Surface studies molecular dynamics

Work is in progress in our laboratory to provide an accurate intermolecular potential surface for molecular dynamics studies of liquid hydrogen fluoride. 

B. Clifton and T. Cosgrove, Simulation of Liquid Benzene between two Graphite Surfaces a Molecular dynamics Study, Mol. Phys. 93 (1998) 767-776. 

L. Perera and M. L. Berkowitz, Free energy profiles for Li+ and I ions approaching the Pt(lOO) surface - A molecular dynamics study, J. Phys. Chem. 97 (1993)13803. 

Weber T A and Stillinger F H 1990 Dynamical branching during fluorination of the dimerized Si (100) surface a molecular dynamics study J. Chem Phys. 92 6239-45... 

Rog T, Murzyn K, Pasenkiewicz-Gierula M (2002) The dynamics of water at the phospholipid bilayer surface a molecular dynamics simulation study. Chem Phys Lett 352 323... 

Baldelli, S. (2008) Surface structure at the ionic liquid-electrified metal interface. Acc. Chem. Res., 41 (3), 421-431. Sieffert, N. and Wipff, G. (2008) Ordering of imidazolium-based ionic liquids at the r-Quartz(OOl) surface a molecular dynamics study. J. Phys. Chem. C, 112, 19560-19603. 

Vrbka L, Jungwirth P, Bauduin P, Touraud D, Kunz W (2006) Specific itm effects at protein surfaces a molecular dynamics study of bovine pancreatic trypsin inhibitor and horseradish peroxidase in selected salt solutions. J Phys Chem B 110 7036-7043... 

Lundgren, M., AUan, N. A., Cosgrove, T., and George, N. 2002. Wetting of water and water/ethanol droplets on a non-polar surface a molecular dynamics study. Langmuir. 18 10462. 

Dutta, R. C., Khan, S., and Singh, J. K. 2011. Wetting transition of Water on Graphite and Boron-Nitride Surfaces A Molecular Dynamics Study. Fluid Phase Equilibria 302 310. 

Lee, S. H., and Rossky, P. J. 1993. A comparison of the structure and dynamics of liquid water at hydrophobic and hydrophilic surfaces-a molecular dynamics simulation study. J. Chem. Phys. 100 3334. 

Lundgren, M., Allan, N. L., and Cosgrove, T. 2002. Wetting of Water and Water/Ethanol Droplets on a Non-Polar Surface A Molecular Dynamics Study. Langmuir 18 10462. 

Huang P, Loew GH (1995) Interaction of an amphiphilic peptide with a phospholipid bilayer surface by molecular dynamics simulation study. J Biomol Struct Dyn 12(5) 937-956 Bemeche S, Nina M, Roux B (1998) Molecular dynamics simulations of melittin in a dimy-ristoylphosphatidylcholine bilayer membrane. Biophys J 75(4) 1603 1618 Woolf TB, Roux B (1994) Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer. PNAS 91(24) 11631 11635... 

Pal, S., Balasubramanian, S., and Bagchi, B. 2002. Temperature dependence of water dynamics at an aqueous micellar surface Atomistic molecular dynamics simulation studies of a complex system. J. Chem. Phys. 117, 2852-2859. 

Electronic structure calculations provide fundamental information on molecular structure and interaction, and the potential energy surfaces necessary for studying molecular dynamics. Description of electrons is necessarily based on quantum mechanics principles. Because of the delocalized nature of quantum particles and the many-body interaction between the electrons, quantum mechanical calculations are demanding in computational effort. Thus the accuracy and efficiency of the methods used are major concerns. We address here the efficiency issue. 

Otsuka I, Yaoita M, Nagashima S, Higano M. Molecular dimensions of dried glucose oxidase on an Au(lll) surface studied by dynamic mode scanning force microscopy. Electrochim Acta 2005 50 4861 867. 

Qiu, B., Sun, L., Ruan, X. L. (2011). Lattice thermal conductivity reduction in Bi2Tc3 quantum wires with smooth and rough surfaces a molecular dynamics study. Physical Review B, 83, 035312. 

Raffaini, G., Ganazzoli, E, 2010. Protein adsorption on a hydrophobic surface a molecular dynamics study of lysozyme on graphite. Langmuir 26, 5679. 

Nada, H. and Furukawa, Y. (1997) Anisotropy in structural phase transitions at ice surfaces a molecular dynamics study. Appl. Surf. Sci., 121/122, 445-447. 

