Simulations of solvent effects

The main adjustable parameter we have is the surface that surrounds the molecule. One approach is to surround each atom by a sphere having a radius Ra 

The dielectric continuum models may allow us to predict speciation in aqueous solutions as a function of temperature simply by changing dielectric constant of the polarizing medium. At first glance, this may simply appear to be a return to the Bom-model formalism. However, the inner sphere solvation would be included explicitly. To include temperature effects on the inner solvation shells, we would have to calculate the partition functions of the cluster defining the metal atom and its first and, possibly, second coordination environment. 

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Sudholt W, Staib A, Sobolewski AL, Domcke W (2000) Molecular-dynamics simulations of solvent effects in the intramolecular charge transfer of 4-(N, N-dimethylamino) benzonitrile. Phys Chem Chem Phys 2(19) 4341-4353... 

J. Gao, Monte Carlo quantum mechanical-configuration interaction and molecular mechanics simulation of solvent effects on the n - n blue shift of acetone. J. Am. Chem. Soc. 116, 9324-9328 (1994)... 

The aim of this chapter is to provide the reader with an overview of the potential of modern computational chemistry in studying catalytic and electro-catalytic reactions. This will take us from state-of-the-art electronic structure calculations of metal-adsorbate interactions, through (ab initio) molecular dynamics simulations of solvent effects in electrode reactions, to lattice-gas-based Monte Carlo simulations of surface reactions taking place on catalyst surfaces. Rather than extensively discussing all the different types of studies that have been carried out, we focus on what we believe to be a few representative examples. We also point out the more general theory principles to be drawn from these studies, as well as refer to some of the relevant experimental literature that supports these conclusions. Examples are primarily taken from our own work other recent review papers, mainly focused on gas-phase catalysis, can be found in [1-3]. 

The theory of solvent-effects and some of its applications are overviewed. The generalized selfcon-sistent reaction field (SCRF)theory has been used to give a unified approach to quantum chemical calculations of subsystems embedded in a given milieu. The statistical mechanical theory of projected equations of motion has been briefly described. This theory underlies applications of molecular dynamics simulations to the study of solvent and thermal bath effects on carefully defined subsystem of interest. The relationship between different approaches used so far to calculate solvent effects and the general SCRF has been established. Recent work using the continuum approach to model the surrounding media is overviewed. Monte Carlo and molecular dynamics studies of solvent effects on molecular properties and chemical reactions together with simulations of solvent effects on protein structure and dynamics are reviewed. 

In Sect. 4, an overview of solvent effects evaluation with the techniques described in the preceding sections is presented. MC and MD studies on molecular properties are overviewed. Of particular interest are recent developments in the simulation of solvent effects on chemical reactions. The focus is in computer simulations. Analytical models for describing chemical reactions have been thoroughly discussed by Hynes [11] and will not be examined here. 

Progress is forseen in the study of solvent effects on chemical reactions in liquids, solids, miscelles, and enzymes. Brute force MD simulations of solvent effects on the dynamics properties of protein summarized in this work will serve as benchmark calculations to gauge model representations of solvent effects on biomacro-molecules. The use of realistic dielectric models can be also be seen as a complementary approach to represent solvent effects on biomolecules. In chemical dynamics, important advances have been made with analytical simple model approaches [11, 104, 105]. The conditions are now ripe for including more sophisticated ab initio studies into the description of time-dependent phenomena. 

Configuration Interaction and Molecular Mechanics Simulation of Solvent Effects on the n — ir Blue Shift of Acetone. 

M. F. Herman and B. J. Berne, /. Chem. Phys., 78,4103 (1983). Monre Carlo Simulation of Solvent Effects on Vibrational and Electronic Spectra. 

Figure 13.2 Thermodynamic cycle used in free-energy perturbation simulations of solvent effects.

Yun-Yu S, W Lu and W F van Gunsteren 1988. On the Approximation of Solvent Effects on Conformation and Dynamics of Cyclosporin A by Stochastic Dynamics Simulation Teclmiqi Molecular Simulation 1 369-383. 

Both of these substitution pathways in MeCN solution have been simulated using the Onsager model (Tables IV and V). Whereas pathway b is favored in the gas phase, inclusion of solvent effects in the calculations causes pathway a to be energetically favored. Substitution of Cl via pathway a is now 1.6 kcal/mol more favorable. In addition, TS(X)/TS(Pyr) calculations (Scheme 15) for the OMe (40) and OSiMes (41) cations have been performed. TS(X) of both 40 and 41 remain significantly disfavored (+66.9 kcal/mol and +46.6 kcakmol, respectively), thus indicating that pathway b should be preferred in MeCN.Tliese calculations are in complete agreement with experimental observations. 

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. 

The several theoretical and/or simulation methods developed for modelling the solvation phenomena can be applied to the treatment of solvent effects on chemical reactivity. A variety of systems - ranging from small molecules to very large ones, such as biomolecules [236-238], biological membranes [239] and polymers [240] -and problems - mechanism of organic reactions [25, 79, 223, 241-247], chemical reactions in supercritical fluids [216, 248-250], ultrafast spectroscopy [251-255], electrochemical processes [256, 257], proton transfer [74, 75, 231], electron transfer [76, 77, 104, 258-261], charge transfer reactions and complexes [262-264], molecular and ionic spectra and excited states [24, 265-268], solvent-induced polarizability [221, 269], reaction dynamics [28, 78, 270-276], isomerization [110, 277-279], tautomeric equilibrium [280-282], conformational changes [283], dissociation reactions [199, 200, 227], stability [284] - have been treated by these techniques. Some of these... 

Tapia, O. and Lluch, J. M. Solvent effects on chemical reaction profiles. Monte Carlo simulation of hydration effects on quantum chemically calculated stationary structures, J. Chem.Phys., 83 (1983, 3970-3982... 

An important advantage of the simulation methods consists in their explicit treatment of solvent effects as the effects of a set of individual... 

Calculation of the B, Al, and Ga hydrides and their dihydrogen-bonded complexes is not a problem for computers. Moreover, as we will see below, some of the approaches can be used for proper simulation of the effect of solvents on dihydrogen bonding. Nevertheless, in the absence of frequency analysis, the nature of a complex often remains unclear Does it act as a transition state or as a minimum on the potential energy surface One of the simplest examples... 

However, it is important to note that the energy values, calculated for gas-phase dihydrogen-bonded complexes are usually overestimated with respect to the experimental measurements carried out in solutions. The latter is connected directly with solvent effects. In fact, the computer simulation of solvent polarity demonstrates significant lowering of the energy of formation for example, from 6.7 to 5.2 and 2.4 kcahmol, computed for niobium trihydride system 1 on going from the gas phase to n-heptane and CH2CI2. 

Vitalis, A., Wang, X., Pappu, R.V. Atomistic simulations of the effects of polyglutamine chain length and solvent quality on conformational equilibria and spontaneous homodimerization. J. Mol. Biol. 2008, 384, 279-97. 

Contemporary computer-assisted molecular simulation methods and modern computer technology has contributed to the actual numerical calculation of solvent effects on chemical reactions and molecular equilibria. Classical statistical mechanics and quantum mechanics are basic pillars on which practical approaches are based. On top of these, numerical methods borrowed from different fields of physics and engineering and computer graphics techniques have been integrated into computer programs running in graphics workstations and modem supercomputers (Zhao et al., 2000). 

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