51
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Willow SY. Path integral molecular dynamics at zero thermal temperature. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.02.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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52
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Katouda M, Nakajima T. MPI/OpenMP hybrid parallel algorithm for resolution of identity second-order Møller-Plesset perturbation calculation of analytical energy gradient for massively parallel multicore supercomputers. J Comput Chem 2017; 38:489-507. [PMID: 28133838 DOI: 10.1002/jcc.24701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 11/16/2016] [Accepted: 11/16/2016] [Indexed: 11/09/2022]
Abstract
A massively parallel algorithm of the analytical energy gradient calculations based the resolution of identity Møller-Plesset perturbation (RI-MP2) method from the restricted Hartree-Fock reference is presented for geometry optimization calculations and one-electron property calculations of large molecules. This algorithm is designed for massively parallel computation on multicore supercomputers applying the Message Passing Interface (MPI) and Open Multi-Processing (OpenMP) hybrid parallel programming model. In this algorithm, the two-dimensional hierarchical MP2 parallelization scheme is applied using a huge number of MPI processes (more than 1000 MPI processes) for acceleration of the computationally demanding O(N5 ) step such as calculations of occupied-occupied and virtual-virtual blocks of MP2 one-particle density matrix and MP2 two-particle density matrices. The new parallel algorithm performance is assessed using test calculations of several large molecules such as buckycatcher C60 @C60 H28 (144 atoms, 1820 atomic orbitals (AOs) for def2-SVP basis set, and 3888 AOs for def2-TZVP), nanographene dimer (C96 H24 )2 (240 atoms, 2928 AOs for def2-SVP, and 6432 AOs for cc-pVTZ), and trp-cage protein 1L2Y (304 atoms and 2906 AOs for def2-SVP) using up to 32,768 nodes and 262,144 central processing unit (CPU) cores of the K computer. The results of geometry optimization calculations of trp-cage protein 1L2Y at the RI-MP2/def2-SVP level using the 3072 nodes and 24,576 cores of the K computer are presented and discussed to assess the efficiency of the proposed algorithm. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Michio Katouda
- Computational Molecular Science Research Team, RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-minami-machi, Chuo-ku, Kobe, 650-0047, Japan
| | - Takahito Nakajima
- Computational Molecular Science Research Team, RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-minami-machi, Chuo-ku, Kobe, 650-0047, Japan
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53
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Watanabe HC, Kubillus M, Kubař T, Stach R, Mizaikoff B, Ishikita H. Cation solvation with quantum chemical effects modeled by a size-consistent multi-partitioning quantum mechanics/molecular mechanics method. Phys Chem Chem Phys 2017; 19:17985-17997. [DOI: 10.1039/c7cp01708a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the condensed phase, quantum chemical properties such as many-body effects and intermolecular charge fluctuations are critical determinants of the solvation structure and dynamics.
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Affiliation(s)
- Hiroshi C. Watanabe
- Research Center for Advanced Science and Technology
- The University of Tokyo
- Tokyo 153-8904
- Japan
- Department of Applied Chemistry
| | - Maximilian Kubillus
- Institute of Physical Chemistry and Center for Functional Nanostructures
- Karlsruhe Institute of Technology
- Karlsruhe 73131
- Germany
| | - Tomáš Kubař
- Institute of Physical Chemistry and Center for Functional Nanostructures
- Karlsruhe Institute of Technology
- Karlsruhe 73131
- Germany
| | - Robert Stach
- Institute of Analytical Bioanalytical Chemistry
- Ulm University
- Ulm 89081
- Germany
| | - Boris Mizaikoff
- Institute of Analytical Bioanalytical Chemistry
- Ulm University
- Ulm 89081
- Germany
| | - Hiroshi Ishikita
- Research Center for Advanced Science and Technology
- The University of Tokyo
- Tokyo 153-8904
- Japan
- Department of Applied Chemistry
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54
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Wilhelm J, Seewald P, Del Ben M, Hutter J. Large-Scale Cubic-Scaling Random Phase Approximation Correlation Energy Calculations Using a Gaussian Basis. J Chem Theory Comput 2016; 12:5851-5859. [DOI: 10.1021/acs.jctc.6b00840] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jan Wilhelm
- Department
of Chemistry and National Centre for Computational Design and Discovery
of Novel Materials (MARVEL), University of Zurich, 8057 Zurich, Switzerland
| | - Patrick Seewald
- Department
of Chemistry and National Centre for Computational Design and Discovery
of Novel Materials (MARVEL), University of Zurich, 8057 Zurich, Switzerland
| | - Mauro Del Ben
- Computational
Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jürg Hutter
- Department
of Chemistry and National Centre for Computational Design and Discovery
of Novel Materials (MARVEL), University of Zurich, 8057 Zurich, Switzerland
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55
