Monte Carlo-quantum mechanical approach

K. Coutinho, S. Canuto, Solvent effects from a sequential Monte Carlo-quantum mechanics approach. Adv. Quantum Chem. 28, 89-105 (1997)... 

K. Coutinho, S. Canuto, Sequential Monte Carlo/quantum mechanics study of the dipole polarizability of atomic liquids The argon case, in Atoms, Molecules and Clusters in Electric Fields. Theoretical Approaches to the Calculation of Electric Polarizabilities, ed. by G. Maroulis (Imperial College Press, London, 2006), pp. 405 120... 

Abstract The chemical activation of light alkanes by acidic zeolites was studied by a combined Classical Mechanics/Quantum Mechanics approach. The diffusion and adsorption steps were investigated by Molecular Mechanics, Molecular Dynamics and Monte Carlo simulations. The chemical reactions step was studied at the DPT (B3LYP) level with 6-31IG basis sets and 3T and 5T clusters to represent the acid site ofthe zeolite. 

This account highlights some of the recent developments in methods and current applications of classical trajectory simulations of molecular collisions. It has been more than 60 years since the first classical trajectory calculation was attempted on a mechanical calculator and almost 40 years since the first ensembles of trajectories were calculated on a digital computer and, even though the real world is quantum mechanical, classical trajectory simulations continue to play a crucial role in studies of chemical dynamics. The classical approximation, fortunately, is valid for many processes and conditions of interest to chemists, and the Monte Carlo quasiclassical trajectory approach is relatively simple and straightforward to apply. The work reviewed here clearly illustrates that it continues to be used productively, creatively, and widely, to study the details of chemical processes. 

Significant progress in the optimization of VDW parameters was associated with the development of the OPLS force field [53]. In those efforts the approach of using Monte Carlo calculations on pure solvents to compute heats of vaporization and molecular volumes and then using that information to refine the VDW parameters was first developed and applied. Subsequently, developers of other force fields have used this same approach for optimization of biomolecular force fields [20,21]. Van der Waals parameters may also be optimized based on calculated heats of sublimation of crystals [68], as has been done for the optimization of some of the VDW parameters in the nucleic acid bases [18]. Alternative approaches to optimizing VDW parameters have been based primarily on the use of QM data. Quantum mechanical data contains detailed information on the electron distribution around a molecule, which, in principle, should be useful for the optimization of VDW... 

Hpp describes the primary system by a quantum-chemical method. The choice is dictated by the system size and the purpose of the calculation. Two approaches of using a finite computer budget are found If an expensive ab-initio or density functional method is used the number of configurations that can be afforded is limited. Hence, the computationally intensive Hamiltonians are mostly used in geometry optimization (molecular mechanics) problems (see, e. g., [66]). The second approach is to use cheaper and less accurate semi-empirical methods. This is the only choice when many conformations are to be evaluated, i. e., when molecular dynamics or Monte Carlo calculations with meaningful statistical sampling are to be performed. The drawback of semi-empirical methods is that they may be inaccurate to the extent that they produce qualitatively incorrect results, so that their applicability to a given problem has to be established first [67]. 

The MD/QM methodology [18] is likely the simplest approach for explicit consideration of quantum effects, and is related to the combination of classical Monte Carlo sampling with quantum mechanics used previously by Coutinho et al. [27] for the treatment of solvent effects in electronic spectra, but with the variation that the MD/QM method applies QM calculations to frames extracted from a classical MD trajectory according to their relative weights. 

Sometimes the theoretical or computational approach to description of molecular structure, properties, and reactivity cannot be based on deterministic equations that can be solved by analytical or computational methods. The properties of a molecule or assembly of molecules may be known or describable only in a statistical sense. Molecules and assemblies of molecules exist in distributions of configuration, composition, momentum, and energy. Sometimes, this statistical character is best captured and studied by computer experiments molecular dynamics, Brownian dynamics, Stokesian dynamics, and Monte Carlo methods. Interaction potentials based on quantum mechanics, classical particle mechanics, continuum mechanics, or empiricism are specified and the evolution of the system is then followed in time by simulation of motions resulting from these direct... 

It is clear from the above that the continuum model can simulate only those aspects of the solvent which are somewhat independent from hydrophobicity, hydrophyUicity, generally the first solvation shell, and specific interactions with the solute. The physical problem is a general one namely, it relates to the validity to use quantities, correctly described and defined at the macroscopic level, in the discrete description of matter at the atomic level. For such study, one needs explicit consideration of the solvent, for example the molecules of water. This can be done either at the quantum-mechanical level, as in cluster computations. Another approach is to simulate the system at the molecular dynamics (or Monte Carlo) level these techniques allow us to consider... 

The second contribution spans an even larger range of length and times scales. Two benchmark examples illustrate the design approach polymer electrolyte fuel cells and hard disk drive (HDD) systems. In the current HDDs, the read/write head flies about 6.5 nm above the surface via the air bearing design. Multi-scale modeling tools include quantum mechanical (i.e., density functional theory (DFT)), atomistic (i.e., Monte Carlo (MC) and molecular dynamics (MD)), mesoscopic (i.e., dissipative particle dynamics (DPD) and lattice Boltzmann method (LBM)), and macroscopic (i.e., LBM, computational fluid mechanics, and system optimization) levels. 

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... 

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