Co-reporter:Shan Jiang, Thomas D. Sewell, and Donald L. Thompson
The Journal of Physical Chemistry C 2016 Volume 120(Issue 40) pp:22989-23000
Publication Date(Web):September 8, 2016
DOI:10.1021/acs.jpcc.6b07002
Molecular dynamics (MD) simulations were used to study shock wave passage with normal incidence through the equilibrium interface between (100)-oriented nitromethane and the melt. The simulations were performed using the fully flexible, nonreactive SRT force field (Sorescu, D. C.; Rice, B. M.; Thompson, D. L. The Journal of Physical Chemistry B 2000, 104, 8406–8419). The local kinetic energies (intermolecular, intramolecular, and total) and stress states differ significantly in the liquid and crystal regions, and depend on whether the shock is initiated in the crystal or liquid. The number and spatial distributions of shock-induced molecular disorientations in the crystal for shocks initiated in the crystal are similar to those obtained for analogous simulations for a completely crystalline sample; however, substantial differences in the extent and distribution of shock-induced molecular disorientations in the crystal region were observed when the shock was initiated in the liquid. All three measures of kinetic temperature in the crystal region are higher when the shock is initiated in the crystal than when it is initiated in the liquid. Kinetic temperature profiles exhibit features in the vicinity of the interface considerably different from those in either bulk phase. The shock-induced local mechanical states (von Mises stress) indicate that the crystal is less able to support shear stresses when the shock is initiated in the crystal than when it is initiated in the liquid. There is a strong reflection back into the liquid when the shock wave passes through the liquid and encounters the interface with the crystal. This causes a large increase in the potential energy of the liquid and limits the amount of energy transmitted into the crystal, which limits the molecular disorientations in the crystal. Thus, a shock from liquid to crystal yields less inelastic deformation in the crystal.
Co-reporter:Albert F. Wagner, Luis A. Rivera-Rivera, Damien Bachellerie, Jamin W. Perry, and Donald L. Thompson
The Journal of Physical Chemistry A 2013 Volume 117(Issue 46) pp:11624-11639
Publication Date(Web):February 28, 2013
DOI:10.1021/jp3099889
Motivated by photodissociation experiments in which non-RRKM nanosecond lifetimes of the ethyl radical were reported, we have performed a classical trajectory study of the dissociation and isomerization of C2H5 over the energy range 100–150 kcal/mol. We used a customized version of the AIREBO semiempirical potential (Stuart, S. J.; et al. J. Chem. Phys. 2000, 112, 6472–6486) to more accurately describe the gas-phase decomposition of C2H5. This study constitutes one of the first gas-phase applications of this potential form. At each energy, 10 000 trajectories were run and all underwent dissociation in less than 100 ps. The calculated dissociation rate constants are consistent with RRKM models; no evidence was found for nanosecond lifetimes. An analytic kinetics model of isomerization/dissociation competition was developed that incorporated incomplete mode mixing through a postulated divided phase space. The fits of the model to the trajectory data are good and represent the trajectory results in detail through repeated isomerizations at all energies. The model correctly displays single exponential decay at lower energies, but at higher energies, multiexponential decay due to incomplete mode mixing becomes more apparent. At both ends of the energy range, we carried out similar trajectory studies on CD2CH3 to examine isotopic scrambling. The results largely support the assumption that a H or a D atom is equally likely to dissociate from the mixed-isotope methyl end of the molecule. The calculated fraction of products that have the D atom dissociation is ∼20%, twice the experimental value available at one energy within our range. The calculated degree of isotopic scrambling is non-monotonic with respect to energy due to a non-monotonic ratio of the isomerization to dissociation rate constants.
