Teaching and Learning of Structural Organic Chemistry with Nomenclature/Structure Software

Bert Ramsay, Antony Williams, Andrey Erin, and Robin Martin

224th ACS National Meeting Boston, MA & International Conference on Chemical Education, Beijing, PRC

17th

Concepts and Models introduced early in Organic Chemistry courses

Molecular formulas 2-D Drawings
Bond-explicit Condensed formulas Line segment
Constitutional (Structural)

Isomers Stereoisomers
Conformational isomers Configurational isomers
Cis/trans Enantiomers Diastereomers

3-D Drawings and Models

Ball-and-stick Space-filling Saw-horse Newman projections

Nomenclature Common Semi-systematic IUPAC (CAS) Index Functional Groups

Tools to help in Organic Structure Recognition

Molecular Models Ball-and-stick Wire-frame Space-filling Molecular Modeling Software or demos MDLChime Nomenclature/Structure Software

Molecular Modeling using the MDLChime plug-in

Molecular modeling exercise taken from: Chemistry in Context:

Laboratory Manuel, 3rd Ed (2000)

Introductory Student Guide to Learning Structural Organic Chemistry with Nomenclature/Structure Software
1. 2. 3. 4. 5.

Recognizing Molecular Structures 2D ! 3D Molecular Viewer Molecular Geometry Alkyl Group structures/names Cis/Trans isomers Alkenes Cycloalkanes

6.

Configurational Isomers:
Compounds with only one stereogenic center Compounds with more than one stereogenic center

7. 8.

9.

Tautomers Functional Group identification and nomenclature Carbohydrates

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The ChemSketch Window

1. Recognizing Molecular Structures

Hydrogen and carbon atom How many terminal methyl

counting Molecular formulas

groups? Naming

Molecular Formula Analysis

Molecular Formula

Locating Terminal Methyl Groups or finding the location of all carbon and hydrogen atoms
Click on the Select/Move button, then double-click on structure to bring up Properties box.

Nomenclature
After selecting a structure, click on the Generate Name

from Structure icon.

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IUPAC Naming Preferences

Common names: YES Click on IUPAC Name

button

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IUPAC Naming Preferences

Common names: NO
Click on IUPAC Name

button

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Introduction to the 3D Molecular Viewer

Question #2

3D Optimization:
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3D Molecular Viewer in ChemSketch

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3D Molecular Viewer
3D Model Styles

Ball-and-stick with dots Wire frame Ball-and-stick Space-filling

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Molecular Geometry in 3D View

Bond distances, Torsional angles, and Bond

angles.

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Name to Structure

Click on the Name to Structure icon. Enter name

and click on the Run button.

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Entering Name and Finding a Structure

"
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Results of Name ! Structure

1. 2.

Clear numbers Find new name

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Finding the correct names

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Common, semi-systematic and IUPAC/CAS Nomenclature

Name to Structure Use Table of Radicals

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Attaching a sec-butyl group to chlorine

1.

HCl
2.

Get s-butyl

3.

Move to ChemSketch

4.

Attach to chlorine
5.

Final product

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Completion of the nomenclature

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Nomenclature of Cis/Trans Configurational Isomers

Structure to Name

Name to Structure

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Cis/Trans Representations in Cyclohexane Derivatives

Some possible answers

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Configurational Priorities (with only one stereogenic center)

Results

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3D View
3D view of molecule 8a

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Configurational Isomers (with more than one stereogenic center)

Results

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3D Views of Molecules in Q#9

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Tautomers

Click on the Tautomer button

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Functional Group Identification

Name to Structure Structure to Name

ACD/Name
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Examples of Name and Structure Scans

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 Recognition of structural identities

Guide to the use of Nomenclature/Structure software helps students

drawings Build their chemical drawing skills Check out nomenclature and structure relationships Make configurational assignments Identify functional groups
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See relationship between 2D and 3D

Communication
Copies of this presentation are available on the

Educators Page at: http://www.acdlabs.com. Or contact Scott MacDonald: info@acdlabs.com Advanced Chemistry Development,
90 Adelaide Street West, Suite 702, Toronto, Canada, M5H 2L3, 416-368-3435

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