Monte Carlo simulations hydration

Jorgenson W L and Ravimohan C 1985 Monte Carlo simulation of the differences in free energy of hydration J. Chem. Phys. 83 3050... 

Jorgensen, W. L. Ravimohan, C., Monte Carlo simulation of differences in free energies of hydration, J. Chem. Phys. 1985, 83, 3050-3054... 

Jorgensen, W. L. Tirado-Rives, J., Free energies of hydration for organic molecules from Monte Carlo simulations, Perspectives in Drug Discovery and Design 1995, 3,123-138. 

W. L. Jorgensen and T. B. Nguyen, Monte Carlo simulations of the hydration of... 

After this computer experiment, a great number of papers followed. Some of them attempted to simulate with the ab-initio data the properties of the ion in solution at room temperature [76,77], others [78] attempted to determine, via Monte Carlo simulations, the free energy, enthalpy and entropy for the reaction (24). The discrepancy between experimental and simulated data was rationalized in terms of the inadequacy of a two-body potential to represent correctly the n-body system. In addition, the radial distribution function for the Li+(H20)6 cluster showed [78] only one maximum, pointing out that the six water molecules are in the first hydration shell of the ion. The Monte Carlo simulation [77] for the system Li+(H20)2oo predicted five water molecules in the first hydration shell. A subsequent MD simulation [79] of a system composed of one Li+ ion and 343 water molecules at T=298 K, with periodic boundary conditions, yielded... 

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... 

X-ray and neutron diffraction methods and EXAFS spectroscopy are very useful in getting structural information of solvated ions. These methods, combined with molecular dynamics and Monte Carlo simulations, have been used extensively to study the structures of hydrated ions in water. Detailed results can be found in the review by Ohtaki and Radnai [17]. The structural study of solvated ions in lion-aqueous solvents has not been as extensive, partly because the low solubility of electrolytes in 11011-aqueous solvents limits the use of X-ray and neutron diffraction methods that need electrolyte of -1 M. However, this situation has been improved by EXAFS (applicable at -0.1 M), at least for ions of the elements with large atomic numbers, and the amount of data on ion-coordinating atom distances and solvation numbers for ions in non-aqueous solvents are growing [15 a, 18]. For example, according to the X-ray diffraction method, the lithium ion in for-mamide (FA) has, on average, 5.4 FA molecules as nearest neighbors with an... 

The different degrees of water inhibition on the ether and olefin formation from ethanol on alumina, and the agreement of ether/ethylene selectivity ratios found experimentally with those calculated by the Monte Carlo simulation of the hydrated surface of alumina [144],... 

Molecular Recognition XIV. Monte Carlo Simulation of the Hydration of the Combining Site of a Lectin, H. Beierbeck,... 

Monte Carlo Simulations of the Hydration of a Protein Receptor for an Oligosaccharide, H. Beierbeck and R. U. Lemieux, Abstr, 75th Canadian Chem. Conf, Edmonton, Alberta, Canada, June 1-4 (1992). 

The main question is whether the hydrated ions behave as hard spheres while this seems plausible for ions much larger than the water molecules, it is probably not entirely applicable to small ions, whose hydration shells continuously change. Marcelj a calculated recently the double layer interaction8 using the anisotropic hypemetted chain method and potentials of mean force between pairs of ions in water, provided by Monte Carlo simulations. This... 

The dependence of the interaction force between two undulating phospholipid bilayers and of the root-mean-square fluctuation of their separation distances on the average separation can be determined once the distribution of the intermembrane separation is known as a function of the applied pressure. However, most of the present theories for interacting membranes start by assuming that the distance distribution is symmetric, a hypothesis invalidated by Monte Carlo simulations. Here we present an approach to calculate the distribution of the intermembrane separation for any arbitrary interaction potential and applied pressure. The procedure is applied to a realistic interaction potential between neutral lipid bilayers in water, involving the hydration repulsion and van der Waals attraction. A comparison with existing experiments is provided. 

Fig. 8. Simulated water uptake from Monte Carlo simulations, adopted from [29 c]. A typical configuration of a hydrated Na+ montmorillonite in the do01=12A stable hydrated state revealed by Monte Carlo simulations [29].

It is worthwhile to present some examples of the types of results available from Monte Carlo simulations of peptide solvent systems. In Figure 6 we present the convergence of the energy of hydration of the lysozyme crystal over a million configurations. 

Figure 6. The average energy of the water of hydration of the triclinic lysozyme crystal as a function of the number of configurations generated in the Monte Carlo simulation. The upper curve (A) corresponds to the cumulative statistical average, and the lower curve fU gives the statistical average over sequential sets of 5,000...

W. L. Jorgensen and C. Ravimohan, /. Chem. Phys., 83, 3050 (1985). Monte Carlo Simulation of Differences in Free Energies of Hydration. 

Molecular modeling using either Monte-Carlo simulations or molecular dynamics is used to apply molecular mechanics energy minimizations to very complex systems [348]. In complex flexible molecules such as proteins or nucleic adds, the number of variable parameters, i.e., bond torsion angles, is such that the global search for energy minima becomes impossible The same problem occurs with theoretical calculations of water structure in aqueous solutions or in heavily hydrated crystals. 

Monte-Carlo simulations have been made of the known water structure in crystalline serine monohydrate, arginine dihydrate homoproline tetrahydrate [331], deoxycytidylyl-3, 5 -guanosine-proflavine hydrate [358] and the spine of hydration in the minor groove of a 5-type oligodeoxynucleotide duplex [359]. They resulted in partial agreement and demonstrated the sensitivity of the method to the pair potentials used. 

Papadimitriou, N.I., Tsimpanogiannis, I.N., Papaioannou, A.Th., and Stubos, A.K. (2008) Evaluation of the hydrogen-storage capacity of pure H2 and binay H2-THF hydrates with Monte Carlo simulations. /. Chem. Phys. C, 112,... 

P. S. Subramanian and D. L. Beveridge, Theor. Chim. Acta, 85, 3 (1993). A Monte Carlo Simulation Study of the Aqueous Hydration of d(CGCGCG) in Z Form. 

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