A molecular mechanics/continuum reaction field investigation of the interactions between polar amino acid side chains in water and organic solvents

Abstract

An integrated procedure that computes in a consistent way both the intermolecular interaction energies and the solvation energies is reported. It interfaces the S u m of Interactions Between Fragments Ab initio computed molecular mechanics and the Langlet

Joint quantum chemical and polarizable molecular mechanics investigation of formate complexes with penta- and hexahydrated Zn2+: Comparison between energetics of model bidentate, monodentate, and through-water Zn2+ binding modes and evaluation of nonadditivity effects

“…24 The DFT computations are done with the B3LYP functional 9 using the Gaussian 94 package. 19 The MNDO, AM1, and PM3 semiempirical computations are done using version 6 of the MOPAC code.…”

Binding of D‐ and L‐captopril inhibitors to metallo‐β‐lactamase studied by polarizable molecular mechanics and quantum mechanics

“…The docking was first done manually using MSI software 26 and the cff91 force field. To explore alternative binding modes of the inhibitor, molecular dynamics (MD) runs at 300 K were launched starting from these complexes with only captopril flexible in the binding pocket.…”

Conformational properties of a model alanyl dipeptide and of alanine-derived oligopeptides: Effects of solvation in water and in organic solvents—A combined SIBFA/continuum reaction field, ab initio self-consistent field, and density functional theory investigation

“…was used, rather than the one published in Ref. 30, A very satisfactory overall agreement occurs, at the which used a more extensive 6-31G* basis set coruncorrelated level, between dE SCF and dE SIBFA0 . The related with the MP2 set.…”

“…30 The inte-There are shortcomings in currently used molecgrated SIBFA/Continuum procedure was applied in ular mechanics force fields, due to an incomplete a series of molecular recognition problems. These representation of the electrostatic term, which is encompass the interactions between polar amino limited to single atom-centered point charges, the acid side chains in water and organic solvents, 30 the lack of anisotropy in the short-range repulsion encooperativity in multiply hydrogen-bonded water ergy, and the absence of polarization and chargeoligomers, 31 and in models of the triose phosphate transfer terms. In an attempt to remedy these shortcomings, we have conceived and elaborated the isomerase enzyme (H. Guo et al, in preparation), 8K41 5557 / 8K41$$5557 02-24-98 10:32:59 bpa W: Biopolymers as well as anticooperativity in polycoordinated Zn 2/ which will be recalled below.…”