Optimal Potential Energy Scan of an Ester Molecule
Josh Rauscher, Aaron Kiefer
Table of Contents
- Purpose of the Project
- Scientific Background
- Computational Approach
- Results
- References
Purpose of the Project
The aim of our project was to graphically compare the relationship between molecular geometry and potential energy. We used an ab initio quantum chemistry software package (Gaussian94) running on a high-performance cluster to scan for optimal molecular energy by manipulating our molecule's two dihedrals. A dihedral is the angle formed between three planar atoms and one non-planar atom. When our dihedrals were at an optimum position, the negative energy or stability of our molecule was maximized.
The ester molecule on the right has its two dihedral angles (carbon 10 and carbon 8) artificially flattened to create a high-energy molecule that would never exist in nature. The eccentric shape creates interference in the molecular orbitals causing positive energy and increasing strain on the molecule,(25.8 Hartrees). The ester on the left is our geometrically optimized version, whose orbitals don't interact. It has a stability of -193 hartrees.
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Scientific Background
We chose a diethyl ester as the subject for our experiments simply because it contains several interesting geometric dihedrals. The term ester refers to a double-bonded oxygen linked to a carbon which in turn is single bonded to another oxygen. Our ester contains five carbons and two oxygens.
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Computational Approach
Using MacSpartan running from a Power Macintosh 5400/200, we assembled an arbitrary ester molecule with five carbons and two oxygens. We then ran a geometric optimization/single point energy scan customized to deliver bond lengths,angles and dihedrals of the molecule. We chose the complex ab initio method at a 3-21G* level of theory to reap comparatively high geometric accuracy. We then converted the cartesian coordinate output into Z-matrix form using the MacBabel conversion program. We modified the z-matrix, then ran a dihedral angular scan on Gaussian94 to give us a series of angle vs. potential energy relationship readouts. Unfortunately, Gaussian94 couldn't handle the format or length of our computations. Never fear! Our instructor, Robert "Bob2" Gotwals, fixed the problems.
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Results
When we were finally able to retrieve our scan, Bob helped us clean up the resulting one megabyte file. We edited out the entire middle portion of the data,saving only the first and last potential energy outputs. We then imported the Gaussian info into a spreadsheet and graphed the results on 3D surface. As earlier mentioned, we changed our experiment to fit the limited computing resources availble to us as students. (Scientists are allocated larger chunks of memory and proscessing power.) According to our graph, the least potential energy occured when the dihedral bond was at a length of 1.6 angstroms and an angle of 125 degrees.
References
START HERE: For a book citation, use:
Hehre, Warren J. Shusterman, Alan J. Huang, Wayne W: A Laboratory Book of Computational Chemistry. Wavefunction Inc: Irvine CA, 1996.
Greenstone, Arthur W. Sutman, Frank X. Hollingworth, Leland G: Concepts in Chemistry. Hardcourt Brace & World: Chicago, IL, 1966.
Gotwals, Robert R. "Personal conversations and much more" Computational Chemistry. Aug. 18-22, 1997.
Thissen, Anne "Personal conversations and much more" Computational Chemistry. Aug. 18-22, 1997.
McCormick, Jamie & Bloemeke, William. "Diastereomers of Butane" (1997) Online. Available: http://www.shodor.org/succeed/projects/compchem/butane.
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