Solvent modeling

Cramer C J and Truhlar D G 1996 Continuum solvation models Solvent Effects and Ohemical Reactivity ed O Tapia and J Bertran (Dordrecht Kluwer) pp 1-80... 

This method was introduced recently as an efficient technique to accurately model solvent and salt effects in an implicit fashion ([Gilson et al. 1993]). The forces are calculated as a sum of three terms ... 

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. 

Smith P E and B M Pettitt 1994. Modelling Solvent in Biomolecular Systems. Journal of Physical Chemistry 98 9700-9711. 

PE Smith, BM Pettitt. Modeling solvent m biomolecular systems. J Phys Chem 98 9700-9711, 1994. 

The photodecomposition and thermodecomposition of nitromethane have been extensively studied as model systems in combustion, explosion and atmosphere pollution processes[l]. On another hand, nitromethane was selected as a model solvent in experiments aimed at examining non hydrogen-bonded solvent effects in a general acid-base theory of organic molecules [2.3]. This selection is based on the electronic and structural characteristics of nitromethane that has a high dielectric constant, and at the same time cannot form hydrogen bonds with solute molecules. 

A CRO may also allow for the in-house introduction of specialized lipophilic scales by transferring routine measurements. While the octanol-water scale is widely applied, it may be advantageous to utilize alternative scales for specific QSAR models. Solvent systems such as alkane or chloroform and biomimetic stationary phases on HPLC columns have both been advocated. Seydel [65] recently reviewed the suitabihty of various systems to describe partitioning into membranes. Through several examples, he concludes that drug-membrane interaction as it relates to transport, distribution and efficacy cannot be well characterized by partition coefficients in bulk solvents alone, including octanol. However, octanol-water partition coefficients will persist in valuable databases and decades of QSAR studies. 

Leahy, D. E. Taylor, P. J. Wait, A. R., Model solvent systems for QSAR. 1. Propylene glycol dipelargonate (PGDP). A new standard for use in partition coefficient determination, Quant. Struct. Act. Relat. 8, 17-31 (1989). 

Polymer Matrix Effects. In order to approximate the environment experienced by the arylcarbamate moieties in coatings based on aromatic diisocyanates, we chose to study the photochemistry of alkyl N-arylcarbamates in polymethacrylate (PMMA) and polypropyl-methacrylate (PPMA) films. First, however, 2a and 3a were irradiated in ethyl propionate (a model solvent for PMMA and PPMA) to determine the effect of the solvent polarity (dielectric) on the photolysis of the carbamates. Upon excitation at 280 nm, where the solvent absorbance was negligible, is 0.006 for 2a and 0j) is 0.005 for 3a. These values are significantly smaller... 

Sytnik A, Del Valle JC (1995) Steady-state and time-resolved study of the proton-transfer fluorescence of 4-hydroxy-5-azaphenanthrene in model solvents and in complexes with human serum albumin. J Phys Chem 99 13028-13032... 

Pandurangi, R.S. et al. (1997b) Chemistry of bifunctional photoprobes Part 1. Perfluoro azido functionalized phosphorus hydrazides as novel photoreactive heterobifunctional chelating agents High efficiency nitrene insertion on model solvents and proteins./. Org. Chem. 62(9), 2798-2807. 

A structural comparison of the calculated (B3LYP/6-311+G ) ts (transition state in the gas phase), ts-wc (transition state in the cluster of five extra water molecules), ts-CPCM (transition state within the CPCM-solvent model (B3LYP(CPCM)/6-311+G )) and ts-PCM (transition state optimized within the PCM-solvent model (B3LYP(PCM)/6-311+G )), shows no large differences (see Fig. 8), which is also valid for the precursor complexes (see Fig. 9). Modeling solvent effects shrinks in all cases the Be-0 bonds of the entering/leaving water molecules (159). 

T. Solmajer and E. L. Mehler, Modeling solvent effects in molecular dynamics... 

We now turn to the electronically adiabatic ET reaction problem (cf. Sec. 2.2). There has been a spate oftheoretical papers [8,11 28,33,35,36,50] dealing with the possible role of solvent dynamics in causing departures from the standard Marcus TST rate theory [27,28] (although many of these deal with nonadiabatic reactions). The ET reaction considered is a simplified symmetric model, A1 2 A1/2 A1/2 A1/2, in a model solvent similar to CH3C1. The technical and computational... 

These block copolymers can act as effective steric stabilizers for the dispersion polymerization in solvents with ultralow cohesion energy density. This was shown with some polymerization experiments in Freon 113 as a model solvent. The dispersion particles are effectively stabilized by our amphi-philes. However, these experiments can only model the technically relevant case of polymerization or precipitation processes in supercritical C02 and further experiments related to stabilization behavior in this sytem are certainly required. 

