Chapter 2

Basics of Organic Chemistry

2.1
Types of Chemical Formulae
Base
Les dirents types de formules chimiques
47
trivial name IUPAC name molecular
formula
condensed
formula
structure formulae
isobutane 2-methylpropane C,H,,
CH, -CH(CH, )-
CH,
isopropyl alcohol propan-2-ol C,H,O CH, -CH(OH)-CH,
acetone propan-2-one C,HO CH,-C(O)- CH, C
C
O
C
C C
C
C
H
3
C
O
CH
3
H
3
C
OH
CH
3
CH
3
CH
3
H
3
C
H
H
H
H
H
H
H
H
H
H
C C
OH
C
H
H
H
H
H
H
H
H
H
H
H
H
H
O
H
H
H
H
H
H
H
H
H
H
OH
H
H
H
H
H
H
H
H
H
H
H
H
H
O
OH
Base
Dierent Types of Chemical Formulae
48
trivial name IUPAC name molecular
formula
condensed
formula
structure formulae
acetic acid ethanoic acid C,H,O,
CH,-C(O)-OH
CH,COOH
benzene benzene CH CH
styrene 1-phenylethene C,H, CH,-CH=CH,
C
C
O
OH
C
C
C C
C
C
C
C
C
C
C
C C
C
H
3
C
O
OH
CH
2
H
H
H
H
H
H H
H
H
H
H
H
H
H
H
H
H
O
OH
H
H
H
H
H
H H
H
H
H
H
H
H
H
H
H
H
O
OH
2.2
Names of Functional Groups
Basics
Overview of Hydrocarbon Derivatives
50
hydrocarbons compounds that only contain C and H
alkanes hydrocarbons that only contain single bonds alkenes alkynes arenes
linear
alkanes
branched
alkanes
cyclic
alkanes
alkanes with a single carbon backbone
without branching points
R
R
R
R R
R
R
R
R
R
R
R
C
m
H
n
Basics
Overview of Functional Groups Monovalent Functional Groups
51
haloalkanes alcohols
amines
miscellaneous
R F
R Br
R Cl
R I
R
N
R
R
N
R
R
R
R OH
R
R
OH
R
R OH
H
H
N
R
H
OH
R
O
R
uoroalkane
bromoalkane
iodooalkane
chloroalkane
primary alcohol
secondary alcohol
tertiary alcohol
primary amine
secondary amine
tertiary amine
phenol
ether
Basics
Overview of Functional Groups Divalent and Trivalent Functional Groups
52
divalent derivatives
carbonyl & related derivatives
trivalent derivatives
carboxyl derivatives
tetravalent derivatives
carbonic acid derivatives
miscellaneous
derivatives
R H
O
R OH
O
HO OH
O
R O
O O
R
aldehyde (carboxylic) acid carbonic acid
carbonate ketone ester
anhydride
R R
O
R OR
O
RO OR
O
acetal
RO NR
2
O
R NR
2
O
R H
RO OR
R C N
nitrile urethane amide
R
2
N NR
2
O
R Hal
O
R R
RO OR
ketal acid halogenide urea
2.3
Basic Rules of Nomenclature
Nomenclature
Nomenclature of Linear Alkanes and the corresponding Alkyl Residues (Radical Groups)
54
methane
hexane
pentane
butane
propane
ethane
mthane
hexane
pentane
butane
propane
thane
H
H H H
H H H
H
H H H
H H H
H
H H H
H H
H
H H H
H H
H
H H
H H
H
H H
H H
H
H H
H
H
H H
H
H
H
H
H
H
H
H
H
H
H
H C
H
H
H
H C
H
C
H
H
H
H
H C
H
C
H
C
H
H
H
H
H
H C
H
C
H
C
H
H
C
H
H
H
H
H
H C
H
C
H
C
H
H
C
H
H
C
H
H
H
H
H
H C
H
C
H
C
H
H
C
H
H
C
H
H
C
H
H
H
H
H
CH
4
CH
3
(CH
2
)
4
CH
3
CH
3
(CH
2
)
3
CH
3
CH
3
(CH
2
)
2
CH
3
CH
3
CH
2
CH
3
CH
3
CH
3
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) ...
X CH
3
X
CH
3
CH
3
X
CH
3
X CH
3
X
CH
3
X
methyl
hexyl
pentyl
butyl
propyl
ethyl
CH
3
H
3
C
CH
3
H
3
C
CH
3
H
3
C
CH
3
H
3
C
CH
3
H
3
C
Nomenclature
Basic Rules of Nomenclature of Branched Alkanes (Rules)
55
1. Find and name the longest carbon chain in the molecule

