Molecular dynamics with polarization

The explicit definition of water molecules seems to be the best way to represent the bulk properties of the solvent correctly. If only a thin layer of explicitly defined solvent molecules is used (due to hmited computational resources), difficulties may rise to reproduce the bulk behavior of water, especially near the border with the vacuum. Even with the definition of a full solvent environment the results depend on the model used for this purpose. In the relative simple case of TIP3P and SPC, which are widely and successfully used, the atoms of the water molecule have fixed charges and fixed relative orientation. Even without internal motions and the charge polarization ability, TIP3P reproduces the bulk properties of water quite well. For a further discussion of other available solvent models, readers are referred to Chapter VII, Section 1.3.2 of the Handbook. Unfortunately, the more sophisticated the water models are (to reproduce the physical properties and thermodynamics of this outstanding solvent correctly), the more impractical they are for being used within molecular dynamics simulations. 

This chapter has given an overview of the structure and dynamics of lipid and water molecules in membrane systems, viewed with atomic resolution by molecular dynamics simulations of fully hydrated phospholipid bilayers. The calculations have permitted a detailed picture of the solvation of the lipid polar groups to be developed, and this picture has been used to elucidate the molecular origins of the dipole potential. The solvation structure has been discussed in terms of a somewhat arbitrary, but useful, definition of bound and bulk water molecules. 

The simulations to investigate electro-osmosis were carried out using the molecular dynamics method of Murad and Powles [22] described earher. For nonionic polar fluids the solvent molecule was modeled as a rigid homo-nuclear diatomic with charges q and —q on the two active LJ sites. The solute molecules were modeled as spherical LJ particles [26], as were the molecules that constituted the single molecular layer membrane. The effect of uniform external fields with directions either perpendicular to the membrane or along the diagonal direction (i.e. Ex = Ey = E ) was monitored. The simulation system is shown in Fig. 2. The density profiles, mean squared displacement, and movement of the solvent molecules across the membrane were examined, with and without an external held, to establish whether electro-osmosis can take place in polar systems. The results clearly estab-hshed that electro-osmosis can indeed take place in such solutions. 

Recent molecular dynamics studies of properties of the water surface have led to predictions of the surface potential of water that differ not only in magnitude but also in sign. The main problem is connected with the difficulty of proper definition of the surface potential of a real polar... 

The availability of thermodynamically reliable quantities at liquid interfaces is advantageous as a reference in examining data obtained by other surface specific techniques. The model-independent solid information about thermodynamics of adsorption can be used as a norm in microscopic interpretation and understanding of currently available surface specific experimental techniques and theoretical approaches such as molecular dynamics simulations. This chapter will focus on the adsorption at the polarized liquid-liquid interfaces, which enable us to externally control the phase-boundary potential, providing an additional degree of freedom in studying the adsorption of electrified interfaces. A main emphasis will be on some aspects that have not been fully dealt with in previous reviews and monographs [8-21]. 

This indicates that the polarity of a medium is a long-range property that goes much further than the first solvation shell and therefore involves the two adjacent bulk media properties. This result is, however, valid for compounds the solvation of which is not determined by specific interactions with the first solvent shell, but rather by long-range forces like dipole interactions. The solvation of DEPNA was determined by molecular dynamics too and similar conclusions were drawn [82]. 

Lamoureux G, Roux B (2003) Modeling induced polarization with classical Drude oscillators theory and molecular dynamics simulation algorithm. J Chem Phys 119(6) 3025-3039... 

Even if we consider a single solvent, e g., water, at a single temperature, say 298K, depends on the solute and in fact on the coordinate of the solute which is under consideration, and we cannot take xF as a constant. Nevertheless, in the absence of a molecular dynamics simulation for the solute motion of interest, XF for polar solvents like water is often approximated by the Debye model. In this model, the dielectric polarization of the solvent relaxes as a single exponential with a relaxation time equal to the rotational (i.e., reorientational) relaxation time of a single molecule, which is called Tp) or the Debye time [32, 347], The Debye time may be associated with the relaxation of the transverse component of the polarization field. However the solvent fluctuations and frictional relaxation occur on a faster scale given by [348,349]... 

The role of the conditions in which these phenomena are observed is now well understood [40, 45], The chromophore should be solvatofluorochromic, that is, its fluorescence spectra should respond to changes in interaction energy with its environment by significant shifts. This environment should be relatively polar, but rigid or highly viscous, so that the relaxation times of its dipoles, tr, are comparable or longer than the fluorescence lifetime tf (in the case of recording the steady-state spectra) or on the time scale of observation (in time-resolved spectroscopy). Thus, these effects are coupled with molecular dynamics in condensed media. 

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