1
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Ojha D, Henao A, Zysk F, Kühne TD. Nuclear quantum effects on the vibrational dynamics of the water-air interface. J Chem Phys 2024; 160:204114. [PMID: 38804494 DOI: 10.1063/5.0204071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/11/2024] [Indexed: 05/29/2024] Open
Abstract
We have applied path-integral molecular dynamics simulations to investigate the impact of nuclear quantum effects on the vibrational dynamics of water molecules at the water-air interface. The instantaneous fluctuations in the frequencies of the O-H stretch modes are calculated using the wavelet method of time series analysis, while the time scales of vibrational spectral diffusion are determined from frequency-time correlation functions and joint probability distributions. We find that the inclusion of nuclear quantum effects leads not only to a redshift in the vibrational frequency distribution by about 120 cm-1 for both the bulk and interfacial water molecules but also to an acceleration of the vibrational dynamics at the water-air interface by as much as 35%. In addition, a blueshift of about 45 cm-1 is seen in the vibrational frequency distribution of interfacial water molecules compared to that of the bulk. Furthermore, the dynamics of water molecules beyond the topmost molecular layer was found to be rather similar to that of bulk water.
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Affiliation(s)
- Deepak Ojha
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Department of Chemistry, University of Paderborn, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Andrés Henao
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Department of Chemistry, University of Paderborn, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Frederik Zysk
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Department of Chemistry, University of Paderborn, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Thomas D Kühne
- Center for Advanced Systems Understanding (CASUS), Untermarkt 20, D-02826 Görlitz, Germany, Helmholtz Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, D-01328 Dresden, Germany, and TU Dresden, Institute of Artificial Intelligence, Chair of Computational System Sciences, Nöthnitzer Straße 46, D-01187 Dresden, Germany
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2
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Wickramasinghe S, Hoehn A, Wetthasinghe ST, Lin H, Wang Q, Jakowski J, Rassolov V, Tang C, Garashchuk S. Theoretical Examination of the Hydroxide Transport in Cobaltocenium-Containing Polyelectrolytes. J Phys Chem B 2023; 127:10129-10141. [PMID: 37972315 DOI: 10.1021/acs.jpcb.3c04118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Polymers incorporating cobaltocenium groups have received attention as promising components of anion-exchange membranes (AEMs), exhibiting a good balance of chemical stability and high ionic conductivity. In this work, we analyze the hydroxide diffusion in the presence of cobaltocenium cations in an aqueous environment based on the molecular dynamics of model systems confined in one dimension to mimic the AEM channels. In order to describe the proton hopping mechanism, the forces are obtained from the electronic structure computed at the density-functional tight-binding level. We find that the hydroxide diffusion depends on the channel size, modulation of the electrostatic interactions by the solvation shell, and its rearrangement ability. Hydroxide diffusion proceeds via both the vehicular and structural diffusion mechanisms with the latter playing a larger role at low diffusion coefficients. The highest diffusion coefficient is observed under moderate water densities (around half the density of liquid water) when there are enough water molecules to form the solvation shell, reducing the electrostatic interaction between ions, yet there is enough space for the water rearrangements during the proton hopping. The effects of cobaltocenium separation, orientation, chemical modifications, and the role of nuclear quantum effects are also discussed.
