Teaching and Learning of Structural Organic Chemistry with Nomenclature/Structure Software Bert Ramsay, Antony Williams, Andrey Erin, and Robin Martin 224 th ACS National Meeting Boston, MA & 17 th International Conference on Chemical Education, Beijing, PRC
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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
♦ 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: [email protected]♦ Advanced Chemistry Development,
– 90 Adelaide Street West, Suite 702, Toronto, Canada, M5H 2L3,