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Chapter 3 Molecular Structure 3.1 Basic Rules of Nomenclature Hydrocarbons hydrocarbons compounds that only contain C and H CmHn arenes R alkynes alkenes R R R cyclic alkanes alkanes R R branched alkanes R R R “saturated” hydrocarbons that only contain single bonds R alkanes with a single carbon backbone without branching points linear alkanes R R 73 Nomenclature of Linear Alkanes and the corresponding Alkyl Residues (“Radical Groups”) methane méthane CH4 H H C H H ethane éthane CH3CH3 H H H C C H H H propane propane CH3CH2CH3 butane butane CH3(CH2)2CH3 pentane pentane CH3(CH2)3CH3 hexane hexane CH3(CH2)4CH3 H H H H C C C H H H H H H H H H C C C C H H H H H H H H H H H C C C C C H H H H H H H H H H H H H C C C C C C H H H H H H H HH H H HH H X H H3C HH HH HH H HH HH HH H H3C H H H3C HH HH HH HH HH H HH HH H HH HH HH H H3C HH HH HH H H3C X CH3 CH3 methyl CH3 ethyl X CH3 CH3 propyl X CH3 CH3 butyl CH3 CH3 X pentyl CH3 X CH3 hexyl analogous for the higher alkanes: heptane, octane,nonane, decane, undecane, dodecane, tridecane, tetradecane, pentadecane, hexadecane, heptadecane, octadecane, nondecane, eicosane (C20H42), heneicosane (C21H44), docosane (C22H46), tricosane (C23H48) ... tricontane (C30H62), ... tetracontane (C40H82) ... 74 Basic Rules of Nomenclature of Branched Alkanes 1. find and name the longest carbon chain in the molecule • if two chains are equally long, choose the one that has more substituents 2. name all residues attached to this main chain as “alkyl” residues • if the side chains are branched, apply the same rules iteratively: find the longest carbon chain, etc. 3. number the atoms of the main chain starting with the end that is closest to first substituent • • if two substituents at the same distance from the two ends, alphabetic order of these substituents decides if two identical substituents at the same distance from the two ends, next substituents along the chain decide (iterative) 4. number the atoms in the substituents starting with the first atom attached to the main chain 5. put the substituents into alphabetic order • • the substituents are preceded with a numbering indicating the atom of the main chain they are attached to if the same type of substituents is found multiple times, name is preceded with a numbering prefix (di-, tri-, tetra-, etc.) 4 1 2 3 2-methylpropane 3 5 2 4 6 1 3-methylhexane not 2-propylbutane not 4-methylhexane 1 2 5 3 6 3 3-ethyl-4-methylhexane 7 6 5 2 1 4 3-methyl-4-propylheptane not 4-propyl-5-methylheptane not 4-(1-methylpropyl)heptane 75 Nomenclature of Branched Alkanes (Examples) 76 Nomenclature of Branched Alkanes (Examples) 4 1 2 3 4 2,2-dimethylbutane 1 2 3 4 5 6 3 2,2,4-trimethylhexane 7 3 1 4 2 3 2 4 6 1 5 8 1 9 10 11 12 2 13 2 1 5 3 6 2 7 1 8 9 5-(2,2-dimethylpropyl)nonane 3 14 15 16 3-methyl-7-(3,3-dimethylbutyl)12-(1-ethyl-2-methylpropyl)hexadecane 77 Trivial Names of Alkyl Groups CH3 CH3 isopropyl (1-methylethyl) CH3 CH3 isobutyl (2-methylpropyl) CH3 CH3 isopentyl (3-methylbutyl) CH3 CH3 CH3 CH3 CH3 sec.-butyl (1-methylpropyl) tert.-butyl (1,1-dimethylethyl) CH3 CH3 CH3 neopentyl (2,2-dimethylpropyl) H3C CH3 CH3 H3C CH3 cyclohexyl tert.-hexyl (1,1,2,2-tetramethylpropyl) 78 Nomenclature of Alkanes Using Trivial Names of Alkyl Groups 1 2 1 1 2-cyclohexylhexane or 1-(2-hexyl)-cyclohexane 1 1 2 3 4 2 3 1 6 7 8 4-(1,1-dimethylethyl)octane or 4-(tert.