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Affiliation(s)
- Sachith Wickramasinghe
- Department of Chemistry & Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Alexandria Hoehn
- Department of Chemistry & Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Shehani T Wetthasinghe
- Department of Chemistry & Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Huina Lin
- Department of Chemistry & Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Qi Wang
- Department of Mathematics, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Jacek Jakowski
- Center for Nanophase Materials Science, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Vitaly Rassolov
- Department of Chemistry & Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Chuanbing Tang
- Department of Chemistry & Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Sophya Garashchuk
- Department of Chemistry & Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
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3
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Cinq N, Simon A, Louisnard F, Cuny J. Accurate SCC-DFTB Parametrization of Liquid Water with Improved Atomic Charges and Iterative Boltzmann Inversion. J Phys Chem B 2023; 127:7590-7601. [PMID: 37603798 DOI: 10.1021/acs.jpcb.3c03479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
This work presents improvements of the description of liquid water within the self-consistent-charge density-functional based tight-binding scheme combining the use of Weighted Mulliken (WMull) charges and optimized O-H repulsive potential through the iterative Boltzmann inversion (IBI) process. The quality of the newly developed models is validated considering pair radial distribution functions (RDFs), as well as other structural, energetic, thermodynamic, and dynamic properties. The use of WMull charges certainly improves the agreement with experimental data, however leading to over-structured RDFs at short distance, that can be further improved by considering an optimized O-H repulsive potential obtained by the IBI process. Three different schemes were used to optimize this potential: (i) optimization including short O-H distances. This led to accurate RDFs as well as improved self-diffusion coefficient and heat of vaporization, while the proton transfer energy barrier is severely deteriorated; (ii) optimization starting at long distance. The proton transfer energy barrier is recovered while the heat of vaporization is deteriorated and the O-H RDF is less accurate at short distance; (iii) optimization within the path-integral molecular dynamics scheme which allows us to exclude nuclear quantum effects from the repulsive potential. The latter potential, in conjunction with the WMull improved atomic charges, provides similar results as (i) for structural, dynamic, and thermodynamic properties while recovering a large part of the proton transfer energy barrier. It therefore offers a good compromise to study both dynamic properties and chemistry within liquid water at a quantum chemical level.
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Affiliation(s)
- Nicolas Cinq
- Laboratoire de Chimie et Physique Quantiques (LCPQ), FeRMI Institute, Université de Toulouse [UT3] and CNRS, Toulouse F-31062, France
| | - Aude Simon
- Laboratoire de Chimie et Physique Quantiques (LCPQ), FeRMI Institute, Université de Toulouse [UT3] and CNRS, Toulouse F-31062, France
| | - Fernand Louisnard
- Laboratoire de Chimie et Physique Quantiques (LCPQ), FeRMI Institute, Université de Toulouse [UT3] and CNRS, Toulouse F-31062, France
| | - Jérôme Cuny
- Laboratoire de Chimie et Physique Quantiques (LCPQ), FeRMI Institute, Université de Toulouse [UT3] and CNRS, Toulouse F-31062, France
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4
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Panagiotopoulos AZ, Yue S. Dynamics of Aqueous Electrolyte Solutions: Challenges for Simulations. J Phys Chem B 2023; 127:430-437. [PMID: 36607836 DOI: 10.1021/acs.jpcb.2c07477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
This Perspective article focuses on recent simulation work on the dynamics of aqueous electrolytes. It is well-established that full-charge, nonpolarizable models for water and ions generally predict solution dynamics that are too slow in comparison to experiments. Models with reduced (scaled) charges do better for solution diffusivities and viscosities but encounter issues describing other dynamic phenomena such as nucleation rates of crystals from solution. Polarizable models show promise, especially when appropriately parametrized, but may still miss important physical effects such as charge transfer. First-principles calculations are starting to emerge for these properties that are in principle able to capture polarization, charge transfer, and chemical transformations in solution. While direct ab initio simulations are still too slow for simulations of large systems over long time scales, machine-learning models trained on appropriate first-principles data show significant promise for accurate and transferable modeling of electrolyte solution dynamics.
