José C. Corchado

Potential energy surface, thermal, and state-selected rate coefficients, and kinetic isotope effects for Cl+CH4→HCl+CH3

A new potential energy surface is reported for the gas-phase reaction Cl+CH4→HCl+CH3. It is based on the analytical function of Jordan and Gilbert for the analog reaction H+CH4→H2+CH3, and it is calibrated by using the experimental thermal rate coefficients and kinetic isotope effects. The forward and reverse thermal rate coefficients were calculated using variational transition state theory with semiclassical transmission coefficients over a wide temperature range, 200–2500 K. This surface is also used to analyze dynamical features, such as reaction-path curvature, the coupling between the reaction coordinate and vibrational modes, and the effect of vibrational excitation on the rate coefficients. We find that excitation of C–H stretching modes and Cl–H stretching modes enhances the rate of both the forward and the reverse reactions, and excitation of the lowest frequency bending mode in the CH4 reactant also enhances the rate coefficient for the forward reaction. However, the vibrational excitation of t...

Multiconfiguration molecular mechanics algorithm for potential energy surfaces of chemical reactions

We present an efficient algorithm for generating semiglobal potential energy surfaces of reactive systems. The method takes as input molecular mechanics force fields for reactants and products and a quadratic expansion of the potential energy surface around a small number of geometries whose locations are determined by an iterative process. These Hessian expansions might come, for example, from ab initio electronic structure calculations, density functional theory, or semiempirical molecular orbital theory. A 2×2 electronic diabatic Hamiltonian matrix is constructed from these data such that, by construction, the lowest eigenvalue of this matrix provides a semiglobal approximation to the lowest electronically adiabatic potential energy surface. The theory is illustrated and tested by applications to rate constant calculations for three gas-phase test reactions, namely, the isomerization of 1,3-cis-pentadiene, OH+CH4→H2O+CH3, and CH2Cl+CH3F→CH3Cl+CH2F.

Analytical potential energy surface for the NH3+H↔NH2+H2 reaction: Application of variational transition-state theory and analysis of the equilibrium constants and kinetic isotope effects using curvilinear and rectilinear coordinates

The potential energy surface (PES) for the gas-phase NH3+H↔NH2+H2 reaction is constructed with suitable functional forms to represent the stretching and bending modes, and using as calibration criterion the reactant and product experimental properties and the ab initio saddle point properties. This surface is then used to calculate rate constants with variational transition-state theory over the temperature range 300–2000 K. While the forward rate constants agree with experimental results, the reverse ones are lower by factors of between 4 and 6. Since the same PES is used and these rates are related by detailed balance, this disagreement could indicate an uncertainty in the few available experimental studies for the reverse reaction. We also provide a detailed analysis of the equilibrium constants and of the kinetic isotope effects and compare the results of this analytical PES with earlier ab initio reaction-path calculations. Finally, for the vibrational frequency calculations, we analyze the consequen...

Analytical potential energy surface for the CH4+Cl→CH3+ClH reaction: Application of the variational transition state theory and analysis of the kinetic isotope effects

We present a potential energy surface for the CH4+Cl→CH3+Cl reaction, based on the analytical function J1 for the analog CH4+H→CH3+H2 reaction by Joseph et al. To calibrate the new surface we chose the reactant and product experimental properties as reference data. The forward and reverse rate constants were calculated using variational transition state theory with large curvature transmission coefficients over a wide temperature range, 200–1000 K. The variational effects were concluded to be small for this reaction, and good agreement with experimental rate constants was found in both forward and reverse reactions. The kinetic isotope effects (KIEs) at different temperatures for the forward and reverse reactions were also analyzed showing always a ‘‘normal’’ behavior. The factor analysis of the KIEs in the forward reactions indicated high vibrational and tunneling contributions at low temperatures.