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Chen W, Ambrosio F, Miceli G, Pasquarello A. Ab initio Electronic Structure of Liquid Water. PHYSICAL REVIEW LETTERS 2016; 117:186401. [PMID: 27835004 DOI: 10.1103/physrevlett.117.186401] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Indexed: 05/26/2023]
Abstract
Self-consistent GW calculations with efficient vertex corrections are employed to determine the electronic structure of liquid water. Nuclear quantum effects are taken into account through ab initio path-integral molecular dynamics simulations. We reveal a sizable band-gap renormalization of up to 0.7 eV due to hydrogen-bond quantum fluctuations. Our calculations lead to a band gap of 8.9 eV, in accord with the experimental estimate. We further resolve the ambiguities in the band-edge positions of liquid water. The valence-band maximum and the conduction-band minimum are found at -9.4 and -0.5 eV with respect to the vacuum level, respectively.
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Affiliation(s)
- Wei Chen
- Chaire de Simulation à l'Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Francesco Ambrosio
- Chaire de Simulation à l'Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Giacomo Miceli
- Chaire de Simulation à l'Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Alfredo Pasquarello
- Chaire de Simulation à l'Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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56
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Pham TA, Ogitsu T, Lau EY, Schwegler E. Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations. J Chem Phys 2016; 145:154501. [DOI: 10.1063/1.4964865] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Tuan Anh Pham
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94551, USA
| | - Tadashi Ogitsu
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94551, USA
| | - Edmond Y. Lau
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94551, USA
| | - Eric Schwegler
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94551, USA
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57
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Schreck S, Wernet P. Isotope effects in liquid water probed by transmission mode x-ray absorption spectroscopy at the oxygen K-edge. J Chem Phys 2016; 145:104502. [PMID: 27634266 DOI: 10.1063/1.4962237] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- Simon Schreck
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Philippe Wernet
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Str. 15, 12489 Berlin, Germany
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58
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Ziaei V, Bredow T. Red and blue shift of liquid water’s excited states: A many body perturbation study. J Chem Phys 2016. [DOI: 10.1063/1.4960561] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Vafa Ziaei
- Mulliken Center for Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Thomas Bredow
- Mulliken Center for Theoretical Chemistry, University of Bonn, Bonn, Germany
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59
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Miceli G, Hutter J, Pasquarello A. Liquid Water through Density-Functional Molecular Dynamics: Plane-Wave vs Atomic-Orbital Basis Sets. J Chem Theory Comput 2016; 12:3456-62. [DOI: 10.1021/acs.jctc.6b00271] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Giacomo Miceli
- Chaire
de Simulation à l’Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jürg Hutter
- Department
of Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Alfredo Pasquarello
- Chaire
de Simulation à l’Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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60
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Ambrosio F, Miceli G, Pasquarello A. Structural, Dynamical, and Electronic Properties of Liquid Water: A Hybrid Functional Study. J Phys Chem B 2016; 120:7456-70. [DOI: 10.1021/acs.jpcb.6b03876] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Francesco Ambrosio
- Chaire de Simulation à
l’Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Giacomo Miceli
- Chaire de Simulation à
l’Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Alfredo Pasquarello
- Chaire de Simulation à
l’Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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61
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Abstract
Whereas the interactions between water molecules are dominated by strongly directional hydrogen bonds (HBs), it was recently proposed that relatively weak, isotropic van der Waals (vdW) forces are essential for understanding the properties of liquid water and ice. This insight was derived from ab initio computer simulations, which provide an unbiased description of water at the atomic level and yield information on the underlying molecular forces. However, the high computational cost of such simulations prevents the systematic investigation of the influence of vdW forces on the thermodynamic anomalies of water. Here, we develop efficient ab initio-quality neural network potentials and use them to demonstrate that vdW interactions are crucial for the formation of water's density maximum and its negative volume of melting. Both phenomena can be explained by the flexibility of the HB network, which is the result of a delicate balance of weak vdW forces, causing, e.g., a pronounced expansion of the second solvation shell upon cooling that induces the density maximum.
