Molecular dynamics simulation structural properties

Subject areas for the Series include solutions of electrolytes, liquid mixtures, chemical equilibria in solution, acid-base equilibria, vapour-liquid equilibria, liquid-liquid equilibria, solid-liquid equilibria, equilibria in analytical chemistry, dissolution of gases in liquids, dissolution and precipitation, solubility in cryogenic solvents, molten salt systems, solubility measurement techniques, solid solutions, reactions within the solid phase, ion transport reactions away from the interface (i.e. in homogeneous, bulk systems), liquid crystalline systems, solutions of macrocyclic compounds (including macrocyclic electrolytes), polymer systems, molecular dynamic simulations, structural chemistry of liquids and solutions, predictive techniques for properties of solutions, complex and multi-component solutions applications, of solution chemistry to materials and metallurgy (oxide solutions, alloys, mattes etc.), medical aspects of solubility, and environmental issues involving solution phenomena and homogeneous component phenomena. 

To calculate the properties of a molecule, you need to generate a well-defined structure. A calculation often requires a structure that represents a minimum on a potential energy surface. HyperChem contains several geometry optimizers to do this. You can then calculate single point properties of a molecule or use the optimized structure as a starting point for subsequent calculations, such as molecular dynamics simulations. 

T Ichiye, RB Yelle, JB Koerner, PD Swartz, BW Beck. Molecular dynamics simulation studies of electron transfer properties of Ee-S proteins. Biomacromolecules Erom 3-D Structure to Applications. Hanford Symposium on Health and the Environment 34, Pasco, WA, 1995, pp 203-213. 

Thermodynamic properties. A molecular-dynamics simulation method (using a steepest decent method) with Stillinger-Weber potential is employed to optimize structures and to obtain the cohesive en-... 

A good understanding of the properties of water is thus essential as we move to more complicated systems. We have been involving in the study of aqueous solution of many important biological molecules, such as acetylcholine, Gramicidin, deoxydinucleoside phosphate and proflavin, and DNA, etc., first at the Monte Carlo level and slowly moving to the molecular dynamics simulations. We will discuss some of the new results on the hydration structure and the dynamics of B- and Z-DNA in the presence of counterions in the following. 

Molecular dynamics simulations, with quantum-mechanically derived energy and forces, can provide valuable insights into the dynamics and structure of systems in which electronic excitations or bond breaking processes are important. In these cases, conventional techniques with classical analytical potentials, are not appropriate. Since the quantum mechanical calculation has to be performed many times, one at each time step, the choice of a computationally fast method is crucial. Moreover, the method should be able to simulate electronic excitations and breaking or forming of bonds, in order to provide a proper treatment of those properties for which classical potentials fail. 

Hyvonen, M. T., Rantala, T. T. and Ala-Korpela, M. (1997). Structure and dynamic properties of diunsaturated l-palmitoyl-2-linoleoyl-,sM-glycero-3-phosphatidylcholine lipid bilayer from molecular dynamics simulation, Biophys. J., 73, 2907-2923. 

Monte Carlo and Molecular Dynamics simulations of water near hydrophobic surfaces have yielded a wealth of information about the structure, thermodynamics and transport properties of interfacial water. In particular, they have demonstrated the presence of molecular layering and density oscillations which extend many Angstroms away from the surfaces. These oscillations have recently been verified experimentally. Ordered dipolar orientations and reduced dipole relaxation times are observed in most of the simulations, indicating that interfacial water is not a uniform dielectric continuum. Reduced dipole relaxation times near the surfaces indicate that interfacial water experiences hindered rotation. The majority of simulation results indicate that water near hydrophobic surfaces exhibits fewer hydrogen bonds than water near the midplane. 

As described above, silicon crystals can be grown from a variety of gas sources. Because the rate of growth can be modulated using these techniques, dopants can be efficiently incorporated into a growing crystal. This results in control of the atomic structure of the crystal, and allows the production of samples which have specific electronic properties. The mechanisms by which gas-phase silicon species are incorporated into the crystal, however, are still unclear, and so molecular dynamics simulations have been used to help understand these microscopic reaction events. 

At the mesoscopic scale, interactions between molecular components in membranes and catalyst layers control the self-organization into nanophase-segregated media, structural correlations, and adhesion properties of phase domains. Such complex processes can be studied by various theoretical tools and simulation techniques (e.g., by coarse-grained molecular dynamics simulations). Complex morphologies of the emerging media can be related to effective physicochemical properties that characterize transport and reaction at the macroscopic scale, using concepts from the theory of random heterogeneous media and percolation theory. 

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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