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First Year Chemistry Theory (Organic) Starting date: 20 th October (Every Mon, Wed, Thu) Finishing Date: 17th November Teacher: Prof. A. Basak Reference book: Clayden/T.W.G. Solomons Peter Sykes Topics to be covered: 1) Structure / stereochemistry 2) Ionic rxns– addition/ elimination/substitution/ rearrangements 3) Free radical reactions 4) Concerted reactions(Diels Alder/electrocyclic) 5) Amino acids /peptides/enzymes (chymotrypsin) 6) Carbohydrates/ nucleic acids Lecture 1 Why read organic chemistry? O Life is organic chemistry Organic chemistry is the chemistry of the compounds of carbon Deoxyribonucleic acids or DNA RNA Proteins R1 O H N H2N N H O R2 Base O O O O Drug molecules: P O O O Base O NHCOCH 3 H N R OCOCH3 H H S CH3 COOH O N CH3 O COOH Penicillins OH Aspirin Paracetamol H 3C COOH Ibuprofen Stereochemistry: Chemistry in space, as a function of molecular geometry. Constitution based chemistry: OH OH OH All these alcohols behave differently to certain reagents. That is due to their different modes of connectivity. A B A C X X C D B D x = functional group with same connectivity. However, reactivity of X may differ again certain reagents. OH H OH Reactivity of the hydroxyl groups somewhat different. H Stereoisomerism Isomerism constitutional chain C-C-C-C C-C-C stereo C-O-C C-C-C C - C -O O C - C- C C Enantiomers: enantiomers diastereomers positional functional O Stereoisomers that are mirror images of one another H3C CH 3 COOH HOOC H H OH OH enantiomers If a molecule is nonsuperimposable with its mirror image, then it becomes optically active and is called a chiral molecule. 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 X Z X Me C C Y R R Y Me C Z Stereogenic centre H Me C H C H H Stereogenic centre C Me Representation in 2D: Projection Formula : Fischer, Newman…………. R Fischer Projection : R Y X Y X Z Suppose a molecule is drawn as : Z X X Z R Y Y X R R Z X R Rules: Z Y Y Z (1) Exchange in a group of three allowed X R X Y Z Z R Y (2) 1800 in plane rotation is allowed Z X R Y Y Z (3) 900 in plane rotation (4) 1800 out of plane rotation R X ? 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 1 S 4 3 2 R 4 3 2 Sequence Rules: (1)If the four atoms directly attached to the stereogenic centre are different, higher atomic number takes precedence over lower. (3) H3C H (4) S C (1)Br Cl (2) (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 (1) reached. (4) Br CH 2CH 2CH3 s CH3 Cl (2) CH 2CH (3) CH3 (3) Double and triple bonds are treated by assuming that each such bonded atom is duplicated or triplicated. O O C C H C H O > OH C OH H CH CH2 C H C C C > H H CH3 C H CH3 What are absolute configurations of the following compounds : O H3CHC HC C H3C C H HC H OH H C H3C CN H3C Cl More rules: R H (2) (4) H Br Br C C OH R precedes S Cl (1) (3) S S H 1 1 Br CH3 2 Cl H2 E precedes Z cis precedes trans 1 2 Br H 2 Cl CH3 E Z Isotopic discrimination to be applied only when atomic no. fails HO CH2CD2CH3 C H CD2CH2CH3 C CH2CH2CH3 1 CH2 CH CH3 CH3