-butyl)octane 5 6 7 8 4-(1-methylethyl)octane or 4-isopropyloctane 2 5 4 1 2 3 4 5 2 6 3 7 8 9 10 5-(2,2-dimethylpropyl)decane or 5-neopentyldecane 79 Nomenclature of Alkenes and Alkynes (Rules) 1. name the longest chain that contains the double/triple bond • the molecule may well contain longer carbon chains, but the one that contains the double/triple bond has priority 2. indicate the position of the double/triple bond • give the number of the carbon atom of the double/triple bond that is closer to the end of the chain 3. replace the suffix “ane” by “ene” or “yne” • if more than one double/triple bond exists, the suffix is preceded with a numbering prefix (di-, tri-, tetra-, etc.) 3 2 1 3 4 1 2 3 2-butene or but-2-ene 6 4 5 3 2 3 1-butyne or but-1-yne 2 1 4-propyl-3-heptene 4 1 5 2 3 2-butyne or but-2-yne 1 2 3 4 5-methyl-2-hexyne 4 4-ethyl-3-methyl-2-hexene 1 5 6 1 1 4 7 1-butene or but-1-ene 2 6 5 4 2 3 2-ethylhex-1-ene-4-yne 80 Nomenclature of Aromatic Compounds 1. The aromatic or heteroaromatic residue is (typically) considered to be the core of the molecule • • typically, trivial names are used all other residues attached to it are treated as substituents to this core, using previous rules benzene naphthalene anthracene tetracene pentacene phenanthrene pyrene benzopyrene perylene pyridine pyrrol furan thiophene N N H O S 81 Important Trivial Names of Alkenyl, Alkynyl, and Aromatic Substituents vinyl (1-ethenyl) ethynyl (1-ethynyl) phenyl allyl (2-propenyl) propargyl (2-propynyl) benzyl (1-phenylmethyl) 82 Naming of Unsaturated Compounds (Including Trivial Names) 6 5 6 5 4 1 2 4 2 3 1 2 3 4 5 4 3 1-butyl-4-ethylbenzene 1-hexylbenzene 1-phenylhexane 1 6 6 7 8 4-vinyl-1,7-octadiene or 4-(eth-1-enyl)-1,7-octadiene 1 2 3 4 5 6 7 8 4-phenyl-1,7-octadiene or (1-(prop-2-enyl)pent-4-enyl)-benzene 1 5 2 3 4 5 6 1 2 3 1-(4-ethylhexyl)benzene 1 2 3 4 5 6 7 8 4-benzyl-1,7-octadiene or (2-(prop-2-enyl)hex-5-enyl)-benzene 2 1 1-phenyl-1-ethene or vinylbenzene or styrene 83 Monovalent Functional Groups R F R NH 2 R OH fluoroalkane alkyl amine aminoalkane alkyl alcohol, alkanol hydroxyalkane R Cl R PH 2 R SH chloroalkane alkyl phospine alkyl mercaptane alkanthiol R Br bromoalkane OH R I iodoalkane phenol • in monovalent functional groups, carbon has one single bond connected to a heteroatom 84 Nomenclature of Amines and Alcohols R N H H N H R N R primary alcohol R OH R H secondary amine R OH R H H primary amine R R R tertiary amine secondary alcohol R O R dialkyl ether R S R dialkyl thioether OH R R secondary alcohol • in primary, secondary, tertiary amines, the amine nitrogen is bonded to one, two, three alkyl groups • in primary, secondary, tertiary alcohols, the OH group is bonded to a primary, secondary, tertiary carbon • primary, secondary, tertiary carbons are connected to one, two, three alkyl groups 85 Nomenclature of Haloalkanes • identify the longest chain to which the halogen atom is attached, and name it as usual • use the prefix “fluoro”, “chloro”, “bromo”, “iodo”, indicate its position with number • if different halogen atoms attached to the same chain, sort alphabetically • if multiple halogen atoms of the same type attached to same chain, use number prefix (di, tri, tetra) F 1 2 3 Cl 3 2-fluoropropane 1 2 3 4 2-chlorobutane 2 4 I 5 Br 1 1-bromo-2-methylpentane non 2-(1-bromomethyl)pentane Br 1 2 1 3 2 4 5 Cl 1-bromo-5-chloro -3-(1-iodoethyl)pentane • priority rules: alkene, alkyne > haloalkane • if a molecule contains an alkene or alkyne, they take precedence for longest chain and suffix 86 Nomenclature of Amines • identify the longest chain to which the amine is attached, name it, append suffix “amine” • indicate its position on the chain with number • if multiple amines attached to same chain, use number prefix (di, tri, tetra) • if higher priority groups present, use prefix “amino” and indicate position with number 1 NH2 NH2 NH2 1 2 3 2-propanamine or propan-2-amine or 2-aminopropane or isopropylamine 5 4 3 2 2 3 N 1 2,4-pentandiamine or pentan-2,4-diamine or 2,4-diaminopentane 2-propan-(N,N-diethyl)amine or 2-(N,N-diethyl)aminopropane or diethylisopropylamine HO H2N 1 1 2 3 4 OH 2-(1-aminomethyl)-1,4-butandiol not 2-(1-hydroxymethyl)4-hydroxy-1-butanamine • priority rules: amine > alkene, alkyne > haloalkane • amine takes precedence over alkene, alkyne, halogen for longest