Solvent dynamics, computer simulations

Supercritical water (SCW) presents a unique combination of aqueous and non-aqueous character, thus being able to replace an organic solvent in certain kinds of chemical synthesis. In order to allow for a better understanding of the particular properties of SCW and of its influence on the rate of chemical reactions, molecular dynamics computer simulations were used to determine the free energy of the SN2 substitution reaction of Cl- and CH3C1 in SCW as a function of the reaction coordinate [216]. The free energy surface of this reaction was compared with that for the gas-phase and ambient water (AW) [248], In the gas phase, an ion-dipole complex and a symmetric transition... 

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. 

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. 

Recently, detailed molecular pictures of the interfacial structure on the time and distance scales of the ion-crossing event, as well as of ion transfer dynamics, have been provided by Benjamin s molecular dynamics computer simulations [71, 75, 128, 136]. The system studied [71, 75, 136] included 343 water molecules and 108 1,2-dichloroethane molecules, which were separately equilibrated in two liquid slabs, and then brought into contact to form a box about 4 nm long and of cross-section 2.17 nmx2.17 nm. In a previous study [128], the dynamics of ion transfer were studied in a system including 256 polar and 256 nonpolar diatomic molecules. Solvent-solvent and ion-solvent interactions were described with standard potential functions, comprising coulombic and Lennard-Jones 6-12 pairwise potentials for electrostatic and nonbonded interactions, respectively. While in the first study [128] the intramolecular bond vibration of both polar and nonpolar solvent molecules was modeled as a harmonic oscillator, the next studies [71,75,136] used a more advanced model [137] for water and a four-atom model, with a united atom for each of two... 

While the difference in the upwards and downwards solvent responses presented in Figure 3 is striking, this is not the first time that variations in solvation dynamics for the same solvent have been observed. Experimental studies have shown differences in solvation response for different probe molecules in the same solvent. This is a direct indication that probe molecules which have different excited state charge distributions and different mechanical interactions with the solvent produce differing relaxation dynamics. Computer simulations have also observed differing solvation dynamics for the forward and reverse transitions of the sudden appearance of charge, indicative of a solute-dependent solvent response. Moreover, theoretical work has shown that dielectric solvation dynamics is sensitive to the shape of a solute, and that solute size is intimately connected to viscoelastic relaxation. It is these effects which are manifest in the... 

Computer simulations are generally made with one ion and 256-1024 solvent molecules, that is, in fairly dilute solutions. They have the advantage that counter ions are absent, and the results pertain directly to the individual ions studied. Earlier studies of ion hydration by classical (Monte Carlo and molecular dynamics) computer simulations are summarized in Refs. 31 and 53, but recently results... 

While the long-standing picture of the solvent as a structureless medium has been very useful for offering a qualitative understanding of the solvent s effect on structure and dynamics, computer simulations and experiments clearly suggest that a microscopic molecular description of the solvent is necessary. This is particularly so for interfacial phenomena, because the interfacial region itself is only a few molecular diameters thick. 

In general, the rate of permeation of the permeating species is difficult to calculate. It is a complex matter which intimately involves a knowledge of the structure and dynamics of the membrane and the structure and dynamics of the complex fluid mixture in contact with it on one side and the solvent on the other side. Realistic membranes with realistic fluids are beyond the possibihties of theoretical treatment at this time. The only way of dealing with anything at all reahstic is by computer simulation. Even then one is restricted to rather simplified models for the membrane. 

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. 

Presently, only the molecular dynamics approach suffers from a computational bottleneck [58-60]. This stems from the inclusion of thousands of solvent molecules in simulation. By using implicit solvation potentials, in which solvent degrees of freedom are averaged out, the computational problem is eliminated. It is presently an open question whether a potential without explicit solvent can approximate the true potential sufficiently well to qualify as a sound protein folding theory [61]. A toy model study claims that it cannot [62], but like many other negative results, it is of relatively little use as it is based on numerous assumptions, none of which are true in all-atom representations. 

In the case of molten salts, no obvious model based on statistical mechanics is available because the absence of solvent results in very strong pair correlation effects. It will be shown that the fundamental properties of these liquids can be described by quasi-chemical models or, alternatively, by computer simulation of molecular dynamics (MD). 

Beyond the clusters, to microscopically model a reaction in solution, we need to include a very big number of solvent molecules in the system to represent the bulk. The problem stems from the fact that it is computationally impossible, with our current capabilities, to locate the transition state structure of the reaction on the complete quantum mechanical potential energy hypersurface, if all the degrees of freedom are explicitly included. Moreover, the effect of thermal statistical averaging should be incorporated. Then, classical mechanical computer simulation techniques (Monte Carlo or Molecular Dynamics) appear to be the most suitable procedures to attack the above problems. In short, and applied to the computer simulation of chemical reactions in solution, the Monte Carlo [18-21] technique is a numerical method in the frame of the classical Statistical Mechanics, which allows to generate a set of system configurations... 

Finally, for the PT problem, dynamical friction effects have been examined for a model for a phenol-amine acid-base reaction in methyl chloride solvent [12]. With the quantization of the proton and the O-N vibration, the problem can be reduced to a one-dimensional solvent coordinate problem, similar to the ET case. Again, GH theory is found to agree with the MD results to within the error bars of the computer simulation. 

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 ... 

When structural and dynamical information about the solvent molecules themselves is not of primary interest, the solute-solvent system may be made simpler by modeling the secondary subsystem as an infinite (usually isotropic) medium characterized by the same dielecttic constant as the bulk solvent, that is, a dielectric continuum. Theoretical interpretation of chemical reaction rates has a long history already. Until recently, however, only the chemical reactions of systems containing a few atoms in the gas phase could be studied using molecular quantum mechanics due to computational expense. Fortunately, very important advances have been made in the power of computer-simulation techniques for chemical reactions in the condensed phase, accompanied by an impressive progress in computer speed (Gonzalez-Lafont et al., 1996). 

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