Surface force molecular dynamic simulation

S. B. Sinnott, R. J. Colton, C. T. White, and D. W. Brennei Surf. Set., 316, L1055 (1994). Surface Patterning with Atomically-Controlled Chemical Forces Molecular Dynamics Simulations. 

As discussed in the previous section a brute-force molecular-dynamics simulation of gas-surface dynamics, although simple in principle, is a large computational problem. Though these direct methods will continue to be of use, particularly in providing numerical benchmarks for the calibration of more approximate methods, it will prove useful to search for more efficient methods. The chief defect of direct methods when applied to gas-solid scattering is that the essentially harmonic chatracter of the lattice is not fully exploited. We expect that the strong, direct interaction with the solid will involve a relatively small number of lattice... 

Importantly, all biological procedures are operating at a temperature of 310 Kelvin, not at 0 Kelvin as the potential energy is calculated by the force fields. The kinetic energy must also be considered. Molecules and proteins at room temperature change the conformation at least at the surface and in loop region. Molecular dynamics simulation (MD) is an approach to tackle these kinetic and stability problems. 

The rapid rise in computer speed over recent years has led to atom-based simulations of liquid crystals becoming an important new area of research. Molecular mechanics and Monte Carlo studies of isolated liquid crystal molecules are now routine. However, care must be taken to model properly the influence of a nematic mean field if information about molecular structure in a mesophase is required. The current state-of-the-art consists of studies of (in the order of) 100 molecules in the bulk, in contact with a surface, or in a bilayer in contact with a solvent. Current simulation times can extend to around 10 ns and are sufficient to observe the growth of mesophases from an isotropic liquid. The results from a number of studies look very promising, and a wealth of structural and dynamic data now exists for bulk phases, monolayers and bilayers. Continued development of force fields for liquid crystals will be particularly important in the next few years, and particular emphasis must be placed on the development of all-atom force fields that are able to reproduce liquid phase densities for small molecules. Without these it will be difficult to obtain accurate phase transition temperatures. It will also be necessary to extend atomistic models to several thousand molecules to remove major system size effects which are present in all current work. This will be greatly facilitated by modern parallel simulation methods that allow molecular dynamics simulations to be carried out in parallel on multi-processor systems [115]. 

Medium-range interactions can be defined as those which dominate the dynamics when atoms interact with energies within a few eV of their molecular binding energies. These forces determine a majority of the physical and chemical properties of surface reactions which are of interest, and so their incorporation in computer simulations can be very important. Unfortunately, they are usually many-body in nature, and can require complicated functional forms to be adequately represented. This means that severe approximations are often required when one is interested in performing molecular dynamics simulations. Recently, several potentials have been semi-empirically developed which have proven to be sufficiently simple to be useful in computer simulations while still capturing the essentials of chemical bonding. 

Abstract. The physical nature of nonadditivity in many-particle systems and the methods of calculations of many-body forces are discussed. The special attention is devoted to the electron correlation contributions to many-body forces and their role in the Be r and Li r cluster formation. The procedure is described for founding a model potential for metal clusters with parameters fitted to ab initio energetic surfaces. The proposed potential comprises two-body, three-body, and four body interation energies each one consisting of exchange and dispersion terms. Such kind of ab initio model potentials can be used in the molecular dynamics simulation studies and in the cinalysis of binding in small metal clusters. 

Anions bind also to other metals, like gold, platinum, or silver [74,81], Why do anions adsorb specifically to metals, while cations do not The explanation is a strong hydration of cations. A cation would have to give up its hydration shell for an adsorption. This is energetically disadvantageous. Anions are barely hydrated and can therefore bind more easily to metals [82], Another possible explanation is the stronger van der Waals force between anions and metals. The binding of ions to metallic surfaces is not yet understood and even the idea that cations are not directly bound to the metal, was questioned based on molecular-dynamics simulations [83],... 

In order to overcome the limitations of currently available empirical force field param-eterizations, we performed Car-Parrinello (CP) Molecular Dynamic simulations [36]. In the framework of DFT, the Car-Parrinello method is well recognized as a powerful tool to investigate the dynamical behaviour of chemical systems. This method is based on an extended Lagrangian MD scheme, where the potential energy surface is evaluated at the DFT level and both the electronic and nuclear degrees of freedom are propagated as dynamical variables. Moreover, the implementation of such MD scheme with localized basis sets for expanding the electronic wavefunctions has provided the chance to perform effective and reliable simulations of liquid systems with more accurate hybrid density functionals and nonperiodic boundary conditions [37]. Here we present the results of the CPMD/QM/PCM approach for the three nitroxide derivatives sketched above details on computational parameters can be found in specific papers [13]. 

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