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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