Molecular dynamics simulation liquid water

The importance of three-body effects in the determination of macroscopic properties has also been studied. Recently, nonadditive molecular dynamics simulation of water and organic liquids has been performed [86]. 

Rovere M, Ricci MA, Vellati D, Bruni F. (1998) A molecular dynamics simulation of water confined in a cylindrical Si02 pore. / Chem Phys 108 9859-9867. Delville A. (1993) Structure and properties of confined liquids A molecular model of the clay-water interface. J Phys Chem 97 9703-9712. 

Postma, J.P.M., Berendsen, H.J.C., Straatsma, T.P. Intramolecular vibrations from molecular dynamics simulations of liquid water. Journal de Physique C7 (1984) 31-40. 

TIte NCC water model. (After Corongiu G 1992. Molecular Dynamics Simulation fir Liquid Water Using risable and Flexible Potential. International Journal of Quantum Chemistry 42 1209-1235.)... 

The correct treatment of boundaries and boundary effects is crucial to simulation methods because it enables macroscopic properties to be calculated from simulations using relatively small numbers of particles. The importance of boundary effects can be illustrated by considering the following simple example. Suppose we have a cube of volume 1 litre which is filled with water at room temperature. The cube contains approximately 3.3 X 10 molecules. Interactions with the walls can extend up to 10 molecular diameters into the fluid. The diameter of the water molecule is approximately 2.8 A and so the number of water molecules that are interacting with the boundary is about 2 x 10. So only about one in 1.5 million water molecules is influenced by interactions with the walls of the container. The number of particles in a Monte Carlo or molecular dynamics simulation is far fewer than 10 -10 and is frequently less than 1000. In a system of 1000 water molecules most, if not all of them, would be within the influence of the walls of the boundary. Clecirly, a simulation of 1000 water molecules in a vessel would not be an appropriate way to derive bulk properties. The alternative is to dispense with the container altogether. Now, approximately three-quarters of the molecules would be at the surface of the sample rather than being in the bulk. Such a situation would be relevcUit to studies of liquid drops, but not to studies of bulk phenomena. 

Fig. 7.12 Experimental and calculated infrared spectra for liquid water. The black dots are the experimental values. The thick curve is the classical profile produced by the molecular dynamics simulation. The thin curve is obtained by applying quantum corrections. (Figure redrawn from Guilbt B 1991. A Molecular Dynamics Study of the Infrared Spectrum of Water. Journal of Chemical Physics 95 1543-1551.)...

Tarek et al. [388] studied a system with some similarities to the work of Bocker et al. described earlier—a monolayer of n-tetradecyltrimethylammonium bromide. They also used explicit representations of the water molecules in a slab orientation, with the mono-layer on either side, in a molecular dynamics simulation. Their goal was to model more disordered, liquid states, so they chose two larger molecular areas, 0.45 and 0.67 nm molecule Density profiles normal to the interface were calculated and compared to neutron reflectivity data, with good agreement reported. The hydrocarbon chains were seen as highly disordered, and the diffusion was seen at both areas, with a factor of about 2.5 increase from the smaller molecular area to the larger area. They report no evidence of a tendency for the chains to aggregate into ordered islands, so perhaps this work can be seen as a realistic computer simulation depiction of a monolayer in an LE state. 

Vassilev P, Hartnig C, Koper MTM, Frechard F, van Santen RA. 2001. Ab initio molecular dynamics simulation of liquid water and water-vapor interface. J Chem Phys 115 9815-9820. 

The flat interface model employed by Marcus does not seem to be in agreement with the rough picture obtained from molecular dynamics simulations [19,21,64-66]. Benjamin examined the main assumptions of work terms [Eq. (19)] and the reorganization energy [Eq. (18)] by MD simulations of the water-DCE junction [8,19]. It was found that the electric field induced by both liquids underestimates the effect of water molecules and overestimates the effect of DCE molecules in the case of the continuum approach. However, the total field as a function of the charge of the reactants is consistent in both analyses. In conclusion, the continuum model remains as a good approximation despite the crude description of the liquid-liquid boundary. 