if two chains are equally long, choose the one that has more substitutents
2. Name all residues attached to this chains as alkyl chains

if the side chains are further bracnhed, the same rules apply: lnd the longest carbon chain, then name the subsittuents to it (iterative)
3. Number the atoms of the main chain starting with the end that is closest to rst substituent

if two substituents are at the same distance from the two ends, one decides on the basis of the alphabetic order of these substituents

if there is more than one substitutent, the one chooses the one (of two) possibilities that results in the lowest number for the lrst case of dierence
4. Number the atoms in the substituents starting with the rst 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 a molecule contains the same type of substituents multiple times, its name is preceded with a numbering prelx (di-, tri-, tetra-, etc.)
Nomenclature
Nomenclature of Branched Alkanes (Examples)
56
Nomenclature
Nomenclature of Branched Alkanes (Examples)
57
1 3
2
1 3
2 4 3
4 6
5
2
3
4 6
5
5
4
3 1
2
1
7
6
2
1
2-methylpropane
2-methylbutane
not 3-methylbutane
3-methylhexane
not 2-propylbutane
3-ethyl-4-methylhexane 3-methyl-4-propylheptane
not 4-propyl-5-methylheptane
not 4-(1-methylpropyl)heptane
Nomenclature
Nomenclature of Branched Alkanes (Examples)
58
Nomenclature
Nomenclature of Branched Alkanes (Examples)
59
1 3
2
1
2
1
3
2
4
1 3
2 4
5
6
4 2
3
3
4
5
6
7
8
10
11
12
13
14
15
9
1 3
4 2
3 1
2 5
6
7
8
9
16
1
2,2-dimethylbutane 2,2,4-trimethylhexane 5-(2,2-dimethylpropyl)nonane
3-methyl-7-(3,3-dimethylbutyl)-
12-(1-ethyl-2-methylpropyl)hexadecane
Nomenclature
Important Trivial Names of Alkyl Groups
60
isopropyl (1-methylethyl)
isobutyl (2-methylproyl)
isopentyl (3-methylbutyl)
cyclohexyl
sec.-butyl (1-methylproyl)
CH
3
CH
3
CH
3
CH
3
CH
3
CH
3
CH
3
CH
3
CH
3
CH
3
CH
3
CH
3
CH
3
CH
3
H
3
C CH
3
H
3
C CH
3
CH
3
tert.-butyl (1-methylproyl)
neopentyl (2,2-dimethylpropyl)
tert.-hexyl (1,1,2,2-tetramethylpropyl)
Nomenclature
Nomenclature of Alkanes Using Trivial Names of Alkyl Groups
61
1
1 3
2 4
5
6 1 3
2 4
5
6
1
2
1 3
2
7
8 7
8
9
10
1 3
2 4
5
6
1
2
7
8
2-cyclohexylhexane
or 1-(2-hexyl)-cyclohexane
4-(1-methylethyl)octane
or 4-isopropyloctane
4-(1,1-dimethylethyl)octane
or 4-(tert.-butyl)octane
5-(2,2-dimethylpropyl)decane
or 5-neopentyldecane
La nomenclature des alcnes et alcynes
Nomenclature
Nomenclature of Alkenes and Alkynes (Rules)
62
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 sux ane by ene or yne

if a molecule contains more than one double/triple bond, the sulx is preceded with a numbering prelx (di-, tri-, tetra-, etc.)
Nomenclature
Nomenclature of Alkenes and Alkynes (Examples)
63
Nomenclature
Nomenclature of Alkenes and Alkynes (Examples)
64
1 3
2 4
1
2
1 3
2 4
3
4
5
1 2 3 1 2 3
4
1 2 3 4
5 6
6
7
1-butene
or but-1-ene
4-propyl-3-heptene
2-butene
or but-2-ene
1-butyne
or but-1-yne
2-butyne
or but-2-yne
5-mthyl-2-hexyne
Nomenclature
Nomenclature of Alkenes and Alkynes (Examples)
65
Nomenclature
Nomenclature of Alkenes and Alkynes (Examples)
66
5
4
3 1
2
5
4
3 1
2
6
6 5 4 3
2
1
2
3
4
6
5
1
4-ethyl-3-methyl-2-hexene
3-ethyl-4-propyl-1,5-hexadiene
not 3,4-di(ethenyl)heptane
2-ethylhex-1-ene-4-yne 4-ethyl-3-propylhex-1-ene-5-yne
not 3-ethyl-4-propylhex-5-ene-1-yne
Nomenclature
Nomenclature of Aromatic Compounds
67
1. The aromatic 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

