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

Hua, Duy P.; Leverentz, Hannah R.; Amin, Elizabeth A.; Truhlar, Donald G.

doi:10.1021/ct100491q

Cited by 11 publications

(27 citation statements)

References 33 publications

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“…First, our calculations on neutral and negatively charged Zn systems demonstrate, consistently with our previous findings, 30 that one must choose a fragmentation scheme where one of the monomers is Zn 2+ coordinated to at least two ligands. We rationalize this rule in terms of partial atomic charges.…”

supporting

confidence: 88%

“…12–24 The electrostatically embedded many-body expansion (EE-MB) method has emerged as a particularly promising approach. 10,17,25–29 As described in our previous work, 10,17,25–30 EE-MB addresses the challenge of system size by partitioning larger complexes into a series of fragments, embedding fragment energies in a field of point charges, and running calculations in parallel.…”

mentioning

confidence: 99%

“…30 In the present work, we recommend a set of specific fragmentation strategies to enhance the accuracy of EE-MB for coordination chemistry, and we assess the suitability of the EE-3B method for the more challenging neutral and negatively charged penta- and hexacoordinate Zn systems of biological importance; we also present EE-PA results for comparison.…”

mentioning

confidence: 99%

“…Here we calculate charges using Merz-Kollman (MK) electrostatic fitting, 37 as in previous work on Zn compounds. 30 …”

mentioning

confidence: 99%

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

Kurbanov

Leverentz

Truhlar

et al. 2011

J. Chem. Theory Comput.

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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.

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supporting

confidence: 88%

mentioning

confidence: 99%

mentioning

confidence: 99%

“…Here we calculate charges using Merz-Kollman (MK) electrostatic fitting, 37 as in previous work on Zn compounds. 30 …”

mentioning

confidence: 99%

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

Kurbanov

Leverentz

Truhlar

et al. 2011

J. Chem. Theory Comput.

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“…The EE-3B method is able to predict bond energies obtained by conventional full-system calculations done at the same level of theory to within 1.0 kcal/mol for cationic, neutral, and negatively charged Zn 2+ complexes. 44,45 In EE-MB-CE, one applies the many-body expansion only to the correlation energy, that is, to the post-Hartree–Fock part of the energy calculation. Here we apply the EE-MB-CE method to predict MP2 correlation energies for a variety of pentacoordinate and hexacoordinate Zn 2+ and Cd 2+ systems, and we compare its performance to the EE-MB method.…”

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confidence: 99%

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

Kurbanov

Leverentz

Truhlar

et al. 2013

J. Chem. Theory Comput.

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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.

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Two‐step evaluation of binding energy and potential energy surface of van der Waals complexes

Deshmukh

Sakaki

2012

J Comput Chem

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Evaluation of intermolecular distance and binding energy (BE) of van der Waals complex/cluster at ab initio level of theory is computationally demanding when many monomers are involved. Starting from MP2 energy, we reached a two-step evaluation method of BE of van der Waals complex/cluster through reasonable approximations; BE = BE(HF) + sum Mi> Mj{BE (Mi- Mj)(MP2 or MP2.5) - BE(Mi-Mj)(HF)} where HF represents the Hartree-Fock calculation, Mi, Mj, etc. are interacting monomers, and MP2.5 represents the arithmetic mean of MP2 and MP3. The first term is the usual BE of the complex/cluster evaluated at the HF level. The second term is the sum of the difference in two-body BE between the correlated and HF levels of theory. This equation was applied to various van der Waals complexes consisting of up-to-four monomers at MP2 and MP2.5 levels of theory. We found that this method is capable of providing precise estimate of the BE and reproducing well the potential energy surface of van der Waals complexes/clusters; the maximum error of the BE is less than 1 kcal/mol and 1% in most cases except for several limited cases. The origins of error in these cases are discussed in detail.

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

Cited by 11 publications

References 33 publications

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

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

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

Two‐step evaluation of binding energy and potential energy surface of van der Waals complexes

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