chain and suffix 87 Nomenclature of Alcohols and Thiols • identify the longest chain to which the alcohol/thiol is attached, name it, append suffix “ol”/“thiol” • indicate its position on the chain with number • if multiple alcohols/thiols attached to same chain, use number prefix (di, tri, tetra) • if higher priority groups present, use prefix “hydroxy”/“mercapto” and indicate position with number OH 1 2 3 2-propanol or propan-2-ol or 2-hydroxypropane ou isopropanol OH OH 4 3 2 1 1,3-butandiol or butan-1,3-diol or 1,3-dihydroxybutane 3 2 4 5 OH 1 HO 4 3 5 2 6 1 OH 2-ethyl-1-pentanol 3-propyl-1,4-hexandiol or 2-ethylpentan-1-ol not 4-(2-hydroxyethyl)-3-heptanol or 3-(1-hydroxymethyl)hexane • priority rules: alcohol > amine > alkene, alkyne > haloalkane • alcohol takes precedence over amine, alkene, alkyne, halogen for longest chain and suffix 88 Divalent Functional Groups NH R R (H) O O R H R R imine aldehyde alkanal ketone alkanone R 2N NR 2 RO OR RO OR R R R R (H) aminal H acetal R ketal • in divalent functional groups, carbon has two bonds connected to heteroatom(s) • the C=O group is called “carbonyl” group 89 Nomenclature of Ketones and Aldehydes • identify the longest chain to which the ketone/aldehyde is attached, name it, append suffix “one”/“al” • indicate the position of the ketone on the chain with number (aldehyde is always terminal, no number) • if multiple ketones/aldehydes attached to same chain, use number prefix (di, tri, tetra) • if higher priority groups present, use prefix “oxy” and indicate position with number 1 O O 2 1 propanone O propanal 3 4 H 3 5 2,4-pentandione O H O O propandial O 4 O 5 6 3-propylhexan-2-one 3 H 2 6 5 4 2 4 3 5 6 2 1 OH 3-ethyl-1-hydroxyhexan-4-one OH 1 O H 3,4-dimethylhexanal 5 4 3 H 2 1 O 3-ethyl-5-hydroxypentanal • priority rules: aldehyde > ketone > alcohol > amine > alkene, alkyne > haloalkane • aldehyde, then ketone takes precedence over other functional groups for longest chain and suffix 90 Nomenclature of Carboxylic Acids • identify the longest chain to which the acid is attached, name it, append suffix “oic acid” • carboxylic acid(s) is always terminal, no number needed • if two acids attached to same chain, use number prefix (di) • if more carboxylic acid groups are present in side chains, use prefix “carboxy” and indicate position O O OH propanoic acid HO 2 O OH propandioic acid old: methanedicarboxylic acid HO 1 3 O 4 OH O 2-propylbutandioic acid old: pentane-1,2-dicarboxylic acid HO 4 3 5 OH 2 1 O 3-ethyl-4hydroxypentanoic acid • priority rules: acid > ester > amide > aldehyde > ketone > alcohol > amine > alkene, alkyne > … • acids take precedence over other functional groups for longest chain and suffix 91 Important Trivial Names for Aldehydes, Acids, Esters, and Acyl Residues aldehydes carboxylic acids esters acyl residues formaldehyde methanal formic acid methanoic acid formate methanoate formyl methanoyl O O H acetaldehyde ethanal O OH acetic acid ethanoic acid O O H propionaldehyde propanal O butyraldehyde butanal O valeraldehyde pentanal acetate ethanoate OH propionic acid propanoic acid OH butyric acid butanoic acid O propionate propanoate valeric acid pentanoic acid propionyl propanoyl O O butyrate butanoate O OH acetyl ethanoyl O O O H O O O H O butyryl butanoyl O O valerate pentanoate valeryl pentanoyl 92 Nomenclature of Carboxylic Acid Esters • identify the longest chain to which the ester is attached, name it, append suffix “oate” • prepend the name with the remaining residue ended by “yl” (use number prefix if necessary) • carboxylic acid ester(s) always terminal, no number needed • if two carboxylic acid esters attached to same chain, use number prefix (di) Cl O 4 3 2 1 O 1 2 3 4 hexyl butanoate old: butanoic acid hexyl ester 5 6 4 3 O 2 1 O 1 O 2 3 4 5 6 hex-2-yl 3-chlorobutanoate or: 1-methylpentyl 3-chlorobutanoate old: 3-chlorobutanoic acid 