A comparison of conformational energies calculated by molecular mechanics (MM2(85), Sybyl 5.1, Sybyl 5.21, and ChemX) and semiempirical (AM1 and PM3) methods

Abstract

Conformational energies of different conformers have been calculated for a series of molecules using various molecular mechanics and semiempirical methods. The quality of the force fields has also been tested by calculating barriers to rotation about carbon-carbon bonds. The molecular mechanics force fields used are MM2(85), Syby15.1, Sybyl5.21, and ChemX, ver. Jan 89. The semiempirical methods used are AM1 and PM3. Molecules with different functional groups, for which good experimental data exist, have been selected. The semiempirical methods generally calculate barriers to rotation which are lower than the experimentally determined. The conformational energies for hydrocarbons are reasonably well reproduced by all tested methods although MMZ(85) gives the quantitatively best agreement with experiments. For compounds containing oxygen, nitrogen and halogens MMZ(85) gives results which are in best agreement with the experimentally determined values.

So you want to do molecular modeling? A consumer's guide to desktop modeling programs for the Macintosh

“…A summary of conformational energy differences calculated by these packages is provided in Table 2. All of the programs calculate energies comparable to the reported experimental values (5)(6)(7). As one would expect, the MM2 based programs give almost identical results.…”

“…ometries determined by the various programs for sulfonamide [HSO2NH2L Although the structure can be constructed in MacMimic, Nemesis, and C hem 3D, necessary parameters are missing to perform the energy minimization. The results from Alchemy and PC-Model are compared to the optimized geometry obtained from ab initio calculations using a 6-31G*basis set (7). Bond lengths, angles, and torsions differ markedly among the programs.…”

Reaction of Resorcinol With Acetone

“…This Δ S seems reasonable. By contrast, PM3 gives the wrong sign and would demand Δ S = +8.6 eu, which seems rather large …”

London Dispersion Helps Refine Steric A-Values: The Halogens

“…These interactions are present in both the diaxial trans-1,2 and trans-1,4 isomers, while in the diequatorial form, electron withdrawal from the hydrogens is not so efficient. Previous computations on dihalocyclohexanes using either molecular mechanics or semiempirical methods 73 did not favor the diaxial conformer form, especially not for trans-1,4-dichloro and -dibromocyclohexane.…”