Co-reporter:Richard Dawes, Albert F. Wagner and Donald L. Thompson
The Journal of Physical Chemistry A 2009 Volume 113(Issue 16) pp:4709-4721
Publication Date(Web):March 16, 2009
DOI:10.1021/jp900409r
We report here calculated J = 0 vibrational frequencies for 1CH2 and HCN with root-mean-square error relative to available measurements of 2.0 cm−1 and 3.2 cm−1, respectively. These results are obtained with DVR calculations with a dense grid on ab initio potential energy surfaces (PESs). The ab initio electronic structure calculations employed are Davidson-corrected MRCI calculations with double-, triple-, and quadruple-ζ basis sets extrapolated to the complete basis set (CBS) limit. In the 1CH2 case, Full CI tests of the Davidson correction at small basis set levels lead to a scaling of the correction with the bend angle that can be profitably applied at the CBS limit. Core-valence corrections are added derived from CCSD(T) calculations with and without frozen cores. Relativistic and non-Born−Oppenheimer corrections are available for HCN and were applied. CBS limit CCSD(T) and CASPT2 calculations with the same basis sets were also tried for HCN. The CCSD(T) results are noticeably less accurate than the MRCI results while the CASPT2 results are much poorer. The PESs were generated automatically using the local interpolative moving least-squares method (L-IMLS). A general triatomic code is described where the L-IMLS method is interfaced with several common electronic structure packages. All PESs were computed with this code running in parallel on eight processors. The L-IMLS method provides global and local fitting error measures important in automatically growing the PES from initial ab initio seed points. The reliability of this approach was tested for 1CH2 by comparing DVR-calculated vibrational levels on an L-IMLS ab initio surface with levels generated by an explicit ab initio calculation at each DVR grid point. For all levels (∼200) below 20 000 cm−1, the mean unsigned difference between the levels of these two calculations was 0.1 cm−1, consistent with the L-IMLS estimated mean unsigned fitting error of 0.3 cm−1. All L-IMLS PESs used in this work have comparable mean unsigned fitting errors, implying that fitting errors have a negligible role in the final errors of the computed vibrational levels with experiment. Less than 500 ab initio calculations of the energy and gradients are required to achieve this level of accuracy.
Co-reporter:Aristophanes Metropoulos, Donald L. Thompson
Journal of Molecular Structure: THEOCHEM 2007 Volume 822(1–3) pp:125-132
Publication Date(Web):15 November 2007
DOI:10.1016/j.theochem.2007.08.010
Quantum chemistry calculations at the MP2 and MRCI levels have been used to compute the energies of the stationary points and the minimum energy pathways (MEPs) between them for the dissociation and isomerization reactions of the methylene amido-gene radical. The MEPs for H2CN → trans-HCNH → cis-HCNH, H2CN → H + HCN, cis-HCNH → H + {HCN, HNC}, trans-HCNH → H + {HCN, HNC} and collinear CN + H2 → HCN + H are reported. The absence of a transition state for the dissociation of the trans isomer has been verified. Also, some calculations for the concerted H2CN ↔ H2 + CN are reported.
Co-reporter:Igor V. Tokmakov;Albert F. Wagner;Michael Minkoff
Theoretical Chemistry Accounts 2007 Volume 118( Issue 4) pp:755-767
Publication Date(Web):2007 October
DOI:10.1007/s00214-007-0358-7
We present several approaches to use gradients in higher degree interpolating moving least squares (IMLS) methods for representing a potential energy surface (PES). General procedures are developed to obtain smooth approximations of the PES and its derivatives from quasi-uniform sets of energy and gradient data points. These methods are illustrated and analyzed for the Morse oscillator and a 1-D slice of the ground-state PES for the HCO radical computed using density functional theory. Variations in the IMLS fits with the number and distribution of points and the degree of the polynomial fitting basis set are examined. We determine the effects of gradient inclusion on the accuracy of the IMLS values of the energy, first and second derivatives for two 1-D test cases. Gradient inclusion reduces the number of data points required by up to 40%.
Co-reporter:Yin Guo, Donald L. Thompson
Chemical Physics Letters 2006 Volume 418(4–6) pp:351-354
Publication Date(Web):6 February 2006
DOI:10.1016/j.cplett.2005.11.001
Abstract
We investigate a theoretical approach that combines molecular dynamics and stochastic dynamics simulations for computing reaction rates in liquids. The approach has the potential for providing a practical computational tool at considerable savings of computer time than that required by using the full-dimensional molecular dynamics calculations alone. Building upon our previous studies on the cis–trans isomerization of HONO in liquid krypton [Y. Guo, D.L. Thompson, J. Chem. Phys. 120 (2004), 898], we further investigate the approach by applying it to the O–N bond dissociation of HONO in liquid krypton. It is shown that the approach provides accurate rates for the bond dissociation as well.