Literature DB >> 23814509

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.

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

Abstract

In the present paper, we apply the electrostatically embedded many-body expansion of the correlation energy (EE-MB-CE) to the calculation of zinc-ligand and cadmium-ligand bond dissociation energies, and we analyze the errors due to various fragmentation schemes in a variety of neutral, positively charged, and negatively charged Zn2+ and Cd2+ coordination complexes. As a result of the analysis, we are able to present a new, simple, and unambiguous fragmentation strategy. Following this strategy, we show that both methods perform well for zinc-ligand and cadmium-ligand bond dissociation energies for all systems studied in the paper, including a model of the catalytic site of the zinc-bearing anthrax toxin lethal factor (LF), which has garnered substantial attention as a target for drug development. To draw general conclusions we consider ten pentacoordinate and hexacoordinate zinc and cadmium containing coordination complexes, each with 10 or 15 different fragmentation schemes. By analyzing errors, we developed a prescription for the optimal fragmentation strategy. With this scheme, and using MP2 correlation energies as a test, we find that the electrostatically embedded three-body expansion of the correlation energy (EE-3B-CE) method is able to reproduce all 53 conventionally calculated bond energies with an average absolute error of only 0.59 kcal/mol. The paper also presents EE-MB-CE calculations using the CCSD(T) level of theory on an LF model system. With CCSD(T), EE-3B-CE has an average error of 0.30 kcal/mol.

Entities:  

Year:  2013        PMID: 23814509      PMCID: PMC3694631          DOI: 10.1021/ct4001872

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


  45 in total

1.  A local second-order Møller-Plesset method with localized orbitals: a parallelized efficient electron correlation method.

Authors:  Yoshihide Nakao; Kimihiko Hirao
Journal:  J Chem Phys       Date:  2004-04-08       Impact factor: 3.488

2.  Large scale electronic structure calculations.

Authors: 
Journal:  Phys Rev Lett       Date:  1992-12-14       Impact factor: 9.161

3.  Thermochemical Fragment Energy Method for Biomolecules: Application to a Collagen Model Peptide.

Authors:  Ernesto Suárez; Natalia Díaz; Dimas Suárez
Journal:  J Chem Theory Comput       Date:  2009-06-09       Impact factor: 6.006

4.  Many-Overlapping-Body (MOB) Expansion: A Generalized Many Body Expansion for Nondisjoint Monomers in Molecular Fragmentation Calculations of Covalent Molecules.

Authors:  Nicholas J Mayhall; Krishnan Raghavachari
Journal:  J Chem Theory Comput       Date:  2012-07-06       Impact factor: 6.006

5.  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

6.  A generalized many-body expansion and a unified view of fragment-based methods in electronic structure theory.

Authors:  Ryan M Richard; John M Herbert
Journal:  J Chem Phys       Date:  2012-08-14       Impact factor: 3.488

7.  Density functional theory for transition metals and transition metal chemistry.

Authors:  Christopher J Cramer; Donald G Truhlar
Journal:  Phys Chem Chem Phys       Date:  2009-10-21       Impact factor: 3.676

8.  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

9.  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

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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