Electrostatic interactions molecular modeling

The electrostatic interaction is modeled using a coulombic potential. The electrostatic energy is a function of the charge on the nonbonded atoms, their interatomic distance, and a molecular dielectric expression that accounts for the attenuation of electrostatic interaction by the environment (e.g., a solvent or the molecule itself). 

The models used in our own work[40, 47-51]are of the interaction site type, where the intermolecular interactions result from a sum over pairwise interactions among sites in each molecule. Typically, each atom of the system is associated with a short ranged potential consisting of a Lennard-Jones 6-12 form, describing molecular shape and dispersion effects, and separately a partial charge describing a contribution to the electrostatic interactions. Such models dominate the descriptions used successfully for systems as diverse as CO2 and biopolymers. 

Independent molecules and atoms interact through non-bonded forces, which also play an important role in determining the structure of individual molecular species. The non-bonded interactions do not depend upon a specific bonding relationship between atoms, they are through-space interactions and are usually modelled as a function of some inverse power of the distance. The non-bonded terms in a force field are usually considered in two groups, one comprising electrostatic interactions and the other van der Waals interactions. 

Morishima et al. [75, 76] have shown a remarkable effect of the polyelectrolyte surface potential on photoinduced ET in the laser photolysis of APh-x (8) and QPh-x (12) with viologens as electron acceptors. Decay profiles for the SPV (14) radical anion (SPV- ) generated by the photoinduced ET following a 347.1-nm laser excitation were monitored at 602 nm (Fig. 13) [75], For APh-9, the SPV- transient absorption persisted for several hundred microseconds after the laser pulse. The second-order rate constant (kb) for the back ET from SPV- to the oxidized Phen residue (Phen+) was estimated to be 8.7 x 107 M 1 s-1 for the APh-9-SPV system. For the monomer model system (AM(15)-SPV), on the other hand, kb was 2.8 x 109 M-1 s-1. This marked retardation of the back ET in the APh-9-SPV system is attributed to the electrostatic repulsion of SPV- by the electric field on the molecular surface of APh-9. The addition of NaCl decreases the electrostatic interaction. In fact, it increased the back ET rate. For example, at NaCl concentrations of 0.025 and 0.2 M, the value of kb increased to 2.5 x 108 and... 

A common feature of many mesogenic molecules is the presence of polar substituents and aromatic cores [3]. The electrostatic interactions between such groups can be incorporated into a molecular potential with the addition of dipolar and quadrupolar terms, respectively. Rather than represent these permanent electrostatic interactions by using a model in which a charge distribution is scattered over the surface of the molecule, it is very common to use one (or more) point multipoles [2,29]. Thus for an electrostatic Gay-Berne model, the pair potential is given by the sum... 

Theoretical studies aimed at rationalizing the interaction between the chiral modifier and the pyruvate have been undertaken using quantum chemistry techniques, at both ab initio and semi-empirical levels, and molecular mechanics. The studies were based on the experimental observation that the quinuclidine nitrogen is the main interaction center between cinchonidine and the reactant pyruvate. This center can either act as a nucleophile or after protonation (protic solvent) as an electrophile. In a first step, NH3 and NH4 have been used as models of this reaction center, and the optimal structures and complexation energies of the pyruvate with NH3 and NHa, respectively, were calculated [40]. The pyruvate—NHa complex was found to be much more stable (by 25 kcal/mol) due to favorable electrostatic interaction, indicating that in acidic solvents the protonated cinchonidine will interact with the pyruvate. 

One of the most popular applications of molecular rotors is the quantitative determination of solvent viscosity (for some examples, see references [18, 23-27] and Sect. 5). Viscosity refers to a bulk property, but molecular rotors change their behavior under the influence of the solvent on the molecular scale. Most commonly, the diffusivity of a fluorophore is related to bulk viscosity through the Debye-Stokes-Einstein relationship where the diffusion constant D is inversely proportional to bulk viscosity rj. Established techniques such as fluorescent recovery after photobleaching (FRAP) and fluorescence anisotropy build on the diffusivity of a fluorophore. However, the relationship between diffusivity on a molecular scale and bulk viscosity is always an approximation, because it does not consider molecular-scale effects such as size differences between fluorophore and solvent, electrostatic interactions, hydrogen bond formation, or a possible anisotropy of the environment. Nonetheless, approaches exist to resolve this conflict between bulk viscosity and apparent microviscosity at the molecular scale. Forster and Hoffmann examined some triphenylamine dyes with TICT characteristics. These dyes are characterized by radiationless relaxation from the TICT state. Forster and Hoffmann found a power-law relationship between quantum yield and solvent viscosity both analytically and experimentally [28]. For a quantitative derivation of the power-law relationship, Forster and Hoffmann define the solvent s microfriction k by applying the Debye-Stokes-Einstein diffusion model (2)... 

The second necessary ingredient in the primitive quasichemical formulation is the excess chemical potential of the metal-water clusters and of water by itself. These quantities p Wm — can typically be obtained from widely available computational packages for molecular simulation [52], In hydration problems where electrostatic interactions dominate, dielectric models of those hydration free energies are usually satisfactory. The combination /t xWm — m//, wx is typically insensitive to computational approximations because the water molecules coat the surface of the awm complex, and computational errors can compensate between the bound and free ligands. 

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