2-hexyl ester 5 4 3 2 1 O 1 2 3 OH 3 4 2-hydroxybutyl pent-4-enoate old: 4-pentenoic acid 2-hydroxybutyl ester 2 1 O 4 O O 3 2 1 O 1 2 3 di(2-propenyl) butandioate or diallyl butandioate old: butandioic acid di(2-propenyl) ester • alternatively, you name like a carboxylic acid, append the residue ended by “yl”, and append “ester” • naming of compounds with more than two esters (i.e., in side chains) complex, but rarely needed 93 Nomenclature of Carboxylic Acid Amides • identify the longest chain to which the amide is attached, name it, append suffix “amide” • prepend the name with the remaining residue ended by “yl” (use number prefix if necessary) • carboxylic acid amide(s) always terminal, no number needed • if two carboxylic acid amides attached to same chain, use number prefix (di) Cl O 4 3 2 1 N H 1 2 3 4 hexyl butanamide old: butanoic acid hexyl amide 5 6 4 3 O 2 1 O 1 N H 2 3 4 5 6 5 4 3 2 1 N H 1 2 3 OH 3 4 2 1 O 4 O O 3 2 1 N H 1 2 3 hex-2-yl 3-chlorobutanamide 2-hydroxybutyl pent-4-enamide di(2-propenyl) butandiamide old: 4-pentenoic acid or diallyl butandiooate or: 1-methylpentyl 2-hydroxybutyl amide old: butandioic acid 3-chlorobutanamide di(2-propenyl) amide old: 3-chlorobutanoic acid 2-hexyl amide • alternatively, you name like a carboxylic acid, append the residue ended by “yl”, and append “amide” • naming of compounds with more than two amides (i.e., in side chains) complex, but rarely needed 94 Summary of the Priority Rules O OH > O OR O > H > O > R OH > > NH 2 > Hal group acid ester aldhyde ketone alcohol amine alkene, alkyne halide suffix -oic acid -oate -al -one -ol -amine -ene, -yne – prefix – oxycarbonyl- oxo- oxo- hydroxy- amino- en-, yn- halo- H2N 1 2 3 Br 4 4-bromo-butanamine not: 4-aminobutylbromide H2N 4 3 2 OH 1 4-amino-butanol not: 4-hydroxybutanamine O HO 4 3 2 O 1 4-hydroxy-butan-2-one not: 3-oxobutanol not: but-3-one-1-ol H 1 O 2 3 O 4 3-oxo-butanal not: 4-oxobut-2-one not: but-3-one-1-al HO 1 O 2 3 O 3-ethyloxycarbonylpropanoic acid • the functional group with the higher priority defines the base name (using the suffix) • any functional group with a lower priority treated as a substituent (using prefix nomenclature) 95 Naming of Simple Compounds with Tetravalent Functional Groups • in tetravalent functional groups, carbon has four bonds connected to heteroatom(s) HO O O O OH RO carbonic acid carbonate O O RO NR 2 urethane (carbamate) R 2N O OR di(but-2-yl) carbonate O NR 2 urea O O N H OH N-(4-hydroxybutyl) O-tert.-butyl urethane • tetravalent functions are relevant in polymers (polycarbonates, polyurethanes, polyureas) 96 2.4 Isomerism Isomers H3C O O OH CH3 O H3C OH O H3C CH3 OH H HO HO H3C H3C CH3 O H OH O HO HO OH OH HO OH HO OH H OH O H • isomers have the same molecular formula (e.g., C H 5 10O2) but different structural formula 98 Types of Isomers chemical compounds same molecular formula? no different compounds yes isomers same connectivity of atoms? constitution isomers no yes same functional groups? yes chain isomers same carbon skeleton? no yes stereoisomers conversion without breaking bonds? functional isomers no no yes rotation around one single bond? yes configuration isomers position isomers difference in spatial orientation at double bond? no yes conformers rotamers geometric isomers isomers like object and mirror image? diastereomers no yes enantiomers 99 Chemical Compounds versus Isomers chemical compounds same molecular formula? no different compounds O H3 C OH H3 C C5H10 O2 H3 C OH H3 C C4H 8O2 CH3 C5H10 O O OH C5H10 O2 H3 C H HO H3 C CH3 C5H 8 CH3 OH C5H10 O2 OH O H3 C O OH C5H10 O2 C5H10 O H3 C C5H10 O2 CH3 O O OH H3 C CH3 O isomers C6H12 O2 O H3 C yes HO OH H C5H10 O2 C5H10 O2 • all types of isomers have the same molecular formula but different structural formula Isomers 100 Constitution Isomers versus Stereoisomers isomers same connectivity of atoms? no constitution