Molecular dynamics simulation organic molecules

The Merck molecular force field (MMFF) is one of the more recently published force fields in the literature. It is a general-purpose method, particularly popular for organic molecules. MMFF94 was originally intended for molecular dynamics simulations, but has also seen much use for geometry optimization. It uses five valence terms, one of which is an electrostatic term, and one cross tenn. 

DG was primarily developed as a mathematical tool for obtaining spahal structures when pairwise distance information is given [118]. The DG method does not use any classical force fields. Thus, the conformational energy of a molecule is neglected and all 3D structures which are compatible with the distance restraints are presented. Nowadays, it is often used in the determination of 3D structures of small and medium-sized organic molecules. Gompared to force field-based methods, DG is a fast computational technique in order to scan the global conformational space. To get optimized structures, DG mostly has to be followed by various molecular dynamic simulation. 

Even for purely adiabatic reactions, the inadequacies of classical MD simulations are well known. The inability to keep zero-point energy in all of the oscillators of a molecule leads to unphysical behavior of classical trajectories after more than about a picosecond of their time evolution." It also means that some important physical organic phenomena, such as isotope effects, which are easily explained in a TST model, cannot be reproduced with classical molecular dynamics. So it is clear that there is much room for improvement of both the computational and experimental methods currently employed by those of us interested in reaction dynamics of organic molecules. Perhaps some of the readers of this book will be provide some of the solutions to these problems. 

Considering these results and the contributions by Broos [125], Watanabe [126], and Ueji [55, 77], it may be concluded that the relation between enzyme flexibility and enanhoselective performance in organic solvents is now firmly established. Molecular dynamic simulations on the flexibility of subtilisin and the mobility of bound water molecules in carbon tetrachloride corroborate the idea that organic solvents reduce molecular flexibility via interactions at specific binding sites [127]. Whether predictive tools can be developed on the basis of this knowledge remains to be seen. 

Solvent effects can significantly influence the function and reactivity of organic molecules.1 Because of the complexity and size of the molecular system, it presents a great challenge in theoretical chemistry to accurately calculate the rates for complex reactions in solution. Although continuum solvation models that treat the solvent as a structureless medium with a characteristic dielectric constant have been successfully used for studying solvent effects,2,3 these methods do not provide detailed information on specific intermolecular interactions. An alternative approach is to use statistical mechanical Monte Carlo and molecular dynamics simulation to model solute-solvent interactions explicitly.4 8 In this article, we review a combined quantum mechanical and molecular mechanical (QM/MM) method that couples molecular orbital and valence bond theories, called the MOVB method, to determine the free energy reaction profiles, or potentials of mean force (PMF), for chemical reactions in solution. We apply the combined QM-MOVB/MM method to... 

At the liquid-liquid interface, completely different properties of water and organic phases can be met in the two-dimensional boundary with a thickness of only 1 nm. In practical two-phase systems with highly miscible components, however, the formation of nano- and micro-droplets at the interfacial nano-region is suggested. The structural and dynamic properties of molecules at the interface are the most important subject in the study of physics and chemistry at the interface. The solution theory of the liquid-liquid interface has not been established yet, though the molecular dynamics simulations have been developed as a useful tool for depicting the molecular picture of the solvent and solute molecules in the interfacial region. 

Soc., 114, 10024 (1992). UFF, a Full Periodic Table Force Field for Molecular Mechanics and Molecular Dynamics Simulations. C. J. Casewit, K. S. Colwell, and A. K. Rappe,/. Am. Chem. Soc., 114, 10035 (1992). Application of a Universal Force Field to Organic Molecules. C. J. Casewit, K. S. Colwell, and A. K. Rappe,/. Am. Chem. Soc., 114,10046 (1992). Application of a Universal Force Field to Main Group Compounds. 

Nitrobenzene (NB) is ahighly polarizable molecule and so is carbon tetrachloride, the interface of which with water was studied by molecular dynamics simulation by Chang and Dang (1996). Whereas the density profile of the water in both systems is rather smooth, that of the organic liquid exhibits fluctuations. The interface induces... 

Explaining Behavior with Structure. To answer the question of why these materials behave so differently, we must revisit the issue of the polymer interphase (or bound polymer). These nanocomposite systems can be prepared such that nearly the entire polymer in the system is interphase polymer, due to the large specific surface area of the layered silicates (when properly dispersed) and the large amount of interface thus created. Coupled with the many descriptions of bound polymer reported in composite literature, molecular dynamics simulations of nanocomposite systems also indicate that local density variations occur in proximity to organically modified layered silicates, both in the absence and presence of intercalated polymer chains. In fact, such interlayer density variations (albeit with small molecules rather than polymers) have been reported for many years in field of clay science. ... 

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