On the curvature in logarithmic plots of rate coefficients for chemical reactions

In terms of the reduced potential energy barrier ζ = ΔuTS/kT, the rate coefficients for chemical reactions are usually expressed as proportional to e-ζ. The coupling between vibrational modes of the medium to the reaction coordinate leads to a proportionality of the regularized gamma function of Euler Q(a,ζ) = Γ(a,ζ)/Γ(a), with a being the number of modes coupled to the reaction coordinate. In this work, the experimental rate coefficients at various temperatures for several chemical reactions were fitted to the theoretical expression in terms of Q(a,ζ) to determine the extent of its validity and generality. The new expression affords lower deviations from the experimental points in 29 cases out of 38 and it accounts for the curvature in the logarithmic plots of rate coefficients versus inverse temperature. In the absence of tunneling, conventional theories predict the curvature of these plots to be identically zero

Improving the study of proton transfers between amino acid sidechains in solution: choosing appropriate DFT functionals and avoiding hidden pitfalls

We have studied the influence of implicit solvent models, inclusion of explicit water molecules, inclusion of vibrational effects, and density functionals on the quality of the predicted pK a of small amino acid side chain models. We found that the inclusion of vibrational effects and explicit water molecules is crucial to improve the correlation between the computed and the experimental values. In these micro-solvated systems, the best agreement between DFT-computed electronic energies and benchmark values is afforded by BHHLYP and B97-2. However, approaching experimental results requires the addition of more than three explicit water molecules, which generates new problems related to the presence of multiple minima in the potential energy surface. It thus appears that a satisfactory ab initio prediction of amino acid side chain pK a will require methods that sample the configurational space in the presence of large solvation shells, while at the same time computing vibrational contributions to the enthalpy and entropy of the system under study in all points of that surface. Pending development of efficient algorithms for those computations, we strongly suggest that whenever counterintuitive protonation states are found in a computational study (e.g., the presence of a neutral aspartate/neutral histidine dyad instead of a deprotonated aspartate/protonated histidine pair), the reaction profile should be computed under each of the different protonation micro-states by constraining the relevant N–H or O–H bonds, in order to avoid artifacts inherent to the complex nature of the factors contributing to the pK a

Symmetry numbers and chemical reaction rates

Abstract This article shows how to evaluate rotational symmetry numbers for different molecular configurations and how to apply them to transition state theory. In general, the symmetry number is given by the ratio of the reactant and transition state rotational symmetry numbers. However, special care is advised in the evaluation of symmetry numbers in the following situations: (i) if the reaction is symmetric, (ii) if reactants and/or transition states are chiral, (iii) if the reaction has multiple conformers for reactants and/or transition states and, (iv) if there is an internal rotation of part of the molecular system. All these four situations are treated systematically and analyzed in detail in the present article. We also include a large number of examples to clarify some complicated situations, and in the last section we discuss an example involving an achiral diasteroisomer

New methods for potential functions for simulating biological molecules

We use the CM1A class IV charge model and the SM5.4/A and SM5.4PD/A solvation models to calculate atomic charges and solvation energies for 9-methyladenine and thymine and for alanine and serine dipeptides. The CM1A quantum mechanical charge model provides atomic charges as accurate as or more accurate than those used in popular molecular dynamics force fields but is very economical in both computer time and effort required to generate charges; thus it is very promising for examining effects of conformational changes, substituents, solvation, binding, and even reaction. The solvation models have been parameterized over multiple functionalities and are well suited to rapid calculations on large systems

ENFORCED HYDROPHOBIC INTERACTIONS AND HYDROGEN-BONDING IN THE ACCELERATION OF DIELS-ALDER REACTIONS IN WATER

Following pioneering work of Breslow, Grieco and others, we find that intermolecular Diels-Alder (DA) reactions of cyclopentadiene with alkyl vinyl ketones and 5-substituted-1,4 naphthoquinones as well as intramolecular DA reactions of N-furfuryl-N-alkylacrylamides are greatly accelerated in water as compared with traditional organic solvents. Isobaric activation parameters in combination with thermodynamic quantities for transfer of reactants and activated complex from alcohols and alcohol-water mixtures to water indicate, that the decrease of the hydrophobic surface area of the reactants during the activation process (''enforced hydrophobic interactions'') is an important factor determining the rate enhancement in water. A second factor involves hydrogen-bond stabilization of the polarized activated complex. Aggregation or stacking of the reactants do not play a role at the concentrations used for the kinetic measurements. In alcohol-water mixtures the rate accelerations are confined to the highly water-rich solvent composition range and result from favorable changes in both Delta(#)H(circle minus) and Delta(#)S(circle minus)