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Automated parametrization of AMBER force field terms from vibrational analysis with a focus on functionalizing dinuclear zinc(II) scaffolds

Steven K Burger, Mike Lacasse, Toon Verstraelen UGent, Joel Drewry, Patrick Gunning and Paul W Ayers (2012) JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 8(2). p.554-562
abstract
A procedure for determining force constants that is independent of the internal redundant coordinate choice is presented. The procedure is based on solving each bond and angle term separately, using the Wilson B matrix. The method only requires a single ab initio frequency calculation at the minimum energy structure and is made available in the software "parafreq". The methodology is validated with a set of small molecules, by showing it can reproduce ab initio frequencies better than other methods such as taking the diagonal terms of the Hessian in internal coordinates or by using standard AMBER force fields. Finally, the utility of the method is demonstrated by parametrizing the dizinc scaffold of bis-dipicolylamine (BDPA) bound to phosphotyrosine, which is then functionalized into promising antitumor drug proteomimetics.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
PHOSPHODIESTER LINKAGE, MOLECULAR-DYNAMICS SIMULATIONS, COORDINATION-COMPLEXES, AQUEOUS-SOLUTION, PARAMETERIZATION, METALLOPROTEINS, OPTIMIZATION, MECHANICS, PROTEINS, HYDROLYSIS
journal title
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
J. Chem. Theory Comput.
volume
8
issue
2
pages
554 - 562
Web of Science type
Article
Web of Science id
000300141600018
JCR category
PHYSICS, ATOMIC, MOLECULAR & CHEMICAL
JCR impact factor
5.389 (2012)
JCR rank
3/34 (2012)
JCR quartile
1 (2012)
ISSN
1549-9618
DOI
10.1021/ct2007742
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
1999597
handle
http://hdl.handle.net/1854/LU-1999597
date created
2012-01-23 10:14:03
date last changed
2012-05-31 13:21:20
@article{1999597,
  abstract     = {A procedure for determining force constants that is independent of the internal redundant coordinate choice is presented. The procedure is based on solving each bond and angle term separately, using the Wilson B matrix. The method only requires a single ab initio frequency calculation at the minimum energy structure and is made available in the software {\textacutedbl}parafreq{\textacutedbl}. The methodology is validated with a set of small molecules, by showing it can reproduce ab initio frequencies better than other methods such as taking the diagonal terms of the Hessian in internal coordinates or by using standard AMBER force fields. Finally, the utility of the method is demonstrated by parametrizing the dizinc scaffold of bis-dipicolylamine (BDPA) bound to phosphotyrosine, which is then functionalized into promising antitumor drug proteomimetics.},
  author       = {Burger, Steven K and Lacasse, Mike and Verstraelen, Toon and Drewry, Joel and Gunning, Patrick and Ayers, Paul W},
  issn         = {1549-9618},
  journal      = {JOURNAL OF CHEMICAL THEORY AND COMPUTATION},
  keyword      = {PHOSPHODIESTER LINKAGE,MOLECULAR-DYNAMICS SIMULATIONS,COORDINATION-COMPLEXES,AQUEOUS-SOLUTION,PARAMETERIZATION,METALLOPROTEINS,OPTIMIZATION,MECHANICS,PROTEINS,HYDROLYSIS},
  language     = {eng},
  number       = {2},
  pages        = {554--562},
  title        = {Automated parametrization of AMBER force field terms from vibrational analysis with a focus on functionalizing dinuclear zinc(II) scaffolds},
  url          = {http://dx.doi.org/10.1021/ct2007742},
  volume       = {8},
  year         = {2012},
}

Chicago
Burger, Steven K, Mike Lacasse, Toon Verstraelen, Joel Drewry, Patrick Gunning, and Paul W Ayers. 2012. “Automated Parametrization of AMBER Force Field Terms from Vibrational Analysis with a Focus on Functionalizing Dinuclear zinc(II) Scaffolds.” Journal of Chemical Theory and Computation 8 (2): 554–562.
APA
Burger, S. K., Lacasse, M., Verstraelen, T., Drewry, J., Gunning, P., & Ayers, P. W. (2012). Automated parametrization of AMBER force field terms from vibrational analysis with a focus on functionalizing dinuclear zinc(II) scaffolds. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8(2), 554–562.
Vancouver
1.
Burger SK, Lacasse M, Verstraelen T, Drewry J, Gunning P, Ayers PW. Automated parametrization of AMBER force field terms from vibrational analysis with a focus on functionalizing dinuclear zinc(II) scaffolds. JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 2012;8(2):554–62.
MLA
Burger, Steven K, Mike Lacasse, Toon Verstraelen, et al. “Automated Parametrization of AMBER Force Field Terms from Vibrational Analysis with a Focus on Functionalizing Dinuclear zinc(II) Scaffolds.” JOURNAL OF CHEMICAL THEORY AND COMPUTATION 8.2 (2012): 554–562. Print.