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Chem 380.37 Assignment 1

Chem 380.37 Assignment 1 - C hemistry 3 80.37 May 2 013 Dr...

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Chemistry 380.37 May 2013 Dr. Jean M. Standard May 13, 2013 Assignment 1: Molecular Mechanics (PART 1 – 25 points) In this assignment, you will perform some molecular mechanics calculations using the Avogadro software package. One of the objectives of this assignment is to explore the ability of molecular mechanics force fields to adequately represent the energies of molecules as their geometries are varied. Another objective is to learn how to extract information about force field parameters from calculations. In addition, the use of Avogadro to build simple organic molecules and perform equilibrium geometry and energy calculations will be illustrated. THIS PORTION OF ASSIGNMENT 1 IS DUE WEDNESDAY, MAY 15, 2013. Using the Avogadro Software Package The computer program that you will use for these molecular mechanics simulations is a software package called called Avogadro . You will be able to access Avogadro on the Macintosh computers located in Julian Hall Room 216. Alternately, since Avogadro is freely available and includes the molecular mechanics routines as a built-in feature, you may choose to download Avogadro to your personal computer. The software package is available for Windows, Macintosh, and Linux platforms. Please see Appendix 1 for details on downloading the software package. To use Avogadro on the Macs in JH 216, log in using your ULID and password. The Avogadro software package may be started by clicking on its icon in the Dock. PART A (7 points) – Conformations of 2,3-dimethylbutane How many stable conformers are there of 2,3-dimethylbutane? Draw sketches (by hand) of each of the stable conformers –Newman projections probably would be best. Which of the conformers do you expect to have the lowest energy? Why? Provide some physical explanation as to your predicted energy ordering. Next, build all the predicted stable conformers of 2,3-dimethylbutane using the Avogadro package (see Appendix 2 for a tutorial on building organic molecules). Determine the equilibrium geometries of each of the conformers using the MMFF94 Molecular Mechanics force field (see Appendix 3 for instructions on performing molecular mechanics calculations). Record the total energy of each one in kcal/mol. Discuss whether or not the results agree with your qualitative predictions. PART B (7 points) - Equilibrium Geometry of Biphenyl and Substituted Biphenyl What is the equilibrium torsional angle of biphenyl? To find out, first build the biphenyl molecule using Avogadro . biphenyl
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2 The torsional angle in question is for rotation about the central C-C bond. In order to build biphenyl, it is helpful to start with pre-built benzene rings available in the Avogadro library. To locate the fragment library, select "Build Insert Fragment". Open the aromatics folder, select benzene, and then click "Insert Fragment". At this point a benzene molecule should appear in the display window highlighted in blue. Use the mouse buttons to translate and
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