Activation volume and quantum tunneling in the hydrogen transfer reaction between methyl radical and methane: A first computational study

We present a theory of the effect of quantum tunneling on the basic parameter that characterizes the effect of pressure on the rate constant of chemical reactions in a dense phase, the activation volume. This theory results in combining, on the one hand, the extreme pressure polarizable continuum model, a quantum chemical method to describe the effect of pressure on the reaction energy profile in a dense medium, and, on the other hand, the semiclassical version of the transition state theory, which includes the effect of quantum tunneling through a transmission coefficient. The theory has been applied to the study of the activation volume of the model reaction of hydrogen transfer between methyl radical and methane, including the primary isotope substitution of hydrogen with deuterium (H/D). The analysis of the numerical results offers, for the first time, a clear insight into the effect of quantum tunneling on the activation volume for this hydrogen transfer reaction: this effect results from the different influences that pressure has on the competing thermal and tunneling reaction mechanisms. Furthermore, the computed kinetic isotope effect (H/D) on the activation volume for this model hydrogen transfer correlates well with the experimental data for more complex hydrogen transfer reactions.

High-Pressure Reaction Profiles and Activation Volumes of 1,3-Cyclohexadiene Dimerizations Computed by the Extreme Pressure-Polarizable Continuum Model (XP-PCM)

Quantum chemical calculations are reported for the thermal dimerizations of 1,3-cyclohexadiene at 1 atm and high pressures up to the GPa range. Computed activation enthalpies of plausible dimerization pathways at 1 atm agree well with the experiment activation energies and the values from previous calculations. High-pressure reaction profiles, computed by the recently developed extreme pressure-polarizable continuum model (XP-PCM), show that the reduction of reaction barrier is more profound in concerted reactions than in stepwise reactions, which is rationalized on the basis of the volume profiles of different mechanisms. A clear shift of the transition state towards the reactant under pressure is revealed for the [6+4]-ene reaction by the calculations. The computed activation volumes by XP-PCM agree excellently with the experimental values, confirming the existence of competing mechanisms in the thermal dimerization of 1,3-cyclohexadiene.

Molecular Dynamics Calculations of Partial Molar Volumes of Amino Acids in Aqueous Solutions

Partial molar volumes of amino acids in their zwitterionic and molecular forms have been calculated using molecular dynamics simulations of these systems in aqueous solutions. Calculations performed with the TIP4P, SPC (rigid and flexible), SPC/E, and polarizable water models show that the choice of water model can have a significant impact on the calculated volumes. The effect of treatment of long-range electrostatic interactions on the calculated results was also investigated. Volumes obtained in simulations with a properly chosen water model fit well the experimental data for both molecular and zwitterionic forms of amino acids.

Static Combinatorial Chemistry: A High-Pressure Approach to the Synthesis of Macrocyclic Benzoamide Libraries

We investigated the yield and distribution of macrocyclic products formed in combinatorial libraries (CLs) obtained via double-amidation reactions of methyl diesters with α,ω-diamines. The application of the static combinatorial chemistry (SCC) approach allowed us to generate a large number of macrocyclic diamides and tetraamides in single experiments. We show that high-pressure conditions accelerate the macrocyclization process but also have a great impact on the distribution of macrocyclic products in the presented libraries, promoting the formation of macrocyclic compounds and eliminating the linear ones. The distribution of macrocyclic products was also found to be strongly dependent on the structural features of the substrates employed. Furthermore, in three- and four-substrate CLs we observed the formation of a new type of hybrid tetraamides consisting of three different components.

A General Method for High-Pressure-Promoted Postfunctionalization of Unclosed Cryptands: Potential Phase-Transfer Catalysts

We report a high-pressure approach to facile late-stage functionalization of unclosed cryptands (UCs) (11 examples, yield up to 99%). Direct comparison of classic and high-pressure conditions of the quaternization reaction in a sterically crowded intraannular position is investigated, and differences in the reactivity of tertiary amine substrates are discussed. Finally, we demonstrated the application of UCs as catalysts for synthetically important alkylation reactions under phase-transfer conditions.

Theoretical analysis of high-pressure effects on conformational equilibria

Along with temperature, pressure is the most important physical parameter determining the thermodynamic properties and reactivity of chemical systems. In this work, we discuss the effects of high pressure on conformational properties of organic molecules and propose an approach toward calculation of conformational volume changes based on molecular dynamics simulations. The results agree well with the experimental data. Furthermore, we demonstrate that pressure can be used as an instrument for fine-tuning of molecular conformations and to propel a properly constructed molecular rotor possessing a suitable combination of energy and volume profiles.

High pressure-assisted low-loading asymmetric organocatalytic conjugate addition of nitroalkanes to chalcones

A highly enantioselective and relatively fast (1–5 h) Michael reaction with substantial reduction of organocatalyst loading (0.2–1 mol%) was developed under high-pressure conditions (up to 9 kbar) and at room temperature.

Effect of high pressure on the topography of potential energy surfaces

Properties and reactivity of chemical compounds change dramatically at elevated pressures. Since kinetics and mechanisms of condensed-phase reactions are described in terms of their potential energy (PESs) or Gibbs energy (GESs) surfaces, chemical effects of high pressure can be assessed through analysis of pressure-induced deformations of GESs of solvated reaction systems. We discuss general trends expected for such changes and use quantum mechanical calculations to construct PESs of compressed species for hydrogen and methyl transfer reactions.

