Water molecular simulations

Our understanding of supercritical water and its properties has improved dramatically over the past decade. This is due, in no small part, to a constructive interplay between molecular-based simulations and neutron scattering experiments on supercritical water that has resulted in a thorough re-examination of both techniques. Better models for simulating water and better techniques for processing raw scattering data have resulted. Important implications have also resulted for studies of ambient water. Molecular simulation has played an indispensable and unprecedented role in these developments. 

Dang L X, J E Rice, J Caldwell and P A Kollman 1991. Ion Solvation in Polarisable Water Molecular Dynamics Simulations. Journal of the American Chemical Society 113 2481-2486. 

However, theories that are based on a basis set expansion do have a serious limitation with respect to the number of electrons. Even if one considers the rapid development of computer technology, it will be virtually impossible to treat by the MO method a small system of a size typical of classical molecular simulation, say 1000 water molecules. A logical solution to such a problem would be to employ a hybrid approach in which a chemical species of interest is handled by quantum chemistry while the solvent is treated classically. 

The molecular and liquid properties of water have been subjects of intensive research in the field of molecular science. Most theoretical approaches, including molecular simulation and integral equation methods, have relied on the effective potential, which was determined empirically or semiempirically with the aid of ab initio MO calculations for isolated molecules. The potential parameters so determined from the ab initio MO in vacuum should have been readjusted so as to reproduce experimental observables in solutions. An obvious problem in such a way of determining molecular parameters is that it requires the reevaluation of the parameters whenever the thermodynamic conditions such as temperature and pressure are changed, because the effective potentials are state properties. 

Electro-osmosis has been defined in the literature in many indirect ways, but the simplest definition comes from the Oxford English Dictionary, which defines it as the effect of an external electric held on a system undergoing osmosis or reverse osmosis. Electro-osmosis is not a well-understood phenomenon, and this especially apphes to polar non-ionic solutions. Recent hterature and many standard text and reference books present a rather confused picture, and some imply directly or indirectly that it cannot take place in uniform electric fields [31-35]. This assumption is perhaps based on the fact that the interaction of an external electric held on a polar molecule can produce only a net torque, but no net force. This therefore appears to be an ideal problem for molecular simulation to address, and we will describe here how molecular simulation has helped to understand this phenomenon [26]. Electro-osmosis has many important applications in both the hfe and physical sciences, including processes as diverse as water desahnation, soil purification, and drug delivery. 

One of the most remarkable results from the molecular simulation studies of aqueous electrolyte solutions was that no additional molecular forces needed to be introduced to prevent the much smaller ions (Na has a molecular diameter of less than 0.2 nm) from permeating the membrane, while permitting the larger water molecules (about 0.3 nm in diameter) to permeate the membrane. This appeared to be due to the large ionic clusters formed. The ions were surrounded by water molecules, thus increasing their effective size quite considerably to almost 1 nm. A typical cluster formed due to the interaction between the ions and a polar solvent is shown in Fig. 7. These clusters were found to be quite stable, with a fairly high energy of desolvation. The inability of the ions to permeate the membrane is also shown... 

Third, as the size and complexity of the biomolecular systems at hand further expand, there are more uncertainties in the molecular model itself. For example, the resolution of the X-ray structure may not be sufficiently high for identifying the locations of critical water molecules, ions and other components in the system the oxidation states and/or titration states of key reactive groups might be unclear. In those cases, it is important to couple QM/MM to other molecular simulation techniques to establish and to validate the microscopic models before elaborate calculations on the reactive mechanisms are investigated. In this context, pKa and various spectroscopic calculations [113,114] can be very relevant. 

Chialvo AA, Cummings PT (1996) Engineering a simple polarizable model for the molecular simulation of water applicable over wide ranges of state conditions. J Chem Phys 105(18) ... 

The second necessary ingredient in the primitive quasichemical formulation is the excess chemical potential of the metal-water clusters and of water by itself. These quantities p Wm — can typically be obtained from widely available computational packages for molecular simulation [52], In hydration problems where electrostatic interactions dominate, dielectric models of those hydration free energies are usually satisfactory. The combination /t xWm — m//, wx is typically insensitive to computational approximations because the water molecules coat the surface of the awm complex, and computational errors can compensate between the bound and free ligands. 