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Affiliation(s)
| | - Shuwen Yue
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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5
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Liu J, He X. Ab initio molecular dynamics simulation of liquid water with fragment-based quantum mechanical approach under periodic boundary conditions. CHINESE J CHEM PHYS 2021. [DOI: 10.1063/1674-0068/cjcp2110183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- New York University-East China Normal University Center for Computational Chemistry at New York University Shanghai, Shanghai 200062, China
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6
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Bakó I, Madarász Á, Pusztai L. Nuclear quantum effects: Their relevance in neutron diffraction studies of liquid water. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.115192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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7
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Ojha D, Kühne TD. Hydrogen bond dynamics of interfacial water molecules revealed from two-dimensional vibrational sum-frequency generation spectroscopy. Sci Rep 2021; 11:2456. [PMID: 33510246 PMCID: PMC7844302 DOI: 10.1038/s41598-021-81635-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 01/06/2021] [Indexed: 11/17/2022] Open
Abstract
Vibrational sum-frequency generation (vSFG) spectroscopy allows the study of the structure and dynamics of interfacial systems. In the present work, we provide a simple recipe, based on a narrowband IR pump and broadband vSFG probe technique, to computationally obtain the two-dimensional vSFG spectrum of water molecules at the air-water interface. Using this technique, to study the time-dependent spectral evolution of hydrogen-bonded and free water molecules, we demonstrate that at the interface, the vibrational spectral dynamics of the free OH bond is faster than that of the bonded OH mode.
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Affiliation(s)
- Deepak Ojha
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Thomas D Kühne
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany.
- Paderborn Center for Parallel Computing and Institute for Lightweight Design, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany.
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8
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Yao Y, Kanai Y. Temperature dependence of nuclear quantum effects on liquid water via artificial neural network model based on SCAN meta-GGA functional. J Chem Phys 2020; 153:044114. [DOI: 10.1063/5.0012815] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yi Yao
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
| | - Yosuke Kanai
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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9
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Berta D, Ferenc D, Bakó I, Madarász Á. Nuclear Quantum Effects from the Analysis of Smoothed Trajectories: Pilot Study for Water. J Chem Theory Comput 2020; 16:3316-3334. [PMID: 32268067 PMCID: PMC7304866 DOI: 10.1021/acs.jctc.9b00703] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Nuclear quantum effects
have significant contributions to thermodynamic
quantities and structural properties; furthermore, very expensive
methods are necessary for their accurate computation. In most calculations,
these effects, for instance, zero-point energies, are simply neglected
or only taken into account within the quantum harmonic oscillator
approximation. Herein, we present a new method, Generalized Smoothed
Trajectory Analysis, to determine nuclear quantum effects from molecular
dynamics simulations. The broad applicability is demonstrated with
the examples of a harmonic oscillator and different states of water.
Ab initio molecular dynamics simulations have been performed for ideal
gas up to the temperature of 5000 K. Classical molecular dynamics
have been carried out for hexagonal ice, liquid water, and vapor at
atmospheric pressure. With respect to the experimental heat capacity,
our method outperforms previous calculations in the literature in
a wide temperature range at lower computational cost than other alternatives.
Dynamic and structural nuclear quantum effects of water are also discussed.
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Affiliation(s)
- Dénes Berta
- Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary.,Department of Chemistry, Kings College London, 7 Trinity Street, SE1 1DB London, United Kingdom
| | - Dávid Ferenc
- Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary
| | - Imre Bakó
- Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary
| | - Ádám Madarász
- Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary
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10
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Tsimpanogiannis IN, Jamali SH, Economou IG, Vlugt TJH, Moultos OA. On the validity of the Stokes–Einstein relation for various water force fields. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1702729] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Ioannis N. Tsimpanogiannis
- Chemical Process & Energy Resources Institute (CPERI), Centre for Research & Technology Hellas (CERTH) Thermi-Thessaloniki, Greece
| | - Seyed Hossein Jamali
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
| | | | - Thijs J. H. Vlugt
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
| | - Othonas A. Moultos
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
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11
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Clark T, Heske J, Kühne TD. Opposing Electronic and Nuclear Quantum Effects on Hydrogen Bonds in H 2 O and D 2 O. Chemphyschem 2019; 20:2461-2465. [PMID: 31449714 PMCID: PMC6790677 DOI: 10.1002/cphc.201900839] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Indexed: 11/09/2022]
Abstract
The effect of extending the O-H bond length(s) in water on the hydrogen-bonding strength has been investigated using static ab initio molecular orbital calculations. The "polar flattening" effect that causes a slight σ-hole to form on hydrogen atoms is strengthened when the bond is stretched, so that the σ-hole becomes more positive and hydrogen bonding stronger. In opposition to this electronic effect, path-integral ab initio molecular-dynamics simulations show that the nuclear quantum effect weakens the hydrogen bond in the water dimer. Thus, static electronic effects strengthen the hydrogen bond in H2 O relative to D2 O, whereas nuclear quantum effects weaken it. These quantum fluctuations are stronger for the water dimer than in bulk water.
