Organic Molecular Modeling Lab coat and goggle are not necessary - - PowerPoint PPT Presentation

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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 Set White ball: 20 Green ball: 4 Black ball: 12 Yellow ball: 2 Red ball: 6 Grey ball: 1 Blue ball: 4 Purple ball: 1 Short white link: 26 Medium grey link: 26 Long grey link: 12 Link 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 H H H H

C H H H H

Wedge- and-dash

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C H O N Cl Space-filling Ball-and-stick Link remover

Multiple bond Single bond

MOLYMOLD Organic Set

Specific color for element

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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 1 1 1 1 1 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 3 6 4 5 1 2 3 4 6 5

H H H H H H H H H H H 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 Cl Cl Different skeleton Same skeleton, but different spatial arrangement

Same formula, but different structures CH3OCH CH3CH2OH

Cl Cl

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C H Cl C H Cl

Cis-form

C H Cl C Cl H

Trans-form

1,2-Dichloroethene

Geometric Isomers

Geometric 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-

* *

Chiral carbon

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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 CH3 CH3CH2 H * C OH C H3 CH2CH3 H *

25 D

[ ] +13.52 

25 D

[ ] -13.52 

      R- S-



Counter- clockwise

IUPAC



Clockwise

Compare the Enantiomers

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• 1. Assemble the molecules
• 2. Compare and take picture
• 3. 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 or draw by software

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• Chemsketch

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

 Draw chemical structure

C H3 CH2

• Avogadro

http://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)