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TAMkin: a versatile package for vibrational analysis and chemical kinetics

An Ghysels UGent, Toon Verstraelen UGent, Karen Hemelsoet UGent, Michel Waroquier UGent and Veronique Van Speybroeck UGent (2010) JOURNAL OF CHEMICAL INFORMATION AND MODELING. 50(9). p.1736-1750
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
BASIS-SET, THERMOCHEMICAL KINETICS, LARGE SYSTEMS, HARMONIC-ANALYSIS, PHASE N-ALKANES, AB-INITIO CALCULATION, FREQUENCY NORMAL-MODES, BLOCK HESSIAN APPROACH, FREE-RADICAL POLYMERIZATIONS, MOLECULAR-ORBITAL METHODS
journal title
JOURNAL OF CHEMICAL INFORMATION AND MODELING
J. Chem Inf. Model.
volume
50
issue
9
pages
1736 - 1750
Web of Science type
Article
Web of Science id
000282087300021
JCR category
COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS
JCR impact factor
3.822 (2010)
JCR rank
2/97 (2010)
JCR quartile
1 (2010)
ISSN
1549-9596
DOI
10.1021/ci100099g
project
HPC-UGent: the central High Performance Computing infrastructure of Ghent University
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
1055592
handle
http://hdl.handle.net/1854/LU-1055592
date created
2010-10-08 09:31:15
date last changed
2013-09-17 10:47:06
@article{1055592,
  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.},
  author       = {Ghysels, An and Verstraelen, Toon and Hemelsoet, Karen and Waroquier, Michel and Van Speybroeck, Veronique},
  issn         = {1549-9596},
  journal      = {JOURNAL OF CHEMICAL INFORMATION AND MODELING},
  keyword      = {BASIS-SET,THERMOCHEMICAL KINETICS,LARGE SYSTEMS,HARMONIC-ANALYSIS,PHASE N-ALKANES,AB-INITIO CALCULATION,FREQUENCY NORMAL-MODES,BLOCK HESSIAN APPROACH,FREE-RADICAL POLYMERIZATIONS,MOLECULAR-ORBITAL METHODS},
  language     = {eng},
  number       = {9},
  pages        = {1736--1750},
  title        = {TAMkin: a versatile package for vibrational analysis and chemical kinetics},
  url          = {http://dx.doi.org/10.1021/ci100099g},
  volume       = {50},
  year         = {2010},
}

Chicago
Ghysels, An, Toon Verstraelen, Karen Hemelsoet, Michel Waroquier, and Veronique Van Speybroeck. 2010. “TAMkin: a Versatile Package for Vibrational Analysis and Chemical Kinetics.” Journal of Chemical Information and Modeling 50 (9): 1736–1750.
APA
Ghysels, A., Verstraelen, T., Hemelsoet, K., Waroquier, M., & Van Speybroeck, V. (2010). TAMkin: a versatile package for vibrational analysis and chemical kinetics. JOURNAL OF CHEMICAL INFORMATION AND MODELING, 50(9), 1736–1750.
Vancouver
1.
Ghysels A, Verstraelen T, Hemelsoet K, Waroquier M, Van Speybroeck V. TAMkin: a versatile package for vibrational analysis and chemical kinetics. JOURNAL OF CHEMICAL INFORMATION AND MODELING. 2010;50(9):1736–50.
MLA
Ghysels, An, Toon Verstraelen, Karen Hemelsoet, et al. “TAMkin: a Versatile Package for Vibrational Analysis and Chemical Kinetics.” JOURNAL OF CHEMICAL INFORMATION AND MODELING 50.9 (2010): 1736–1750. Print.