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Affiliation(s)
- Timothy Clark
- Computer-Chemie-Centrum, Department Chemie und PharmazieFriedrich-Alexander-Universität Erlangen-NürnbergNägelsbachstr. 2591052ErlangenGermany
| | - Julian Heske
- Chair of Theoretical Chemistry, Dynamics of Condensed Matter, Department of ChemistryUniversity of PaderbornWarburger Str. 10033098PaderbornGermany
| | - Thomas D. Kühne
- Chair of Theoretical Chemistry, Dynamics of Condensed Matter, Department of ChemistryUniversity of PaderbornWarburger Str. 10033098PaderbornGermany
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12
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Kaliannan NK, Henao Aristizabal A, Wiebeler H, Zysk F, Ohto T, Nagata Y, Kühne TD. Impact of intermolecular vibrational coupling effects on the sum-frequency generation spectra of the water/air interface. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1620358] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Naveen Kumar Kaliannan
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, University of Paderborn, Paderborn, Germany
| | - Andres Henao Aristizabal
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, University of Paderborn, Paderborn, Germany
| | - Hendrik Wiebeler
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, University of Paderborn, Paderborn, Germany
| | - Frederik Zysk
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, University of Paderborn, Paderborn, Germany
| | - Tatsuhiko Ohto
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan
| | - Yuki Nagata
- Max-Planck Institute for Polymer Research, Mainz, Germany
| | - Thomas D. Kühne
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, University of Paderborn, Paderborn, Germany
- Paderborn Center for Parallel Computing and Institute for Lightweight Design, University of Paderborn, Paderborn, Germany
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13
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Cheng B, Engel EA, Behler J, Dellago C, Ceriotti M. Ab initio thermodynamics of liquid and solid water. Proc Natl Acad Sci U S A 2019; 116:1110-1115. [PMID: 30610171 PMCID: PMC6347673 DOI: 10.1073/pnas.1815117116] [Citation(s) in RCA: 172] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Thermodynamic properties of liquid water as well as hexagonal (Ih) and cubic (Ic) ice are predicted based on density functional theory at the hybrid-functional level, rigorously taking into account quantum nuclear motion, anharmonic fluctuations, and proton disorder. This is made possible by combining advanced free-energy methods and state-of-the-art machine-learning techniques. The ab initio description leads to structural properties in excellent agreement with experiments and reliable estimates of the melting points of light and heavy water. We observe that nuclear-quantum effects contribute a crucial [Formula: see text] to the stability of ice Ih, making it more stable than ice Ic. Our computational approach is general and transferable, providing a comprehensive framework for quantitative predictions of ab initio thermodynamic properties using machine-learning potentials as an intermediate step.
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Affiliation(s)
- Bingqing Cheng
- Laboratory of Computational Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland;
| | - Edgar A Engel
- Laboratory of Computational Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Jörg Behler
- Universität Göttingen, Institut für Physikalische Chemie, Theoretische Chemie, 37077 Göttingen, Germany
- International Center for Advanced Studies of Energy Conversion, Universität Göttingen, 37073 Göttingen, Germany
| | | | - Michele Ceriotti
- Laboratory of Computational Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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14
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Elton DC, Fritz M, Fernández-Serra M. Using a monomer potential energy surface to perform approximate path integral molecular dynamics simulation of ab initio water at near-zero added cost. Phys Chem Chem Phys 2018; 21:409-417. [PMID: 30534683 DOI: 10.1039/c8cp06077k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
It is now established that nuclear quantum motion plays an important role in determining water's hydrogen bonding, structure, and dynamics. Such effects are important to include in density functional theory (DFT) based molecular dynamics simulation of water. The standard way of treating nuclear quantum effects, path integral molecular dynamics (PIMD), multiplies the number of energy/force calculations by the number of beads required. In this work we introduce a method whereby PIMD can be incorporated into a DFT simulation with little extra cost and little loss in accuracy. The method is based on the many body expansion of the energy and has the benefit of including a monomer level correction to the DFT energy. Our method calculates intramolecular forces using the highly accurate monomer potential energy surface developed by Partridge-Schwenke, which is cheap to evaluate. Intermolecular forces and energies are calculated with DFT only once per timestep using the centroid positions. We show how our method may be used in conjunction with a multiple time step algorithm for an additional speedup and how it relates to ring polymer contraction and other schemes that have been introduced recently to speed up PIMD simulations. We show that our method, which we call "monomer PIMD", correctly captures changes in the structure of water found in a full PIMD simulation but at much lower computational cost.
