Molecular Modeling

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  • Topic: Molecule, Atom, Molecular physics
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  • Published : July 4, 2007
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Molecular Modeling Exercise

The purpose of the is lab was to practice modeling molecules and exploring the capabilities of the ChemOffice programs. The minimum energy was found for each of the three molecules tested and the strain energy at different dihedral angles was plotted. The first molecule, butane, was easily completed but amphetamine and U4EA caused some difficulty. The results of the last two were not very conclusive.

The purpose of this lab was to explore the capabilities of ChemOffice in the realm of modeling molecules. The strain energy was then taken at different dihedral angles to compare with each molecule and the text. Three molecules were used: butane, amphetamine, U4EA.

NameAmount (g)Molecular WeightAmount (mol)Density (g/cm3)Boiling Point (°C)Melting Point (°C) Butane58.1230.6011-0.45-138.35

For part A butane was easily drawn in Chem3D and the molecular energy minimized. The dihedral angle was then changed to find the strain energy at each angle. These values were recorded and plotted.

In part B amphetamine and U4EA were drawn in ChemDraw and then transferred into Chem3D. Both molecules were minimized and the dihedral angle was found. It was then attempted to find the strain energy of different dihedral angles. Eventually data was recorded and plotted.

The three molecules were each adjusted to the minimum energy. The results are in the table below. The strain energy for each molecule at the specific dihedral angle is attached in both chart and graph form.

NameMinimized Strain Energy (kcal/mole)Minimized Dihedral Angle Butane2.173180°

The process of minimizing the energy of each molecule was interesting to observe. The strain energy was fairly low for all three molecules. Amphetamine was unique because the strain energy was negative. This was very surprising and it is...
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