Towards large scale hybrid QM/MM dynamics of complex systems with advanced point dipole polarizable embeddings
| Autor: | Louis Lagardère, Giovanni Scalmani, Filippo Lipparini, Benedetta Mennucci, Jean-Philip Piquemal, Michael J. Frisch, Daniele Loco, Gerardo Andrés Cisneros |
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| Přispěvatelé: | Laboratoire de chimie théorique (LCT), Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), 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), Institut des Sciences du Calcul et des Données (ISCD), Sorbonne Université (SU), University of North Texas (UNT), Gaussian, Inc., University of Pisa - Università di Pisa, Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), Biomedical Engineering [Austin], University of Texas at Austin [Austin], ANR-11-IDEX-0004,SUPER,Sorbonne Universités à Paris pour l'Enseignement et la Recherche(2011) |
| Rok vydání: | 2019 |
| Předmět: |
Physics
010405 organic chemistry Complex system General Chemistry Polarizable force field AMOEBA 010402 general chemistry QM/MM 01 natural sciences molecular dynamics Force field (chemistry) 0104 chemical sciences Born-Oppenheimer molecular dynamics quantum chemistry [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry Molecular dynamics Chemistry Classical mechanics Polarizability Embedding Density functional theory polarizable force fields Quantum |
| Zdroj: | Chemical Science Chemical Science, The Royal Society of Chemistry, 2019, ⟨10.1039/C9SC01745C⟩ |
| ISSN: | 2041-6520 2041-6539 |
| DOI: | 10.1039/C9SC01745C⟩ |
| Popis: | Hybrid DFT(Gaussian)/AMOEBA(Tinker/Tinker-HP) polarizable molecular dynamics including the QM/MM mutual polarization on large complex systems. Example of the thiazole orange dye buried in a DNA double helix, embedded in a sphere of water (16 500 atoms). In this work, we present a general route to hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Molecular Dynamics for complex systems using a polarizable embedding. We extend the capabilities of our hybrid framework, combining the Gaussian and Tinker/Tinker-HP packages in the context of the AMOEBA polarizable force field to treat large (bio)systems where the QM and the MM subsystems are covalently bound, adopting pseudopotentials at the boundaries between the two regions. We discuss in detail the implementation and demonstrate the global energy conservation of our QM/MM Born–Oppenheimer molecular dynamics approach using Density Functional Theory. Finally, the approach is assessed on the electronic absorption properties of a 16 500 atom complex encompassing an organic dye embedded in a DNA matrix in solution, extending the hybrid method to a time-dependent Density Functional Theory approach. The results obtained comparing different partitions between the quantum and the classical subsystems also suggest that large QM portions are not necessary if accurate polarizable force fields are used in a variational formulation of the embedding, properly including the QM/MM mutual polarization. |
| Databáze: | OpenAIRE |
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