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62
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Abstract
Hydrogen bond directionality in the water dimer is explained on the basis of symmetry-adapted intermolecular perturbation theory which directly separates the intermolecular interaction energy into four physically interpretable components: electrostatics, exchange-repulsion, dispersion, and induction. Analysis of these four main contributions to the binding energy allows a deeper understanding of the dominant factors ruling the mutual arrangement of the two monomers. A preference for the linear configuration is shown to be due to a subtle interplay of all four energy components. While the first-order terms, electrostatic and exchange-repulsion, almost perfectly cancel each other near the equilibrium geometry of the dimer, the importance of the second- and higher-order terms, induction and dispersion, becomes evident.
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Affiliation(s)
- Maxim Tafipolsky
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Campus Hubland Nord , Emil-Fischer-Strasse 42, D-97074 Würzburg, Germany
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63
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Tikhonov DS, Otlyotov AA, Rybkin VV. The effect of molecular dynamics sampling on the calculated observable gas-phase structures. Phys Chem Chem Phys 2016; 18:18237-45. [PMID: 27331660 DOI: 10.1039/c6cp02973f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In this study, we compare the performance of various ab initio molecular dynamics (MD) sampling methods for the calculation of the observable vibrationally-averaged gas-phase structures of benzene, naphthalene and anthracene molecules. Nose-Hoover (NH), canonical and quantum generalized-Langevin-equation (GLE) thermostats as well as the a posteriori quantum correction to the classical trajectories have been tested and compared to the accurate path-integral molecular dynamics (PIMD), static anharmonic vibrational calculations as well as to the experimental gas electron diffraction data. Classical sampling methods neglecting quantum effects (NH and canonical GLE thermostats) dramatically underestimate vibrational amplitudes for the bonded atom pairs, both C-H and C-C, the resulting radial distribution functions exhibit nonphysically narrow peaks. This deficiency is almost completely removed by taking the quantum effects on the nuclei into account. The quantum GLE thermostat and a posteriori correction to the canonical GLE and NH thermostatted trajectories capture most vibrational quantum effects and closely reproduce computationally expensive PIMD and experimental radial distribution functions. These methods are both computationally feasible and accurate and are therefore recommended for calculations of the observable gas-phase structures. A good performance of the quantum GLE thermostat for the gas-phase calculations is encouraging since its parameters have been originally fitted for the condensed-phase calculations. Very accurate molecular structures can be predicted by combining the equilibrium geometry obtained at a high level of electronic structure theory with vibrational amplitudes and corrections calculated using MD driven by a lower level of electronic structure theory.
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Affiliation(s)
- Denis S Tikhonov
- Universität Bielefeld, Lehrstuhl für Anorganische Chemie und Strukturchemie, Universitätsstrasse 25, 33615, Bielefeld, Germany.
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64
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Torres-Carbajal A, Castañeda-Priego R. Characterisation of the thermodynamics, structure and dynamics of a water-like model in 2- and 3-dimensions. Phys Chem Chem Phys 2016; 18:17335-40. [PMID: 27232761 DOI: 10.1039/c6cp01565d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The physical properties of colloidal particles suspended in an aqueous environment are well-understood when the latter is considered to be a continuum and a structureless medium. However, this approach fails to explain complex phenomena, for example, the critical Casimir forces among colloids and the colloidal self-assembly near critical solvents, and the inertial contribution of the solvent molecules on the diffusion of non-spherical Brownian particles. Therefore, the role played by the solvent on the physical properties of colloidal dispersions is of paramount relevance. Recently, there has been an interest in the (non-trivial) diffusion mechanisms of a nano-colloidal particle in a solvent that undergoes a vapour-liquid transition. Nonetheless, the models typically used to incorporate the solvent details do not capture quantitatively the thermodynamic properties of real substances. It is then important to study the Brownian motion of colloids in more realistic models. To reach such goal, one first has to characterise the thermodynamic states and the microscopic features of the solvent. Hence, in this contribution, we have investigated the coexistence densities of a core-softened potential in two- and three-dimensions, whose potential parameters are able to capture some anomalies of water. We show that in the two-dimensional case, the potential model exhibits, besides the normal vapour-liquid coexistence region, additional liquid-liquid coexistence densities. We particularly focus our attention to the structural properties and the dynamical behaviour of the solvent around the liquid-liquid critical point and assess the differences with the three-dimensional case.