benzene naphthalene anthracene
tetracene pentacene
Nomenclature
Nomenclature of Aromatic Compounds
68
1-hexylbenzene 1-butyl-2-ethylbenzene 1-(4-ethylhexyl)benzene
1
2
3
4
5
6
1
2
3
4
5
6
1
2
3
4
5
6 1 3 5
2 6 4
Nomenclature
Important Trivial Names of Alkenyl, Alkynyl, and Aromatic Substituents
69
vinyl (1-ethenyl) ethynyl (1-ethynyl) phenyl
allyl (2-propenyl) propargyl (2-propynyl) benzyl (1-phenylmethyl)
Nomenclature
Naming of Unsaturated Compounds with Trivial Names
70
1 3
2 4
5
6
7
8
1 3
2 4
5
6
7
8
1 3
2 4
5
6
7
8
2
1
4-vinyl-1,7-octadiene
or 4-(eth-1-enyl)-1,7-octadiene
4-phenyl-1,7-octadiene 4-benzyl-1,7-octadiene
1-phenyl-1-ethene
or vinylbenzene
or styrene
Nomenclature
Nomenclature of Haloalkanes
71

indicate the position of the halogen and its nature with a prex (uoro, chloro, bromo, iodo)
2-uoropropane 2-chlorobutane
1-bromo-2-methylpentane
non 2-(1-bromomethyl)pentane
1-bromo-5-chloro
-3-(1-iodoethyl)pentane
F Cl
1 3
2
1 3
2 4
Br
2
3 5
4
2
3
1
2
I
1
Cl
4
5
1
Br
Nomenclature
Nomenclature of Alcohols
72

nd the longest chain that contains the alcohol, name it, and append the sux ol

alternatively, indicate its position on the alkane (or alkyl residue) and use prex hydroxy
2-propanol
or propan-2-ol
or 2-hydroxypropane
ou isopropanol
1,3-butandiol
or butan-1,3-diol
or 1,3-dihydroxybutane
2-ethyl-1-pentanol
or 2-ethylpentan-1-ol
or 3-(1-hydroxymethyl)hexane
3-propyl-1,4-hexandiol
not 4-(2-hydroxyethyl)-3-heptanol
OH OH
1 3
2
4 2
3 1
OH
2
3 5
4
3
4 6
5
HO
OH
2
1
1
OH
Nomenclature
Nomenclature of Amines
73
2-propanamine
or propan-2-amine
or 2-aminopropane
or isopropylamine
2,4-pentandiamine
or pentan-2,4-diamine
or 2,4-diaminopentane
2-propan-(N,N-dithyl)amine
or 2-(N,N-diethyl)aminopropane
or dithylisopropylamine
2-(1-aminomthyl)-1,4-butandiol
not 2-(1-hydroxymthyl)-
4-hydroxy-1-butanamine
NH
2
NH
2
1 3
2
5 3
4 2
N
2
H
2
N
OH
3
4
NH
2
1
2
1 3
1
HO
1

nd the longest chain that contains the amine, name it, and append the sux amine

alternatively, indicate its position on the alkane (or alkyl residue) and use prex amino
Nomenclature
Nomenclature of Aldehydes
74

nd the longest chain that contains the aldehyde, name it, and append the sux al
propanal propandial 3,4-dimethylhexanal
not 3,4-dimethyl-5-hexanal
not 2-ethyl-3-methyl-5-pentanal
3-ethyl-5-hydroxypentanal
or 3-ethyl-pentanal-5-ol
not 3-ethyl-pentan-5-al-1-ol
H
O
H
O
4
3 1
2
3
OH
4
5
O
2
1
5
O
H
O
H
H
6

Nomenclature of Ketones
75

nd the longest chain that contains the ketone, name it, and append the sux one
propanone 2,4-pentandione
3-propylhexan-2-one
not 4-(2-acetyl)heptane
3-ethylhexanal-4-one
O
O
O
2
3 5
4
3
4 6
5
O
O
2
1
O
1
1 3
2 4
5 6

