Solvation computer simulation

Keywords electron crystallography, polymorphs, solvate, computer simulation, x-ray powder... 

Modern techniques of studying solvation computer simulations... 

Elamrani et al. 1996] Elamrani, S., Berry, M.B., Phillips Jr., G.N., McCammon, J.A. Study of Global Motions in Proteins by Weighted Masses Molecular Dynamics Adenylate Kinase as a Test Case. Proteins 25 (1996) 79-88 [Elcock et al. 1997] Elcock, A.H., Potter, M.J., McCammon, J.A. Application of Poisson-Boltzmann Solvation Forces to Macromolecular Simulations. In Computer Simulation of Biomoleeular Systems, Vol. 3, A.J. Wilkinson et al. eds., ESCOM Science Publishers B.V., Leiden... 

Caution Solvation in simulations can significantly increase computation time so that the simulation may be impractical. 

Modem understanding of the hydrophobic effect attributes it primarily to a decrease in the number of hydrogen bonds that can be achieved by the water molecules when they are near a nonpolar surface. This view is confirmed by computer simulations of nonpolar solutes in water [15]. To a first approximation, the magnimde of the free energy associated with the nonpolar contribution can thus be considered to be proportional to the number of solvent molecules in the first solvation shell. This idea leads to a convenient and attractive approximation that is used extensively in biophysical applications [9,16-18]. It consists in assuming that the nonpolar free energy contribution is directly related to the SASA [9],... 

To illustrate the relationship between the microscopic structure and experimentally accessible information, we compute pseudo-experimental solvation-force curves F h)/R [see Eq. (22)] as they would be determined in SEA experiments from computer-simulation data for T z [see Eqs. (93), (94), (97)]. Numerical values indicated by an asterisk are given in the customary dimensionless (i.e., reduced) units (see [33,75,78] for definitions in various model systems). Results are correlated with the microscopic structure of a thin film confined between plane parallel substrates separated by a distance = h. Here the focus is specifically on a simple fluid in which the interaction between a pair of film molecules is governed by the Lennard-Jones (12,6) potential [33,58,59,77,79-84]. A confined simple fluid serves as a suitable model for approximately spherical OMCTS molecules confined... 

Levy (Chapter 6) has also explored the use of supercomputers to study detailed properties of biological macromolecule that are only Indirectly accessible to experiment, with particular emphasis on solvent effects and on the Interplay between computer simulations and experimental techniques such as NMR, X-ray structures, and vltratlonal spectra. The chapter by Jorgensen (Chapter 12) summarizes recent work on the kinetics of simple reactions In solutions. This kind of calculation provides examples of how simulations can address questions that are hard to address experimentally. For example Jorgensen s simulations predicted the existence of an Intermediate for the reaction of chloride Ion with methyl chloride In DMF which had not been anticipated experimentally, and they Indicate that the weaker solvation of the transition state as compared to reactants for this reaction In aqueous solution Is not due to a decrease In the number of hydrogen bonds, but rather due to a weakening of the hydrogen bonds. 

The use of computer simulations to study internal motions and thermodynamic properties is receiving increased attention. One important use of the method is to provide a more fundamental understanding of the molecular information contained in various kinds of experiments on these complex systems. In the first part of this paper we review recent work in our laboratory concerned with the use of computer simulations for the interpretation of experimental probes of molecular structure and dynamics of proteins and nucleic acids. The interplay between computer simulations and three experimental techniques is emphasized (1) nuclear magnetic resonance relaxation spectroscopy, (2) refinement of macro-molecular x-ray structures, and (3) vibrational spectroscopy. The treatment of solvent effects in biopolymer simulations is a difficult problem. It is not possible to study systematically the effect of solvent conditions, e.g. added salt concentration, on biopolymer properties by means of simulations alone. In the last part of the paper we review a more analytical approach we have developed to study polyelectrolyte properties of solvated biopolymers. The results are compared with computer simulations. 

Mentus S, Maroncelli M (1998) Solvation and the excited-state tautomerization of 7-azaindole and 1-azacarbazole computer simulations in water and alcohol solvents. J Phys Chem A 102 3860-3876... 