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Affiliation(s)
- Daniel C Elton
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA.
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15
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Lindsey RK, Fried LE, Goldman N. Application of the ChIMES Force Field to Nonreactive Molecular Systems: Water at Ambient Conditions. J Chem Theory Comput 2018; 15:436-447. [DOI: 10.1021/acs.jctc.8b00831] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rebecca K. Lindsey
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Laurence E. Fried
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Nir Goldman
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
- Department of Chemical Engineering, University of California, Davis, California 95616, United States
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16
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Tsimpanogiannis IN, Moultos OA, Franco LFM, Spera MBDM, Erdős M, Economou IG. Self-diffusion coefficient of bulk and confined water: a critical review of classical molecular simulation studies. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1511903] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Ioannis N. Tsimpanogiannis
- Environmental Research Laboratory, National Center for Scientific Research “Demokritos”, Aghia Paraskevi Attikis, Greece
- Institute of Nanoscience and Nanotechnology, National Center for Scientific Research “Demokritos”, Aghia Paraskevi Attikis, Greece
| | - Othonas A. Moultos
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
| | - Luís F. M. Franco
- School of Chemical Engineering, University of Campinas, Campinas, Brazil
| | | | - Máté Erdős
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
| | - Ioannis G. Economou
- Institute of Nanoscience and Nanotechnology, National Center for Scientific Research “Demokritos”, Aghia Paraskevi Attikis, Greece
- Chemical Engineering Program, Texas A&M University at Qatar, Doha, Qatar
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17
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Abstract
Ab initio molecular dynamics is an irreplaceable technique for the realistic simulation of complex molecular systems and processes from first principles. This paper proposes a comprehensive and self-contained review of ab initio molecular dynamics from a computational perspective and from first principles. Quantum mechanics is presented from a molecular dynamics perspective. Various approximations and formulations are proposed, including the Ehrenfest, Born–Oppenheimer, and Hartree–Fock molecular dynamics. Subsequently, the Kohn–Sham formulation of molecular dynamics is introduced as well as the afferent concept of density functional. As a result, Car–Parrinello molecular dynamics is discussed, together with its extension to isothermal and isobaric processes. Car–Parrinello molecular dynamics is then reformulated in terms of path integrals. Finally, some implementation issues are analysed, namely, the pseudopotential, the orbital functional basis, and hybrid molecular dynamics.
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18
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Robertson C, Habershon S. Harmonic-phase path-integral approximation of thermal quantum correlation functions. J Chem Phys 2018; 148:102316. [PMID: 29544325 DOI: 10.1063/1.5002189] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present an approximation to the thermal symmetric form of the quantum time-correlation function in the standard position path-integral representation. By transforming to a sum-and-difference position representation and then Taylor-expanding the potential energy surface of the system to second order, the resulting expression provides a harmonic weighting function that approximately recovers the contribution of the phase to the time-correlation function. This method is readily implemented in a Monte Carlo sampling scheme and provides exact results for harmonic potentials (for both linear and non-linear operators) and near-quantitative results for anharmonic systems for low temperatures and times that are likely to be relevant to condensed phase experiments. This article focuses on one-dimensional examples to provide insights into convergence and sampling properties, and we also discuss how this approximation method may be extended to many-dimensional systems.