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Affiliation(s)
- Alexis Torres-Carbajal
- División de Ciencias e Ingenierías, Campus León, Universidad de Guanajuato, Loma del Bosque 103, Lomas del Campestre, 37150 León, Guanajuato, México.
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65
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Köster A, Spura T, Rutkai G, Kessler J, Wiebeler H, Vrabec J, Kühne TD. Assessing the accuracy of improved force-matched water models derived fromAb initiomolecular dynamics simulations. J Comput Chem 2016; 37:1828-38. [DOI: 10.1002/jcc.24398] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 04/08/2016] [Accepted: 04/14/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Andreas Köster
- Thermodynamics and Energy Technology; Department of Mechanical Engineering, University of Paderborn; Warburger Str. 100 Paderborn D-33098 Germany
| | - Thomas Spura
- Dynamics of Condensed Matter, Department of Chemistry; University of Paderborn; Warburger Str. 100 Paderborn D-33098 Germany
| | - Gábor Rutkai
- Thermodynamics and Energy Technology; Department of Mechanical Engineering, University of Paderborn; Warburger Str. 100 Paderborn D-33098 Germany
| | - Jan Kessler
- Dynamics of Condensed Matter, Department of Chemistry; University of Paderborn; Warburger Str. 100 Paderborn D-33098 Germany
| | - Hendrik Wiebeler
- Dynamics of Condensed Matter, Department of Chemistry; University of Paderborn; Warburger Str. 100 Paderborn D-33098 Germany
| | - Jadran Vrabec
- Thermodynamics and Energy Technology; Department of Mechanical Engineering, University of Paderborn; Warburger Str. 100 Paderborn D-33098 Germany
| | - Thomas D. Kühne
- Dynamics of Condensed Matter, Department of Chemistry; University of Paderborn; Warburger Str. 100 Paderborn D-33098 Germany
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66
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Gillan MJ, Alfè D, Michaelides A. Perspective: How good is DFT for water? J Chem Phys 2016; 144:130901. [DOI: 10.1063/1.4944633] [Citation(s) in RCA: 478] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Michael J. Gillan
- London Centre for Nanotechnology, Gordon St., London WC1H 0AH, United Kingdom
- Thomas Young Centre, University College London, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Dario Alfè
- London Centre for Nanotechnology, Gordon St., London WC1H 0AH, United Kingdom
- Thomas Young Centre, University College London, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
- Department of Earth Sciences, University College London, London WC1E 6BT, United Kingdom
| | - Angelos Michaelides
- London Centre for Nanotechnology, Gordon St., London WC1H 0AH, United Kingdom
- Thomas Young Centre, University College London, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
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67
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Ceriotti M, Fang W, Kusalik PG, McKenzie RH, Michaelides A, Morales MA, Markland TE. Nuclear Quantum Effects in Water and Aqueous Systems: Experiment, Theory, and Current Challenges. Chem Rev 2016; 116:7529-50. [DOI: 10.1021/acs.chemrev.5b00674] [Citation(s) in RCA: 339] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Michele Ceriotti
- Laboratory
of Computational Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Wei Fang
- Thomas
Young Centre, London Centre for Nanotechnology and Department of Physics
and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Peter G. Kusalik
- Department
of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Ross H. McKenzie
- School
of Mathematics and Physics, University of Queensland, Brisbane, 4072 Queensland Australia
| | - Angelos Michaelides
- Thomas
Young Centre, London Centre for Nanotechnology and Department of Physics
and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Miguel A. Morales
- Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Thomas E. Markland
- Department
of Chemistry, Stanford University, 333 Campus Drive, Stanford, California 94305, United States
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68
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Rybkin VV, VandeVondele J. Spin-Unrestricted Second-Order Møller–Plesset (MP2) Forces for the Condensed Phase: From Molecular Radicals to F-Centers in Solids. J Chem Theory Comput 2016; 12:2214-23. [DOI: 10.1021/acs.jctc.6b00015] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vladimir V. Rybkin
- Nanoscale Simulations, Department
of Materials, ETH Zürich, Wolfgang-Pauli-Str. 27, CH-8093 Zürich, Switzerland
| | - Joost VandeVondele
- Nanoscale Simulations, Department
of Materials, ETH Zürich, Wolfgang-Pauli-Str. 27, CH-8093 Zürich, Switzerland
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69
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Cheng J, VandeVondele J. Calculation of Electrochemical Energy Levels in Water Using the Random Phase Approximation and a Double Hybrid Functional. PHYSICAL REVIEW LETTERS 2016; 116:086402. [PMID: 26967430 DOI: 10.1103/physrevlett.116.086402] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Indexed: 06/05/2023]
