Solvents, models for

B Roux, T Simonson, eds. Implicit Solvent Models for Biomolecular Simulations. Special Issue of Biophys Chem Amsterdam Elsevier, 1999. 

Pratt, L. R., and Rempe, S. B. (1999). Quasi-chemical theory and implicit solvent models for simulations. In Simulation and Theory of Electrostatic Interactions in Solution. Computational Chemistry, Biophysics, and Aqueous Solutions (L. R. Pratt and G. Hummer, eds.), vol. 492 of AIP Conference Proceedings, pp. 172-201. American Institute of Physics, Melville, NY... 

Torrie, G. M. and Patey, G. N. Molecular solvent model for an electrical double layer asymmetric solvent effects, J.Phys.Chem., 97(1993). 12909-12918... 

In general, continuum models perform very well wherever interactions between solvent and solute are only moderately strong, including for many nonpolar solvents as are frequently used in organometallic chemistry. They also work quite well for water, as a lot of effort has been invested in obtaining accurate solvent models for this important solvent. This allows the calculation of acid and base pA values with reasonable accuracy. 

G. Scalmani, N. Rega, M. Cossi and V. Barone, Finite elements molecular surface in continuum solvent models for large chemical systems, J. Comput. Meth. Science Eng., 2 (2001) 159-164. 

Homogeneous and Heterogeneous Solvent Models for Nonlinear Optical Properties... 

B. Roux and T. Simonson, Biophys. Chem., 78, (1999). Implicit Solvent Models for... 

Zhang L, Gallicchio E, Levy RM (1999) Implicit Solvent Models for Protein-Ligand Binding, Insights Based on Explicit Solvent Simulations, (AIP Conference Proceedings, Simulation and Theory of Electrostatic Interactions in Solutions), 192 151 172... 

Ferrara P, J Apostolakis, A Caflisch (2002) Evaluation of a fast implicit solvent model for molecular dynamics simulations. Proteins Struct., Funct., Genet. 46 (1) 24—33... 

AN EXPLICIT QUANTUM CHEMICAL SOLVENT MODEL FOR STRONGLY COUPLED SOLUTE-SOLVENT SYSTEMS IN GROUND OR EXCITED STATE... 

The solvent is a necessary part of the physical problem for computational studies of larger-scale structures in solution. But often the solvent is of secondary interest. Therefore, there has been extended attention to implicit solvent models for those computational studies, models that provide the proper statistical description of the macromolecule but without the solvent explicitly present (Roux and Simonson, 1999). Equation (3.38), p. 45, provides a fundamental basis for implicit solvent models. 

G. King and A. Warshel, J. Chem. Phys., 91, 3647 (1989). A Surface Constrained All-Arom Solvent Model for Effective Simulations of Polar Solutions. 

The choice of a solvent model for the hydrophobic interaction. Obviously the selectivity of the biological system cannot be modeled by a solvent. However, solvents can be chosen to model the partial desolvation observed in protein-protein interactions (see above) because there is a qualitative analogy between water and non-polar solvents and the interaction of small molecules with biological systems. This can be expressed as a quantitative relation between partition coefficients and the binding to biological systems (receptors, proteins, membranes, etc.) It... 

Schmidt am Busch M, Lopes A, Amara N, Bathelt C, Simonson T (2008) Testing the Coulomb/accessible surface area solvent model for protein stability, ligand binding, and protein design. BMC Bioinform 9 148-163... 

Zhang LY, Gallicchio E, Friesner RA, Levy RM. Solvent models for protein-ligand binding comparison of implicit solvent Poisson and surface generalized Born models with explicit solvent simulations. J Comput Chem 2001 22 591-607. 

Wang, T, Wade, R. Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation. Proteins 2003, 50,158-69. 

G. M. Torrie and G. N. Patey, /. Phys. Chem., 97,12909 (1993). Molecular Solvent Model for an Electrical Double Layer Asymmetric Solvent Effects. 

Basdevant, N., Borgis, D., Ha-Duong, T. A semi-implicit solvent model for the simulation of peptides and proteins. J. Comput. Chem. 25, 1015-1029 (2004)... 

Recall that this protocol uses OLYP/3-21G geometries combined with single-point OLYP/6-311+G calculations with the COSMO solvent model. The excellent results obtained appear to support the use of the small basis set for the geometry optimizations, as well as the use of the COSMO solvent model for the aqueous solvent. 

Wei J, Li C, van der Vegt NFA, Peter C (2011) Transferability of coarse grained potentials implicit solvent models for hydrated ions. J Chem Theory Comput, Doi 10.1021/ct2001396... 

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