Monte Carlo simulation chemical reactions

Another method of simulating chemical reactions is to separate the reaction and particle displacement steps. This kind of algorithm has been considered in Refs. 90, 153-156. In particular. Smith and Triska [153] have initiated a new route to simulate chemical equilibria in bulk systems. Their method, being in fact a generalization of the Gibbs ensemble Monte Carlo technique [157], has also been used to study chemical reactions at solid surfaces [90]. However, due to space limitations of the chapter, we have decided not to present these results. 

A. P. J. Jansen. Monte Carlo simulation of chemical reactions on a surface with time-dependent reaction-rate constants. Comp Phys Commun 56 1-12, 1995. 

Enzyme reactions, like all chemical events, are dynamic. Information coming to us from experiments is not dynamic even though the intervals of time separating observations may be quite small. In addition, much information is denied to us because of technological limitations in the detection of chemical changes. Our models would be improved if we could observe and record all concentrations at very small intervals of time. One approach to this information lies in the creation of a model in which we know all of the concentrations at any time and know something of the structural attributes of each ingredient. A class of models based on computer simulations, such as molecular dynamics, Monte Carlo simulations, and cellular automata, offer such a possibility. 

Although the collision and transition state theories represent two important methods of attacking the theoretical calculation of reaction rates, they are not the only approaches available. Alternative methods include theories based on nonequilibrium statistical mechanics, stochastic theories, and Monte Carlo simulations of chemical dynamics. Consult the texts by Johnson (62), Laidler (60), and Benson (59) and the review by Wayne (63) for a further introduction to the theoretical aspects of reaction kinetics. 

MONTE CARLO SIMULATIONS OF CHEMICAL REACTIONS IN SOLUTION... 

Monte Carlo simulations were carried out to determine the free energy curve for the reaction in solution. The simulations were executed for the solute surrounded by 250 water molecules (or 180 DMF molecules) in the isothermal-isobaric ensemble at 25 °C and 1 atm, including periodic boundary conditions. As a consequence, the Gibbs free energy is obtained in this case. There is sufficient solvent to adequately represent the bulk participation in the chemical reaction. 

The combined QM/MM model can be used along with Statistical Perturbation Theory to carry out a Monte Carlo simulation of a chemical reaction in solution, with the advantage of allowing solute electronic structure relaxation in solution. Particularly, the combined AM1/TIP3P force field has recently been applied to simulate several chemical processes in solution. We will refer here briefly to the Claisen rearrangement and to the Menshutkin reaction. 

Beyond Transition State Theory (and, therefore, beyond Monte Carlo simulations) dynamical effects coming from recrossings should be introduced. Furthermore, additional quantum mechanical aspects, like tunneling, should be taken into account in some chemical reactions. 

Tapia, O. and Lluch, J. M. Solvent effects on chemical reaction profiles. Monte Carlo simulation of hydration effects on quantum chemically calculated stationary structures, J. Chem.Phys., 83 (1983, 3970-3982... 

In chapter 3, Profs. A. Gonzalez-Lafont, Lluch and Bertran present an overview of Monte Carlo simulations for chemical reactions in solution. First of all, the authors briefly review the main aspects of the Monte Carlo methodology when it is applied to the treatment of liquid state and solution. Special attention is paid to the calculations of the free energy differences and potential energy through pair potentials and many-body corrections. The applications of this methodology to different chemical reactions in solution are... 

To evaluate solvent effeets, statistieal meehanical Monte Carlo simulations have been carried out. An important quantity to be computed is the potential of mean force, or free energy profile, as a funetion of the reaction coordinate, X, for a chemical reaction in solution using free energy perturbation method. (44) A straightforward approaeh is to determine free energy differences for incremental changes of certain geometrieal variables that characteristically reflect the... 

Note that careful evaluation and minimization of uncertainties and errors in CTMs is requested to enable the application of these CTMs to the study of observed changes in 03 as small as < 1.5 %/yr. However, actually 03 concentrations are simulated by the models within 20-50%. Chemical reaction rates are also uncertain, for instance in the 90 s determinations of the rates of CH4 and CH3CC13 reactions with OH suggested that these reactions are about 20% slower than believed. Similarly OH reaction with N02 which is an important sink for NOx in the troposphere is measured to be 10-30% lower than earlier estimates [23]. Thus, the past years a number of studies (mainly based on Monte Carlo simulations) focused on the identification and evaluation of the importance of various chemical reactions on oxidant levels to highlight topics crucial for error minimization. Temperature dependence of reaction rates can also introduce a 20-40% uncertainty in 03 and H20 computations in the upper troposphere. It has been also shown that 03 simulations are particularly sensitive to the photolysis rates of N02 and 03 and to PAN chemistry. 

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