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Affiliation(s)
- Christopher Robertson
- Department of Chemistry and Centre for Scientific Computing, University Of Warwick, Coventry CV4 7AL, United Kingdom
| | - Scott Habershon
- Department of Chemistry and Centre for Scientific Computing, University Of Warwick, Coventry CV4 7AL, United Kingdom
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19
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Ojha D, Henao A, Kühne TD. Nuclear quantum effects on the vibrational dynamics of liquid water. J Chem Phys 2018; 148:102328. [PMID: 29544291 DOI: 10.1063/1.5005500] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Based on quantum-mechanical path-integral molecular dynamics simulations, the impact of nuclear quantum effects on the vibrational and hydrogen bond dynamics in liquid water is investigated. The instantaneous fluctuations in the frequencies of the O-H stretch modes are calculated using the wavelet method of time-series analysis, while the time scales of the vibrational spectral diffusion are determined from frequency-time correlation functions, joint probability distributions, and the slope of three-pulse photon echo. We find that the inclusion of nuclear quantum effects leads not only to a redshift of the vibrational frequency distribution by around 130 cm-1 but also to an acceleration of the vibrational dynamics by as much as 30%. In addition, quantum fluctuations also entail a significantly faster decay of correlation in the initial diffusive regime, which is in agreement with recent vibrational echo experiments.
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Affiliation(s)
- Deepak Ojha
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Department of Chemistry, University of Paderborn, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Andrés Henao
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Department of Chemistry, University of Paderborn, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Thomas D Kühne
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Department of Chemistry, University of Paderborn, Warburger Str. 100, D-33098 Paderborn, Germany
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20
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Affiliation(s)
- Xinzijian Liu
- Beijing National Laboratory For Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Jian Liu
- Beijing National Laboratory For Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
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21
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Buxton SJ, Habershon S. Accelerated path-integral simulations using ring-polymer interpolation. J Chem Phys 2017; 147:224107. [DOI: 10.1063/1.5006465] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Samuel J. Buxton
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Scott Habershon
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, United Kingdom
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22
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Kondratyuk ND, Norman GE, Stegailov VV. Self-consistent molecular dynamics calculation of diffusion in higher n-alkanes. J Chem Phys 2016; 145:204504. [PMID: 27908129 DOI: 10.1063/1.4967873] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Diffusion is one of the key subjects of molecular modeling and simulation studies. However, there is an unresolved lack of consistency between Einstein-Smoluchowski (E-S) and Green-Kubo (G-K) methods for diffusion coefficient calculations in systems of complex molecules. In this paper, we analyze this problem for the case of liquid n-triacontane. The non-conventional long-time tails of the velocity autocorrelation function (VACF) are found for this system. Temperature dependence of the VACF tail decay exponent is defined. The proper inclusion of the long-time tail contributions to the diffusion coefficient calculation results in the consistency between G-K and E-S methods. Having considered the major factors influencing the precision of the diffusion rate calculations in comparison with experimental data (system size effects and force field parameters), we point to hydrogen nuclear quantum effects as, presumably, the last obstacle to fully consistent n-alkane description.
