AMOEBA Polarizable Force Field Parameters of the Heme Cofactor in Its Ferrous and Ferric Forms
In: Journal of Chemical Theory and Computation Journal of Chemical Theory and Computation, American Chemical Society, 2018, 14 (5), pp.2705-2720. ⟨10.1021/acs.jctc.7b01128⟩; (2018-03-22)
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Zugriff:
We report the first parameters of the heme redox cofactors for the polarizable AMOEBA force field in both the ferric and ferrous forms. We consider two types of complexes, one with two histidine side chains as axial ligands and one with a histidine and a methionine side chain as ligands. We have derived permanent multipoles from second-order Moller–Plesset perturbation theory (MP2). The sets of parameters have been validated in a first step by comparison of AMOEBA interaction energies of heme and a collection of biologically relevant molecules with MP2 and Density Functional Theory (DFT) calculations. In a second validation step, we consider interaction energies with large aggregates comprising around 80 H2O molecules. These calculations are repeated for 30 structures extracted from semiempirical PM7 DM simulations. Very encouraging agreement is found between DFT and the AMOEBA force field, which results from an accurate treatment of electrostatic interactions. We finally report long (10 ns) MD simulation...
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AMOEBA Polarizable Force Field Parameters of the Heme Cofactor in Its Ferrous and Ferric Forms
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Autor/in / Beteiligte Person: | Piquemal, Jean-Philip ; Lagardère, Louis ; Clavaguéra, Carine ; Aurélien de la Lande ; Wu, Xiaojing ; Laboratoire de Chimie Physique D'Orsay (LCPO) ; Université Paris-Sud - Paris 11 (UP11)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS) ; Laboratoire de chimie moléculaire (LCM) ; Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X) ; Institut des Sciences du Calcul et des Données (ISCD) ; Sorbonne Université (SU) ; Institut Parisien de Chimie Physique et Théorique (IP2CT) ; Université Pierre et Marie Curie - Paris 6 (UPMC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS) ; Laboratoire de chimie théorique (LCT) ; Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS) ; Institut Universitaire de France (IUF) ; Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.) |
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Quelle: | Journal of Chemical Theory and Computation Journal of Chemical Theory and Computation, American Chemical Society, 2018, 14 (5), pp.2705-2720. ⟨10.1021/acs.jctc.7b01128⟩; (2018-03-22) |
Veröffentlichung: | HAL CCSD, 2018 |
Medientyp: | unknown |
ISSN: | 1549-9618 (print) ; 1549-9626 (print) |
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