Solvation/solvents molecular dynamics simulation

Specific solute-solvent interactions involving the first solvation shell only can be treated in detail by discrete solvent models. The various approaches like point charge models, siipennoleciilar calculations, quantum theories of reactions in solution, and their implementations in Monte Carlo methods and molecular dynamics simulations like the Car-Parrinello method are discussed elsewhere in this encyclopedia. Here only some points will be briefly mentioned that seem of relevance for later sections. 

Often you need to add solvent molecules to a solute before running a molecular dynamics simulation (see also Solvation and Periodic Boundary Conditions on page 62). In HyperChem, choose Periodic Box on the Setup menu to enclose a solute in a periodic box filled appropriately with TIP3P models of water molecules. 

Molecular dynamics simulations have also been used to interpret phase behavior of DNA as a function of temperature. From a series of simulations on a fully solvated DNA hex-amer duplex at temperatures ranging from 20 to 340 K, a glass transition was observed at 220-230 K in the dynamics of the DNA, as reflected in the RMS positional fluctuations of all the DNA atoms [88]. The effect was correlated with the number of hydrogen bonds between DNA and solvent, which had its maximum at the glass transition. Similar transitions have also been found in proteins. 

TvaroSka, KoS r and Hricovini in this book). One way to account for the effect of solvent on conforxnation might be to represent the molecule without environmental influences, and then explicitly include the solvent or other environmental molecules in the calculation. While avoiding built-in influences of environment is a satisfying concept, it is difficult to obtain by experiment parameters that lack those influences. Several methods have been used to study solvation effects, including continuum descriptions (24) and the explicit treatment of solvent molecules in Monte Carlo and molecular dynamics simulation. 

In this work we presented the results of Molecular Dynamics simulations performed to study the solvatochromism and the dynamic stokes-shift of coumarin 153 in mixtures of solvents. We showed the ability of MD to reproduce available data of the time-dependent Stokes-shifts. Moreover, MD allowed us to interpret these dynamics in benzene-acetonitrile mixtures in terms of motions of benzene around the coumarin or rotation of acetonitrile. The role of benzene in the solvation process of Cl53 seems to be more important than usually assumed. 

The COSMO solvent model has been used to simulate the influence of water on the electronic spectrum of A -methylacetamide [81], and the results was compared with the results of molecular dynamics simulations (where the electronic spectrum were calculated as an average over 90 snapshots from MD simulations). Most of the hydration effects were found to come from the first solvation shell hydrogen-bonded water molecules, and the continuum model does not properly account for these effects. The rotatory strengths were not calculated directly in ref. [81]. However, the results were used to model ECD spectra of peptides via the coupled oscillator model, with satisfactory result. 

K. Ando and S. Kato, Dielectric relaxation dynamics of water and methanol solutions associated with the ionization of /V,/V-dimcltiylanilinc theoretical analyses, J. Chem. Phys., 95 (1991) 5966-82 D. K. Phelps, M. J. Weaver and B. M. Ladanyi, Solvent dynamic effects in electron transfer molecular dynamics simulations of reactions in methanol, Chem. Phys., 176 (1993) 575-88 M. S. Skaf and B. M. Ladanyi, Molecular dynamics simulation of solvation dynamics in methanol-water mixtures, J. Phys. Chem., 100 (1996) 18258-68 D. Aheme, V. Tran and B. J. Schwartz, Nonlinear, nonpolar solvation dynamics in water the roles of elec-trostriction and solvent translation in the breakdown of linear response, J. Phys. Chem. B, 104 (2000) 5382-94. 

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. 

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