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Affiliation(s)
- Nikolay D Kondratyuk
- Joint Institute for High Temperatures of the Russian Academy of Sciences, Moscow 125412, Russia
| | - Genri E Norman
- Joint Institute for High Temperatures of the Russian Academy of Sciences, Moscow 125412, Russia
| | - Vladimir V Stegailov
- Joint Institute for High Temperatures of the Russian Academy of Sciences, Moscow 125412, Russia
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23
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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: 1.1] [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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24
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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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25
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Nagata Y, Ohto T, Bonn M, Kühne TD. Surface tension of ab initio liquid water at the water-air interface. J Chem Phys 2016; 144:204705. [DOI: 10.1063/1.4951710] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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26
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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: 1.1] [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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27
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Perakis F, De Marco L, Shalit A, Tang F, Kann ZR, Kühne TD, Torre R, Bonn M, Nagata Y. Vibrational Spectroscopy and Dynamics of Water. Chem Rev 2016; 116:7590-607. [DOI: 10.1021/acs.chemrev.5b00640] [Citation(s) in RCA: 225] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Fivos Perakis
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Luigi De Marco
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Department of Chemistry and James Franck Institute, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Andrey Shalit
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Fujie Tang
- International Center for Quantum Materials, Peking University, 5 Yiheyuan Road, Haidian, Beijing 100871, China
| | - Zachary R. Kann
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States,
| | - Thomas D. Kühne
- Department of Chemistry, University of Paderborn, Warburger Strasse 100, D-33098 Paderborn, Germany
| | - Renato Torre
- European Lab for Nonlinear Spectroscopy and Dipartimento di Fisica e Astronomia, Università di Firenze, Via Nello Carrara 1, Sesto Fiorentino (Firenze) I-50019, Italy
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Yuki Nagata
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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28
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John C, Spura T, Habershon S, Kühne TD. Quantum ring-polymer contraction method: Including nuclear quantum effects at no additional computational cost in comparison to ab initio molecular dynamics. Phys Rev E 2016; 93:043305. [PMID: 27176426 DOI: 10.1103/physreve.93.043305] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Indexed: 06/05/2023]
Abstract
We present a simple and accurate computational method which facilitates ab initio path-integral molecular dynamics simulations, where the quantum-mechanical nature of the nuclei is explicitly taken into account, at essentially no additional computational cost in comparison to the corresponding calculation using classical nuclei. The predictive power of the proposed quantum ring-polymer contraction method is demonstrated by computing various static and dynamic properties of liquid water at ambient conditions using density functional theory. This development will enable routine inclusion of nuclear quantum effects in ab initio molecular dynamics simulations of condensed-phase systems.
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Affiliation(s)
- Christopher John
- Dynamics of Condensed Matter, Department of Chemistry, University of Paderborn, Warburger Strasse 100, D-33098 Paderborn, Germany
| | - Thomas Spura
- Dynamics of Condensed Matter, Department of Chemistry, University of Paderborn, Warburger Strasse 100, D-33098 Paderborn, Germany
| | - Scott Habershon
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Thomas D Kühne
- Dynamics of Condensed Matter, Department of Chemistry, University of Paderborn, Warburger Strasse 100, D-33098 Paderborn, Germany and Paderborn Center for Parallel Computing and Institute for Lightweight Design, Department of Chemistry, University of Paderborn, Warburger Strasse 100, D-33098 Paderborn, Germany
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29
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30
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Kessler J, Elgabarty H, Spura T, Karhan K, Partovi-Azar P, Hassanali AA, Kühne TD. Structure and Dynamics of the Instantaneous Water/Vapor Interface Revisited by Path-Integral and Ab Initio Molecular Dynamics Simulations. J Phys Chem B 2015; 119:10079-86. [DOI: 10.1021/acs.jpcb.5b04185] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jan Kessler
- Institute
of Physical Chemistry and Center of Computational Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 9, D-55128 Mainz, Germany
| | - Hossam Elgabarty
- Institute
of Physical Chemistry and Center of Computational Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 9, D-55128 Mainz, Germany
| | - Thomas Spura
- Dynamics
of Condensed Matter, Department of Chemistry, University of Paderborn, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Kristof Karhan
- Dynamics
of Condensed Matter, Department of Chemistry, University of Paderborn, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Pouya Partovi-Azar
- Dynamics
of Condensed Matter, Department of Chemistry, University of Paderborn, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Ali A. Hassanali
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, I-34151 Trieste, Italy
| | - Thomas D. Kühne
- Dynamics
of Condensed Matter, Department of Chemistry, University of Paderborn, Warburger Str. 100, D-33098 Paderborn, Germany
- Paderborn Center for Parallel Computing and Institute for Lightweight Design with Hybrid Systems, Warburger Str. 100, D-33098 Paderborn, Germany
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