Grid-Based Projector Augmented Wave (GPAW) Implementation of Quantum Mechanics/Molecular Mechanics (QM/MM) Electrostatic Embedding and Application to a Solvated Diplatinum Complex

A. O. Dohn, E. O. Jónsson, G. Levi, J. J. Mortensen, O. Lopez-Acevedo, K. S. Thygesen, K. W. Jacobsen, J. Ulstrup, N. E. Henriksen, K. B. Møller, H. Jónsson

Resultado de la investigación: Contribución a una revistaArtículoInvestigaciónrevisión exhaustiva

7 Citas (Scopus)

Resumen

© 2017 American Chemical Society. A multiscale density functional theory-quantum mechanics/molecular mechanics (DFT-QM/MM) scheme is presented, based on an efficient electrostatic coupling between the electronic density obtained from a grid-based projector augmented wave (GPAW) implementation of density functional theory and a classical potential energy function. The scheme is implemented in a general fashion and can be used with various choices for the descriptions of the QM or MM regions. Tests on H2O clusters, ranging from dimer to decamer show that no systematic energy errors are introduced by the coupling that exceeds the differences in the QM and MM descriptions. Over 1 ns of liquid water, Born-Oppenheimer QM/MM molecular dynamics (MD) are sampled combining 10 parallel simulations, showing consistent liquid water structure over the QM/MM border. The method is applied in extensive parallel MD simulations of an aqueous solution of the diplatinum [Pt2(P2O5H2)4]4-complex (PtPOP), spanning a total time period of roughly half a nanosecond. An average Pt-Pt distance deviating only 0.01 Å from experimental results, and a ground-state Pt-Pt oscillation frequency deviating by <2% from experimental results were obtained. The simulations highlight a remarkable harmonicity of the Pt-Pt oscillation, while also showing clear signs of Pt-H hydrogen bonding and directional coordination of water molecules along the Pt-Pt axis of the complex.
Idioma originalInglés estadounidense
Páginas (desde-hasta)6010-6022
Número de páginas13
PublicaciónJournal of Chemical Theory and Computation
DOI
EstadoPublicada - 12 dic 2017

Huella dactilar

Molecular mechanics
Quantum theory
projectors
embedding
quantum mechanics
Electrostatics
grids
electrostatics
Density functional theory
Molecular dynamics
Water
Potential energy functions
water
molecular dynamics
density functional theory
oscillations
simulation
Liquids
liquids
borders

Citar esto

Dohn, A. O. ; Jónsson, E. O. ; Levi, G. ; Mortensen, J. J. ; Lopez-Acevedo, O. ; Thygesen, K. S. ; Jacobsen, K. W. ; Ulstrup, J. ; Henriksen, N. E. ; Møller, K. B. ; Jónsson, H. / Grid-Based Projector Augmented Wave (GPAW) Implementation of Quantum Mechanics/Molecular Mechanics (QM/MM) Electrostatic Embedding and Application to a Solvated Diplatinum Complex. En: Journal of Chemical Theory and Computation. 2017 ; pp. 6010-6022.
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title = "Grid-Based Projector Augmented Wave (GPAW) Implementation of Quantum Mechanics/Molecular Mechanics (QM/MM) Electrostatic Embedding and Application to a Solvated Diplatinum Complex",
abstract = "{\circledC} 2017 American Chemical Society. A multiscale density functional theory-quantum mechanics/molecular mechanics (DFT-QM/MM) scheme is presented, based on an efficient electrostatic coupling between the electronic density obtained from a grid-based projector augmented wave (GPAW) implementation of density functional theory and a classical potential energy function. The scheme is implemented in a general fashion and can be used with various choices for the descriptions of the QM or MM regions. Tests on H2O clusters, ranging from dimer to decamer show that no systematic energy errors are introduced by the coupling that exceeds the differences in the QM and MM descriptions. Over 1 ns of liquid water, Born-Oppenheimer QM/MM molecular dynamics (MD) are sampled combining 10 parallel simulations, showing consistent liquid water structure over the QM/MM border. The method is applied in extensive parallel MD simulations of an aqueous solution of the diplatinum [Pt2(P2O5H2)4]4-complex (PtPOP), spanning a total time period of roughly half a nanosecond. An average Pt-Pt distance deviating only 0.01 {\AA} from experimental results, and a ground-state Pt-Pt oscillation frequency deviating by <2{\%} from experimental results were obtained. The simulations highlight a remarkable harmonicity of the Pt-Pt oscillation, while also showing clear signs of Pt-H hydrogen bonding and directional coordination of water molecules along the Pt-Pt axis of the complex.",
author = "Dohn, {A. O.} and J{\'o}nsson, {E. O.} and G. Levi and Mortensen, {J. J.} and O. Lopez-Acevedo and Thygesen, {K. S.} and Jacobsen, {K. W.} and J. Ulstrup and Henriksen, {N. E.} and M{\o}ller, {K. B.} and H. J{\'o}nsson",
year = "2017",
month = "12",
day = "12",
doi = "10.1021/acs.jctc.7b00621",
language = "American English",
pages = "6010--6022",
journal = "Journal of Chemical Theory and Computation",
issn = "1549-9618",
publisher = "American Chemical Society",

