1
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Quoika PK, Zacharias M. Liquid-Vapor Coexistence and Spontaneous Evaporation at Atmospheric Pressure of Common Rigid Three-Point Water Models in Molecular Simulations. J Phys Chem B 2024; 128:2457-2468. [PMID: 38427971 PMCID: PMC10945489 DOI: 10.1021/acs.jpcb.3c08183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/03/2024]
Abstract
Molecular dynamics (MD) simulations are widely used to investigate molecular systems at atomic resolution including biomolecular structures, drug-receptor interactions, and novel materials. Frequently, MD simulations are performed in an aqueous solution with explicit models of water molecules. Commonly, such models are parameterized to reproduce the liquid phase of water under ambient conditions. However, often, simulations at significantly higher temperatures are also of interest. Hence, it is important to investigate the equilibrium of the liquid and vapor phases of molecular models of water at elevated temperatures. Here, we evaluate the behavior of 11 common rigid three-point water models over a wide range of temperatures. From liquid-vapor coexistence simulations, we estimated the critical points and studied the spontaneous evaporation of these water models. Moreover, we investigated the influence of the system size, choice of the pressure-coupling algorithm, and rate of heating on the process and compared them with the experimental data. We found that modern rigid three-point water models reproduce the critical point surprisingly well. Furthermore, we discovered that the critical temperature correlates with the quadrupole moment of the respective water model. This indicates that the spatial arrangement of the partial charges is important for reproducing the liquid-vapor phase transition. Our findings may guide the selection of water models for simulations conducted at high temperatures.
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Affiliation(s)
- Patrick K. Quoika
- Center for Functional Protein
Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, Garching 85748, Germany
| | - Martin Zacharias
- Center for Functional Protein
Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, Garching 85748, Germany
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2
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Ajide MT, English NJ. Nonequilibrium Ab Initio Molecular Dynamics Simulation of Water Splitting at Fe 2O 3-Hematite/Water Interfaces in an External Electric Field. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2023; 127:24088-24105. [PMID: 38148852 PMCID: PMC10749450 DOI: 10.1021/acs.jpcc.3c05119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 12/28/2023]
Abstract
In the exploration of the optimal material for achieving the photoelectrochemical dissociation of water into hydrogen, hematite (α-Fe2O3) emerges as a highly promising candidate for proof-of-concept demonstrations. Recent studies suggest that the concurrent application of external electric fields could enhance the photoelectrochemical (PEC) process. To delve into this, we conducted nonequilibrium ab initio molecular dynamics (NE-AIMD) simulations in this study, focusing on hematite-water interfaces at room temperature under progressively stronger electric fields. Our findings reveal intriguing evidence of water molecule adsorption and dissociation, as evidenced by an analysis of the structural properties of the hydrated layered surface of the hematite-water interface. Additionally, we scrutinized intermolecular structures using radial distribution functions (RDFs) to explore the interaction between the hematite slab and water. Notably, the presence of a Grotthuss hopping mechanism became apparent as the electric field strength increased. A comprehensive discussion based on intramolecular geometry highlighted aspects such as hydrogen-bond lengths, H-bond angles, average H-bond numbers, and the observed correlation existing among the hydrogen-bond strength, bond-dissociation energy, and H-bond lifetime. Furthermore, we assessed the impact of electric fields on the librational, bending, and stretching modes of hydrogen atoms in water by calculating the vibrational density of states (VDOS). This analysis revealed distinct field effects for the three characteristic band modes, both in the bulk region and at the hematite-water interface. We also evaluated the charge density of active elements at the aqueous hematite surface, delving into field-induced electronic charge-density variations through the Hirshfeld charge density analysis of atomic elements. Throughout this work, we drew clear distinctions between parallel and antiparallel field alignments at the hematite-water interface, aiming to elucidate crucial differences in local behavior for each surface direction of the hematite-water interface.