Wallqvist and Mountain (1999) explored molecular models of water, beginning with the precomputer-era models, but mainly focused on the computer-era models. Computer simulations, which have been available since the 1960s, have contributed the missing dimension of time to the picture (or should we say movie) of the molecular structure of water. Computer simulations are powerful additions to the previous combination... 

Coordination of Uranyl in Water A Combined Ab Initio and Molecular Simulation Study. 

Membrane-Interaction (MI)-QSAR approach developed by Iyer et al. was used to develop predictive models of some organic compounds through BBB, and to simulate the interaction of a solute with the phospholipide-rich regions of cellular membranes surrounded by a layer of water. Molecular dynamics simulations were used to determine the explicit interaction of each test compound with the DMPC-water model (a model of dimyristoylphosphatidylcholine membrane monolayer, constructed using the software Material Studio according to the work done by van der Ploeg and Berendsen). Six MI-QSAR equations were constructed (Eqs. 74-79) ... 

To estimate how many dye molecules fit into the dendritic micelles, UV-titra-tion experiments have been employed. In comparison with the spectra of a pure pinacyanol chloride solution in water, the peaks of the absorption maxima of the dye in the presence of the dendrimer are shifted bathochromically due to solvatochromic effects, which indicates the incorporation of the dye within the branches of the dendrimer. At dye-to-dendrimer molar ratios higher than 4 1, in addition to the bathochromic shifts, hypsochromically shifted peaks start to appear, indicating that the dendrimer is not incorporating further dyes. We interpret this as an incorporation of up to four dyes within the branches of the dendrimer. This observation correlates with the calculated available space within the dendrimer, obtained from the molecular simulations. Further studies of the interactions of the dyes within the dendritic micelle are in progress. 

The of Fe +aq is affected by the presence of anions due to their interactions with the aquacation formation quotients have been estimated. Fe " "aq is hydrolyzed to a much smaller extent in 80% (w/w) DMSO + water than in water. Molecular dynamics simulation of iron(III) and its hydrolysis products successfully matched the known pKi value, but was unsuccessful in reproducing... 

Muller EA, Rull LE, Vega LF, Gubbins KE et al (1996) Adsorption of water on activated carbons A molecular simulation study. J Phys Chem 100 1189-1196... 

Tmskett and Dill (2002) proposed a two-dimensional water-like model to interpret the thermodynamics of supercooled water. This model is consistent with model (1) for liquid water. Cage-like and dense fluid configurations correspond to transient structured and unstructured regions, observed in molecular simulations of water (Errington and Debenedetti, 2001). Truskett and Dill s model provides a microscopic theory for the global phase behavior of water, which predicts the liquid-phase anomalies and expansion upon freezing. 

Molecular simulation methods have been applied to investigate the nucleation mechanism of gas hydrates in the bulk water phase (Baez and Clancy, 1994), and more recently at the water-hydrocarbon interface (Radhakrishnan and Trout, 2002 Moon et al., 2003). The recent simulations performed at the water-hydrocarbon interface provide support for a local structuring nucleation hypothesis, rather than the previously described labile cluster model. 

Anomalous properties—thermal expansivity and thermal conductivity. Molecular simulation has been integral in evaluating physical behaviors of hydrate compared with ice, specifically a larger thermal expansivity (Tse, et al., 1987 Tanaka, et al., 1997) and a glasslike thermal conductivity (Tse, et al., 1983 1984 Inoue, et al., 1996). These properties have been explained by the coupling between the water and the guest molecules. 

A series of articles were published by Ennari et al. on MD simulation of transport processes in Poly(Ethylene Oxide) and sulfonic acid-based polymer electrolyte.136,137 The work was started by the determination of the parameters for the ions missing from the PCFF forcefield made by MSI (Molecular Simulations Inc.), to create a new forcefield, NJPCFF. In the models, the proton is represented as a hard ball with a positive charge. Zhou et al. used the similar approach to model Nation.138 The repeating unit of Nafion (Fig. 17) was optimized using ab initio VAMP scheme. The protons were modeled with hydronium ions. Three unit cell or molecular models were used for the MD simulation. The unit cell contains 5000 atoms 20 pendent side chains, and branched Nafion backbone created with the repeating unit. Their water uptakes or water contents were 3, 13, or 22 IEO/SO3, which correspond to the room temperature water uptakes at 50% relative humidity (RH), at 100% RH, and in liquid water respectively.18 The temperature was initially set at a value between 298.15 and 423.15 K under NVE ensemble with constant particle number, constant volume (1 bar), and constant energy. 

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