Experiment 2 Handout

Experiment 2 Handout - AN INTRODUCTION TO MOLECULAR...

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AN INTRODUCTION TO MOLECULAR MODELING USING CHEM 3D ON THE PC http://www.chem.umass.edu/~samal/mm/chem3d.pdf OBJECTIVES Conformational analysis of alkanes using Chem 3D software. BACKGROUND ChemBio3D Ultra is a computer program that is used to visualize models of molecules and to calculate molecular energies by the molecular mechanics (MM2) method. The program is use- ful for predicting relative stabilities of reaction products and con- formational isomers and for modeling biological systems, e.g., calculating the stabilities of specific enzyme-substrate complexes. The MM2 method assumes that for a given molecule, the atoms will adjust their positions by stretching and bending bonds away from standard values so as to produce a minimum energy configu- ration. Deviation from those standard values results in what is known as strain energy or steric energy. Calculation of the strain energy for different molecules or conformations, for example, allows for an assessment of the relative stabilities of those mole- cules or conformations. The following factors are considered by the MM2 program in minimizing the energies: bond stretching and compression, bond bending, torsional strain, van der Waals interactions, and electrostatic interactions. As an example, con- sider butane (Figure 1). Your chemical intuition should tell you that the two methyl groups (C1 and C4) if in close proximity cause steric hindrance. According to MM2, the molecule relieves this strain as much as possible through a combination of bond stretching and bending over the entire molecule. This allows the methyl groups to move as far away from one another as possible forming the anti-conformation, thereby minimizing the steric strain and leading to a minimum energy (more stable geometry). Staggered Anti Eclipsed Figure 1. Newman projections of butane. As you proceed through the following exercises and record ener- gies for various conformations, notice how energy is broken down among the various factors that make up total energy, and observe which factor contributes most to overall energy of the particular conformation you are looking at. This may help you to gain some insight into how certain molecules relieve steric strain. You will find that ChemBio3D Ultra is a useful tool for analyzing confor- mational equilibria and visualizing three-dimensional models of molecules. Be careful however in the interpretation of results. Often, the program will lead to a local minimum that is not neces- sarily the lowest energy conformation of that molecule. The user’s own chemical knowledge must always be applied in the interpre- tation of the results obtained with ChemBio3D Ultra or other MM2 programs. Introduction to ChemDraw
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This note was uploaded on 09/26/2011 for the course MATH 120508 taught by Professor Jdoug during the Fall '08 term at Drexel.

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Experiment 2 Handout - AN INTRODUCTION TO MOLECULAR...

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