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Affiliation(s)
- Mary T. Ajide
- School of Chemical &
Bioprocess Engineering, University College
Dublin, Belfield, Dublin 4, Ireland
| | - Niall J. English
- School of Chemical &
Bioprocess Engineering, University College
Dublin, Belfield, Dublin 4, Ireland
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3
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Alwaleedy S, Kabara KB, Karale RR, Kamble S, Al-Hamdani S, Kumbharkhane AC, Sarode AV. Water dynamics on the structural properties of some NSAID's with leucine in the picosecond region using time domain spectroscopy. J Biomol Struct Dyn 2023:1-18. [PMID: 37897192 DOI: 10.1080/07391102.2023.2273987] [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: 07/10/2023] [Accepted: 10/14/2023] [Indexed: 10/29/2023]
Abstract
Concentration-dependent dielectric response for non-steroidal anti-inflammatory drugs (NSAIDs): Aceclofenac (ACF) and Diclofenac (DCF) in the aqueous leucine solution have been reported at different concentrations and temperatures (298.15 K to 283.15 K). The time domain reflectometry technique in the frequency region of 1 GHz to 30 GHz was used for the present study. Complex permittivity (ε*), static dielectric constant (ε), dielectric relaxation time (τ), dipole moment (μ) and Kirkwood correlation factor (g) have been calculated and discussed in terms of the molecular interaction of water and the used drugs. To give more insights into the structural dynamics of drug-induced amino acids, the study includes molar enthalpy of activation (ΔH), entropy of activation (ΔS), and free energy of activation (ΔF). The overall study concludes that the drug (DCF) having a potent inhibitor of cyclooxygenase found a higher static dielectric constant (ε0) than that of the drug (ACF) having more carbon (C), hydrogen (H), and oxygen (O) in the chain, which is more efficient in controlling pain.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Suad Alwaleedy
- School of Physical Sciences, Swami Ramanand Teerth Marathwada University, Nanded, MS, India
- Department of Physics, Taiz University, Yemen
| | - Komal B Kabara
- School of Physical Sciences, Swami Ramanand Teerth Marathwada University, Nanded, MS, India
| | - Ravikant R Karale
- School of Physical Sciences, Swami Ramanand Teerth Marathwada University, Nanded, MS, India
| | - Savita Kamble
- School of Physical Sciences, Swami Ramanand Teerth Marathwada University, Nanded, MS, India
| | - Saeed Al-Hamdani
- School of Physical Sciences, Swami Ramanand Teerth Marathwada University, Nanded, MS, India
| | - Ashok C Kumbharkhane
- School of Physical Sciences, Swami Ramanand Teerth Marathwada University, Nanded, MS, India
| | - Arvind V Sarode
- School of Physical Sciences, Swami Ramanand Teerth Marathwada University, Nanded, MS, India
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4
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Liu R, Chen M. Characterization of the Hydrogen-Bond Network in High-Pressure Water by Deep Potential Molecular Dynamics. J Chem Theory Comput 2023; 19:5602-5608. [PMID: 37535904 DOI: 10.1021/acs.jctc.3c00445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
The hydrogen-bond (H-bond) network of high-pressure water is investigated by neural-network-based molecular dynamics (MD) simulations with first-principles accuracy. The static structure factors (SSFs) of water at three densities, i.e., 1, 1.115, and 1.24 g/cm3, are directly evaluated from 512 water MD trajectories, which are in quantitative agreement with the experiments. We propose a new method to decompose the computed SSF and identify the changes in the SSF with respect to the changes in H-bond structures. We find that a larger water density results in a higher probability for one or two non-H-bonded water molecules to be inserted into the inner shell, explaining the changes in the tetrahedrality of water under pressure. We predict that the structure of the accepting end of water molecules is more easily influenced by the pressure than by the donating end. Our work sheds new light on explaining the SSF and H-bond properties in related fields.
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Affiliation(s)
- Renxi Liu
- HEDPS, CAPT, College of Engineering, Peking University, Beijing 100871, P. R. China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 90871, P. R. China
| | - Mohan Chen
- HEDPS, CAPT, College of Engineering, Peking University, Beijing 100871, P. R. China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 90871, P. R. China
- AI for Science Institute, Beijing 100080, P. R. China
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5
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Neethirajan J, Hache T, Paone D, Pinto D, Denisenko A, Stöhr R, Udvarhelyi P, Pershin A, Gali A, Wrachtrup J, Kern K, Singha A. Controlled Surface Modification to Revive Shallow NV - Centers. NANO LETTERS 2023; 23:2563-2569. [PMID: 36927005 PMCID: PMC10103335 DOI: 10.1021/acs.nanolett.2c04733] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/14/2023] [Indexed: 06/18/2023]
Abstract
Near-surface negatively charged nitrogen vacancy (NV) centers hold excellent promise for nanoscale magnetic imaging and quantum sensing. However, they often experience charge-state instabilities, leading to strongly reduced fluorescence and NV coherence time, which negatively impact magnetic imaging sensitivity. This occurs even more severely at 4 K and ultrahigh vacuum (UHV, p = 2 × 10-10 mbar). We demonstrate that in situ adsorption of H2O on the diamond surface allows the partial recovery of the shallow NV sensors. Combining these with band-bending calculations, we conclude that controlled surface treatments are essential for implementing NV-based quantum sensing protocols under cryogenic UHV conditions.
