Monte Carlo statistical mechanics

A complete set of intermolecular potential functions has been developed for use in computer simulations of proteins in their native environment. Parameters have been reported for 25 peptide residues as well as the common neutral and charged terminal groups. The potential functions have the simple Coulomb plus Lennard-Jones form and are compatible with the widely used models for water, TIP4P, TIP3P and SPC. The parameters were obtained and tested primarily in conjunction with Monte Carlo statistical mechanics simulations of 36 pure organic liquids and numerous aqueous solutions of organic ions representative of subunits in the side chains and backbones of proteins... 

The addition of Me3C+ to Me2C=CH2 has been investigated hr the gas phase and in solution with ab initio calculations and Monte Carlo statistical mechanics simulations. The reaction is exothermic by 20 kcal mol-1 and proceeds without activation energy in the gas phase. By contrast, solvation introduces a 3 1 kcal mol 1 barrier at a C C separation near- 5 A in CH2CI2, THF, and MeOH. An intermediate with a shallow energy well was found at near 3 A separation. Implications for sterol biosynthesis were also discussed in this paper 44... 

Methods Using 3D Descriptors Advances in quantum-chemical calculations and the increasing power of personal computers have made a great impact on the development of methods to predict aqueous solubility directly from the 3D structures of molecules. Monte Carlo statistical mechanics simulations by Jorgensen and Duffy [45] were used to predict the solubility of 150 compounds (MAE = 0.56) using the equation... 

Robinson and Dalton use Monte Carlo statistical mechanics to explore concentration and shape dependencies of the chromophores. Monte Carlo methods provide valuable information about the distribution of a collection of chromophores but are not able to provide atomistic information about the systems. The Monte Carlo simulations performed by Robinson and Dalton employ an array of point dipoles on a periodic lattice with the given parameters for the shape of the chromophores and the chromophore spacing adjustable to achieve the desired chromophore concentration. The model system consisted of 1000 chromophores on a body-centered cubic... 

Robinson, B.H., Dalton, L.R. Monte carlo statistical mechanical simulations of the competition of intermolecular electrostatic and poling-field interactions in defining macroscopic electro-optic activity for organic chromophore/polymer materials, J. Phys. Chem. A 104(20), 4785 795 (2000)... 

Computer simulation techniques have been applied to such solution systems. The Monte Carlo statistical mechanics have provided much useful information about the energetics, structure, and molecular interactions. The computations suggested that at the hexanol-water interface minimal water penetration into the hydrocarbon regions takes place. 

A wide variety of different models of the pure water/solid interface have been investigated by Molecular Dynamics or Monte Carlo statistical mechanical simulations. The most realistic models are constructed on the basis of semiempirical or ab initio quantum chemical calculations and use an atomic representation of the substrate lattice. Nevertheless, the understanding of the structure of the liquid/metal surface is only at its beginning as (i) the underlying potential energy surfaces are not known very well and (ii) detailed experimental information of the interfacial structure of the solvent is not available at the moment (with the notable exception of the controversial study of the water density oscillations near the silver surface by Toney et al. [140, 176]). 

As an example, such a methodology has been applied by Essex and Jorgensen to the calculation of the dielectric constant of formamide and dimethylformamide using Monte Carlo statistical mechanics simulations (see Section 8.7.2 for details). The simulation result for dimethylformamide, 32 2, is reasonably in agreement with respect to the experimental value, 37. However, in the case of formamide, the obtained value, 56 2, underestimates the experimental value of 109.3. The poor performance here addresses the fact that force field models with fixed charges underestimate the dielectric constant for hydrogen-bonded liquids. 

Abstract. An overview is given of the paper by Metropolis et al. that has formed the basis for Monte Carlo statistical mechanics simulations of atomic and molecular systems. 

Key words Monte Carlo - Statistical mechanics -Metropolis sampling... 

Overall, Metropolis et al. introduced the sampling method and periodic boundary conditions that remain at the heart of Monte Carlo statistical mechanics simulations of fluids. This was one of the major contributions to theoretical chemistry of the twentieth century. 

Despite these problems, however, some techniques of computerized molecular dynamics and Monte-Carlo statistical mechanical treatments have been applied to solvent systems with over 200 water molecules [9, 10]. In addition, small clusters of... 

The focus in development of the OPLS-UA model was on the non-bonded parameters, which historically had been the most problematic, and the new approach was to perform large numbers of Monte Carlo statistical mechanics simulations of pure liquids for their refinement. This advance was made possible by increases in computer resources and the development of flexible, efficient software, namely, the BOSS program and its predecessors, that allowed rapid setup of simulations for new systems. The key point was that a principal application of such force fields was in condensed-phase simulations including protein dynamics, and testing of the force fields on prediction of well-characterized condensed-phase properties was needed. Minimally, reproduction of liquid densities and heats of vaporization provides some confidence in both the size of the molecules and the strengths of their intermolecular interactions. Furthermore, these quantities are obtained from both experiment and simulation with high precision. 

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