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HyperChem in the Physical Chemistry Laboratory


David Whisnant
Wofford College
Spartanburg, SC 29307

Note: This article was scanned using OCR from the Fall 1996 CCCE Newsletter. Please contact us if you identify any OCR errors.
HyperChem is a molecular modeling program that runs on a variety of platforms, including a Windows 3.1 or Windows 95 based PC. The version we use at Wofford (HyperChem, Release 3) includes several molecular mechanics and semi-empirical molecular orbital methods. A more recent version also includes ab initio calculations. We have three copies of HyperChem available, two on 66 MHz 80486 machines and one on a 75 MHz Pentium, which we use in our general chemistry and physical chemistry laboratories.
In physical chemistry, my students use molecular modeling in two experiments. The first is an addition to a traditional experiment in which the students record the visible spectra of three conjugated cyanine dyes (e.g., Shoemaker, Garland and Nibler, 5th Ed., pp 440- 446). They obtain the wavelengths of maximum absorbance from the spectra and calculate the photon energies corresponding to the transitions. These energies can be fitted to a particle-in-a-box model and used to estimate average bond lengths for the molecules (Moog. R. S. J. Chern. Educ. 1991, 68, 506). At the end of this experiment, my students use the MM+ molecular mechanics option in HyperChem to calculate an alternate model of the smallest dye molecule. They then use the ChemPius extensions for HyperChem to vary the torsion angle between the two ring systems in the dye. The molecular modeling calculations add around an hour to the experiment when the program is run on the 75 MHZ Pentium and somewhat longer on a 486 machine, mainly because of the time required for the torsion angle search. The bond lengths obtained from molecular mechanics and the average value estimated from the particle¬∑ in-a-box model diller by less than 1%. They also are within 4% of the bond length in benzene.
Small carbon clusters have been of considerable interest in the last decade, due to their relevance to interstellar and combustion chemistry, and because of the synthesis of the fullerenes. Our second physical chemistry experiment involving molecular modeling is a semiempirical MO study of the Cs molecule, based on the description of such calculations in Wellner and van Zee, Chemical Reviews 1989, 89, 1713-1747. The students begin by using MIND0/3 to calculate heats of formation for several possible Cs isomers- linear, pentagonal, trigonal bipyramidal, square pyramidal, trapezium, and tetrahedral. They then use the heat offormation values to predict that the linear structure is the most stable.
Having decided that the linear structure is the most stable form of Cs. the students then use PM3 calculations to make predlcions about this isomer. They lind that the calculated bond lengths are around 1.28 A, consistent with the model :C=C=C=C=C:. They calculate the energies of the molecular orbitals and use contour plots to draw pictures of the orbitals, to which they assign , , and inversion symmetry labels. They also calculate the wavelengths and oscillator strengths of the three most intense visible-UV peaks, as well as the wavelengths of peaks in the IR spectrum. These predictions can be compared with theoretical and experimental results in the literature.
The C5 computational chemistry experiment, on which the students work in pairs near the end of the second semester, is useful because it ties together several topics which we have discussed in lecture throughout the year. First, it gives the students experience with a practical application of molecular orbital theory, which I find it difficult to cover effectively in lecture. The students also make a brief return to thermodynamics (which they have learned in the first semester) when they use heats of formation to predict the most stable isomer. They use group theory to identify the point groups of the six C5 isomers and apply symmetry to label the different molecular orbitals. The predicted oscillator strengths ofthe vlsible-UV peaks lead them to discuss allowed, symmetry-forbidden, and spin-forbidden transitions. Finally, HyperChem shows animated pictures of the vibrations corresponding to the infrared transitions. This gives the students the opportunity to think about vibrational modes and the relationship of changing dipole moment to the intensity of the transitions in the infrared.
10/05/96 to 10/09/96