Nomenclature of Carboxylic Acids
76
OH
O
HO
O
HO O
2 4
3
3
4
5
HO
O
2
1
O
OH
1
O
OH
OH
propanoic acid
propandioic acid
old: methanedicarboxylic acid
2-propyl-
butandioic acid
old: pentane-1,2-dicarboxylic acid
3-ethyl-4-
hydroxypentanoic acid

nd the longest chain that contains the acid function, and append the sux oic acid
Nomenclature
Important Trivial Names for Aldehydes, Acids, Esters, and Acyl Residues
77
aldehydes carboxylic acids esters acyl residues examples
H H
O
H OH
O
H O
O
H
O
O
O
H
O
OH
O
O
O O
H
O
OH
O
O
O O
H
O
OH
O
O
O O
H
O
OH
O
O
O O
O
O
H
NH
O
formaldehyde
methanal
acetate
ethanoate
propionate
propanoate
valeryl
pentanoyl
butyryl
butanoyl
propionyl
propanoyl
acetyl
ethanoyl
formate
methanoate
formyl
methanoyl
thyl propanoate
ou acide thyl ester
propionique
phnyl formate
ou acide phnyl ester
mthanoque
N-actyl-2-
pentanamine
valeric acid
acide pentanoic acid
butyric acid
butanoic acid
propionic acid
propanoic acid
valerate
pentanoate
butyrate
butanoate
acetic acid
ethanoic acid
valeraldehyde
pentanal
butyraldehyde
butanal
propionaldehyde
propanal
acetaldehyde
ethanal
formic acid
methanoic acid
2.4
Isomerism
Isomers
Isomers
79

Isomers have the same molecular formula (e.g., C

5
H
10
O
2
) but dierent structural formula
H
3
C
O
OH
O
H
H
3
C
O
OH
CH
3
H
3
C
O
OH
CH
3
HO
O
H
HO
CH
3
H
3
C
O
H
OH
HO OH
HO
OH
OH HO
OH HO
H
3
C
O
H
OH
Isomers
Types of Isomers (1)
80
chemical compounds
same molecular formula?
no yes
isomers
same connectivity of atoms?
dierent compounds
stereoisomers
conversion without breaking bonds?
constitution isomers
same functional groups?
enantiomers
functional
isomers
same carbon skeleton?
no yes
conguration isomers
dierence in spatial orientation at double bond?
chain
isomers
position
isomers
conformers
rotation around one single bond?
yes
rotamers
no yes
no yes yes no
no yes
geometric isomers
no yes
diastereomers
isomers like object and mirror image?
Isomers
Types of Isomers (2)
81
chemical compounds
same molecular formula?
no yes
isomers
dierent compounds
H
3
C
O
OH
H
3
C
O
OH
CH
3
H
3
C
O
OH
H
3
C
O
H
CH
3
H
3
C
CH
3
H
3
C
C
5
H
10
O
2
C
6
H
12
O
2
C
4
H
8
O
2
C
5
H
10
O
C
5
H
10
C
5
H
8

All types of isomers have the same molecular formula but dierent structural formula
H
3
C
O
OH
H
3
C
O
OH
CH
3
H
3
C
O
O CH
3
H
3
C
O
H
OH
OH
OH
C
5
H
10
O
2
C
5
H
10
O
2
HO
HO
C
5
H
10
O
2
C
5
H
10
O
2
C
5
H
10
O
2
C
5
H
10
O
2
Isomers
Types of Isomers (3)
82
isomers
same connectivity of atoms?
stereoisomers constitution isomers
no yes
functional isomers
chain isomers
position isomers
H
3
C
O
OH
O
H HO
acid alcohol aldehyde
O
H HO H
3
C
O
H
OH
pentanoic acid methylbutanoic acid
5-hydroxypentanal 3-hydroxypentanal
conformers
geometric isomers
diastereomers or enantiomers
H
3
C
O
H
OH
H
CH
3
O
H HO
H
interconversion without breaking bonds
interconversion would require rotation around double bond
H
3
C
CH
3
H
3
C
CH
3
no interconversion by real or hypothetical bond rotation
CH
3
O
H HO
H H
3
C
O
H HO
H
H
3
C
O
OH
CH
3
H
3
C
O
OH
Isomers
Types of Isomers (4)
83
stereoisomers
conversion without breaking bonds?
conguration isomers conformers
no yes
Natta projection
Sawhorse projection
Newman projection
geometric isomers
diastereomers
enantiomers
H
3
C
Et HO
H
COOH
Br
H
3
C
COOH HO
H
Et
Br
H
3
C
H OH
Br HOOC
Et
H
3
C
H OH
Et
COOH Br
Br
COOH
Et CH
3
H OH
Br HOOC
Et
CH
3
H OH
CH
3
O
H HO
H H
3
C
O
H HO
H
OH HO OH HO
H
3
C
CH
3
H
3
C
CH
3
no mirror images
mirror images
Isomers
Types of Isomers (5)
84
conguration isomers
dierence in spatial orientation at double bond?
no yes
geometric isomers diastereomers or enantiomers
but not
but not
N
CH
3
N
CH
3
H
3
C
CH
3
H
3
C
CH
3
H
3
C
OH CH
3
H
3
C
CH
3
O
H
H
3
C
HO
CH
3
O
H
H
3
C
O
CH
3
OH
H
(E) (Z)
(E) (Z)
(E) (Z)
diastereomers
enantiomers
CH
3
O
H HO
H H
3
C
O
H HO
H
OH HO OH HO
no mirror images
mirror images
Isomers
Enantiomers and Diasteromers
85

