K. Hemelsoet

TAMkin: A Versatile Package for Vibrational Analysis and Chemical Kinetics

A. Ghysels, T. Verstraelen, K. Hemelsoet, M. Waroquier, V. Van Speybroeck
Journal of Chemical Information and Modeling (JCIM)
50 (9), 1736–1750


TAMkin is a program for the calculation and analysis of normal modes, thermochemical properties and chemical reaction rates. At present, the output from the frequently applied software programs ADF, CHARMM, CPMD, CP2K, Gaussian, Q-Chem, and VASP can be analyzed. The normal-mode analysis can be performed using a broad variety of advanced models, including the standard full Hessian, the Mobile Block Hessian, the Partial Hessian Vibrational approach, the Vibrational Subsystem Analysis with or without mass matrix correction, the Elastic Network Model, and other combinations. TAMkin is readily extensible because of its modular structure. Chemical kinetics of unimolecular and bimolecular reactions can be analyzed in a straightforward way using conventional transition state theory, including tunneling corrections and internal rotor refinements. A sensitivity analysis can also be performed, providing important insight into the theoretical error margins on the kinetic parameters. Two extensive examples demonstrate the capabilities of TAMkin: the conformational change of the biological system adenylate kinase is studied, as well as the reaction kinetics of the addition of ethene to the ethyl radical. The important feature of batch processing large amounts of data is highlighted by performing an extended level of theory study, which TAMkin can automate significantly.

First principle kinetic studies of zeolite-catalyzed methylation reactions

V. Van Speybroeck, J. Van der Mynsbrugge, M. Vandichel, K. Hemelsoet, D. Lesthaeghe, A. Ghysels, G.B. Marin, M. Waroquier
JACS (Journal of the American Chemical Society)
133 (4), 888–899


Methylations of ethene, propene, and butene by methanol over the acidic microporous H-ZSM-5 catalyst are studied by means of state of the art computational techniques, to derive Arrhenius plots and rate constants from first principles that can directly be compared with the experimental data. For these key elementary reactions in the methanol to hydrocarbons (MTH) process, direct kinetic data became available only recently [J. Catal.2005, 224, 115−123; J. Catal.2005, 234, 385−400]. At 350 °C, apparent activation energies of 103, 69, and 45 kJ/mol and rate constants of 2.6 × 10−4, 4.5 × 10−3, and 1.3 × 10−2 mol/(g h mbar) for ethene, propene, and butene were derived, giving following relative ratios for methylation kethene/kpropene/kbutene = 1:17:50. In this work, rate constants including pre-exponential factors are calculated which give very good agreement with the experimental data: apparent activation energies of 94, 62, and 37 kJ/mol for ethene, propene, and butene are found, and relative ratios of methylation kethene/kpropene/kbutene = 1:23:763. The entropies of gas phase alkenes are underestimated in the harmonic oscillator approximation due to the occurrence of internal rotations. These low vibrational modes were substituted by manually constructed partition functions. Overall, the absolute reaction rates can be calculated with near chemical accuracy, and qualitative trends are very well reproduced. In addition, the proposed scheme is computationally very efficient and constitutes significant progress in kinetic modeling of reactions in heterogeneous catalysis.

Validation of DFT-Based Methods for Predicting Qualitative Thermochemistry of Large Polyaromatics

K. Hemelsoet, F. De Vleeschouwer, V. Van Speybroeck, F. De Proft, P. Geerlings, M. Waroquier
12(6), 1100-1108


We present a validation of computationally efficient density functional-based methods for the reproduction of relative bond dissociation energies of large polyaromatic hydrocarbons. Through the calculation of intrinsic radical stabilities and the computation of spin densities, the extent of delocalization of the unpaired electron in the benzylic radicals is examined. We focus on the influence of the level of theory choice applied for the geometry optimization and the role of van der Waals corrections on thermochemical properties. The dispersion effects mainly influence the energetics, causing a small upward shift of the bond dissociation energies. The long-range corrected CAM-B3LYP functional does not improve the traditional B3LYP results for the geometry description of the large delocalized radicals, however a non-negligible influence was encountered when applied for the energetics. It is reported that the f polarization functions present in the 6-311+G(3df,2p) basis set lead to an erroneous trend when combined with the B2PLYP functional for the computation of the single point energies.


Subscribe to RSS - K. Hemelsoet