Organic and Biochemistry

Development of Complex Curricula for Molecular Bionics and Infobionics Programs within a consortial* framework**

Consortium leader

PETER PAZMANY CATHOLIC UNIVERSITY

Consortium members

SEMMELWEIS UNIVERSITY, DIALOG CAMPUS PUBLISHER

The Project has been realised with the support of the European Union and has been co-financed by the European Social Fund ***

**Molekuláris bionika és Infobionika Szakok tananyagának komplex fejlesztése konzorciumi keretben

***A projekt az Európai Unió támogatásával, az Európai Szociális Alap társfinanszírozásával valósul meg.

PETER PAZMANY CATHOLIC UNIVERSITY SEMMELWEIS

UNIVERSITY

Isomerism: 2D and 3D. Configuration, conformation; 3D representation

(Izoméria: 2D és 3D nézetben. Konfiguráció, konformáció; térbeli ábrázolás)

Organic and Biochemistry

(Szerves és Biokémia )

semmelweis-egyetem.hu

Compiled by dr. Péter Mátyus

Table of Contents

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Organic and Biochemistry: isomerism, configuration, conformation

Isomerism 4 – 8

Stereochemistry 9 – 16

Types of isomerism

Two compounds are

with the same general formula

Are they superimposable on each other?

their structures are the same

they are isomeric structures

yes not

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Organic and Biochemistry: isomerism, configuration, conformation

Is their connectivity different?

the compounds are con- stitutional isomers

the compounds are stereoisomers

Is their relationship the same as an object and its nonidentical mirror-image?

yes yes

not not

Enantiomers Diastereomers

Are they superimposable by simple rotation around a single bond?

Are they superimposable by simple rotation around a single bond?

Conformational enantiomers

Configurational enantiomers

Conformational diastereomers

Configurational diastereomers

yes not yes not

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Organic and Biochemistry: isomerism, configuration, conformation

CONSTITUTIONAL ISOMERISM

Configurational isomerism STEREOISOMERISM

Conformational isomerism

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Organic and Biochemistry: isomerism, configuration, conformation

Isomerism

These compounds possess the same molecular formula, but the connectivity of atoms is different.

Different 2D structures

2. Stereoisomers

These compounds possess the same general formula and connectivity, they differ in the spatial arrangement of their atoms/groups.

Different 3D structures

Enantiomers: nonsuperimposable mirror-images of each other

Diastereomers: stereoisomers but not with enantiomeric relationship (not mirror-images of each other)

1. Constitutional isomers

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Organic and Biochemistry: isomerism, configuration, conformation

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Organic and Biochemistry: isomerism, configuration, conformation

C

H₃ CH₂ CH₂ CH₃ 1° 2°

n-butane

C

H₃ CH₂ CH₂

C

H₃ CH CH₂ CH₃

n-butyl

sec-butyl

C

H₃ CH CH₃ CH₃

3° H₃C CH CH₂

CH₃

isobutane

isobutyl

C H₃ C

CH₃ 1°

Stereochemistry

Configuration:

A particular spatial arrangement of atoms, usually disregarding the rotation around the single bonds.

Conformation:

A particular arrangement that originates from rotation around the single bonds.

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Organic and Biochemistry: isomerism, configuration, conformation

The difference in properties of isomers is due to the difference in the relative arrangements of various atoms or groups present in their molecules.

- stretching

- bending

- torsion

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Organic and Biochemistry: isomerism, configuration, conformation

O O H

H r₁

r₃ r₂

O O H

H α

O O H

τ(φ)

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Organic and Biochemistry: isomerism, configuration, conformation

HOO + ^H +^H

O H

~90 ~50 kcal/mol E

r

E

α

~30 kcal/mol

O O H

H

O O

H

H O

O

H H

stretching

dissociation

bending

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Organic and Biochemistry: isomerism, configuration, conformation

H H H

H

τ (torsional angle)

H

H

H H

HH O O

H

H

O O

H

H

~10 kcal/mol

~1 kcal/mol

Newman projection:

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Organic and Biochemistry: isomerism, configuration, conformation

H H YZ

H H Y Z

H Z

H Y

H Y

H Z

H Z

H Y

H Y H

Z

H H YZ

60° 120° 180° 240° 300° 360°

0°

-180° -60°

-240°

-360° -300° -120° 0°

clockwise

counterclockwise

CH₂ CH₂ Z

Y Y = Z = H ethane

Y = Z = CH₃ n-butane

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Organic and Biochemistry: isomerism, configuration, conformation

H H

H H H

H

60° 120° 180° 240° 300° 360°

0°

C H H₃

H H

H H H CH

3

H CH

3

H H

H H

H H H H

M M

m m m

1/2 M 1/2 M

minimum

E(Θ)

Θ

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Organic and Biochemistry: isomerism, configuration, conformation

H H YZ

H H Y Z

H Z

H Y

H Y

H Z

H Z

H Y

H YH

Z

H H YZ

60° 120° 180° 240° 300° 360°

0°

H H

H H H

H

H H

H H C H₃

CH₃

anti effect

gauche effect

extreme gauche effect

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Organic and Biochemistry: isomerism, configuration, conformation

H H

H CH₃ H

CH₃ H H

H CH₃ CHH₃

CH₃ H

H CH₃ HH

H

CH₃

H CH₃ H

H

C

H₃ H H CH₃ HH

H H

H CH₃ H

C H₃

H H

H CH₃ CHH₃

0.7 2.9 5.8 E (kcal)

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Organic and Biochemistry: isomerism, configuration, conformation

2

1

G

G

ΔG ° = ° − °

RT ΔG

e K

− °

=

S TΔ ΔH

ΔG

RTlnK ΔG

−

=

−

=

0.74 ΔS =

1.9 K

2

ΔS = =

G −Gibbs free energy H − enthalpy

S − entropy T − temperature R − gas contans

K − equilibrium constant

Gibbs free energy is the enthalpy minus the product of thermodynamic temperature and entropy. It was formerly called free energy or free enthalpy.

Entropy is the quantity the change in which is equal to the heat brought to the system in a reversible

process at constant temperature divided by that temperature.

Enthalpy is the internal energy of a system plus the product of pressure and volume. Its change in a system is equal to the heat brought to the system at constant pressure.