Explicit solvation structure

Protein-DNA complexes present demanding challenges to computational biophysics The delicate balance of forces within and between the protein, DNA, and solvent has to be faithfully reproduced by the force field, and the systems are generally very large owing to the use of explicit solvation, which so far seems to be necessary for detailed simulations. Simulations of such systems, however, are feasible on a nanosecond time scale and yield structural, dynamic, and thermodynamic results that agree well with available experimen-... 

On balance, the FF derived from a reasonably large and diverse training set gives accurate structures (Fig. 11). Any significant discrepancies suggest interesting behavior due to environmental effects. In such cases, explicit solvation improves the computed results (45). 

DFT was employed to study the mechanism of ammonolysis of phenyl formate in the gas phase, and the effect of various solvents on the title reaction was assessed by the polarizable continuum model (PCM). The calculated results show that the neutral concerted pathway is the most favourable one in the gas phase and in solution.24 The structure and stability of putative zwitterionic complexes in the ammonolysis of phenyl acetate were examined using DFT and ab initio methods by applying the explicit, up to 7H20, and implicit PCM solvation models. The stability of the zwitterionic tetrahedral intermediate required an explicit solvation by at least five water molecules with stabilization energy of approximately 35 kcalmol-1 25... 

Sulfite addition in water can be treated but here it seems necessary to use nine explicit waters solvating the C-O- in the initial product of sulfite addition in order to avoid breakdown of the adduct. Clearly it would be better to include a large number of waters in every case but the cost of the optimizations goes up as the number of waters increases. From a practical perspective it is better to allow a bit of empiricism to find the number of waters needed to reliably give a good result. This reaction is still under investigation as we seek to find a general way to carry out structure optimizations with reaction intermediates that have a lifetime in solution but are unstable in the gas phase unless explicitly solvated. 

Solvent effect can have a profound effect on chemical reactions, yet we do not at the moment have a proven methodology (as in the case of electronic structure theory) that by well-known routes can converge to chemical accuracy. Continuum methods are going to carry the bulk of the workload in the foreseeable future. However, it will be one of the major challenges within the next decade to develop solvation theories that by standard procedures will converge to chemical accuracy. Such methods are likely to combine explicit solvation for the first few solvation shelves with bulk descriptions (continuum or mean-field) for the remaining part of the solvent. 

Effective ways to estimate tree energies since solvent degrees ot treedom are taken into account implicitly, estimating tree energies ot solvated structures is much more straightforward than with explicit water models. 

An analogous approach to the solvation quantities derived for non-electrolyte systems [41,181], based on Kusalik and Patey s version of the Kirkwood-Buff fluctuation theory of mixtures [210], was developed recently [42] to make explicit contact not only between the solvation structure of individual ions and its corresponding macroscopic properties, but also between the individual ion s and the salt s properties without invoking any extrathermodynamic assumption [173,212]. 

A great deal of effort has been placed in determining the solvation structure of ions, i.e, the solvent structure in their vicinity, from a variety of spectroscopic techniques such as NMR, XAFS [258-260], Mossbauer, IR, and Raman [261] scattering techniques such as X-rays, electron and neutron diffraction [261,262] electrochemical techniques [2,36] and simulation methods [261]. The rationale behind these studies hinges upon the idea that a realistic description of the thermophysical properties of electrolyte solutions must take into account the ion-induced local distortion of the solvent properties, i.., it should go beyond the so-called continuum or primitive models. The challenge resides in our ability to probe the properties of the solvent in the vicinity of ions, and then, to make explicit contact with meaningful solvation-related macroscopic properties. 

Machesky ML, Predota M, Wesolowski DJ, Vlcek L, Cummings PT, Rosenqvist J, Ridley MK, Kubicki JD, Bandura AV, Kumar N, Sofo JO (2008) Surface protonation at the rutile (110) interface explicit incorporation of solvation structure within the refined MUSIC model framework. Langmuir 24 12331-12339... 

It is possible to go beyond the SASA/PB approximation and develop better approximations to current implicit solvent representations with sophisticated statistical mechanical models based on distribution functions or integral equations (see Section V.A). An alternative intermediate approach consists in including a small number of explicit solvent molecules near the solute while the influence of the remain bulk solvent molecules is taken into account implicitly (see Section V.B). On the other hand, in some cases it is necessary to use a treatment that is markedly simpler than SASA/PB to carry out extensive conformational searches. In such situations, it possible to use empirical models that describe the entire solvation free energy on the basis of the SASA (see Section V.C). An even simpler class of approximations consists in using infonnation-based potentials constructed to mimic and reproduce the statistical trends observed in macromolecular structures (see Section V.D). Although the microscopic basis of these approximations is not yet formally linked to a statistical mechanical formulation of implicit solvent, full SASA models and empirical information-based potentials may be very effective for particular problems. 

A. Schiiurmann, G. COSMO a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. J. Chem. Soc., Perkins Trans. 1993, 799-805. (c) Klamt, A. Jonas, V. Burger, T. Lohrenz, J. C. W. Refinement and parametrization of COSMO-RS. J. Phys. Chem. A 1998, 102, 5074—5085. (d) For a more comprehensive treatment of solvation models, see Cramer, C. J. Truhlar, D. G. Implicit solvation models equilibria, structure, spectra, and dynamics. Chem. Rev. 1999, 99, 2161— 2200. 

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