... edition Hybrid version with access (24 months) to oWlv2 with Mindtap reader isBn: 978-1-285-86784-7 A briefer, paperbound version of Organic Chemistry with Biological Applications, third edition,... greater emphasis on those organic reactions and topics that are relevant to biological chemistry than on those that are not Organic chemistry, which began historically as the chemistry of living organisms,