Molecular dynamics calculation of molecular volumes and volumes of activation

Abstract

Experimentally, the effects of pressure on reaction rates are described by their pressure derivatives, known as volumes of activation. Transition state theory directly links activation volumes to partial molar volumes of reactants and transition states. We discuss a molecular dynamics method for the accurate calculation of molecular volumes, within which the volumes of molecular species are obtained as a difference between the volumes of pure solvent and solvent with a single molecule inserted. The volumes thus obtained depend on the molecular geometry, the strength and type of the solute-solvent interactions, as well as temperature and pressure. The partial molar volumes calculated using this approach agree well with experimental data. Since this method can also be applied to transition state species, it allows for quantitative analysis of experimental volumes of activation in terms of structural parameters of the corresponding transition states. The efficiency of the approach is illustrated by calculation of volumes of activation for three nonpolar reactions in nonpolar solvents. The results agree well with the experimental data.

Determination of partial molar volumes from free energy perturbation theory

“…Benzene was selected for study in all three solvents due to its hydrophobic nature, the availability of experimental data, 34,35,38,63–65 and its inclusion in previous studies. 11,17,18,38,48,66–68 Water and CCl 4 were also examined in their pure liquids to help validate the methodology. To annihilate a molecule, all force field intermolecular interactions for the solute must be scaled to zero.…”

“…Since 2007, Weinberg and coworkers have similarly applied this methodology using molecular dynamics to analyze partial molar volumes of hydrocarbon solutes in a variety of solvents and volumes of activation for three reactions. 17,18 Additionaly, Ashbaugh and co-workers recently used the direct method in conjunction with other techniques to compute V ° values for amino acid side chains and volumes of micellization. 16 Others have employed this method to study thermodynamic properties of small proteins.…”

CHAPTER 9. Partial Molar Volumes of Gases Dissolved in Liquids

“…Using molecular dynamics simulations [183][184][185] in combination with solvent OPLS-AA (Optimized Potentials for Liquid Simulations-All Atom) force field parameters 186,187 and customised force field parameters for the solutes, V LN 2 is computed by the direct method, that is, the volume difference between the pure liquid solvent and a solution containing a single solute molecule is calculated. [188][189][190] In addition, the simulation results may also be used to derive the solute (2)-solvent (1) pair distribution function g 21 (r), 189,191 where r denotes the solute-solvent centre-of-mass distance. At infinite dilution, in the grand canonical ensemble, V LN 2 is given by the Kirkwood-Buff expression 192,193 as is determined only by the spatial solvent structure around the solute and the isothermal compressibility of the pure solvent.…”

High-pressure reaction profiles and activation volumes of 1,3-cyclohexadiene dimerizations computed by the extreme pressure-polarizable continuum model (XP-PCM)

“…Molecular dynamics (MD) simulations or Monte Carlo simulations (an early example by Klärner et al 25 ) are performed to obtain reaction profiles at high pressures and activation volumes. Due to the large size of the system using a simulation box, the MD simulations were usually done with force fields, as illustrated in the works from the Weinberg group, 45,46,47,48 or by a hybrid quantum mechanics/molecular mechanics (QM/MM) approach, as shown in the work by Plotnikov and Martinez 49 and a recent work by Loco et al 50 We now report a thorough consideration of the potential energy surface (PES) of the thermal dimerization 1,3-cyclohexadiene, including [4+2]-ene pathways that were not considered previously. In addition, we report, for the first time, XP-PCM calculations on the activation volumes for the various dimerization reactions of 1,3-cyclohexadiene, offering a new approach for computationally studying the competing mechanisms of this reaction.…”