Simulation of conformational dynamics with the MM3 force field: the pseudorotation of cyclopentane

Numerical determination of pseudorotation constants

“…11 An MM3 study by Cui, Li, and Allinger 11 gave a average cycle time ϭ0.2 ps at 298 K, corresponding to a phase velocity ϭ1700°ps Ϫ1 or a pseudorotational constant of B ϭ66 cm Ϫ1 . This is hardly surprising, as the force field must reproduce the extremely flat potential energy surface over a large range of dihedral angles.…”

“…Molecular dynamics simulations provide an entirely different approach to thermodynamic functions of a pseudorotating system, [11][12][13] as the latter are calculated from ensemble averages and fluctuations, without constructing a partition function explicitly. Furthermore, the result contains pseudorotation-vibration coupling at no extra cost.…”

Molecular Modeling of Energetic Materials: The Parameterization and Validation of Nitrate Esters in the COMPASS Force Field

“…Popular force fields, such as MM3 [3][4][5][6][7][8][9][10][11][12][13], AMBER [14][15], and CHARMM [16], have been designed mainly to study biologically interesting molecules. The COMPASS force field, on the other hand, has been specifically designed for material science applications.…”

Unnaturally configured 13‐epi steroids: full 1H and 13C assignments and ring C–D conformations from 1H, 1H vicinal couplings

“…Altona et al 34 have written the definitive treatise on ring D steroid geometry. The concept of pseudorotation, 35 devised to explain the conformation of cyclopentane rings, applies and the geometry of the five-membered ring can be described by the maximum puckering amplitude ( m , a measure of how far a given atom has moved above or below the average plane of the ring), and the phase angle of pseudorotation (P, how far the puckering has moved around the ring). The ring C/D junction puts constraints on the conformational flexibility compared to cyclopentane and hence in regular steroids ring D is generally somewhere in between a 13ˇenvelope and 14˛envelope conformation (solid phase), 36 or is a continuum of states between these two (solution).…”