Post on 02-Jan-2016
First Year ChemistryFirst Year ChemistryTheory (Organic)Theory (Organic)
Starting date: 20 th October (Every Mon, Wed, Thu)
Finishing Date: 17th NovemberTeacher: Prof. A. BasakReference book: Clayden/T.W.G. Solomons
Peter Sykes
Topics to be covered:1) Structure / stereochemistry2) Ionic rxns– addition/
elimination/substitution/ rearrangements3) Free radical reactions4) Concerted reactions(Diels
Alder/electrocyclic)5) Amino acids /peptides/enzymes
(chymotrypsin)6) Carbohydrates/ nucleic acids
Lecture 1Lecture 1
Why read organic Why read organic chemistry?chemistry?
Life is organic chemistry Organic chemistry is the
chemistry of the compounds of carbon
Deoxyribonucleic acids or DNA
RNA Proteins
Drug molecules:
BaseO
O
OBase
O
O
O
PO O
H2N
NH
HN
O
O
O
R2
R1
OCOCH3
COOH
Aspirin
N
S
HN
O
CH3
CH3
H H
O
COOH
R
Penicillins
NHCOCH3
OH
Paracetamol
COOHH3C
Ibuprofen
StereochemistrStereochemistry:y:
Chemistry in space, as a function of molecular geometry.
Constitution based chemistry:
All these alcohols behave differently to certain reagents. That is due to their different modes of connectivity.
x = functional group with same connectivity. However, reactivity of X may differ again certain reagents.
Reactivity of the hydroxyl groups somewhat different.
OH
OH OH
C X
D
A
B X C
D
A
B
H
HOH
OH
Stereoisomerism Isomerism
constitutional stereo
chain functional positional enantiomersdiastereomers
Enantiomers: Stereoisomers that are mirror images of one another
enantiomers
If a molecule is nonsuperimposable with its mirror image, then it becomes optically active and is called a chiral molecule.
H3C
OH
HOOC
CH3
HH
COOH
OH
C - C - C - C
C - C - C C
C - O - C
C - C -O
C - C - C
OC - C - C
O
Chiral Centre (Asymmetric Centre): An atom, usually carbon
attached to four different ligands (atoms or groups)
Stereogenic Centre: An atom, again usually carbon, in which interchanging the position of two ligands gives rise to a stereoisomer.
This includes the carbon atom attached to four different ligands as also the sp2 carbon which can show cis-trans isomerism
Z
C
R
X
Y
R
C
Z
X
Y
C C
Me
H
Me
H
C C
H
Me
Me
H
Stereogenic centre Stereogenic centre
Representation in 2D:
Projection Formula :Fischer, Newman………….
Fischer Projection :
Suppose a molecule is drawn as :
Rules:
(1) Exchange in a group of three allowed
R
Z
XY
R
Z
XY
Z
R
X
Y
X
Y
ZR
XR
ZY
X
Y
ZR
X
Z
YR
X
Y
RZ
(2) 1800 in plane rotation is allowed
(3) 900 in plane rotation ?
(4) 1800 out of plane rotation ?
X
Z
YR
Z
X
RY
Not Allowed
Not Allowed
Absolute configuration : The R,S - notation
(1)Assign priority sequence to the four groups attached to a stereogenic carbon following the sequence rule.
(2) Observe the stereogenic centre from a direction opposite to the group of lowest priority.
(3) Trace the path from 1 to 2 to 3
If clockwise R ( rectus, right)
If anticlockwise S (sinister, left)1
4
23
1
4
23
S R
Sequence Rules:
(1)If the four atoms directly attached to the stereogenic centre are different, higher atomic number takes precedence over lower.
(2) If the atoms directly attached to the stereocentre are same, then work outward along the two chains atom by atom until a point of difference is reached.
(3) Double and triple bonds are treated by assuming that each such bonded atom is duplicated or triplicated.
H3C
C
Br Cl
H(3) (4)
(2)(1)
S
Br
Cl
CH2CH2CH3
CH2CH
CH3
CH3
(1)
(2)(3)
(4)
s
C
O
H C
O C
O
H COH
HOH> CH CH2 C
H
C
C
H
H
C > CCH3
CH3
H
What are absolute configurations of the following compounds :
More rules:
R precedes S
HC
CHC OH
HH3CHC
H3C
H3CH
C
O
C
H3C
H
CN
C
H
OH
Cl
Cl
H
H
BrBr
C
R
S
(2)(4)
(3)(1)
S
C
CH2CH2CH3
HO CH2CD2CH3
H
C
CD2CH2CH3
CH2 CHCH3
CH3
E precedes Z
cis precedes trans
Isotopic discrimination to be applied only when atomic no. fails
CH3
H
Br
Cl
1
22
1
Z
H
CH3
Br
Cl 1
2
2
1
E