Solvation dynamics computer simulation

The upshot is that the Born theory of solvation fails because it regards the solvent as a continuous dielectric, whereas in fact solute ions (especially metal cations with z > 1) often interact in a specific manner with solvent molecules. In any event the molecular dielectric is obviously very lumpy on the scale of the ions themselves. The Born theory and other continuous dielectric models work reasonably well when metal ion solute species are treated as solvent complexes such as Cr(OH2)63+ rather than naked ions such as Cr3+, but the emerging approach to solvation phenomena is to simulate solvation dynamically at the molecular level using computer methods. 

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... 

For 25 years, molecular dynamics simulations of proteins have provided detailed insights into the role of dynamics in biological activity and function [1-3]. The earliest simulations of proteins probed fast vibrational dynamics on a picosecond time scale. Fifteen years later, it proved possible to simulate protein dynamics on a nanosecond time scale. At present it is possible to simulate the dynamics of a solvated protein on the microsecond time scale [4]. These gains have been made through a combination of improved computer processing (Moore s law) and clever computational algorithms [5]. 

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. 

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. 

The need for computer simulations introduces some constraints in the description of solvent-solvent interactions. A simulation performed with due care requires millions of moves in the Monte Carlo method or an equivalent number of time steps of elementary trajectories in Molecular Dynamics, and each move or step requires a new calculation of the solvent-solvent interactions. Considerations of computer time are necessary, because methodological efforts on the calculation of solvation energies are motivated by the need to have reliable information on this property for a very large number of molecules of different sizes, and the application of methods cannot be limited to a few benchmark examples. There are essentially two different strategies. 

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. 

B. M. Ladanyi and B. C. Perng, Solvation dynamics in dipolar-quadrupolar mixtures A computer simulation study of dipole creation in mixtures of acetonitrile and benzene, J. Phys. Chem. A, 106 (2002) 6922-34. 

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

G. Cinacchi, F. Ingrosso and A. Tani, Solvation dynamics by computer simulation coumarin C153 in 1,4-dioxane, J. Phys. Chem. B, 110 (2006) 13633-41. 

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. 

As most chemical and virtually all biochemical processes occur in liquid state, solvation of the reaction partners is one of the most prominent topics for the determination of chemical reactivity and reaction mechanisms and for the control of reaction conditions and resulting materials. Besides an exhaustive investigation by various experimental methods [1,2,3], theoretical approaches have gained an increasing importance in the treatment of solvation effects [4,5,6,7,8], The reason for this is not only the need for sufficiently accurate models for a physically correct interpretation of the experimental data (Theory determines, what we observe ), but also the limitation of experimental methods in dealing with ultrafast reaction dynamics in the pico- or even subpicosecond regime. These processes have become more and more the domain of computational simulations and a critical evaluation of the accuracy of simulation methods covering experimentally inaccessible systems is of utmost importance, therefore. 

In this chapter, we will review some of the work that we have been doing in recent years in the context of solvation and dynamical properties in polar and non-polar supercritical solutions using molecular dynamics computer simulations. First we will discuss solvation of alkaloids in SC-CO2 and provide detailed molecular views of the main structural features of the local density augmentation around simple alkaloids... 

In this chapter, we have reviewed some of our own work on solvation properties in supercritical fluids using molecular dynamics computer simulations. We have presented the main aspects associated with the solvation structures of purine alkaloids in CO2 under different supercritical conditions and in the presence of ethanol as co-solvent, highlighting the phenomena of solvent density augmentation in the immediate neighborhood of the solute and the effects from the strong preferential solvation by the polar co-solvent. We have also presented a summary of our results for the structure and dynamics of supercritical water and ammonia, focusing on the dielectric behavior of supercritical water as functions of density and temperature and the behavior of excess solvated electrons in aqueous and non-aqueous associative environments. 

The same computer revolution that started in the middle of the last century also plays an important, in fact crucial, role in the development of methods and algorithms to study solvation problems. Dealing, for instance, with a liquid system means the inclusion of explicit molecules, in different thermodynamic conditions. The number of possible arrangements of atoms or molecules is enormous, demanding the use of statistical mechanics. Here is where computer simulation, Monte Carlo (MC) or molecular dynamics (MD), makes its entry to treat liquid systems. Computer simulation is now an important, if not central, tool to study solvation phenomena. The last two decades have seen a remarkable development of methods, techniques and algorithms to study solvation problems. Most of the recent developments have focused on combining quantum mechanics and statistical mechanics using MC or... 

---