Quantum molecular dynamic water

The above-described features are reproduced in a high level quantum-molecular-dynamics simulation of an excess proton in water [30, 31]. In accordance with results from several other groups, this finds the excess proton either as part of a dimer (H5O2+, Zundel -ion) or as part of a hydrated hydronium ion (H9O4+, Eigen -ion) (Fig. 23.3). 

In this chapter we will review the recent developments in simulating and modelling proton transport. We will put a special emphasis on studies employing classical and quantum molecular-dynamics simulations, but also include basic studies that have focussed on model systems using accurate quantum-chemical methods. Proton-transport and dilfusion phenomena in liquids - such as water, inorganic acids, or organic liquids - will be discussed as well as in biomolecules, solid-state materials, and at the solid-liquid interface. Many of these materials are used in proton-transporting fuel-cell membranes, so that membrane materials will be the focus of the last section. 

Wohlgemuth M, Bonacic-Koutecky V, Mitric R (2011) Time-dependent density functional theory excited state nonadiabatic d5mamics combined with quantum mechanital/molecular mechanical approach photrxlynamics of indole in water. J Chem Phys 135 054105 Ben Nun M, Quenneville J, Martinez TJ (2000) Ab initio multiple spawning photochemistry from first principles quantum molecular dynamics. J Phys Chem A 104 5161-5175... 

Behrens, P.H., Mackay, D.H.J., White, G.M., Wilson, K.R. Thermodynamics and quantum corrections from molecular dynamics for liquid water. J. Chem. Phys. 79 (1983) 2375-2389. 

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.)... 

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.)...

Quantum chemical calculations, molecular dynamics (MD) simulations, and other model approaches have been used to describe the state of water on the surface of metals. It is not within the scope of this chapter to review the existing literature only the general, qualitative conclusions will be analyzed. 

Below we shall start with our problem — namely the prediction of the properties of a molecular liquid — first at the quantum mechanical and then at the statistical level up to hydrodynamic limit. We shall then conclude by showing the feasibility of using molecular dynamics to solve problems of fluid mechanics and the results obtained by using water as a solvent for DNA in the presence of counterions. 

Besides these generalities, little is known about proton transfer towards an electrode surface. Based on classical molecular dynamics, it has been suggested that the ratedetermining step is the orientation of the HsO with one proton towards the surface [Pecina and Schmickler, 1998] this would be in line with proton transport in bulk water, where the proton transfer itself occurs without a barrier, once the participating molecules have a suitable orientation. This is also supported by a recent quantum chemical study of hydrogen evolution on a Pt(lll) surface [Skulason et al., 2007], in which the barrier for proton transfer to the surface was found to be lower than 0.15 eV. This extensive study used a highly idealized model for the solution—a bilayer of water with a few protons added—and it is not clear how this simplification affects the result. However, a fully quantum chemical model must necessarily limit the number of particles, and this study is probably among the best that one can do at present. 

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. 

Equation (4-5) can be directly utilized in statistical mechanical Monte Carlo and molecular dynamics simulations by choosing an appropriate QM model, balancing computational efficiency and accuracy, and MM force fields for biomacromolecules and the solvent water. Our group has extensively explored various QM/MM methods using different quantum models, ranging from semiempirical methods to ab initio molecular orbital and valence bond theories to density functional theory, applied to a wide range of applications in chemistry and biology. Some of these studies have been discussed before and they are not emphasized in this article. We focus on developments that have not been often discussed. 

Fig. 13 Results from the quantum calculations on the duplex sequence 5 -GAGG-3. In a, the sodium ions and their solvating water molecules are located at positions near the phosphate anions of the DNA backbone. In b, one sodium ion is moved from near a phosphate anion to N-7 of a guanine, which molecular dynamics calculations show to be a preferred site. The balloons represent the hole density on the GAGG sequences with the two different sodium ion orientations. The radical cation clearly changes its average location with movement of the sodium ion...

Diffusion constants are enhanced with the approximate inclusion of quantum effects. Changes in the ratio of diffusion constants for water and D2O with decreasing temperature are accurately reproduced with the QFF1 model. This ratio computed with the QFF1 model agrees well with the centroid molecular dynamics result at room temperature. Fully quantum path integral dynamical simulations of diffusion in liquid water are not presently possible. 

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. 

Figure 11. The solid line depicts the quantum adiabatic free energy curve for the Fe /Fe electron transfer at the water/Pt(lll) interface (obtained by using the Anderson-Newns model, path integral quantum transition state theory, and the umbrella sampling of molecular dynamics. The dashed line shows the curve from the classical calculation as given in Fig. 5. (Reprinted from Ref 14.)...

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