Structural properties of liquid N-methylacetamide via ab initio, path integral, and classical molecular dynamics.
In order to better understand the physical interactions that stabilize protein secondary structure, the neat liquid state of a peptidic fragment, N-methylacetamide (NMA), was studied using computer simulation. Three different descriptions of the molecular liquid were examined: an empirical force field treatment with classical nuclei, an empirical force field treatment with quantum mechanical nuclei, and an ab initio density functional theory (DFT) treatment. The DFT electronic structure was evaluated using the BLYP approximate functional and a plane wave basis set. The different physical effects probed by the three models, such as quantum dispersion, many-body polarization, and nontrivial charge distributions on the liquid properties, were compared. Much of the structural ordering in the liquid is characterized by hydrogen bonded chains of NMA molecules. Modest structural differences are present among the three models of liquid NMA. The average molecular dipole in the liquid under the ab initio treatment, however, is enhanced by 60% over the gas phase value.
Whitfield
T W
TW
IBM T. J. Watson Research Center, Yorktown Heights, New York 10598, USA.
Crain
J
J
Martyna
G J
GJ
D000081:Acetamides / Q000737:chemistry*; D003198:Computer Simulation; D006860:Hydrogen Bonding; D008958:Models, Molecular; D015394:Molecular Structure; D017433:Protein Structure, Secondary
D000081:Acetamides; C018595:N-methylacetamide