Monte Carlo simulations free-energy perturbation

C02(aq) Parameterization Through Free Energy Perturbation/Monte Carlo Simulations for Use in C02 Sequestration... 

Free Energy Perturbation Monte Carlo Simulations... 

To finalize the development of the aqueous CO2 force field parameters, the C02 model was used in free energy perturbation Monte Carlo (FEP/MC) simulations to determine the solubility of C02 in water. The solubility of C02 in water is calculated as a function of temperature in the development process to maintain transferability of the C02 model to different simulation techniques and to quantify the robustness of the technique used in the solubility calculations. It is also noted that the calculated solubility is based upon the change in the Gibbs energy of the system and that parameter development must account for the entropy/enthalpy balance that contributes to the overall structure of the solute and solvent over the temperature range being modeled [17]. 

What has been developed within the last 20 years is the computation of thermodynamic properties including free energy and entropy [12, 13, 14]. But the ground work for free energy perturbation was done by Valleau and Torrie in 1977 [15], for particle insertion by Widom in 1963 and 1982 [16, 17] and for umbrella sampling by Torrie and Valleau in 1974 and 1977 [18, 19]. These methods were primarily developed for use with Monte Carlo simulations continuous thermodynamic integration in MD was first described in 1986 [20]. 

Fig. 5. To generate an ensemble using Molecular Dynamics or Monte-Carlo simulation techniques the interaction between all pairs of atoms within a given cutoff radius must be considered. In contrast, to estimate changes in free energy using a stored trajectory only those interactions which are perturbed need be determined making the approach highly efficient.

Calculations of relative partition coefficients have been reported using the free energy perturbation method with the molecular dynamics and Monte Carlo simulation methods. For example, Essex, Reynolds and Richards calculated the difference in partition coefficients of methanol and ethanol partitioned between water and carbon tetrachloride with molecular dynamics sampling [Essex et al. 1989]. The results agreed remarkably well with experiment... 

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... 

A review cataloging intramolecular Diels-Alder reactions as key steps in the total synthesis of natural products has been published.78 A key step in the total synthesis (g) of (+)-dihydrocompactin (66) is the intramolecular ionic Diels-Alder reaction of the trienone (63) to yield the (+)-compactin core compound (65) via the intermediate cyclic vinyloxocarbenium ion (64) (Scheme 17).79 The intramolecular Diels-Alder reaction of the Asp-Thr tethered compound (67) produced the cycloadduct (68) with high regio- and stereo-selectivity (Scheme 18).80 Mixed quantum and molec- (g) ular mechanics (QM/MM) combined with Monte Carlo simulations and free-energy perturbation (FEP) calculations have been used to show that macrophomate synthase... 

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