A. Ghysels

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
2010
A1

Abstract 

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.

DOI 

http://dx.doi.org/10.1021/ci100099g

Efficient Calculation of QM/MM Frequencies with the Mobile Block Hessian

A. Ghysels, H. Lee Woodcock III, J.D. Larkin, B.T. Miller, Y. Shao, J. Kong, D. Van Neck, V. Van Speybroeck, M. Waroquier, B.R. Brooks
Journal of Chemical Theory and Computation (JCTC)
7 (2), 496–514
2011
A1

Abstract 

The calculation of the analytical second derivative matrix (Hessian) is the bottleneck for vibrational analysis in QM/MM systems when an electrostatic embedding scheme is employed. Even with a small number of QM atoms in the system, the presence of MM atoms increases the computational cost dramatically: the long-range Coulomb interactions require that additional coupled perturbed self-consistent field (CPSCF) equations need to be solved for each MM atom displacement. This paper presents an extension to the Mobile Block Hessian (MBH) formalism for QM/MM calculations with blocks in the MM region and its implementation in a parallel version of the Q-Chem/CHARMM interface. MBH reduces both the CPU time and the memory requirements compared to the standard full Hessian QM/MM analysis, without the need to use a cutoff distance for the electrostatic interactions. Special attention is given to the treatment of link atoms which are usually present when the QM/MM border cuts through a covalent bond. Computational efficiency improvements are highlighted using a reduced chorismate mutase enzyme system, consisting of 24 QM atoms and 306 MM atoms, as a test example. In addition, the drug bortezomib, used for cancer treatment of myeloma, has been studied as a test case with multiple MBH block choices and both a QM and QM/MM description. The accuracy of the calculated Hessians is quantified by imposing Eckart constraints, which allows for the assessment of numerical errors in second derivative procedures. The results show that MBH within the QM/MM description not only is a computationally attractive method but also produces accurate results.

DOI 

http://dx.doi.org/10.1021/ct100473f

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
2011
A1

Abstract 

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.

DOI 

http://dx.doi.org/10.1021/ja1073992

Normal Mode Analysis in Zeolites: Toward an Efficient Calculation of Adsorption Entropies

B. De Moor, A. Ghysels, M-F. Reyniers, V. Van Speybroeck, M. Waroquier, G.B. Marin
Journal of Chemical Theory and Computation (JCTC)
7(4), 1090-1101
2011
A1

Abstract 

An efficient procedure for normal-mode analysis of extended systems, such as zeolites, is developed and illustrated for the physisorption and chemisorption of n-octane and isobutene in H-ZSM-22 and H-FAU using periodic DFT calculations employing the Vienna Ab Initio Simulation Package. Physisorption and chemisorption entropies resulting from partial Hessian vibrational analysis (PHVA) differ at most 10 J mol−1 K−1 from those resulting from full Hessian vibrational analysis, even for PHVA schemes in which only a very limited number of atoms are considered free. To acquire a well-conditioned Hessian, much tighter optimization criteria than commonly used for electronic energy calculations in zeolites are required, i.e., at least an energy cutoff of 400 eV, maximum force of 0.02 eV/Å, and self-consistent field loop convergence criteria of 10−8 eV. For loosely bonded complexes the mobile adsorbate method is applied, in which frequency contributions originating from translational or rotational motions of the adsorbate are removed from the total partition function and replaced by free translational and/or rotational contributions. The frequencies corresponding with these translational and rotational modes can be selected unambiguously based on a mobile block Hessian−PHVA calculation, allowing the prediction of physisorption entropies within an accuracy of 10−15 J mol−1 K−1 as compared to experimental values. The approach presented in this study is useful for studies on other extended catalytic systems.

DOI 

http://dx.doi.org/10.1021/ct1005505

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