Six-site model

H. Nada and Y. Furukawa, Anisotropy in growth kinetics at interfaces between proton-disordered hexagonal ice and water, A molecular dynamics study using the six-site model of H20, J. Crystal Growth, Article in press (2005). 

Grabuleda, X. Jaime, C. Kollman, P. A., Molecular dynamics simulation studies of liquid acetonitrile new six-site model,./. Comput. Chem. 2000, 21, 901-908... 

The intermolecular interaction between pairs of H2O molecules was estimated using a six-site model, which was developed for simulations of ice and water near 0 °C. Recently, using the six-site model, the growth of an ice crystal from water near 0 °C was successfully... 

H2O molecide in the six-site model (b) The potential energy, U, of the system as a function of time (upper panel) and snapshots ofH20 molecules near the interface at 2.0 ns. The black and gray spheres, respectively, show the H2O molecules that were included in the ice and the water at the beginning of the simulation. 

Second, the Q-dependence of the measured elastic incoherent structure factor (EISF) appears to be in excellent agreement with the predictions of the model of localized atomic motion over a hexagon (Eq. (26.13)) with the distance between the nearest-neighbor sites equal to the experimental value. As an example of these results, Eig. 26.5 shows the behavior of the EISE for TaV2Hj j as a function of Q at several temperatures. The solid curves represent the fits of the six-site model to the data. In these fits the distance between the nearest-neighbor sites has been fixed to its value resulting from the structure, = 0.99 A, so that the... 

Figure 26.5 The elastic incoherent structure factor for TaVjH,, as a function of Q at T = 105, 200, 250 and 300 K [76], The solid lines represent the fits ofthe six-site model with the fixed r, = 0.99 A to the data.

The interaction sites are often fixed at the position of the nuclei, but it is also possible to include additional sites in the middle of a bond to model the repulsion of the electron cloud [18]. As we tackle larger molecules it may be necessary to combine several atoms in an interaction group. In a recent simulation of a lipid bilayer [19], CH3 and CH2 units are represented as single sites and this idea has been applied to a simple six-site model of benzene [20]. There are complete sets of transferable potential parameters available for aromatic and aliphatic hydrocarbons [21] and for hydrogen-bonded fluids [22]. The William s potentials for hydrocarbons [21] have been used in a simulation of CHi, [23], but the exponential repulsion is most profitably calculated using a table look-up. 

Here, and are the contributions of translational and rotational degrees of freedom to the thermal conductivity of the dilute gas evaluated from the six-site model, im.exp experimental internal heat capacity at constant volume, whereas is the equipartition value obtained by assuming the benzene molecule is rigid, that is, — 3/2)R, where R is the universal gas constant. It turns out that... 

Nada, H., 8c van der Eerden, J. R J. M. (2003). An intermolecular potential model for the simulation of ice and water near the melting point A six-site model of H2O. Journal of Chemical Physics, 118, 7401. 

H. Nada and J. P. J. M. van der Eerden,/. Chem. Phys., 118, 7401 (2003). An Intermolecular Potential Model for the Simulation of Ice and Water Near the Melting Point A Six-Site Model ofH20. 

Figure 17.11 Geometry of an H2O molecule in the (a) SPC/E, (b) TIP4P, (c) TIP5P, and (d) six-site models.

Molecular Dynamics Simulation of the Ice Suiface and Inteiface 325 Table 17.1 Parameters in the SPC/E, TIP4P, TIP5P, and six-site models. 

Nada and van der Eerden [60] proposed a six-site model of rigid H2O for the simulation of ice and water near the real at 1 atm. In this model, an H2O molecule has six interaction sites an O atom, two H atoms, two lone-pair sites (L), and a site M located on the bisector of ZHOH (Figure 17.11). A positive charge is placed on each H atom, and a negative charge is placed on each of the L and M sites. The intermolecular interaction between a pair of H2O molecules is calculated as the sum of the Coulomb potentials between the charges plus the sum of the LJ potentials between the atoms. Parameters in the six-site model were optimized by assuming truncation of the intermolecular interaction at the intermolecular distance around 1 nm (Table 17.1). 

The strength of the six-site model is that the model provides proton-disordered hexagonal ice as a thermodynamically stable phase near at 1 atm. Moreover, Tjjj of ice in the six-site model is close to the real of 273.15 K that is, = 271 9 K was estimated from free energy calculations of ice and water [60], and Tjjj = 280-285 K was estimated from MD simulations of the growth and melting of ice over a wide range of temperatures [61]. Abascal et al. [62] estimated Tjjj of ice in the six-site model with the Ewald summation method as 289 K. The densities of ice and water near T, the structure of water near T, and the... 

Besides the six-site model, there are several other models that have been proposed for simulations of ice and water. The KKY (Kumagai, Kawamura, and Yokokawa) potential model is an atomistic model for simulations of ice and water [63]. This model enables analysis of the lattice vibrations of H2O molecules not only for their translational and rotational motions but also for their internal vibrations [64]. The TIP4P/Ice model [65] is a modification of the TIP4P model that can reproduce the real of ice. 

Figure 17.12 Structures of the (a) basal and (b) prismatic plane surfaces near T. Each surface structure was obtained by a 2 ns MD simulation at 280 K using the six-site model. In the simulation, the Ewald...

Nada and Furukawa also performed MD simulations of the interface for basal, prismatic, and 1120 secondary prismatic planes at 268 K, which is close to the real T at 1 atm, using the six-site model. Growth of ice, which was sufficient to determine R, occurred on the interface for all planes within a mn of only several nanoseconds (Figure 17.13) [61, 77]. The anisotropy in R among the planes, which was obtained by the simulations, was qualitatively consistent with experimental measurements that is, R was smaller for the basal plane than that for the prismatic and secondary prismatic planes [2], Carignano et al. [78] also performed MD simulations of the interfaces for basal, prismatic, and secondary prismatic planes using the six-site model and reported qualitatively the same anisotropic R among the planes as that in the MD simulation study by Nada and Furukawa [74],... 

MD simulations were carried out at — 10°C and 1 atm using the six-site model and CHARMM force field param 19 [101] for estimations of the intermolecular interactions. The total run was 4 ns. Simulation results indicated that the AFP was partially surrounded by ice grown at the interface (Figure 17.22) [102]. Initial... 

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