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

http://www.chem.ox.ac.uk/proteins/images/carboxypeptidase.pdb

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