Small metal clusters are also of interest because of their importance in catalysis. Despite the fact that small clusters should consist of mostly surface atoms, measurement of the photon ionization threshold for Hg clusters suggest that a transition from van der Waals to metallic properties occurs in the range of 20-70 atoms per cluster [88] and near-bulk magnetic properties are expected for Ni, Pd, and Pt clusters of only 13 atoms [89] Theoretical calculations on Sin and other semiconductors predict that the stmcture reflects the bulk lattice for 1000 atoms but the bulk electronic wave functions are not obtained [90]. Bartell and co-workers [91] study beams of molecular clusters with electron dirfraction and molecular dynamics simulations and find new phases not observed in the bulk. Bulk models appear to be valid for their clusters of several thousand atoms (see Section IX-3). 

The direct dissociation of diatomic molecules is the most well studied process in gas-surface dynamics, the one for which the combination of surface science and molecular beam teclmiques allied to the computation of total energies and detailed and painstaking solution of the molecular dynamics has been most successful. The result is a substantial body of knowledge concerning the importance of the various degrees of freedom (e.g. molecular rotation) to the reaction dynamics, the details of which are contained in a number of review articles [2, 36, 37, 38, 39, 40 and 41]. 

Many of the fiindamental physical and chemical processes at surfaces and interfaces occur on extremely fast time scales. For example, atomic and molecular motions take place on time scales as short as 100 fs, while surface electronic states may have lifetimes as short as 10 fs. With the dramatic recent advances in laser tecluiology, however, such time scales have become increasingly accessible. Surface nonlinear optics provides an attractive approach to capture such events directly in the time domain. Some examples of application of the method include probing the dynamics of melting on the time scale of phonon vibrations [82], photoisomerization of molecules [88], molecular dynamics of adsorbates [89, 90], interfacial solvent dynamics [91], transient band-flattening in semiconductors [92] and laser-induced desorption [93]. A review article discussing such time-resolved studies in metals can be found in... 

The dynamics of fast processes such as electron and energy transfers and vibrational and electronic deexcitations can be probed by using short-pulsed lasers. The experimental developments that have made possible the direct probing of molecular dissociation steps and other ultrafast processes in real time (in the femtosecond time range) have, in a few cases, been extended to the study of surface phenomena. For instance, two-photon photoemission has been used to study the dynamics of electrons at interfaces [ ]. Vibrational relaxation times have also been measured for a number of modes such as the 0-Fl stretching m silica and the C-0 stretching in carbon monoxide adsorbed on transition metals [ ]. Pump-probe laser experiments such as these are difficult, but the field is still in its infancy, and much is expected in this direction m the near fiitiire. 

Weakliem P C and Carter E A 1993 Surface chemical reactions studied via ab /n/f/o-derived molecular dynamics simulations fluorine etching of Si(IOO) J. Chem Phys. 98 737-45... 

In this chapter, we look at the techniques known as direct, or on-the-fly, molecular dynamics and their application to non-adiabatic processes in photochemistry. In contrast to standard techniques that require a predefined potential energy surface (PES) over which the nuclei move, the PES is provided here by explicit evaluation of the electronic wave function for the states of interest. This makes the method very general and powerful, particularly for the study of polyatomic systems where the calculation of a multidimensional potential function is an impossible task. For a recent review of standard non-adiabatic dynamics methods using analytical PES functions see [1]. 

The full quantum mechanical study of nuclear dynamics in molecules has received considerable attention in recent years. An important example of such developments is the work carried out on the prototypical systems H3 [1-5] and its isotopic variant HD2 [5-8], Li3 [9-12], Na3 [13,14], and HO2 [15-18], In particular, for the alkali metal trimers, the possibility of a conical intersection between the two lowest doublet potential energy surfaces introduces a complication that makes their theoretical study fairly challenging. Thus, alkali metal trimers have recently emerged as ideal systems to study molecular vibronic dynamics, especially the so-called geometric phase (GP) effect [13,19,20] (often referred to as the molecular Aharonov-Bohm effect [19] or Berry s phase effect [21]) for further discussion on this topic see [22-25], and references cited therein. The same features also turn out to be present in the case of HO2, and their exact treatment assumes even further complexity [18],... 

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. 

Molecular dynamics studies can be done to examine how the path and orientation of approaching reactants lead to a chemical reaction. These studies require an accurate potential energy surface, which is most often an analytic... 

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