Abstract
Understanding charge transfer at electrochemical interfaces requires consistent treatment of electronic energy levels in solids and in water at the same level of the electronic structure theory. Using density-functional-theory-based molecular dynamics and thermodynamic integration, the free energy levels of six redox couples in water are calculated at the level of the random phase approximation and a double hybrid density functional. The redox levels, together with the water band positions, are aligned against a computational standard hydrogen electrode, allowing for critical analysis of errors compared to the experiment. It is encouraging that both methods offer a good description of the electronic structures of the solutes and water, showing promise for a full treatment of electrochemical interfaces.
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Affiliation(s)
- Jun Cheng
- Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China and Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, United Kingdom
| | - Joost VandeVondele
- Department of Materials, ETH Zurich, Wolfgang-Pauli-Strasse 27, CH-8093 Zurich, Switzerland
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70
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Willow SY, Zeng XC, Xantheas SS, Kim KS, Hirata S. Why Is MP2-Water "Cooler" and "Denser" than DFT-Water? J Phys Chem Lett 2016; 7:680-684. [PMID: 26821830 DOI: 10.1021/acs.jpclett.5b02430] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Density functional theory (DFT) with a dispersionless generalized gradient approximation (GGA) needs much higher temperature and pressure than the ambient conditions to maintain water in the liquid phase at the correct (1 g/cm(3)) density during first-principles simulations. Conversely, ab initio second-order many-body perturbation (MP2) calculations of liquid water require lower temperature and pressure than DFT/GGA to keep water liquid. Here we present a unifying explanation of these trends derived from classical water simulations using a polarizable force field with different sets of parameters. We show that the different temperatures and pressures between DFT/GGA and MP2 at which the simulated water displays the experimentally observed liquid structure under the ambient conditions can be largely explained by their differences in polarizability and dispersion interaction, respectively. In DFT/GGA, the polarizability and thus the induced dipole moments and the hydrogen-bond strength are all overestimated. This hinders the rotational motion of molecules and requires a higher temperature for DFT-water to be liquid. MP2 gives a stronger dispersion interaction and thus shorter intermolecular distances than dispersionless DFT/GGA, which is why MP2-water is denser than DFT-water under the same external pressure.
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Affiliation(s)
- Soohaeng Yoo Willow
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Xiao Cheng Zeng
- Department of Chemistry, University of Nebraska at Lincoln , 536 Hamilton Hall, Lincoln, Nebraska 68588, United States
| | - Sotiris S Xantheas
- Physical Sciences Division, Pacific Northwest National Laboratory , 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352, United States
| | - Kwang S Kim
- Center for Superfunctional Materials, Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST) , Ulsan 689-798, Korea
| | - So Hirata
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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71
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Kapil V, VandeVondele J, Ceriotti M. Accurate molecular dynamics and nuclear quantum effects at low cost by multiple steps in real and imaginary time: Using density functional theory to accelerate wavefunction methods. J Chem Phys 2016; 144:054111. [DOI: 10.1063/1.4941091] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- V. Kapil
- Laboratory of Computational Science and Modelling, Institute of Materials, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - J. VandeVondele
- Department of Materials, ETH Zurich, Wolfgang-Pauli-Strasse 27, CH-8093 Zurich, Switzerland
| | - M. Ceriotti
- Laboratory of Computational Science and Modelling, Institute of Materials, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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72
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Marsalek O, Markland TE. Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory. J Chem Phys 2016; 144:054112. [DOI: 10.1063/1.4941093] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ondrej Marsalek
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Thomas E. Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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73
