Dispersion corrected density functional theory (DFT-D3) is used for fully ab initio protein-ligand (PL) interaction energy calculation via molecular fractionation with conjugated caps (MFCC) and applied to PL complexes from the PDB comprising 3680, 1798, and 1060 atoms. Molecular fragments with n amino acids instead of one in the original MFCC approach are… (More)
Characterizations and properties of I ˆ g-closed sets and I ˆ g-open sets are given. A characterization of normal spaces is given in terms of I ˆ g-open sets. Also, it is established that an I ˆ g-closed subset of an I-compact space is I-compact.
Stacked dimers of four polycondensed aromatic hydrocarbons, with structures varying from high to reduced symmetries, have been calculated with dispersion-corrected density functional theory. The configurations of the stacked dimers are readily classified by two in-plane displacements and a relative rotation. The potential energy surface in these three… (More)
Using the polarizable molecular mechanics method SIBFA, we have performed a search for the most stable binding modes of D- and L-thiomandelate to a 104-residue model of the metallo-beta-lactamase from B. fragilis, an enzyme involved in the acquired resistance of bacteria to antibiotics. Energy balances taking into account solvation effects computed with a… (More)