Simulation techniques solvation methods

A recent QMCF MD and LAXS (large angle X-ray scattering) study [76] of the sulfate ion has once more demonstrated the reliability of this simulation technique for the description of composite solutes and an accuracy equivalent to best experimental methods. Precise predictions of vibrational spectra as well as the solvation energy of this anion [77] have clearly indicated the ability of the QMCF MD approach to investigate a variety of properties in a general and comprehensive way. 

In this chapter we will mostly focus on the application of molecular dynamics simulation technique to understand solvation process in polymers. The organization of this chapter is as follow. In the first few sections the thermodynamics and statistical mechanics of solvation are introduced. In this regards, Flory s theory of polymer solutions has been compared with the classical solution methods for interpretation of experimental data. Very dilute solution of gases in polymers and the methods of calculation of chemical potentials, and hence calculation of Henry s law constants and sorption isotherms of gases in polymers are discussed in Section 11.6.1. The solution of polymers in solvents, solvent effect on equilibrium and dynamics of polymer-size change in solutions, and the solvation structures are described, with the main emphasis on molecular dynamics simulation method to obtain understanding of solvation of nonpolar polymers in nonpolar solvents and that of polar polymers in polar solvents, in Section 11.6.2. Finally, the dynamics of solvation with a short review of the experimental, theoretical, and simulation methods are explained in Section 11.7. 

Experimental as well as theoretical methods have been widely employed to study such phenomena as solubility, the conformational structures, size change, and so on. Although these methods have been very successful, however, for example the experimental methods cannot reveal the detailed solvation structures to describe the interaction between solvent and polymer. Either theoretical methods are also not completely atomistic or they assume a certain molecular behavior. Molecular simulation methods, on the other hand, can produce most atomistic information about the solvation process. In this section we will mostly focus on the application of molecular dynamics simulation technique to understand solvation process in polymers. 

The Monte Carlo method has been applied more extensively to the study of solvation phenomena. Clementi has looked at solvent distribution around a large variety of amino acids and nucleotides. This work is summarized by Clementi in detail in this volume[l7e]. It should be noted that all this work on solvent using these powerful simulation techniques has appeared within the last five years and most of it even more recently. This is a direct result of the advances in computer technology as well as the adaptation of the... 

An obvious way to combine Monte Carlo with molecular d)mamics is to use each technique for the most appropriate part of a simulation. For example, when simulating a solvated macromolecule, the equilibration phase is usually performed in a series of stages. In the first stage, the solute is kept fixed while the solvent molecules (and any ions, if present) are allowed to move under the influence of the solute s electrostatic field. This solvent equilibration may often be performed more effectively using a Monte Carlo simulation as the solvent and ions do not have any appreciable conformational flexibility. To simulate the whole system, molecular d)maimcs is then the most appropriate method. Such a protocol has been used to perform long simulations of DNA molecules [Swaminathan et al. 1991]. 

The aim of this article is to provide an overview of the range of methodologies that can be used to build qualitative and quantitative models of DNA or RNA-ligand interactions. The construction of such models may resort to computational methods that go beyond 3D-SAR and 3E>-QSAR, and recent reviews of these techniques are available (see Free Energy Calculations Methods and Applications Free Energy Per-turbation Calculations Free Energy Simulations and Solvation Modeling). ... 

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. 

Two remaining problems relating to the treatment of solvation include the slowness of Poisson-Boltzmann calculations, when these are used to treat electrostatic effects, and the difficulty of keeping buried, explicit solvent in equilibrium with the external solvent when, e.g., there are changes in nearby solute groups in an alchemical simulation. Faster methods for solving the Poisson-Boltzmann equation by means of parallel finite element techniques are becoming available, however.22 24... 

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... 

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... 

A novel pump-damp-probe method (PDPM), which allows the characterization of solvation dynamics of a fluorescence probe not only in excited but also in the ground states has been recently developed (Changenet-Barret, 2000 and references therein). In PDPM, a pump produces a nonequilibrium population of the probe excited, which, after media relaxation, is simulated back to the ground states. The solvent relaxation of the nonequlibrium ground state is probed by monitoring with absorption technique. The inramolecular protein dynamics in a solvent-inaccessible region of calmodulin labeled with coumarin 343 peptide was examined by PDPM. In the pump-dump-probe experiments, part of a series of laser output pulses was frequency-doubled and softer beams were used as the probe. The delay of the probe with respect to the pump was fixed at 500 ps. 

Semiempirical techniques are the next level of approximation for computational simulation of molecules. Compared to molecular mechanics, this approach is slow. The formulations of the self-consistent field equations for the molecular orbitals are not rigorous, particularly the various approaches for neglect of integrals for calculation of the elements of the Fock matrix. The emphasis has been on versatility. For the larger molecular systems involved in solvation, the semiempirical implementation of molecular orbital techniques has been used with great success [56,57]. Recent reviews of the semiempirical methods are given by Stewart [58] and by Rivail [59],... 

---