isomers functional isomers OH O O OH acid H HO alcohol aldehyde chain isomers H3C H3C H H H CH3 O H HO interconversion without breaking bonds geometric isomers CH3 O O OH pentanoic acid H3C OH methylbutanoic acid position isomers H3C CH3 H3C CH3 interconversion would require rotation around double bond diastereomers or enantiomers O HO stereoisomers conformers O H3C yes OH O H 5-hydroxypentanal H3C H 3-hydroxypentanal H3C H HO O H H CH3 O H HO no interconversion by real or hypothetical bond rotation • if the connectivity of all atoms is the same, the compounds are stereoisomers 101 Configuration Isomers versus Conformers stereoisomers conversion without breaking bonds? no configuration isomers geometric isomers H3C CH3 H3C CH3 H3C H HO COOH Br Et Et Br COOH H3C H HO Sawhorse projection OH HO OH no mirror images enantiomers H3C H HO conformers Natta projection diastereomers HO yes H3C H Et Br HOOC Et OH Br H3C H COOH OH Newman projection O H H CH3 O H HO mirror images HOOC H CH3 Br Et OH Et CH3 H Br COOH OH • if converting compounds into one another requires breaking of a bond, they are configuration isomers 102 Conformations of Alkanes E eclipsed eclipsed H3C CH3 HH H H 14.2 kJ/mol staggered gauche(–) H3C H eclipsed eclipsed H CH3 H CH3 H3HC H 60 CH H 3 120 H H CH3 180 φ HH H H staggered gauche(+) H H CH3 H H 3.8 kJ/mol 0 HH staggered trans CH3 H H H H H3C CH3 CH3 CH3 H H 14.2 kJ/mol 240 300 360 • fast rotation around single bonds at room temperature, conformers are actually the same compounds 103 Stereoisomers versus Diastereomers and Enantiomers configuration isomers difference in spatial orientation at double bond? diastereomers or enantiomers diastereomers HO yes geometric isomers H3C (E) OH HO CH3 H3C enantiomers H H CH3 O H HO mirror images H3C (Z) HO O H (E) OH CH3 O CH3 CH3 but not H3C OH no mirror images H3C H HO no (E) N CH3 H3C O O (Z) CH3 (Z) H H OH but not H3C CH3 N CH3 • if different spatial orientation of residues due to a double bond, the compounds are geometric isomers 104 Enantiomers and Diasteromers • tetrahedral carbon atoms with four different residues are “chiral centers” or “stereocenters” A A * D B * D B C C • stereocenters, chirality, diastereomers, and enantiomers • chiral centers give rise to two non-superimposable stereoisomers with different “handedness”, or “chirality • molecules with one stereocenter are chiral; they exist as two enantiomers (non-superimposable mirror images) • molecules with multiple stereocenters are not chiral in presence of an intramolecular mirror plane (or inversion center) • molecules with multiple stereocenters are enantiomers if configuration of all stereocenters is inverse diastereomers HO * • OH * HO * OH * HO * OH * HO * OH * enantiomers identical chiral achiral if molecules comprise an internal mirror plane (or inversion center), they are achiral 105 Nomenclature of Stereocenters • IUPAC nomenclature, following the “Cahn-Ingold-Prelog” rules • • • • assign priorities to substituents at stereocenter according to increasing atomic weight of the connecting atom if the first connecting atom is the same, proceed to the substituents on this atom turn the moleule such that the substituent with the lowest priority (i.e., 4) is pointing to the back if the substituents 1→ 2→ 3 are arranged clockwise, the confiuration is (R), and if counterclockwise, it is (S) Br 1 Br H 4 * O H3C 2 3 OH OH H3C 1 4 H Br O O CH3 3 2 OH (S)-2-bromopropanoic acid 1 1 OH OH 3 (S) (S) 22 3 2S,4S-dihydroxypentane HO 2 O 1 OH O (R) (S) 2 OH OH 1 4H 1 Br 4 H Br 1 * O H3C 2 3 OH O H3C 3 HO 2 Br H3C OH O (R)-2-bromopropanoic acid OH OH O (R) (R) (S) (R) 2 H OH OH OH 1 O HO 1 NH2 3 2 OH (S) O 2S,3R-dihydroxypentandioic acid 2R,3S,4R,5R,6-pentahydroxyhexanal 2S-aminobutandioic acid D,L-tartric acid D-glucose L-glutamic acid • stereochemical notation is added to the number prefixes in the compound names 106