Hunenberger, P. H. McCammon, J. A., Ewald artifacts in computer simulations of ionic solvation and ion-ion interactions a continuum electrostatics study, J. Chem. Phys. 1999,110, 1856-1872... 

Voth, G. A., Computer simulation of proton solvation and transport in aqueous and bio-molecular systems, Acc. Chem. Res. 2006, 39, 143-150. 

Schwartz, B. J. and Rossky, P. J. Aqueous solvation dynamics with a quantum mechanical solute computer simulation studies of the photoexcited hydrated electron, J.Chem.Phys., 101 (1994), 6902-6916... 

However, picosecond resolution is insufficient to fully describe solvation dynamics. In fact, computer simulations have shown that in small-molecule solvents (e.g. acetonitrile, water, methyl chloride), the ultrafast part of solvation dynamics (< 300 fs) can be assigned to inertial motion of solvent molecules belonging to the first solvation layer, and can be described by a Gaussian func-tiona) b). An exponential term (or a sum of exponentials) must be added to take into account the contribution of rotational and translational diffusion motions. Therefore, C(t) can be written in the following form ... 

The main goal of the molecular dynamics computer simulation of ionic solvation and adsorption on a metal surface has been to test the above model and to provide more quantitative information about the different factors that influence the structure of hydrated ions at the interface. Unfortunately, most of the experimental information about these issues has been obtained from indirect measurements such as capacity and current-potential plots, although in recent years in situ experimental techniques have begun to provide an accurate test of the above model. For a recent review of experimental techniques and the theory of ionic adsorption at the water/metal interface, see the excellent paper by Philpott. ... 

Although our knowledge of the structure of the electric double layer is based on experimental data collected at finite electrolyte concentrations, understanding the structure of the electric double layer at the microscopic level must begin with knowledge of the structure of a single solvated ion at the interface. This information has been obtained in recent years from molecular dynamics computer simulations. 

The structure of the adsorbed ion coordination shell is determined by the competition between the water-ion and the metal-ion interactions, and by the constraints imposed on the water by the metal surface. This structure can be characterized by water-ion radial distribution functions and water-ion orientational probability distribution functions. Much is known about this structure from X-ray and neutron scattering measurements performed in bulk solutions, and these are generally in agreement with computer simulations. The goal of molecular dynamics simulations of ions at the metal/water interface has been to examine to what degree the structure of the ion solvation shell is modified at the interface. 

The theoretical modeling of electron transfer reactions at the solution/metal interface is challenging because, in addition to the difficulties associated with the quantitative treatment of the water/metal surface and of the electric double layer discussed earlier, one now needs to consider the interactions of the electron with the metal surface and the solvated ions. Most theoretical treatments have focused on electron-metal coupling, while representing the solvent using the continuum dielectric media. In keeping with the scope of this review, we limit our discussion to subjects that have been adi essed in recent years using molecular dynamics computer simulations. 

Such a time scale separation between system and bath may often be appropriate when dealing with intramolecular vibrational motions of molecules but is likely never appropriate for electronic transitions in solution near room temperature. In the past 10 years much effort has been devoted to dynamical aspects of the solvation process in polar liquids utilizing experiments [2-4], theory [5, 6], and computer simulations of molecular dynamics [7-10]. The... 

Indeed, an INM analysis of the optical Kerr signal of acetonitrile by Ladanyi and Klein [43] coupled with a similar analysis of solvation dynamics [12] shows that both processes are dominated by rotational motions and further that p(u) is essentially identical in both cases, providing theoretical backing for earlier guess of Cho et al. that both optical Kerr and Stokes shift responses could be described by a common p(u) in this solvent [44]. Calculations based on computer simulations for water [45] and acetonitrile... 

Recently, several authors have studied solvation dynamics of aqueous solutions using molecular dynamics (MD) computer simulations [36, 57, 58, 112], The simulations offer a detailed molecular approach to interpreting the experimental results, as they focus particularly on the microscopic, molecular aspects of the solvation process. 

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