In the third model, solvent molecules act as a bulk medium and significandy modify the solute properties. In this type, solute-solvent interaction is modeled using the continuum approach [8-11]. A variety of models have been proposed in the literature to treat solvent molecules in different situations. 

Until very recently there was no information about how an MM pair potential should look, based upon calculations from the deeper BO level. In the simplest BO level model for an ionic solution the solvent molecules are represented as hard spheres with centered point dipoles and the ions as hard spheres with centered charges. Now there are two sets of calculations, (16,17) by very different approximation methods, for this model where all of the spheres are 3A in diameter, where the dipole moments are near 1 Debye, and where the ions are singly charged. The temperature is 25° and the solvent concentration is about 50M, corresponding to a liquid state. The dielectric constant of the model solvent is believed to be near 9 6. 

The description of the real process of dipole-orientational relaxation by one parameter xR is a first-order approximation which is far removed from reality even in studies with model solvents.(89) A set of relaxation times would exist in real systems. However, such an approximation is necessary since it allows rather simple models of relaxation to be developed and to be compared with the results of experiments. xR may be considered as a simple effective parameter characterizing the dynamic processes. 

Computational Chemistry in Modeling Solvent Extraction of Metal Ions... 

With this model, it is necessary to assume fast inversion of the two corannulene units within the dimer (or planarity) otherwise the top and bottom bowls would not be equivalent in the NMR spectra. MNDO calculations predict an activation enthalpy of approximately 13 kcal/mol for the concerted inversion process, and this value is inconsistent with the NMR behavior that shows no evidence of freezing out such a dynamic process. These calculations, however, do not take solvation of the exterior lithiums into account, and so the exterior lithiums were removed, and the system was calculated under conditions that would roughly model solvent separation of the lithium cations. Accordingly, the approximate barrier for inversion was lowered to approximately 1 kcal/mol, suggesting that solvation of the exterior lithium cations can indeed greatly reduce the inversion barrier. ... 

Leahy, D.E., Morris, J.J., Taylor, P.J. and Wait, A.R. (1992) Model solvent systems for QSAR. Part 2. Fragment values... 

In order to model the solvent strength parameters of the ODS we used the n-hexane as a model solvent due to its structural similarity with the octadecyl chains of this stationary phase. 

QM/MM approaches where the solute is QM and the solvent MM are in principle useful for computing the effect of the slow reaction field (represented by the solute point charges) but require a polarizable solvent model if electronic equilibration to the excited state is to be included (Gao 1994). With an MM solvent shell, it is no more possible to compute differential dispersion effects directly than for a continuum model. An option is to make the first solvent shell QM too, but computational costs for MC or MD simulations quickly expand with such a model. Large QM simulations with explicit solvent have appeared using the fast semiempirical INDO/S model to evaluate solvatochromic effects, and the results have been promising (Coutinho, Canute, and Zemer 1997 Coutinho and Canute 2003). Such simulations offer the potential to model solvent broadening accurately, since they can compute absorptions for an ensemble of solvent configurations. 

Acetonitrile has been selected as the solvent in this study since it is a possible candidate for a nonaqueous electrolyte battery (5). From this viewpoint, acetonitrile has several attractive physical properties, as shown in Table I. It has a useful liquid state range and a reasonably low vapor pressure and viscosity at ambient temperature. In addition, many common electrolytes are soluble in acetonitrile. Acetonitrile is a good model solvent for solvation studies, as the molecule is a linear aprotic dipole. 

The present work has allowed the direct observation of the transformation of the movements involved in the passage of a conical intersection connecting the V and Z surfaces of a prototype molecule TDMAE by the presence of a model solvent formed by a cage of argon atoms,... 

One example of non-IRC trajectory was reported for the photoisomerization of cA-stilbene.36,37 In this study trajectory calculations were started at stilbene in its first excited state. The initial stilbene structure was obtained at CIS/6-31G, and 2744 argon atoms were used as a model solvent with periodic boundary conditions. In order to save computational time, finite element interpolation method was used, in which all degrees of freedom were frozen except the central ethylenic torsional angle and the two adjacent phenyl torsional angles. The solvent was equilibrated around a fully rigid m-stilbene for 20 ps, and initial configurations were taken every 1 ps intervals from subsequent equilibration. The results of 800 trajectories revealed that, because of the excessive internal potential energy, the trajectories did not cross the barrier at the saddle point. Thus, the prerequisites for common concepts of reaction dynamics such TST or RRKM theory were not satisfied. 

Weitzmann, C. The use of model solvents for evaluating extractables from filters used to process pharmaceutical products. Pharm Tech 21(4) 72-99 (1997). 

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