Paper Citing NAMD - Abstract
Mangold, Martina; Rolland, Leslie; Costanzo, Francesca; Sprik, Michiel; Sulpizi, Marialore; Blumberger, Jochen
Absolute pK(a) Values and Solvation Structure of Amino Acids from Density Functional Based Molecular Dynamics Simulation
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1951-1961, JUN 2011
Absolute pK(a) values of the amino acid side chains of arginine, aspartate, cysteine, histidine, and tyrosine; the C- and N-terminal group of tyrosine; and the tryptophan radical cation are calculated using a revised density functional based molecular dynamics simulation technique introduced previously [Cheng J.; Sulpizi, M.; Sprik, M. J. Chem. Phys. 2009, 131, 154504]. In the revised scheme, acid deprotonation is considered as a dissociation rather than a proton transfer reaction, and a correction term for treating the proton as a hydronium ion is suggested. The acidity constants of the amino acids are obtained from the vertical energy gaps for removal or insertion of the acidic proton and the computed salvation free energy of the proton. The unsigned mean error relative to experimental results is 2.1 pK(a) units with a maximum error of 4.0 pK(a) units. The estimated mean statistical uncertainty due to the finite length of the trajectories is +/-1.1 pK(a) units. The solvation structures of the protonated and deprotonated amino acids are analyzed in terms of radial distribution functions, which can serve as reference data for future force field developments.
