CHEM1602/3 Chemistry for Biologists

Section B: Shapes, dynamics and stereochemistry

Chirality ⇒ chiros (hand in Greek)

mirror image of left hand is not a ball is a ball is a ball

a left hand, but a right hand

An object (molecule) is chiral when it cannot be superimposed on its mirror image

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Section B: Shapes, dynamics and stereochemistry

Chirality and Carbon

Carbon centres with four different substituents lead to chiral molecules

that are non-superimposable with their mirror image.
Molecules whose image and mirror image are non-superimposable are called enantiomers.
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Section B: Shapes, dynamics and stereochemistry

Properties of Enantiomers
Enantiomers rotate plane polarised light by the same degree but in opposite directions

number of degrees = achiral property; direction = chiral property

CH3 CH3

O O

anticlockwise = negative sign clockwise = positive sign

H H
H2 C CH3 H3 C CH2

(–)-carvone (+)-carvone

[α]D25 = –60° (neat) [α]D25 = +60° (neat)

smell: spearmint smell: caraway seed

Achiral molecules are optically inactive

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Section B: Shapes, dynamics and stereochemistry

R,S-Convention
Two enantiomers differ in their configuration at the stereogenic centre
How can we tell which one is which? ⇒ The Cahn-Ingold-Prelog (CIP) Rules

a a

b d d b
c c
I II

Step 1: Assign a priority to the four groups at the stereogenic centre: a a

a > b> c > d

Step 2: look along axis from Carbon ⇒ lowest priority substituent d b c c b

(Mercedes Star) I II
Step 3: if Mercedes Star a → b → c turns clockwise = R -configuration
if Mercedes Star a → b → c turns counterclockwise = S - configuration
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Section B: Shapes, dynamics and stereochemistry

Priority Rules in the R,S-Convention

Rule 1: atoms directly attached to stereogenic centre are ranked by atomic number
e.g.: Cl > O > C > H
(Hint: if one atom is H, it necessarily has lowest priority)

Rule 2: if decision cannot be reached under Rule 1, consider next the next atom in
the chain
e.g.: H3CCH2 > CH3

Rule 3: Multiple bonds are treated as the equal number of single bonds (attach
“dummy” atoms)
C C O C
C C H C C H C O C O
C C
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Section B: Shapes, dynamics and stereochemistry

Examples for applying the R,S-Convention

H H3C H H CH3
HO H
Br
Cl F O

H3C Br
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Section B: Shapes, dynamics and stereochemistry

Fischer - Projections
(used only for amino acids and sugars)
lactic acid
CO2H CO2H CO2H
H OH H OH OH
CH3 H3C H
CH3
what it is what it means how to generate it
Rules
•longest carbon chain vertical
•most oxidized carbon on top
CH=O CH=O

HO H H OH

CH2 OH CH2 OH

L R-(+)-glyceraldehyde D S-(-)-glyceraldehyde

In a given Fischer Projection, look at the stereocentre farthest away from the top carbon
if the substituent of highest priority is to the right: configuration D
if the substituent of highest priority is to the left: configuration L
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Section B: Shapes, dynamics and stereochemistry

D,L - Nomenclature CH=O

(used for sugars and amino acids only!)
H OH

HO H
CH=O CH=O
H OH
HO H H OH
H OH
CH2 OH CH2 OH
CH2 OH
R-(+)-glyceraldehyde S-(-)-glyceraldehyde
glucose

In a given Fischer Projection, look at the stereocentre farthest away from the top carbon

if the substituent of highest priority is to the right: configuration D

if the substituent of highest priority is to the left: configuration L

Note that the DL nomenclature only assigns the configuration at one centre - it assumes that you know the rest.
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Section B: Shapes, dynamics and stereochemistry

The Configuration of Amino Acids

COOH

H2 N H

COOH COOH

H2 N H H2 N H

CH3 CH2 SH

L-(+)-alanine L-(+)-cysteine

Most naturally occurring α-amino acids in living systems have L configuration

Home revision exercise: Assign the configurations of these amino acids using the R & S system?
What about the other amino acids? Are they the same or different?

An unsolved mystery: Why did Nature choose L amino acids? Why not D? Was it just chance or is there a
reason? See Martin Gardner - “The New Ambidextrous Universe” and Chris McManus “Left Hand, Right Hand”.