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Affiliation(s)
| | - Toni Hache
- Max
Planck Institute for Solid State Research, 70569 Stuttgart, Germany
| | - Domenico Paone
- Max
Planck Institute for Solid State Research, 70569 Stuttgart, Germany
- 3rd
Institute of Physics and Research Center SCoPE, University of Stuttgart, 70049 Stuttgart, Germany
| | - Dinesh Pinto
- Max
Planck Institute for Solid State Research, 70569 Stuttgart, Germany
- Institute
de Physique, École Polytechnique
Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Andrej Denisenko
- 3rd
Institute of Physics and Research Center SCoPE, University of Stuttgart, 70049 Stuttgart, Germany
| | - Rainer Stöhr
- 3rd
Institute of Physics and Research Center SCoPE, University of Stuttgart, 70049 Stuttgart, Germany
| | - Péter Udvarhelyi
- Wigner
Research Centre for Physics, Institute for Solid State Physics and Optics, Budapest, POB 49, H-1525, Hungary
- Department
of Atomic Physics, Institute of Physics, Budapest University of Technology and Economics, Műegyetem rakpart 3, H-1111 Budapest, Hungary
| | - Anton Pershin
- Wigner
Research Centre for Physics, Institute for Solid State Physics and Optics, Budapest, POB 49, H-1525, Hungary
- Department
of Atomic Physics, Institute of Physics, Budapest University of Technology and Economics, Műegyetem rakpart 3, H-1111 Budapest, Hungary
| | - Adam Gali
- Wigner
Research Centre for Physics, Institute for Solid State Physics and Optics, Budapest, POB 49, H-1525, Hungary
- Department
of Atomic Physics, Institute of Physics, Budapest University of Technology and Economics, Műegyetem rakpart 3, H-1111 Budapest, Hungary
| | - Joerg Wrachtrup
- Max
Planck Institute for Solid State Research, 70569 Stuttgart, Germany
- 3rd
Institute of Physics and Research Center SCoPE, University of Stuttgart, 70049 Stuttgart, Germany
| | - Klaus Kern
- Max
Planck Institute for Solid State Research, 70569 Stuttgart, Germany
- Institute
de Physique, École Polytechnique
Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Aparajita Singha
- Max
Planck Institute for Solid State Research, 70569 Stuttgart, Germany
- Center
for
Integrated Quantum Science and Technology IQST, University of Stuttgart, 70049 Stuttgart, Germany
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6
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Perturbative vibration of the coupled hydrogen-bond (O:H-O) in water. Adv Colloid Interface Sci 2022; 310:102809. [PMID: 36356480 DOI: 10.1016/j.cis.2022.102809] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 10/30/2022] [Indexed: 11/09/2022]
Abstract
Perturbation Raman spectroscopy has underscored the hydrogen bond (O:H-O or HB) cooperativity and polarizability (HBCP) for water, which offers a proper parameter space for the performance of the HB and electrons in the energy-space-time domains. The OO repulsive coupling drives the O:H-O segmental length and energy to relax cooperatively upon perturbation. Mechanical compression shortens and stiffens the O:H nonbond while lengthens and softens the HO bond associated with polarization. However, electrification by an electric field or charge injection, or molecular undercoordination at a surface, relaxes the O:H-O in a contrasting way to the compression with derivation of the supersolid phase that is viscoelastic, less dense, thermally diffusive, and mechanically and thermally more stable. The HO bond exhibits negative thermal expansivity in the liquid and the ice-I phase while its length responds in proportional to temperature in the quasisolid phase. The O:H-O relaxation modifies the mass densities, phase boundaries, critical temperatures and the polarization endows the slipperiness of ice and superfluidity of water at the nanometer scale. Protons injection by acid solvation creates the H↔H anti-HB and introduction of electron lone pairs derives the O:⇔:O super-HB into the solutions of base or H2O2 hydrogen-peroxide. The repulsive H↔H and O:⇔:O interactions lengthen the solvent HO bond while the solute HO bond contracts because its bond order loss. Differential phonon spectroscopy quantifies the abundance, structure order, and stiffness of the bonds transiting from the mode of pristine water to the perturbed states. The HBCP and the perturbative spectroscopy have enabled the dynamic potentials for the relaxing O:H-O bond. Findings not only amplified the power of the Raman spectroscopy but also substantiated the understanding of anomalies of water subjecting to perturbation.
