Paper Citing NAMD - Abstract
Stachowicz, Anna; Rogalski, Marek; Korchowiec, Jacek
Charge sensitivity approach to mutual polarization of reactants: molecular mechanics perspective
JOURNAL OF MOLECULAR MODELING, 19:4163-4172, OCT 2013
Charge sensitivity analysis (CSA) in force-field atoms resolution was applied to describe the mutual polarization of reactants as well as charge-transfer (CT) effects. An inclusion complex of beta-cyclodextrin with salicylic acid was used as a model system. Three CSA models were taken into account and verified on a Born-Oppenheimer molecular dynamics (BOMD) trajectory. The models differed in terms of the equilibrium conditions imposed on the system. It was demonstrated that mutual polarization is an important source of stabilization, in contrast to the results obtained from static charge calculations. The energy lowering induced by CT was small and comparable to the CT stabilization that occurs in hydrogen-bonded systems. All models correctly described the main topological features of the BOMD energy surface. CSA in force-field atoms resolution qualitatively reproduced the charge reorganization accompanying hydrogen-bond formation. It was shown that CSA parameters are very sensitive to the bond formation process, which suggests that they could be applied in reactive force fields as detectors of newly formed chemical bonds.
