Sum of interactions between fragments

On the basis of a sound analysis of intermolecular interactions, performed by means of a quantum perturbational approach, Claverie derived a force field that could suitably represent intermolecular interactions. The electrostatic interactions are described by means of a distributed multipole analysis, and induction effects are taken into account. The force field sum of interactions between fragments completed ab initio (SIBFA) originated from this study and was subsequently applied successfully to many biophysical problems. 

Accurate energy-decomposition schemes Other force fields build on both atomic multipoles and polarizability to provide an accurate decomposition of intermolecular energies. The sum of interaction between fragments ab initio (sibfa) [83, 84] decomposes the... 

Abstract This chapter discusses molecular mechanics (MM)-based approaches to investigate organometallic complexes. In particular, ligand field MM (LFMM), Sum of Interactions Between Fragments Ab Initio (SIBFA), and VALBOND with its extension to VALBOND-TRANS are presented in some detail. Two particular applications of VALBOND-TRANS to an Ir(III) and a Pt(II) complex are presented. Possible future extensions, including the study of chemical reactions and polarization effects, are briefly discussed at the end. 

SCC-DFTB self-consistent charge-density functional tight binding SCRFPCM self-consistent reaction field polarizable continuum model SIBFA sum of interactions between fragments ab initio computed... 

The theoretical investigations included molecular dynamics, SIBFA (Sum of Interactions Between Fragments initio computed), molecular mechanics, HF and DFT calculations (on models of inhibitor-enzyme complexes on small model complexes including 88 atoms, extracted from the 104-residue complexes [53]. Calculations were carried out both with unconelated (HF) as well as correlated (DFT, MP2) quantum chemical approaches. 

The modifled SIBFA (sum of interactions between fragments ab initio computed) molecular mechanics method has been employed for the study of the conformation at 1 atm and 15kbar of chiral crotonate (131) (Scheme 19) and of the complexes formed with the diphenylmethylamine and the three solvent molecules present in the experiment. The results obtained suggest that the diastereoselectivity of this Michael addition (18% de at 1 atm and 98% de at ISkbar), induced by high pressure and by the presence of methanol, originates from an important stabilization of the pro-R reactive complex in which the crotonate has a stacked-fransoid conformation. This study has demonstrated that it is possible to account theoretically for the influence of pressure on molecular conformation and/or complex sttucture, using a molecular mechanics method that is able to take into account the variation of volumes of the different entities present in the system studied. ... 

SIBFA Sum of interactions between fragments Ab initio computed... 

The SIBFA (sum of interactions between fragments ab initio computed) force field for small molecules and flexible proteins, developed by Gresh, Piquemal et al. is one of the most sophisticated polarizable force fields because it incorporates polarization, electrostatic penetration, " and charge transfer effects. ... 

One area where the concept of atomic charges is deeply rooted is force field methods (Chapter 2). A significant part of the non-bonded interaction between polar molecules is described in terms of electrostatic interactions between fragments having an internal asymmetry in the electron distribution. The fundamental interaction is between the Electrostatic Potential (ESP) generated by one molecule (or fraction of) and the charged particles of another. The electrostatic potential at position r is given as a sum of contributions from the nuclei and the electronic wave function. 

According to the assumption we have made the change in the density matrix, ARX, due to the coulombic interaction between fragments will be more or less localized. It is tempting to set ARX = XL. By doing that, however, one is forced [8] to split off the local space from the remainder of the system to satisfy the idempotency condition. This results in an ordinary cluster model which does not allow electron transfer to or from the surroundings and, as we will see in Sect. 5, is unsuitable for our purposes. In order to properly embed the cluster we take advantage of the fact that the sum of the occupied and unoccupied molecular orbital (MO) spaces is identical to the total AO space. So, instead of ARX = XL, we write... 

We also believe that the analysis of the inclusion complex geometry on the basis of the fluorescence spectra and MM modeling without invoking NOE (or ROE), as is done in [113], is not warranted, and also that the authors interpretation that more than 90% of the stabilization of the 1 1 complexes comes from van der Waals interactions is unfounded since it is based on the partitioning of the difference between the average energies of the complex and the sum of its constituent fragments. 

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