Relative Free Energy Calculations Research Articles

Calculation of relative free energy via indirect pathways

A general method is presented to reduce the simulation time required to compute the relative free energy between two states X and Y of a molecular system by computer simulation. Although the free energy difference ΔAx→y is, in principle, independent of the pathway chosen to change X into Y, in practice its choice strongly affects the accuracy of the obtained ΔA value. The optimum path is the one for which the relaxation time of the system τsystem attains a minimum, allowing the system to remain as close as possible near equilibrium during a simulation. Downscaling the relevant parts of the potential energy function before the change from X to Y is made, and upscaling afterwards is a rather general way to shorten τsystem and thus save computing time. For a model system of butane like molecules the proposed procedure is more than 1 order of magnitude more efficient than the conventional technique of direct interconversion from state X to state Y.

Molecular dynamics of 18-crown-6 complexes with alkali-metal cations: calculation of relative free energies of complexation

Determination des proprietes thermodynamiques lors de la preparation de complexes de Ru, Na et K

Effect of solvent on the reactions of coordination complexes. Part 2.—Kinetics of solvolysis of cis-(chloro)(imidazole)bis(ethylenediamine)-cobalt(III) and cis-(chloro)(benzimidazole)bis(ethylenediamine)cobalt(III) in methanol–water and ethylene glycol–water media

The kinetics of solvolysis of cis-(chloro)(imidazole)bis(ethylenediamine)-cobalt(III) and cis-(chloro)(benzimidazole)bis(ethylenediamine)cobalt(III) have been investigated in aqueous methanol (MeOH) and aqueous ethylene glycol (EG) media (0–80% by weight of MeOH or EG) at 45–64.7 °C. The logarithm of the pseudo-first-order rate constants for MeOH–water media exhibits linear dependence with the reciprocal of the bulk dielectric constant (D–1s), the mole fraction of MeOH (XMeOH) and the solvent ionizing power Y(Y1-AdCl) as determined by the solvolysis rates of 1-adamantyl chloride. Similar plots (log ksobsvs.xEG or D–1s) for EG–water media are non-linear. It is evident that the solvation phenomenon plays dominant role and the rate of solvolysis is mediated by the dual solvent vectors, the overall acidity and basicity of the solvent mixtures. The relative transfer free-energy calculations indicate that the mixed solvent media exert more destabilizing effect on the transition state as compared to the initial state. The activation enthalpy and entropy vs.Xorg(where Xorg is the mole fraction of the organic solvent component) plots display maxima and minima indicating that the solvent structural changes play significant role in the activation process. The activation free energy at a given temperature, however, increases only marginally and linearly with increasing Xorg. The mutual compensatory effect of activation enthalpy and entropy on the activation free energy is in keeping with the fact that the perturbations of the reaction zone and the solvent network remain approximately proportional to each other with increasing Xorg so that the isodelphic and the lyodelphic components of ΔH± and ΔS± correlate well with each other.

Geometric considerations in the calculation of relative free energies of activation

A method that locates transition state structures between homologous reactions and, with the use of the thermodynamic cycle-perturbation technique, determines the relative free energy of activation between the transition states is presented. A simple model system which displays the problem of finding condensed phase transition states is used to illustrate the method.