}

Dohn, AO, Jónsson, EO, Levi, G, Mortensen, JJ, Lopez-Acevedo, O, Thygesen, KS, Jacobsen, KW, Ulstrup, J, Henriksen, NE, Møller, KB & Jónsson, H 2017, 'Grid-Based Projector Augmented Wave (GPAW) Implementation of Quantum Mechanics/Molecular Mechanics (QM/MM) Electrostatic Embedding and Application to a Solvated Diplatinum Complex', Journal of Chemical Theory and Computation, pp. 6010-6022. https://doi.org/10.1021/acs.jctc.7b00621

Grid-Based Projector Augmented Wave (GPAW) Implementation of Quantum Mechanics/Molecular Mechanics (QM/MM) Electrostatic Embedding and Application to a Solvated Diplatinum Complex. / Dohn, A. O.; Jónsson, E. O.; Levi, G.; Mortensen, J. J.; Lopez-Acevedo, O.; Thygesen, K. S.; Jacobsen, K. W.; Ulstrup, J.; Henriksen, N. E.; Møller, K. B.; Jónsson, H.

En: Journal of Chemical Theory and Computation, 12.12.2017, p. 6010-6022.

Resultado de la investigación: Contribución a una revistaArtículoInvestigaciónrevisión exhaustiva

TY - JOUR

T1 - Grid-Based Projector Augmented Wave (GPAW) Implementation of Quantum Mechanics/Molecular Mechanics (QM/MM) Electrostatic Embedding and Application to a Solvated Diplatinum Complex

AU - Dohn, A. O.

AU - Jónsson, E. O.

AU - Levi, G.

AU - Mortensen, J. J.

AU - Lopez-Acevedo, O.

AU - Thygesen, K. S.

AU - Jacobsen, K. W.

AU - Ulstrup, J.

AU - Henriksen, N. E.

AU - Møller, K. B.

AU - Jónsson, H.

PY - 2017/12/12

Y1 - 2017/12/12

N2 - © 2017 American Chemical Society. A multiscale density functional theory-quantum mechanics/molecular mechanics (DFT-QM/MM) scheme is presented, based on an efficient electrostatic coupling between the electronic density obtained from a grid-based projector augmented wave (GPAW) implementation of density functional theory and a classical potential energy function. The scheme is implemented in a general fashion and can be used with various choices for the descriptions of the QM or MM regions. Tests on H2O clusters, ranging from dimer to decamer show that no systematic energy errors are introduced by the coupling that exceeds the differences in the QM and MM descriptions. Over 1 ns of liquid water, Born-Oppenheimer QM/MM molecular dynamics (MD) are sampled combining 10 parallel simulations, showing consistent liquid water structure over the QM/MM border. The method is applied in extensive parallel MD simulations of an aqueous solution of the diplatinum [Pt2(P2O5H2)4]4-complex (PtPOP), spanning a total time period of roughly half a nanosecond. An average Pt-Pt distance deviating only 0.01 Å from experimental results, and a ground-state Pt-Pt oscillation frequency deviating by <2% from experimental results were obtained. The simulations highlight a remarkable harmonicity of the Pt-Pt oscillation, while also showing clear signs of Pt-H hydrogen bonding and directional coordination of water molecules along the Pt-Pt axis of the complex.

AB - © 2017 American Chemical Society. A multiscale density functional theory-quantum mechanics/molecular mechanics (DFT-QM/MM) scheme is presented, based on an efficient electrostatic coupling between the electronic density obtained from a grid-based projector augmented wave (GPAW) implementation of density functional theory and a classical potential energy function. The scheme is implemented in a general fashion and can be used with various choices for the descriptions of the QM or MM regions. Tests on H2O clusters, ranging from dimer to decamer show that no systematic energy errors are introduced by the coupling that exceeds the differences in the QM and MM descriptions. Over 1 ns of liquid water, Born-Oppenheimer QM/MM molecular dynamics (MD) are sampled combining 10 parallel simulations, showing consistent liquid water structure over the QM/MM border. The method is applied in extensive parallel MD simulations of an aqueous solution of the diplatinum [Pt2(P2O5H2)4]4-complex (PtPOP), spanning a total time period of roughly half a nanosecond. An average Pt-Pt distance deviating only 0.01 Å from experimental results, and a ground-state Pt-Pt oscillation frequency deviating by <2% from experimental results were obtained. The simulations highlight a remarkable harmonicity of the Pt-Pt oscillation, while also showing clear signs of Pt-H hydrogen bonding and directional coordination of water molecules along the Pt-Pt axis of the complex.

U2 - 10.1021/acs.jctc.7b00621

DO - 10.1021/acs.jctc.7b00621

M3 - Article

SP - 6010

EP - 6022

JO - Journal of Chemical Theory and Computation

JF - Journal of Chemical Theory and Computation

SN - 1549-9618

ER -