Atom-solvent interactions

The interface between two nonpolar atomic solvents interacting through Lennard-Jones-type potentials has been studied [41] diffusion in the interfacial region was found to be anisotropic. 

Abstract. A smooth empirical potential is constructed for use in off-lattice protein folding studies. Our potential is a function of the amino acid labels and of the distances between the Ca atoms of a protein. The potential is a sum of smooth surface potential terms that model solvent interactions and of pair potentials that are functions of a distance, with a smooth cutoff at 12 Angstrom. Techniques include the use of a fully automatic and reliable estimator for smooth densities, of cluster analysis to group together amino acid pairs with similar distance distributions, and of quadratic progrmnming to find appropriate weights with which the various terms enter the total potential. For nine small test proteins, the new potential has local minima within 1.3-4.7A of the PDB geometry, with one exception that has an error of S.SA. 

Our potential is a sum of smooth surface potentials that model amino acid-solvent interactions and of smooth pair potentials that model amino acid-amino acid interactions. As in [24], we take as essential only the Ca atoms. 

Representative chemical shifts from the large amount of available data on isothiazoles are included in Table 4. The chemical shifts of the ring hydrogens depend on electron density, ring currents and substituent anisotropies, and substituent effects can usually be predicted, at least qualitatively, by comparison with other aromatic systems. The resonance of H(5) is usually at a lower field than that of H(3) but in some cases this order is reversed. As is discussed later (Section 4.17.3.4) the chemical shift of H(5) is more sensitive to substitution in the 4-position than is that of H(3), and it is also worth noting that the resonance of H(5) is shifted downfield (typically 0.5 p.p.m.) when DMSO is used as solvent, a reflection of the ability of this hydrogen atom to interact with proton acceptors. This matter is discussed again in Section 4.17.3.7. 

Suppose we have a physical system with small rigid particles immersed in an atomic solvent. We assume that the densities of the solvent and the colloid material are roughly equal. Then the particles will not settle to the bottom of their container due to gravity. As theorists, we have to model the interactions present in the system. The obvious interaction is the excluded-volume effect caused by the finite volume of the particles. Experimental realizations are suspensions of sterically stabilized PMMA particles, (Fig. 4). Formally, the interaction potential can be written as... 

In the previous chapter we considered a rather simple solvent model, treating each solvent molecule as a Langevin-type dipole. Although this model represents the key solvent effects, it is important to examine more realistic models that include explicitly all the solvent atoms. In principle, we should adopt a model where both the solvent and the solute atoms are treated quantum mechanically. Such a model, however, is entirely impractical for studying large molecules in solution. Furthermore, we are interested here in the effect of the solvent on the solute potential surface and not in quantum mechanical effects of the pure solvent. Fortunately, the contributions to the Born-Oppenheimer potential surface that describe the solvent-solvent and solute-solvent interactions can be approximated by some type of analytical potential functions (rather than by the actual solution of the Schrodinger equation for the entire solute-solvent system). For example, the simplest way to describe the potential surface of a collection of water molecules is to represent it as a sum of two-body interactions (the interac-... 

Now knowing how to evaluate solvation-free energies, we are ready to explore the effect of the solvent on the potential surface of the reacting solute atoms. Adapting the EVB approach we can describe the reaction by including the solute-solvent interaction in the diagonal elements of the solute Hamiltonian, using... 

The author assumed that the Born radii of atoms can be estimated from the solvent exposure factors for sampling spheres around the atoms. Two spheres were used in a five-parameter equahon to calculate the Born radii. The parameters of the equahon were eshmated using numerical calculahons from X-ray protein structures for dihydrofolate reductase. In addition to AGol the author also considered the AGJ term accounting for cavity formahon and dispersion of the solute-solvent interactions as ... 

The coefficients Co, nnd C2 (denoted as mq, ai, and aj in Ref. 33) are influenced by various molecular properties of the solvent and an ion, including their electron-donating or accepting abilities. Hence, these coefficients are specific to the ion. Nevertheless, they may be considered as common to a family of ions such as the polyanions whose surface atoms, directly interacting with solvents, are oxygens. This is the case for hydrated cations or anions whose surfaces are composed of some water molecules that interact with outer water molecules in the W phase or with organic solvents in the O phase. 

Oxidation of the less bulky substituted cyclotrisilene 19 with [Et3Si(C6Hg)]+ TPFPB in benzene surprisingly resulted in the formation of the cyclotetrasileny-lium ion 20+ TPFPB , which was also free from any counterion or solvent interaction in both the solid state and solution (Scheme 2.18). In the cationic portion of the molecule 20+, the Sil, Si2, and Si3 atoms exhibited a planar geometry whereas... 

An alternative approach to calculating the free energy of solvation is to carry out simulations corresponding to the two vertical arrows in the thermodynamic cycle in Fig. 2.6. The transformation to nothing should not be taken literally -this means that the perturbed Hamiltonian contains not only terms responsible for solute-solvent interactions - viz. for the right vertical arrow - but also all the terms that involve intramolecular interactions in the solute. If they vanish, the solvent is reduced to a collection of noninteracting atoms. In this sense, it disappears or is annihilated from both the solution and the gas phase. For this reason, the corresponding computational scheme is called double annihilation. Calculations of... 

Rao and Singh32 calculated relative solvation free energies for normal alkanes, tetra-alkylmethanes, amines and aromatic compounds using AMBER 3.1. Each system was solvated with 216 TIP3P water molecules. The atomic charges were uniformly scaled down by a factor of 0.87 to correct the overestimation of dipole moment by 6-31G basis set. During the perturbation runs, the periodic boundary conditions were applied only for solute-solvent and solvent-solvent interactions with a non-bonded interaction cutoff of 8.5 A. All solute-solute non-bonded interactions were included. Electrostatic decoupling was applied where electrostatic run was completed in 21 windows. Each window included 1 ps of equilibration and 1 ps of data... 

To make an accurate FEP calculation, a good description of the system is required. This means that the parameters for the chosen force field must reproduce the dynamic behaviour of both species correctly. A realistic description of the environment, e.g. size of water box, and the treatment of the solute-solvent interaction energy is also required. The majority of the parameters can usually be taken from the standard atom types of a force field. The electrostatic description of the species at both ends of the perturbation is, however, the key to a good simulation of many systems. This is also the part that usually requires tailoring to the system of interest. Most force fields require atom centered charges obtained by fitting to the molecular electrostatic potential (MEP), usually over the van der Waals surface. Most authors in the studies discussed above used RHF/6-31G or higher methods to obtain the MEP. 

The physical properties of atoms and molecules embedded in polar liquids have usually been described in the frame of the effective medium approximation. Within this model, the solute-solvent interactions are accounted for by means of the RF theory [1-3], The basic quantity of this formalism is the RF potential. It is usually variationally derived from a model energy functional describing the effective energy of the solute in the field of an external electrostatic perturbation. For instance, if a singly negative or positive charged atomic system is considered, the RF potential is simply given by... 

The emphasis thus far has been upon classical approaches to evaluating GC CC,rostatic (although quantum-mechanical methods might be used in some instances to obtain atomic charges or solute molecule electronic densities.) However continuum models lend themselves very well to quantum-mechanical treatments of solute-solvent interactions, and have indeed been incorporated into several standard codes, such as the Gaussian series.29 GC CCtrostatiC is now given by,... 

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