Article ID | Journal | Published Year | Pages | File Type |
---|---|---|---|---|
5416543 | Journal of Molecular Structure: THEOCHEM | 2010 | 22 Pages |
Abstract
Density functional molecular dynamics (DFTMD) is carried out on low-energy conformations of α-maltose. Finite temperature molecular dynamics trajectories are generated with forces obtained from B3LYP/6-31+Gâ electronic structure calculations. The implicit solvent method COSMO is applied to simulate the solution environment. Each simulation is carried out for â¼5 ps, starting from low-energy optimized geometries, including different hydroxymethyl rotamers and hydroxyl clockwise, 'c', and counterclockwise, 'r', orientations. The ggâ²-gg-r solvated form is of lowest relative energy by â¼0.6 kcal/mol relative to the solvated ggâ²-gg-c form, the latter conformation tending to converge to the 'r' form during dynamics. Conformational transitions and conformers residing as 'kink' forms were observed during vacuum runs. In one case, the syn gt'-gt-r + COSMO conformer moved during dynamics into a 'kink' conformation, remaining there for most of the 5 ps simulation. However, when this same conformer was started from a minimum energy 'kink' form, it rapidly reverted into the normal syn conformation in which the H1â²â¯H4 hydrogen atoms across the glycosidic bond were â¼2.15 Ã
on average. Other solvated structures showed a perfunctory preference for the 'kink' conformation during dynamics, even though in previous optimization studies the 'kink' conformations were of higher energy than the syn conformers. Similarly, 'band-flip' conformational studies showed that the 'c' and 'r' forms differed, 'c' undergoing transitions to the syn form, the 'r' form staying in the band-flip conformation over the 5 ps simulation. The trend for the 'r' conformers to be more stable than the 'c' conformers when fully solvated, appears to confirm optimization studies, although transitions to stable partial 'c' forms produces some confusing conformational effects. For example, in one case a hydroxymethyl O6Hâ¯O6â² hydrogen bond locked into a glycosidic 'kink' structure, allowing the O3H and O2â²H' hydroxyl groups between rings to rotate more freely because of the enlarged distances between the groups across the glycosidic bridge.
Related Topics
Physical Sciences and Engineering
Chemistry
Physical and Theoretical Chemistry
Authors
Frank A. Momany, J.L. Willett, Udo Schnupf,