title: 27 ps DFT molecular dynamics simulation of alpha-maltose: A reduced basis set study.
abstract: DFT molecular dynamics simulations are time intensive when carried out on carbohydrates such as alpha-maltose. In a recent publication (Momany et al., J. Mol. Struct. THEOCHEM, submitted) forces for dynamics were generated from B3LYP/6-31+G* electronic structure calculations. The implicit solvent method COSMO was applied to simulate the solution environment. Here we present a modification of the DFT method that keeps the critical aspects of the larger basis set (B3LYP/6-31+G*) while allowing the less-essential atom interactions to be calculated using a smaller basis set, thus allowing for faster completion without sacrificing the interactions dictating the hydrogen bonding networks in alpha-maltose. In previous studies, the gg'-gg-c solvated form quickly converged to the "r" form during a 5 ps dynamics run. This important conformational transition is tested by carrying out a long 27 ps simulation. The trend for the "r" conformer to be most stable during dynamics when fully solvated, is confirmed, resulting in approximately 20/80% c/r population. Further, the study shows that considerable molecular end effects are important, the reducing end being fairly stable, the O6-H pointing at the O5, while the nonreducing end moves freely to take on different conformations. Some "kink" and transition state forms are populated during the simulation. The average H1'...H4 distance of 2.28 A confirms that the syn form is the primary glycosidic conformation, while the average C1'-O1'-C4 bond angle was 118.8 degrees , in excellent agreement with experimental values. The length of this simulation allowed the evaluation of vibrational frequencies by Fourier transform of the velocity correlation function, taken from different time segments along the simulation path.
authors.affiliation: Plant Polymer Research, USDA, ARS, National Center for Agricultural Utilization Research, 1815 N. University St., Peoria, Illinois 61604, USA.
authors.forename: Udo
authors.initials: U
authors.lastname: Schnupf
authors.forename: J L
authors.initials: JL
authors.lastname: Willett
authors.forename: Frank A
authors.initials: FA
authors.lastname: Momany