Tetrahedral carbon atoms with four dierent residues are called chiral centers or stereocenters

Stereocenters, Chirality, Diastereomers, and Enantiomers

Chiral centers give rise to two non-superimposable stereoisomers with dierent 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 the presence of an intramolecular mirror plane

Molecules with multiple stereocenters are enantiomers if conguration of all stereocenters is inverse
diastereomers
enantiomers
chiral
identical
achiral
HO OH
* *
HO OH
* *
HO OH HO OH
* * * *
B
D
A
C
B
D
A
C
* *
Isomers
Nomenclature of Stereocenters (1)
86
H
2
N H
COOH
H
3
C
H
2
N
H
H
3
C
COOH
L-alanine
L-2-aminopropanoic acid
D-alanine
D-2-aminopropanoic acid

Fischer projection (for amino acids, carbohydrates, and related biomolecules)

Most natural amino acids have L-conguration, natural carbohydrates have D-conguration

arrange molecule such that the backbone is bent downwards and project

arrange molecule such that carbon in highest oxidation state points up (in view)

if closest amino/hydroxy function points left, conguration is L, if right, it is D

H H
2
N
COOH
CH
3
H H
2
N
COOH
CH
3
H NH
2
COOH
CH
3
* *
H H
2
N
COOH
CH
3
H
O
OH
NH
2
H H
2
N
COOH
CH
2
OH
*
O
OH
NH
2
OH
O OH
H
OH OH OH
OH
OH H
H HO
OH H
OH H
CH
2
OH
O H
*
glycine
2-aminoethanoic acid
L-serine
L-2-amino-3-hydroxypropanoic acid
D-glucose
D-2,3,4,5,6-pentahydroxyhexanal
Isomers
Nomenclature of Stereocenters (2)
87
(S)-2-bromopropanoic acid

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 rst 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 conuration is (R), and if counterclockwise, it is (S)
CH
3
O
Br
H
OH
4
3 2
1
H
3
C
O
Br
H
HO
4
H
3
C
O
H Br
OH
4
3
2
1
H
3
C
O
Br H
OH
4
3
2
1
* *
3 2
1
H
3
C
O
OH
Br
H
3
C
O
OH
Br
2S,4S-dihydroxypentane 2S,3R-dihydroxypentandioic acid
D,L-tartric acid
2R,3S,4R,5R,6-pentahydroxyhexanal
D-glucose
(S) (S) (S) (S)
OH OH
1 1
2 2
3 3
(R) (R)
(S) (S)
O OH
OH
1
1
2
2
OH
HO
O
(S) (S)
O
OH
NH
2
O
HO
1
2 3
2S-aminobutandioic acid
L-glutamic acid
(R)-2-bromopropanoic acid
(S) (S)
(R) (R) (R) (R)
O OH
H
OH
(R) (R)
OH OH
OH
1
2
Isomers
Conformations of Alkanes
88
E

0 60 120 180
staggered
trans
staggered
gauche()
eclipsed eclipsed
eclipsed eclipsed
staggered
gauche(+)
240 300 360
3.8 kJ/mol
14.2 kJ/mol
14.2 kJ/mol
CH
3
H H
H H
CH
3
CH
3
H H
CH
3
H
H
CH
3
H H
H H
3
C
H
H
H
H
3
CCH
3
H H H
H
H
3
CCH
3
H H
H
3
C
H
HCH
3
H H
H
CH
3
HCH
3
H H