Nonbonding interactions electrostatic

The zeolite framework was described by a specific force field developed by van Santen et al. [11] while the hydrocarbon molecules and their interaction among themselves and with the zeolite lattice were described by the generic force field Drdding n [12]. All the internal coordinates of the alkane molecules were allowed to fully relax. The nonbonded interactions (electrostatic and van der Waals) were computed for aU atoms within a cutoff-radius of 12A. Periodic boundary conditions were imposed along the three axes of the zeolite model to simulate an infinite crystal. 

There are a total of 15 (i.e., (5 x 6)/2) atom-type pairs ifboth interactions between the atoms of the same type and cross-interactions are calculated. For each atom-type pair, two different nonbonding interactions (electrostatic and van der Waals potential) are considered, leading to a final molecular vector comprising of 30 intercations terms. 

In an atomic level simulation, the bond stretch vibrations are usually the fastest motions in the molecular dynamics of biomolecules, so the evolution of the stretch vibration is taken as the reference propagator with the smallest time step. The nonbonded interactions, including van der Waals and electrostatic forces, are the slowest varying interactions, and a much larger time-step may be used. The bending, torsion and hydrogen-bonding forces are treated as intermediate time-scale interactions. 

MOMEC is a force field for describing transition metal coordination compounds. It was originally parameterized to use four valence terms, but not an electrostatic term. The metal-ligand interactions consist of a bond-stretch term only. The coordination sphere is maintained by nonbond interactions between ligands. MOMEC generally works reasonably well for octahedrally coordinated compounds. 

Although interactions between vicinal atoms are nominally treated as nonbonded interactions, most of the force fields treat these somewhat differently from normal 1-5 and greater nonbonded interactions. HyperChem allows each of these nonbonded interactions to be scaled down by a scale factor <1.0 with AMBER or OPLS. For BlO-t the electrostatic may be scaled and different parameters may be used for 1 van der Waals interactions. Th e AMBER force field, for exam p le, norm ally u ses a scalin g factor of 0.5 for both van der Waals and electrostatic interactions. 

SH Bryant, CE Lawrence. The frequency of lon-pair substructures m proteins is quantitatively related to electrostatic potential A statistical model for nonbonded interactions. Proteins 9 108-119, 1991. 

Some authors complement the expressions (5) and (6) for nonbonded interactions by electrostatic terms of the type q y/ y (q,- partial electronic changes) (8,17). At least for the calculation of hydrocarbons it is not clear, however, whether electrostatic terms are actually necessary (19). 

The mechanism of charge reorganization attending the interconversion of geometric isomers due to nonbonded interaction effects has already been discussed before1. The electrostatic effect can be thought of as the effect which forces the distribution of charge in such a way that electrostatic repulsions are minimized. 

Property Sigma conjugative effect Nonbonded interaction effect Electrostatic or steric effect Ab initio... 

Rigid-geometry ab initio MO calculations of 86 torsional isomers of the dimethylphosphate anion (CH30)2P02 led to the determination of parameters for the Lennard-Jones type of nonbonded interaction, two- and three-fold torsional, and electrostatic interaction potential functions (215). Extension of this approach to full relaxation ab initio and MM schemes will be extremely useful, not only for phosphorus but also for other heteroatoms. 

Van der Waals and electrostatic interactions are sometimes called together nonbonded interactions. However, in most works this name refers to the van der Waals interaction only. 

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