Water models five-site

Stern HA, Rittner F, Berne BJ, Friesner RA (2001) Combined fluctuating charge and polarizable dipole models application to a five-site water potential function. J Chem Phys 115(5) 2237-2251... 

M. W. Mahoney and W. L. Jorgensen, A five-site model for liquid water and the... 

Combined Fluctuating-Charge and Polarizable Dipole Models Application to a Five-Site Water Potential Function. 

Mahoney, M.W. and Jorgensen, W.L. (2000) A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions. /. Chem. Phys., 112, 8910. 

Mahoney MW, Jorgensen WL. A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolar-izable potential functions. J. Chem. Phys. 2000 112 8910-8922. Rick SW. A reoptimization of the five-site water potential TIP5P for use with Ewald sums. J. Chem. Phys. 2004 120 6085-6093. Horn HW, Swope WC, Pitera JW, Madura JD, Dick TJ, Hura GL, Head-Gordon T. Development of an improved four-site water model for bio-molecular simulations UP4P-Ew. J. Chem. Phys. 2004 120 9665-9678. 

Figure 9.3 Multisite models of water (a) three-site, (b] four-site, (c) five-site.

Lynch GC, Pettitt BM (1997) Grand canonical ensemble molecular dynamics simulations Reformulation of extended system dynamics approaches. J Chem Phys 107 8594-8610 Madura JD, Pettitt BM, Calef DF (1988) Water under high pressure. Mol Phys 64 325 Mahoney MW, Jorgensen WL (2000) A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions. J ChemPhys 112 8910-8922 March RP, Eyring H (1964) Application of significant stmcture theory to water. J Phys Chem 68 221-228 Martin MG, Chen B, Siepman JI (1998) A novel Monte Carlo algorithm for polarizable force fields. 

Although the liquid-vapor phase transition of bulk water is well studied experimentally, this is not the case for the phase transitions of interfacial and confined water, which we consider in the next sections. Therefore, studies of the phase transitions of confined water by computer simulation gain a special importance. For meaningful computer simulations, it is necessary to have water model, which is able to describe satisfactorily the liquid-vapor and other phase transitions of bulk water. The coexistence curves of some empirical water models, which represent a water molecule as a set of three to five interacting sites, are shown in Fig. 1. Some model adequately reproduces the location of the liquid-vapor critical point and. 

H. A. Stern, F. Rittner, B. J. Berne, and R. A. Friesner,/. Chem. Phys., 115(5), 2237—2251 (2001). Combined Fluctuating Charge and Polarizable Dipole Models Application to a Five-Site Water Potential Function. 

Before our work [39], only one catalytic mechanism for zinc dependent HDACs has been proposed in the literature, which was originated from the crystallographic study of HDLP [47], a histone-deacetylase-like protein that is widely used as a model for class-I HDACs. In the enzyme active site, the catalytic metal zinc is penta-coordinated by two asp residues, one histidine residues as well as the inhibitor [47], Based on their crystal structures, Finnin et al. [47] postulated a catalytic mechanism for HDACs in which the first reaction step is analogous to the hydroxide mechanism for zinc proteases zinc-bound water is a nucleophile and Zn2+ is five-fold coordinated during the reaction process. However, recent experimental studies by Kapustin et al. suggested that the transition state of HDACs may not be analogous to zinc-proteases [48], which cast some doubts on this mechanism. 

Water Potentials. The ST2 (23), MCY (24), and CF (2J5) potentials are computationally tractable and accurate models for two-body water-water interaction potentials. The ST2, MCY and CF models have five, four, and three interaction sites and have four, three and three charge centers, respectively. Neither the ST2 nor the MCY potentials allow OH or HH distances to vary, whereas bond lengths are flexible with the CF model. While both the ST2 and CF potentials are empirical models, the MCY potential is derived from ab initio configuration interaction molecular orbital methods (24) using many geometrical arrangements of water dimers. The MCY+CC+DC water-water potential (28) is a recent modification of the MCY potential which allows four body interactions to be evaluated. In comparison to the two-body potentials described above, the MCY+CC+DC potential requires a supercomputer or array processor in order to be computationally feasible. Therefore, the ST2, MCY and CF potentials are generally more economical to use than the MCY+CC+DC potential. 

USEPA s (2003) Response Protocol Toolbox for water contamination events is the model we use (because of its applicability) to describe the following five-stage chemical site characterization process ... 

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