Electrostatic interaction Nonbonded interactions

Nonbonded interactions are possible between atoms that are neither bound to one another (1,2 interactions) nor bound to a common atom (1,3 interactions). They include both van der Waals and electrostatic interactions. Nonbonded interactions with the metal are often omitted in calculations that have been performed with either the VFF or the POS approach. The reason for the omission is that the majority of metal complexes that have been modeled are coordinatively saturated. In these structures, the metal center is shielded from nonbonded interactions by a shell of donor atoms followed by a second shell of ligand atoms. It is not possible for the outer shells of ligand atoms, i.e., those with 1,4 or greater connection to the metal, to achieve close contacts with the metal center. It has been demonstrated that the inclusion of M-X van der Waals terms does not significantly alter calculated geometries or relative energies for different conformers of hexamine Co(III) and Cr(III) complexes and pentacoordinate nitrogen macrocyclic complexes of Co(III) and Cu(II). ... 

If you are a purist and regard molecular mechanics as a semiempirical method (the theoretical part coming from the physics of springs and the theory of van der Waals and electrostatic and nonbonded interactions) then you will be uncomfortable with any nonexperimental (nonempirical) parameterization. As a practical matter, however, we simply want a method that works, and we can compare the two approaches to parameterizing in this context. 

Recently, detailed molecular pictures of the interfacial structure on the time and distance scales of the ion-crossing event, as well as of ion transfer dynamics, have been provided by Benjamin s molecular dynamics computer simulations [71, 75, 128, 136]. The system studied [71, 75, 136] included 343 water molecules and 108 1,2-dichloroethane molecules, which were separately equilibrated in two liquid slabs, and then brought into contact to form a box about 4 nm long and of cross-section 2.17 nmx2.17 nm. In a previous study [128], the dynamics of ion transfer were studied in a system including 256 polar and 256 nonpolar diatomic molecules. Solvent-solvent and ion-solvent interactions were described with standard potential functions, comprising coulombic and Lennard-Jones 6-12 pairwise potentials for electrostatic and nonbonded interactions, respectively. While in the first study [128] the intramolecular bond vibration of both polar and nonpolar solvent molecules was modeled as a harmonic oscillator, the next studies [71,75,136] used a more advanced model [137] for water and a four-atom model, with a united atom for each of two... 

In the next chapters, one or several of those formalisms are used to describe some aspects of molecular behavior toward other molecules in terms of properties such as electrostatic potential, nonbonded interactions, behavior in solvents, reactivity and behavior during interaction with other molecules, and finally similarity on the basis of nonquantum and quantum properties. 

A priori, one might guess that the partial atomic charges of the oxygens in the carbonyl group would be more similar to each other than to the water oxygen. One would be hard put, however, to decide whether the oxygens in formaldehyde and formamide can be described by the same parameters for electrostatic and nonbonded interactions. The values obtained from the second derivatives (reported in Table 4) allow a direct determination of the answer to... 

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. 

Before running a molecular dynamics simulation with solvent and a molecular mechanics method, choose the appropriate dielectric constant. You specify the type and value of the dielectric constant in the Force Field Options dialog box. The dielectric constant defines the screening effect of solvent molecules on nonbonded (electrostatic) interactions. 

AMBER, BIO-h and OPLS scale 1 van der Waals and 1 electrostatic interactions. Although the value of the 1 nonbonded scale factors is an option in HyperChem, you should generally use recommended values. This is because during parameterization, the force field developers used particular values for the 1 nonbonded scale factors, and their parameters may not be correct for other scale factors. 

This term describes the classical nonbonded electrostatic interactions of charge distributions. 

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. 

The OPLS form of electrostatic interactions is that of equation (26) on page 179. That is, it uses a charge-charge interaction just like AMBER. However, since the nonbonded potentials were developed... 

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. 

The first two terms on the right-hand side of Eq. (83) are usually assumed to be harmonic, as given for example by Eq. (6-74). The third term is often developed in a Fourier series, as given by Eq. (82). The potential function appropriate to the interaction between nonbonded atoms is taken to be of the Lennard-Jones type (Section 6.7.3). In all of these cases the necessary force constants are estimated by comparing the results obtained from a large number of similar molecules. If electrostatic interactions are to be considered, effective atomic charges must be suggested and Coulomb s law applied directly [see Eq. (6-81)]. 

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). 

It is interesting to note that the mS values calculated with the gauche states of all C-C bonds at 120" (solid line) disagree with the NLDE constants measured for all the a,w dibromoalkanes except 1,3-dibromopropane. When the terminal C-C bonds are permitted to adopt g — 80", all other C-C bonds retaining gauche states at 120", the calculated NLDE constants (dashed lines) are in much better agreement with those observed for all the a, —dibromoalkanes except 1,3-dibromopropane. This behavior has a simple explanation in terms of the nonbonded steric and electrostatic interactions (21) resulting from rotation about the terminal C-C bonds. 

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... 

The first three terms, stretch, bend and torsion, are common to most force fields although their explicit form may vary. The nonbonded terms may be further divided into contributions from Van der Waals (VdW), electrostatic and hydrogen-bond interactions. Most force fields include potential functions for the first two interaction types (Lennard-Jones type or Buckingham type functions for VdW interactions and charge-charge or dipole-dipole terms for the electrostatic interactions). Explicit hydrogen-bond functions are less common and such interactions are often modeled by the VdW expression with special parameters for the atoms which participate in the hydrogen bond (see below). 

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