Literature DB >> 22639556

Electrostatically Embedded Many-Body Expansion for Neutral and Charged Metalloenzyme Model Systems.

Elbek K Kurbanov1, Hannah R Leverentz, Donald G Truhlar, Elizabeth A Amin.   

Abstract

The electrostatically embedded many-body (EE-MB) method has proven accurate for calculating cohesive and conformational energies in clusters, and it has recently been extended to obtain bond dissociation energies for metal-ligand bonds in positively charged inorganic coordination complexes. In the present paper, we present four key guidelines that maximize the accuracy and efficiency of EE-MB calculations for metal centers. Then, following these guidelines, we show that the EE-MB method can also perform well for bond dissociation energies in a variety of neutral and negatively charged inorganic coordination systems representing metalloenzyme active sites, including a model of the catalytic site of the zinc-bearing anthrax toxin lethal factor, a popular target for drug development. In particular, we find that the electrostatically embedded three-body (EE-3B) method is able to reproduce conventionally calculated bond-breaking energies in a series of pentacoordinate and hexacoordinate zinc-containing systems with an average absolute error (averaged over 25 cases) of only 0.98 kcal/mol.

Entities:  

Year:  2011        PMID: 22639556      PMCID: PMC3358931          DOI: 10.1021/ct200637v

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  30 in total

Review 1.  The role of zinc in growth and cell proliferation.

Authors:  R S MacDonald
Journal:  J Nutr       Date:  2000-05       Impact factor: 4.798

2.  Multilevel extension of the cluster-in-molecule local correlation methodology: merging coupled-cluster and Møller-Plesset perturbation theories.

Authors:  Wei Li; Piotr Piecuch
Journal:  J Phys Chem A       Date:  2010-06-24       Impact factor: 2.781

3.  Electrostatically Embedded Many-Body Expansion for Simulations.

Authors:  Erin E Dahlke; Donald G Truhlar
Journal:  J Chem Theory Comput       Date:  2008-01       Impact factor: 6.006

4.  Extending the power of quantum chemistry to large systems with the fragment molecular orbital method.

Authors:  Dmitri G Fedorov; Kazuo Kitaura
Journal:  J Phys Chem A       Date:  2007-05-19       Impact factor: 2.781

5.  Editorial: Zinc in wound healing.

Authors:  R I Henkin
Journal:  N Engl J Med       Date:  1974-09-26       Impact factor: 91.245

6.  Assessment and Validation of the Electrostatically Embedded Many-Body Expansion for Metal-Ligand Bonding.

Authors:  Duy Hua; Hannah R Leverentz; Elizabeth A Amin; Donald G Truhlar
Journal:  J Chem Theory Comput       Date:  2010-12-29       Impact factor: 6.006

Review 7.  Zinc deficiency and taste disorders.

Authors:  C A Heyneman
Journal:  Ann Pharmacother       Date:  1996-02       Impact factor: 3.154

8.  Stromelysin-1: three-dimensional structure of the inhibited catalytic domain and of the C-truncated proenzyme.

Authors:  J W Becker; A I Marcy; L L Rokosz; M G Axel; J J Burbaum; P M Fitzgerald; P M Cameron; C K Esser; W K Hagmann; J D Hermes
Journal:  Protein Sci       Date:  1995-10       Impact factor: 6.725

9.  Electrostatically Embedded Many-Body Correlation Energy, with Applications to the Calculation of Accurate Second-Order Møller-Plesset Perturbation Theory Energies for Large Water Clusters.

Authors:  Erin E Dahlke; Donald G Truhlar
Journal:  J Chem Theory Comput       Date:  2007-07       Impact factor: 6.006

10.  Energies, Geometries, and Charge Distributions of Zn Molecules, Clusters, and Biocenters from Coupled Cluster, Density Functional, and Neglect of Diatomic Differential Overlap Models.

Authors:  Anastassia Sorkin; Donald G Truhlar; Elizabeth A Amin
Journal:  J Chem Theory Comput       Date:  2009-04-02       Impact factor: 6.006

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  2 in total

1.  Analysis of the Errors in the Electrostatically Embedded Many-Body Expansion of the Energy and the Correlation Energy for Zn and Cd Coordination Complexes with Five and Six Ligands and Use of the Analysis to Develop a Generally Successful Fragmentation Strategy.

Authors:  Elbek K Kurbanov; Hannah R Leverentz; Donald G Truhlar; Elizabeth A Amin
Journal:  J Chem Theory Comput       Date:  2013-06-11       Impact factor: 6.006

2.  Hybrid RHF/MP2 geometry optimizations with the effective fragment molecular orbital method.

Authors:  Anders S Christensen; Casper Steinmann; Dmitri G Fedorov; Jan H Jensen
Journal:  PLoS One       Date:  2014-02-18       Impact factor: 3.240

  2 in total

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