Quantum mechanical tunneling in methylamine dehydrogenase

We report a calculation for a trideuteration kinetic isotope effect (KIE) for the proton transfer step in the oxidation of methylamine by the quinoprotein methylamine dehydrogenase (MADH). The potential field includes 11 025 atoms, and the dynamics are based on a quantum mechanical/molecular mechanical (QM/MM) direct dynamics simulation and canonical variational transition state theory with small-curvature multidimensional tunneling contributions. About 1% of the reaction occurs by overbarrier processes, with the rest due to tunneling, and the calculated KIE is reduced to 5.9 when we omit tunneling. This provides the most striking evidence yet for the contribution of tunneling processes to enzymatic reactions at physiological temperatures.

Potential energy surface for a seven-atom reaction. Thermal rate constants and kinetic isotope effects for CH4+OH

The potential energy surface for the gas-phase CH4+OH→CH3+H2O reaction and its deuterated analogs was constructed with suitable functional forms to represent vibrational modes, and was calibrated by using the experimental thermal rate constants and kinetic isotope effects. On this surface, the forward and reverse thermal rate constants were calculated using variational transition-state theory with semiclassical transmission coefficients over a wide temperature range, 200–2000 K, finding reasonable agreement with the available experimental data. We also calculated six sets of kinetic isotope effects and, in general, the theoretical results underestimate the few available experiments, with exception of the C-13 isotopic effect values which are overestimated. Finally, this surface is also used to analyze dynamical features, such as reaction-path curvature and coupling between the reaction coordinate and vibrational modes.

The Gaussian-2 method with proper dissociation, improved accuracy, and less cost

The Gaussian-2 method (G2) is modified by deleting the empirical high-level correction and instead using empirical coefficients to extrapolate to full configuration interaction and an infinite basis set. The resulting method, called multicoefficient Gaussian-2 (MCG2) is less expensive than G2 but a factor of 1.7 more accurate for molecules composed of H and first-row atoms.

Test of variational transition state theory with multidimensional tunneling contributions against an accurate full-dimensional rate constant calculation for a six-atom system

We present calculations of the H+CH4 reaction rate on the Jordan–Gilbert surface using canonical variational transition state theory with microcanonical optimized multidimensional tunneling contributions (CVT/μOMT). The purpose of the calculation is to compare the results to the recent accurate dynamical calculations of Bowman, Wang, Huang, Huarte-Larranaga, and Manthe for this potential energy surface. Over the full 200–500 K range for which accurate results are available we find a mean absolute deviation of only 17% and a maximum absolute deviation of 23%. This provides a rigorous validation of this popular method for a larger system than has previously been possible and indicates that previous validations for atom–diatom reactions were indeed indicative of the kind of accuracy one can obtain for larger systems.

Theoretical study of the CH4+F→CH3+FH reaction. I. Abinitio reaction path

Using ab initio information, the reaction path for the CH4+F→CH3+FH reaction was traced and the coupling between the reaction coordinate and normal modes was analyzed along it. The FH product may be vibrationally excited due to the nonadiabatic flow of energy between the reaction coordinate and this bound mode, manifest in the large peak in the coupling term after the saddle point. It was concluded that the variational effects were due only to entropic effects. The rate constants were calculated for the temperature range 100–500 K using the variational transition state theory with different levels of calculation to calibrate the reaction path. Agreement was found with the experimental values when using the QCI/b3 shifted curve, avoiding the errors associated with the use of the single‐point calculation.

Theoretical study of the CH4+F→CH3+FH reaction. II. Semiempirical surfaces

We present two semiempirical surfaces for the CH4+F→CH3+FH reaction. One is based on the PM3 semiempirical molecular orbital theory, using parameters specifically calculated for this reaction (SRP method), and the other is based on the analytic function J1 for the CH4+H→CH3+H2 reaction, slightly modified (MJ1 surface). To calibrate the first surface we chose as reference data the reactant and product experimental properties, while to fit the second, we also used ab initio calculated saddle‐point information. Experimental rate constants were not used in the calibration because of their uncertainty. Because of the flattening of these surfaces in the saddle‐point zone, the variational effects are important and the location of the transition state is concluded to be due to entropy effects. The kinetic isotope effects (KIEs) at different temperatures were also analyzed showing reasonable agreement with the experimental value for both surfaces. The factor analysis of the KIEs indicates an inverse tunneling cont...