Teaching and Learning of Structural Organic Chemistry with

Nomenclature/Structure Software

Bert Ramsay,Antony Williams, Andrey Erin, and Robin

Martin

224th ACS National MeetingBoston, MA

&17th International Conference on Chemical Education,

Beijing, PRC

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Concepts and Models introduced early in Organic Chemistry courses♦ Molecular formulas♦ 2-D Drawings

– Bond-explicit– Condensed formulas– Line segment

♦ 3-D Drawings and Models– Ball-and-stick– Space-filling– Saw-horse– Newman projections

♦ Constitutional (Structural) Isomers

♦ Stereoisomers– Conformational isomers– Configurational isomers

• Cis/trans• Enantiomers• Diastereomers

♦ Nomenclature– Common– Semi-systematic– IUPAC– (CAS) Index

♦ Functional Groups

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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

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Molecular Modeling using the MDLChime plug-in

♦ Molecular modeling exercise taken from: Chemistry in Context: Laboratory Manuel, 3rd Ed (2000)

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Introductory Student Guide to Learning Structural Organic Chemistry with Nomenclature/Structure

Software

1. Recognizing Molecular Structures

2. 2D ! 3D Molecular Viewer

3. Molecular Geometry4. Alkyl Group

structures/names5. Cis/Trans isomers

– Alkenes– Cycloalkanes

6. Configurational Isomers:– Compounds with only one

stereogenic center– Compounds with more

than one stereogeniccenter

7. Tautomers8. Functional Group

identification and nomenclature

9. Carbohydrates

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The ChemSketch Window

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1. Recognizing Molecular Structures

♦ Hydrogen and carbon atom counting

♦ Molecular formulas

♦ How many terminal methyl groups?

♦ Naming

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Molecular Formula Analysis

♦ Molecular Formula

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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.

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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. Clear numbers

2. 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 chlorine1. 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/TransConfigurational Isomers

♦ Name to Structure ♦ Structure to Name

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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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Guide to the use of Nomenclature/Structure software helps

students♦ Recognition of structural identities♦ See relationship between 2D and 3D

drawings♦ Build their chemical drawing skills♦ Check out nomenclature and structure

relationships♦ Make configurational assignments♦ Identify functional groups

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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