Application of a simple diagonal force field to the simulation of cyclopentane conformational dynamics

Abstract

Molecular dynamics simulations have been carried out on the cyclopentane molecule using a diagonal force field and the results compared with both experiment and a recent study which used the MM3 force field [W. Cui, F. Li, and N. L. Allinger, J. Am. Chem. Soc., 115, 2943 (1993)]. The current simulation resulted in an RMS pseudorotational velocity of 1036 deg/ps, compared to the model estimated value of 400 deg/ps and the MM3 result of 1700 deg/ps. The pseudorotation amplitude was calculated to be 0.46 ± 0.02 Å, compared to the experimental value of 0.48 Å and the MM3 value of 0.5 ± 0.03 Å. The two distinct average C(SINGLE BOND)H bond lengths seen for the axial and equatorial conformations in the MM3 simulation were not observed. The energy barrier to passing through the planar conformation was calculated at 4.7 kcal/mol as compared to the experimental value of 5.2 kcal/mol and the MM3 value of 4.2 kcal/mol. During the simulation, the angle bending term dominated the potential energy, followed by the torsion energy, as was seen with MM3. The third largest energy term was the bond stretching, followed by the van der Waals interaction, the reverse of what was seen with MM3. The effects of carrying out the simulation under conditions of constant energy versus constant temperature are discussed. © 1996 by John Wiley & Sons, Inc.