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Lab coat and goggle are not necessary Self-prepare digital camera Download Avogadro and Chemsketch free software

(reference expt.)

Collect and check contents: MOLYMOLD Organic SetWhite ball: 20 Green ball: 4Black ball: 12 Yellow ball: 2Red ball: 6 Grey ball: 1Blue ball: 4 Purple ball: 1Short white link: 26Medium grey link: 26Long grey link: 12Link remover: 1

Organic Molecular Modeling 2016/03/20 revised

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Purpose

Construct and learn spatial arrangement of organic molecules

Use MOLYMOLD organic set to build Ball-and-stick model Observe the conformers and isomers

Use free software to sketch the chemical structures (reference expt.) Chemsketch Avogadro

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Chemical Structure of Organic Compound

Lewis structure

Ball-and-stick

Space-filling

C HH

HH

C

H

HH

H

Wedge-and-dash

4

C

H

O

N

ClSpace-filling

Ball-and-stick

Link remover

Multiple bond

Single bond

MOLYMOLD Organic SetSpecific color for element

5

Flow Chart I. Organic Molecular Modeling

MOLYMOD ball-and-stick model

Check the contents in the set

Draw chemical structures

Construct ball-and-stick model

Compare and take picture

After lab, recheck the set Ball-and-stick model

MOLYMOD organic set

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I. Newman Projection For ethane, C2H6 Newman Projection

1. Staggered

2. Eclipsed

1

111

11

1 2

2

2

2

2

2 1

More stable

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II. Conformation Conformation

Rotate single bond to change the spatial arrangement

Staggered, lower energy Eclipsed, higher energy

1

2 2

1

1

2 36

4

5

12 3

4

6 5

H

H

H

H H

H

H

H

HHH H

Boat form

II. Chair and Boat Form of Cyclohexane

Cyclohexane, C6H12: chair and boat form

Chair form

More stable

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H

Isomers

Structural isomers

Functional group

isomers

Positional isomers

Skeletal isomers

Stereoisomers

Geometric isomers Enantiomers

III. Isomers

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Cl

Cl ClCl

Different skeleton

Same skeleton, but different spatial

arrangement

Same formula, but different structures

CH3OCH

CH3CH2OH

Cl

Cl

10

CH

ClC

H

Cl

Cis-form

CH

ClC

Cl

H

Trans-form

1,2-Dichloroethene

Geometric IsomersGeometric isomers (cis, trans-isomers) Molecule with C=C double bond or ring structure

cis: on the same side trans: on the other side

1,4-dimethylcyclohexane

Cis-form Trans-form

Enantiomers Chiral carbon

Carbon with four different substituents Labeled as C*

Enantiomers (optical isomers) Molecule with chiral carbon is non-superimposable with its

mirror image, named enantiomers Enantiomers could rotate plane-polarized light with same

angle but different direction, and named optical isomers• Rotate clockwise, i.e. dextrorotatory, represent as (+) or d-• Rotate counterclockwise, i.e. levorotatory, represent as (-) or l-

**

Chiralcarbon

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Naming Stereocenters-The R, S System

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Priority rules: Higher atomic number with higher priority (assign 1)

1

2

3 1

2

3

(S)-(＋)-2-Butanol (R)-(－)-2-Butanol

4 4

Enantiomers of 2-butanol

C

OH

CH3CH3CH2

H * COH

CH3 CH2CH3

H*

25D[ ] +13.52 25

D[ ] -13.52

R-S-

Counter-clockwise

IUPAC

Clockwise

Compare the Enantiomers

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1. Assemble the molecules2. Compare and take picture3. Determine the R- or S- configurations

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Notice Construct the molecules and take pictures in the lab Use link remover to take the constructed model apart to

avoid breaking the links After lab, check the contents of MOLYMOD set, hand-in

and rechecked by GTA Hand-in lab report with IUPAC systematic names, the

chemical structures and pictures of modeling next week

Hand-writing ordraw by software

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Chemsketch http://www.youtube.com/watch?v=5kaU5iEqifQ

Draw chemical structureCH3

CH2

Avogadrohttp://www.youtube.com/watch?v=ohdMhGaaP68

Show three-dimensional structure Calculate bond-angle, bond-length, and bond

energy

Flaw Chart II: Free Software for Chemical Structures (Reference)