Experiment 7 - Molecular Mechanics Calculations

Experiment 7 - Molecular Mechanics Calculations - CHEM 257...

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CHEM 257 Experiment 7 Molecular Mechanics Calculations and Conformational Analysis Introduction The study of organic molecules and their reactivity requires a detailed understanding of energies and structures. Medium-to-large organic molecules can exhibit various structures in solution, and this is often important in determining the rate and regiochemistry of a particular chemical process. For a given compound, the various molecular structures are isomers which can be interconverted by rotation about single bonds. These are referred to as “conformers” (or “conformational isomers”). The rotational processes involved in the interconversion of stable conformers force the molecule to cross energy barriers. We often show a map of this process using a potential energy diagram, which is a plot of molecular potential energy vs. a change in some rotational angle. The minima in a potential energy diagram correspond to stable conformers, i.e., those exhibited by a significant fraction of the molecules present. The maxima on a potential energy surface represent “transition states”, i.e., high energy structures with infinitely short lifetimes. It should be remembered that these two-dimensional plots describe the energy as a function of one particular rotation angle; the description of all possible structural changes in a polyatomic molecule would require a multi-dimensional surface that can be difficult to visualize and/or represent. How does one come to understand the energy and structure(s) of an organic molecule? Chemists have traditionally addressed structural problems by preparing the molecule of interest and applying various experimental techniques; these can include spectroscopic analyses such as uv-visible or infrared spectrophotometry, nuclear magnetic resonance spectroscopy, and x-ray or electron diffraction studies. This is clearly a powerful collection of tools, but it is not without some shortcomings. First, it can be difficult to interpret the results of a particular study, and so different techniques can sometimes provide conflicting evidence. Of even more significance, all such techniques suffer from limitations on the number of molecular conformations they can sample. Polyatomic molecules can exist in an infinite number of conformations; as noted above, a few of these will be lower in energy than the others, and these low energy conformers are adopted by the vast majority of the molecules in a sample. Hence, a solution study of a large organic molecule often gives a statistically-weighted measure of the energies of the accessible conformers, and tells one nothing about higher energy structures, or about the relative populations or energies of the accessible conformations. Similarly, x-ray diffraction provides detailed structural information on the lowest energy conformation of a molecule in a crystal, but says nothing about other conformers that may be present in solution. Indeed, most experimental techniques are largely unable to provide much information on the structures or energies of
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Experiment 7 - Molecular Mechanics Calculations - CHEM 257...

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