Computer simulation of solvation dynamics

As discussed in Chapter 3, SD provides information on molecular motions (primarily rotation) by optically studying the energy fluctuations in a solute probe. In the experimental SD studies of the hydration layer of proteins, we need to either place an external probe in the layer, or use a natural probe such as tryptophan, which is a natural amino acid residue. An additional constraint is that the probe must be at least partly exposed to the solvent. However, in computer simulation studies we have the 

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M. Maroncelli, Computer simulations of solvation dynamics in acetonitrile, J. Chem. Phys., 94 (1991) 2084-103. 

D. Michael and I. Benjamin, /. Chem. Phys., 114, 2817 (2001). Molecular Dynamics Computer Simulations of Solvation Dynamics at Liquid/Liquid Interfaces. 

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... 

I. Benjamin, Chemical reactions and solvation at liquid interfaces a microscopic perspective, Chem. Rev. (Washington, D. C.), 96 (1996) 1449-75 I. Benjamin, Theory and computer simulations of solvation and chemical reactions at liquid interfaces, Acc. Chem. Res., 28 (1995) 233-9 L. R. Martins, M. S. Skaf and B. M. Ladanyi, Solvation dynamics at the water/zirconia interface molecular dynamics simulations, J. Phys. Chem. B, 108 (2004) 19687-97 J. Faeder and B. M. Ladanyi, Solvation dynamics in reverse micelles the role of headgroup-solute interactions, J. Phys. Chem. B, 109 (2005) 6732 10 W. H. Thompson, Simulations of time-dependent fluorescence in nano-confined solvents, J. Chem. Phys., 120 (2004) 8125-33. 

Bopp, P. (1987). Molecular dynamics computer simulations of solvation in hydrogen bonded systems. Pure Appl. Chem. 59, 1071-82. 

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... 

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. ... 

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... 

B. M. Ladanyi, Computer simulation studies of solvation dynamics in mixtures, in J. Samios and V. A. Durov (eds), Novel Approaches to the Structure and Dynamics of Liquids Experiments, Theories and Simulations, Kluwer, Dordrecht, 2004, NATO Sci. Ser. II, Vol. 133, p. 560. 

The protein folding problem - the ability to predict a protein fold from its sequence - is one of the major prizes in computational chemistry. Molecular dynamics simulations of solvated proteins is currently not a feasible approach to this problem. However, Duan and Kollman have shown that a 1 ps simulation on a small hydrated protein, here the 36 residue villin headpiece, is now possible using a massively parallel super computer.33 The native protein is estimated to fold in about 10-100 ps and so the simulation can only be used to study the early stages of protein folding. Nevertheless, starting from an extended structure the authors were able to observe hydrophobic collapse and secondary structure formation (helix 2 was well formed, helices 1 and 3 were partially formed and the loop connecting helices 1 and 2 was also partially... 

Many of the systems previously discussed, for example, the S l, and ion pair reactions, involve some type of charge separation, creation, or transfer. This movement of charge has a substantial effect on the polar solvent in which the reaction takes place. These effects are strongly related to those seen in the solvation dynamics studied by several groups through molecular dynamics simulations. The field of solvation dynamics, in its theoretical, computational... 

Some computer simulations of micelles on a molecular level have already been performed with molecular dynamics calculations. The models used in these simulations are based on different approximation levels. In simulations in which solvent molecules were omitted, the solvation shell was simulated by a sphere, and the interactions between the atoms and the sphere was calculated by Lennard-Jones-type potential functions. In more advanced simulations, the solvent molecules were especially considered and specific water models like SPC were used. 

Allen MP, Tildesley DJ (1987) Computer Simulation of Liquids. Oxford University Press, New Yoik Alper HE, Levy RM (1989) Computer simulations of the dielectric properties of water Studies of the simple point chaige and transferable intermolecular potential models. J ChemPhys 91 1242-1251 Balbuena PB, Johnson KP, Rossky PJ (1996a) Molecular dynamics simulation of electrolyte solutions in ambient and supercritical water. 1. Ion solvation. J Phys Chem 100 2706-2715 Balbuena PB, John n KP, Rossky PJ (1996b) Molecular dynamics simulation of electrolyte solutions in ambient and supercritical water. 2. Relative acidity of HCl. J Phys Chem 100 2716-2722... 

Similar stndies have been made on ions in liquid ammonia (at 240K). The mean residence times of ammonia molecules in the second solvation shells of the ions stndied are longer than for water molecules 12.7ps compared to 2.6ps for Ag [116], 28.5 ps compared with 6.5ps for Co [117], but shorter in the case of Cu 3.2ps [118] compared with 7.7ps for water [91]. Molecular dynamics computer simulations of solutions of ions in liquid ammonia [119] yielded the self-diffusion coefficients of ammonia molecules, D/10 m s , in the solvation shells of 6.1 and of R 7.4, shorter than the value for ammonia molecules in the bulk liquid, 11.5 1.5. These studies thus indicate that K and R are structure breakers and Ag" and Co are structure makers regarding the inherent structure of liquid anunonia. 

Extensive theory and computer simulation work has been able to clarify the molecular mechanisms of solvation dynamics in bulk liquids over the past three decades.One of the most important conclusions from this body of work is that most of the contribution to polar solvation dynamics comes from the solute s first solvation shell. This conclusion and the earlier discussion about the prominent role the solute hydration shell plays in understanding vibrational and rotational dynamics at liquid interfaces suggest that surface effects on solvation dynamics will be muted as the solute s polarity is increased. An experimental validation of this are the similar solvation dynamics of C314 at the water liquid/vapor interface and in bulk water, mentioned above, where the highly polar excited state n = 12D) implicates an interfacial hydration structure similar to the bulk. 

Computer simulations of ionic liquids have largely focused on the development of force field parameters specific to an ionic liquid or an ionic liquid family [17-23]. In addition to simulation of structural, dynamical, electric, and thermodynamic properties of several pure ionic liquids [24-26], the solvation of small solutes in ionic liquids has also been investigated [27-31]. Compatibility of ionic liquids and cellulose... 

Abstract. Molecular dynamics (MD) simulations of proteins provide descriptions of atomic motions, which allow to relate observable properties of proteins to microscopic processes. Unfortunately, such MD simulations require an enormous amount of computer time and, therefore, are limited to time scales of nanoseconds. We describe first a fast multiple time step structure adapted multipole method (FA-MUSAMM) to speed up the evaluation of the computationally most demanding Coulomb interactions in solvated protein models, secondly an application of this method aiming at a microscopic understanding of single molecule atomic force microscopy experiments, and, thirdly, a new method to predict slow conformational motions at microsecond time scales. 

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