Raimondi, M., Famulari, A., Gianinetti, E., Sironi, M., Specchio, R. and Vandoni. I. (1998) New ab initio VB interaction potential for molecular dynamics simulation of liquid water, Adv. Quantum Chem., 32, 263-284. 

Yu HB, Geerke DP, Liu HY, van Gunsteren WE (2006) Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models. J Comput Chem 27(13) 1494-1504... 

English NJ (2005) Molecular dynamics simulations of liquid water using various long range electrostatics techniques. Mol Phys 103(14) 1945-1960... 

Curioni et al.148 studied the protonation of 1,3-dioxane and 1,3,5-trioxane by means of CP molecular dynamics similations. The dynamics of both molecules was continued for few ps following protonation. The simulation provided a detailed picture the evolution of both the geometry and the electronic structure, which helped to rationalize some experimental observations. CP molecular dynamics simulations were applied by Tuckerman et al.149,150 to study the dynamics of hydronium (H30+) and hydroxyl (OH-) ions in liquid water. These ions are involved in charge transfer processes in liquid water H20 H+. .. OH2 - H20. .. H+-OH2, and HOH. . . OH- -> HO-. . . HOH. For the solvatetd H30+ ion, a picture consistent with experiment emerged from the simulation. The simulation showed that the HsO+ ion forms a complex with water molecules, the structure of which oscillates between the ones of H502 and I L/ij clusters as a result of frequent proton transfers. During a consid-... 

Hermans, J. Pathiaseril, A. Anderson, A., Excess free-energy of liquids from molecular-dynamics simulations — application to water models, J. Am. Chem. Soc. 1988,110, 5982-5986. 

One of the most convincing tests of the AG relationship appeared in the work of Scala et al.92 for the SPC/E model of water,57 which is known to reproduce many of water s distinctive properties in its super-cooled liquid state qualitatively. In this study, the dynamical quantity used to correlate with the configurational entropy was the self-diffusivity D. Scala et al. computed D via molecular dynamics simulations. The authors calculated the various contributions to the liquid entropy using the methods described above for a wide range of temperature and density [shown in Figure 12(a-c)]. 

Within the mixed quantum/classical approach, at each time step in a classical molecular dynamics simulation (that is, for each configuration of the bath coordinates), for each chromophore one needs the transition frequency and the transition dipole or polarizability, and if there are multiple chromophores, one needs the coupling frequencies between each pair. For water a number of different possible approaches have been used to obtain these quantities in this section we begin with brief discussions of each approach to determine transition frequencies. For definiteness we consider the case of a single OH stretch chromophore on an HOD molecule in liquid D2O. 

The most valuable of all the models of water, by far, is the computer simulated liquid with well defined water-water interaction. To date, molecular dynamics simulations for two pair potentials 3>, and Monte Carlo simulations for three pair potentials 7i>72>, have been published. The details of the methods of simulation can be found in the literature, to which the reader is referred. 

Fig. 29. The OO pair correlation function for the STa potential from molecular dynamics simulation of liquid water (from Ref. 3>)...

The SCF-MI BSSE free method does not take into account dispersion forces, connected to electronic intermolecular correlation effects. By using the SCF-MI wave function as a starting point, however, a non orthogonal BSSE free Cl procedure can be developed. This approach was applied to compute intermolecular interactions in water dimer and trimer the resulting ab initio values were used to generate a new NCC-like potential (Niesar et al, 1990). Molecular dynamics simulation of liquid water were performed and satisfactory results obtained (Raimondi et al, 1997). 

Bjerrum has been used for molecular dynamics simulations of liquid water, to calculate its thermodynamic and structural properties. It turns out that this very important liquid is extremely difficult to model theoretically. 

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