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Moors SLC, Brigou B, Hertsen D, Pinter B, Geerlings P, Van Speybroeck V, Catak S, De Proft F. Influence of Solvation and Dynamics on the Mechanism and Kinetics of Nucleophilic Aromatic Substitution Reactions in Liquid Ammonia. J Org Chem 2016; 81:1635-44. [PMID: 26800020 DOI: 10.1021/acs.joc.5b02794] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The role of the solvent and the influence of dynamics on the kinetics and mechanism of the SNAr reaction of several halonitrobenzenes in liquid ammonia, using both static calculations and dynamic ab initio molecular dynamics simulations, are investigated. A combination of metadynamics and committor analysis methods reveals how this reaction can change from a concerted, one-step mechanism in gas phase to a stepwise pathway, involving a metastable Meisenheimer complex, in liquid ammonia. This clearly establishes, among others, the important role of the solvent and highlights the fact that accurately treating solvation is of crucial importance to correctly unravel the reaction mechanism. It is indeed shown that H-bond formation of the reacting NH3 with the solvent drastically reduces the barrier of NH3 addition. The halide elimination step, however, is greatly facilitated by proton transfer from the reacting NH3 to the solvent. Furthermore, the free energy surface strongly depends on the halide substituent and the number of electron-withdrawing nitro substituents.
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Affiliation(s)
- Samuel L C Moors
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB) , Pleinlaan 2, 1050 Elsene, Brussels, Belgium
| | - Ben Brigou
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB) , Pleinlaan 2, 1050 Elsene, Brussels, Belgium
| | - Dietmar Hertsen
- Center for Molecular Modeling (CMM), Ghent University , Technologiepark 903, 9052 Zwijnaarde, Belgium
| | - Balazs Pinter
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB) , Pleinlaan 2, 1050 Elsene, Brussels, Belgium
| | - Paul Geerlings
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB) , Pleinlaan 2, 1050 Elsene, Brussels, Belgium
| | - Veronique Van Speybroeck
- Center for Molecular Modeling (CMM), Ghent University , Technologiepark 903, 9052 Zwijnaarde, Belgium
| | - Saron Catak
- Department of Chemistry, Bogazici University , Bebek 34342, Istanbul, Turkey
| | - Frank De Proft
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB) , Pleinlaan 2, 1050 Elsene, Brussels, Belgium
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74
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Natarajan SK, Behler J. Neural network molecular dynamics simulations of solid–liquid interfaces: water at low-index copper surfaces. Phys Chem Chem Phys 2016; 18:28704-28725. [DOI: 10.1039/c6cp05711j] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Molecular dynamics simulation of the water–copper interface have been carried out using high-dimensional neural network potential based on density functional theory.
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Affiliation(s)
| | - Jörg Behler
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- D-44780 Bochum
- Germany
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75
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Watanabe HC, Banno M, Sakurai M. An adaptive quantum mechanics/molecular mechanics method for the infrared spectrum of water: incorporation of the quantum effect between solute and solvent. Phys Chem Chem Phys 2016; 18:7318-33. [DOI: 10.1039/c5cp07136d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quantum effects in solute–solvent interactions, such as the many-body effect and the dipole-induced dipole, are known to be critical factors influencing the infrared spectra of species in the liquid phase.
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Affiliation(s)
- Hiroshi C. Watanabe
- Research Center for Advanced Science and Technology
- The University of Tokyo
- Meguro-ku
- Japan
| | - Misa Banno
- Center for Biological Resources and Informatics
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Minoru Sakurai
- Center for Biological Resources and Informatics
- Tokyo Institute of Technology
- Midori-ku
- Japan
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76
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Ambrosio F, Miceli G, Pasquarello A. Redox levels in aqueous solution: Effect of van der Waals interactions and hybrid functionals. J Chem Phys 2015; 143:244508. [DOI: 10.1063/1.4938189] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Francesco Ambrosio
- Chaire de Simulation à l’Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Giacomo Miceli
- Chaire de Simulation à l’Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Alfredo Pasquarello
- Chaire de Simulation à l’Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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77
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Ikeda T, Boero M. Role of van der Waals corrections in first principles simulations of alkali metal ions in aqueous solutions. J Chem Phys 2015; 143:194510. [DOI: 10.1063/1.4935932] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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