Evaluation of semi-empirical methods for calculating conformations of amino-acids

Quantum chemical methods, as a compliment to experiment, offer a deeper insight into understanding structural and energetic features interaction and folding phenomenon [1, 2]. The large size of biomolecules, however, limits the applicability of benchmark methods used in small molecule systems. Semi-empirical methods [3], which use Hartree-Fock formalism with approximations driven from experimental data, are one solution to this problem by decreasing the cost of calculations substantially. The ability of this method for predicting the energy profile of the dihedral angle between amide carbon and alfa-carbon of amino acids is evaluated. Benchmarking against B3LYP shows that using PM6 can lead to errors as large as a few kcal/mol. These errors can be systematic or nonsystematic. In contrast, a similar benchmarking for amide N-H bond shows a much smaller error. These errors can be due to the inability of PM6 in modeling hydrogen bonds, as well as electronic effects. Calculations for rotation around the carbon-carbon single bond in butadiene do not suggest a significant electronic effect. In conjunction with hydrogen bonding effects, however, this effect can lead to nonsystematic and complicated errors. This research suggests that further parametrization of PM6 should be performed and be used with caution and careful evaluation.

کلیدواژه ها:

Semi ، empirical ، Amino acids ، Quantum mechanics ، Semi ، empirical ، Density Functional Theory (DFT)