Note: all handouts are in MSWord  format; all structure files are in PCSpartan Pro format; spreadsheet files are in Excel format

Chem 221b, 222b, 223b (Organic chemistry for non-majors)

PCSpartan Pro computational exercise for calculating energies for butane and for substituted cyclohexanes using pre-built structures; also included understanding isodensity surfaces
version 3 of handout

Chem 321-323 (Organic chemistry sequence for majors)

F 1996-1998:

• Spartan (single SGI machine) exercise in conformational analysis of alkanes used (round robin in groups): original document unavailable; This handout has a table to collect data from each group and distribute to the class, in order to answer questions. OR
• Spartan exercise in conformational analysis of cycloalkanes used round robin in groups; handout

W 1999:
aromatic group exercises involving lab investigations, paper problems, and analyzing surfaces for GS and TS substituted benzenes (no handout available)

W2000
Performed much of Experiment 16, Introduction to Molecular Modelingand Experiment 17, Computational Chemistry from Pavia, et al. (no handout used)

Spring 1999:

1. Friedl Crafts computations, round robin in groups (handout) to complement a "wet" experiment in thermodynamic vs. kinetic control (Experimental Organic Chemistry, Mohrig, Hammond, Morrill, and Neckers, WH Freeman: New York, 1999, pp. 242-247. )
2. First use of PC Spartan Pro, in pairs, to examine the conformations of aldohexoses (newest version of handout)

Fall 2000:

• Pre-made structures; examining polarity and model types; using spreadsheets
• Prepared file with already calculated energies, dipoles, surfaces, and equilibrium structures
• Directions for writeup
• Structures used corresponded to question 1a-c 58-59 in Introduction to Organic Laboratory Techniques: A Microscale Approach,3rd Ed., Pavia, Lampman, Kriz, Engel. These structures were used in subsequent questions for a laboratory experiment on solubility and polarity

• students build ethane, ethene, ethyne; set up and run calculations
• view geometric parameters and energies and surfaces (edensity, homolumo) to answer questions

students perform calculations to look at stabilities of substituted cyclohexanes; some models pre-built files (chair, boat, half-chair), but must be modified, and saved locally;

• build structure of one enantiomer of carvone (partner builds enantiomer) with minimal directions;
• set up and submit calculation;
• view surfaces, properties, and compare;
• view vibrations (intro to IR spectroscopy; correlate to vibrations to reported IR peaks)

• modified from experiment 17B, p. 185 Pavia, et al. (relative energies of ionization of substituted alkyl bromides): an Excel spreadsheet summarizes energies obtained
• using PCSpartan Pro tutorial to build reaction profile for an Sn2 reaction, look at effect of modifying parameters on Sn2 rates (energies of activation);
• exercise looking at anti conformations of alkyl halides that favor E2 (anti) eliminations;
• surfaces generated (html/gif) for first and third parts of exercise are available.

Winter 2001:

1. (Not modeling) completed Sn1 kinetic study, Experiment 20, Pavia; used prepared spreadsheet to complete kinetic calculations;
2. Calculations to augment multistep synthesis: handout

This is a three part modeling exercise examining intermediates in the multistep conversion of limene to carvone, in particular, to look at the instability of the hard-to-isolate intermediate; the relative energies of possible elimination products (the one seen is by far the most stable), and to generate vibrational numbers and animations corresponding to reported IR peaks.

Spring 2001:

• boneol, isoborneol (p. 277),
• carboxylic acids (17C p. 186)
• carbonyl group reactivity (17E)

An exercise to convert straight chain to cyclic monosaccharides in alpha and beta pyranose and furanose forms, and to look critically at the energies (and subsequently the calculated ratios) of the structures

Other exercises appropriate for Organic Chemistry  (used in our Computational Chemistry Course)

• Hot and cool tasting compounds: SARs handout (adapted from . Kimbrough, Doris R. "Hot and Spicy versus Cool and Minty as an Example of Organic Structure-Activity Relationships" J. Chem. Educ. 1997 74 861.) molecular modeling of "hot" and "cool" tasting compounds
• Spartan conformations handout: looking at relative energies of axial and equatorial substituents on cyclohexanes