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

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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.
Keywords
PHOSPHODIESTER LINKAGE, MOLECULAR-DYNAMICS SIMULATIONS, COORDINATION-COMPLEXES, AQUEOUS-SOLUTION, PARAMETERIZATION, METALLOPROTEINS, OPTIMIZATION, MECHANICS, PROTEINS, HYDROLYSIS

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Citation

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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.
@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},
}

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