Determination of partial molar volumes from free energy perturbation theory

Partial molar volume is an important thermodynamic property that gives insights into molecular size and intermolecular interactions in solution. Theoretical frameworks for determining the partial molar volume (V°) of a solvated molecule generally apply Scaled Particle Theory or Kirkwood-Buff theory. With the current abilities to perform long molecular dynamics and Monte Carlo simulations, more direct methods are gaining popularity, such as computing V° directly as the difference in computed volume from two simulations, one with a solute present and another without. Thermodynamically, V° can also be determined as the pressure derivative of the free energy of solvation in the limit of infinite dilution. Both approaches are considered herein with the use of free energy perturbation (FEP) calculations to compute the necessary free energies of solvation at elevated pressures. Absolute and relative partial molar volumes are computed for benzene and benzene derivatives using the OPLS-AA force field. The mean unsigned error for all molecules is 2.8 cm(3) mol(-1). The present methodology should find use in many contexts such as the development and testing of force fields for use in computer simulations of organic and biomolecular systems, as a complement to related experimental studies, and to develop a deeper understanding of solute-solvent interactions.

Theoretical volume profiles as a tool for probing transition states: folding kinetics

The mechanism by which conformational changes, particularly folding and unfolding, occur in proteins and other biopolymers has been widely discussed in the literature. Molecular dynamics (MD) simulations of protein folding present a formidable challenge since these conformational changes occur on a time scale much longer than what can be afforded at the current level of computational technology. Transition state (TS) theory offers a more economic description of kinetic properties of a reaction system by relating them to the properties of the TS, or for flexible systems, the TS ensemble (TSE). The application of TS theory to protein folding is limited by ambiguity in the definition of the TSE for this process. We propose to identify the TSE for conformational changes in flexible systems by comparison of its experimentally determined volumetric property, known as the volume of activation, to the structure-specific volume profile of the process calculated using MD. We illustrate this approach by its successful application to unfolding of a model chain system.

Variation and decomposition of the partial molar volume of small gas molecules in different organic solvents derived from molecular dynamics simulations

The partial molar volumes, V(i), of the gas solutes H2, CO, and CO2, solvated in acetone, methanol, heptane, and diethylether are determined computationally in the limit of infinite dilution and standard conditions. Solutions are described with molecular dynamics simulations in combination with the OPLS-aa force field for solvents and customized force field for solutes. V(i) is determined with the direct method, while the composition of V(i) is studied with Kirkwood-Buff integrals (KBIs). Subsequently, the amount of unoccupied space and size of pre-formed cavities in pure solvents is determined. Additionally, the shape of individual solvent cages is analyzed. Calculated V(i) deviate only 3.4 cm(3) mol(-1) (7.1%) from experimental literature values. Experimental V(i) variations across solutions are reproduced qualitatively and also quantitatively in most cases. The KBI analysis identifies differences in solute induced solvent reorganization in the immediate vicinity of H2 (<0.7 nm) and solvent reorganization up to the third solvation shell of CO and CO2 (<1.6 nm) as the origin of V(i) variations. In all solutions, larger V(i) are found in solvents that exhibit weak internal interactions, low cohesive energy density and large compressibility. Weak internal interactions facilitate solvent displacement by thermal solute movement, which enhances the size of solvent cages and thus V(i). Additionally, attractive electrostatic interactions of CO2 and the solvents, which do not depend on internal solvent interactions only, partially reversed the V(i) trends observed in H2 and CO solutions where electrostatic interactions with the solvents are absent. More empty space and larger pre-formed cavities are found in solvents with weak internal interactions, however, no evidence is found that solutes in any considered solvent are accommodated in pre-formed cavities. Individual solvent cages are found to be elongated in the negative direction of solute movement. This wake behind the moving solute is more pronounced in case of mobile H2 and in solvents with weaker internal interactions. However, deviations from a spherical solvent cage shape do not influence solute-solvent radial distribution functions after averaging over all solvent cage orientations and hence do not change V(i). Overall, the applied methodology reproduces V(i) and its variations reliably and the used V(i) decompositions identify the underlying reasons behind observed V(i) variations.

Partition, sorption and structure activity relation study of dialkoxybenzenes that modulate insect behavior

Some dialkoxybenzenes are promising new insect control agents. These compounds mimic naturally occurring odorants that modulate insect behavior. Before applying these compounds, however, their persistence and biodegradability at the application site and in the environment should be understood. The fate of organic compounds in the environment is a complex phenomenon which is influenced by many processes such as sorption to soil components, sedimentation, volatilization, and uptake by plants, as well as biotic and abiotic chemical degradation. In this study, the octanol-water partition coefficient, volatility and sorption on soil components (sand, clay and organic matter) of selected dialkoxybenzenes as well as structure activity relationships with regard to partition, volatility and sorption were investigated. Additionally, calculations of partition, molar volume and molecular surface areas were done, to understand structure-activity relationships of the physical properties.

Hydrogen transfer reactions in viscous media — Potential and free energy surfaces in solvent–solute coordinates and their kinetic implications

Two-dimensional potential energy and free energy surfaces are obtained using quantum mechanical and molecular dynamics calculations for four hydrogen transfer reactions in n-hexane solvent: the methyl–methane, n-propyl–n-propane, n-pentyl–n-pentane, and t-butyl–isobutane systems. The resultant surfaces have similar landscapes despite the fact the equilibrated solvent cavities for these systems are notably different in size and shape. The kinetic implications of these landscapes are discussed. The Arrhenius and tunneling kinetics of hydrogen transfer in nonpolar hydrocarbon solute–solvent systems are not expected to show any significant viscosity dependence.