Spin‐driven activation of dioxygen in various metalloenzymes and their inspired models

Lande, Aurélien de la; Salahub, Dennis R.; Maddaluno, Jacques; Scemama, Anthony; Pilmé, Julien; Parisel, Olivier; Gérard, Hélène; Caffarel, Michel; Piquemal, Jean‐Philip

doi:10.1002/jcc.21698

Cited by 15 publications

(22 citation statements)

References 35 publications

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“…In addition kinases, the SIBFA protein force field has been used to study a variety of metalloproteins encompassing cations such as Cu + , Zn ++ , Ca ++ or Mg ++ , as well as enabling inhibition studies. 91,[209][210][211] Future molecular dynamics simulations should extend the applicability of SIBFA to proteinligand binding.…”

Section: Proteinsmentioning

confidence: 99%

Polarizable Force Fields for Biomolecular Modeling

Shi¹,

Ren²,

Schnieders³

et al. 2015

Reviews in Computational Chemistry

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110

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Classical electrostatics models that take into account polarization appeared as early as the 1950s. Barker in his 1953 paper "Statistical Mechanics of Interacting Dipoles" discussed the electrostatic energy of molecules in terms of "permanent and induced dipoles". 13 Currently, polarizable models generally fall into three categories: those based on induced point dipoles, 9, 14-23 the classical Drude oscillators, 24-26 and fluctuating charges. 27-30 More sophisticated force fields that are "electronic structure-based" 31, 32 or use "machine learning methods" 33 also exist, but incur higher computational costs. Discussions of the advantages and disadvantages of each model and their applications will be presented in the following sections. Compared to fixed charge models, the polarizable models are still in a relatively early stage. Only in the past decade or so has there been a systematic effort to develop general polarizable force fields for molecular modeling. A number of reviews have been published to discuss various aspects of polarizable force fields and their development. 9, 34-40 Here, we focus on the recent development and applications of different polarizable force fields. We begin with a brief introduction to the basic principles and formulae underlying alternative models. Next, the recent progress of several well-developed polarizable force fields is reviewed. Finally, applications of polarizable models to a range of molecular systems, including water and other small molecules, ion solvation, peptides, proteins and lipid systems are presented.

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Section: Proteinsmentioning

confidence: 99%

Polarizable Force Fields for Biomolecular Modeling

Shi¹,

Ren²,

Schnieders³

et al. 2015

Reviews in Computational Chemistry

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110

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“…Therefore, the interested reader can refer to existing recent publications that deal with the QMC-EPLF analysis of covalent, ionic, and multicenter bonds. [11][12][13]16,20 We focus in this section on some illustrative applications highlighting the specific capabilities of the EPLF as compared to Becke and Edgecombe's ELF.…”

Section: Some Applicationsmentioning

confidence: 99%

Electron Pair Localization Function (EPLF) for Density Functional Theory andab InitioWave Function-Based Methods: A New Tool for Chemical Interpretation

Scemama

Caffarel

Chaudret

et al. 2011

J. Chem. Theory Comput.

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We present a modified definition of the Electron Pair Localization Function (EPLF), initially defined within the framework of quantum Monte Carlo approaches Chaquin, P. J. Chem. Phys. 2004, 121, 1725 to be used in Density Functional Theories (DFT) and ab initio wave-function-based methods. This modified version of the EPLF-while keeping the same physical and chemical contents-is built to be analytically computable with standard wave functions or Kohn-Sham representations. It is illustrated that the EPLF defines a simple and powerful tool for chemical interpretation via selected applications including atomic and molecular closed-shell systems, σ and π bonds, radical and singlet open-shell systems, and molecules having a strong multiconfigurational character. Some applications of the EPLF are presented at various levels of theory and compared to Becke and Edgecombe's Electron Localization Function (ELF). Our open-source parallel software implementation of the EPLF opens the possibility of its use by a large community of chemists interested in the chemical interpretation of complex electronic structures.

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“…[38][39][40][41][42][43] Combined enzymatic and model studies have been used to unveil the mechanisms of dioxygen activation by copper proteins. 5,25,[44][45][46][47] It has been suggested for the most of the copper enzymes that the first step in dioxygen activation is the coordinationof dioxygen to copper ion and formation of the metal superoxo species. 18 Although, several modes of dioxygen ligation to copper have been observed in model compounds, only the  1 -superoxide and the - 2 : 2 -peroxide modes of ligation have been identified crystallographically in mononuclear and dinuclear copper metalloprotein active sites respectively (Scheme 1A).…”

Section: Introductionmentioning

confidence: 99%