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7
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Eeckhoudt J, Bettens T, Geerlings P, Cammi R, Chen B, Alonso M, De Proft F. Conceptual Density Functional Theory under Pressure: Part I. XP-PCM Method Applied to Atoms. Chem Sci 2022; 13:9329-9350. [PMID: 36093025 PMCID: PMC9384819 DOI: 10.1039/d2sc00641c] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 07/14/2022] [Indexed: 11/21/2022] Open
Abstract
High pressure chemistry offers the chemical community a range of possibilities to control chemical reactivity, develop new materials and fine-tune chemical properties. Despite the large changes that extreme pressure brings to the table, the field has mainly been restricted to the effects of volume changes and thermodynamics with less attention devoted to electronic effects at the molecular scale. This paper combines the conceptual DFT framework for analyzing chemical reactivity with the XP-PCM method for simulating pressures in the GPa range. Starting from the new derivatives of the energy with respect to external pressure, an electronic atomic volume and an atomic compressibility are found, comparable to their enthalpy analogues, respectively. The corresponding radii correlate well with major known sets of this quantity. The ionization potential and electron affinity are both found to decrease with pressure using two different methods. For the electronegativity and chemical hardness, a decreasing and increasing trend is obtained, respectively, and an electronic volume-based argument is proposed to rationalize the observed periodic trends. The cube of the softness is found to correlate well with the polarizability, both decreasing under pressure, while the interpretation of the electrophilicity becomes ambiguous at extreme pressures. Regarding the electron density, the radial distribution function shows a clear concentration of the electron density towards the inner region of the atom and periodic trends can be found in the density using the Carbó quantum similarity index and the Kullback–Leibler information deficiency. Overall, the extension of the CDFT framework with pressure yields clear periodic patterns. Conceptual DFT has provided a framework in which to study chemical reactivity. Since high pressure is more and more a tool to control reactions and fine-tune chemical properties, this variable is introduced into the CDFT framework.![]()
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Affiliation(s)
- J Eeckhoudt
- General Chemistry Department (ALGC), Vrije Universiteit Brussel (VUB) Brussels Belgium
| | - T Bettens
- General Chemistry Department (ALGC), Vrije Universiteit Brussel (VUB) Brussels Belgium
| | - P Geerlings
- General Chemistry Department (ALGC), Vrije Universiteit Brussel (VUB) Brussels Belgium
| | - R Cammi
- Department of Chemical Science, Life Science and Environmental Sustainability, University of Parma Parma Italy
| | - B Chen
- Donostia International Physics Center Donostia-San Sebastian Spain
- IKERBASQUE, Basque Foundation for Science Plaza Euskadi 5 48009 Bilbao Spain
| | - M Alonso
- General Chemistry Department (ALGC), Vrije Universiteit Brussel (VUB) Brussels Belgium
| | - F De Proft
- General Chemistry Department (ALGC), Vrije Universiteit Brussel (VUB) Brussels Belgium
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8
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Scheurer M, Dreuw A, Epifanovsky E, Head-Gordon M, Stauch T. Modeling Molecules under Pressure with Gaussian Potentials. J Chem Theory Comput 2021; 17:583-597. [PMID: 33350311 DOI: 10.1021/acs.jctc.0c01212] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The computational modeling of molecules under high pressure is a growing research area that augments experimental high-pressure chemistry. Here, a new electronic structure method for modeling atoms and molecules under pressure, Gaussians On Surface Tesserae Simulate HYdrostatic Pressure (GOSTSHYP) approach, is introduced. In this method, a set of Gaussian potentials is distributed evenly on the van der Waals surface of the investigated chemical system, leading to a compression of the electron density and the atomic scaffold. Since no parameters other than pressure need to be specified, GOSTSHYP allows straightforward geometry optimizations and ab initio molecular dynamics simulations of chemical systems under pressure for nonexpert users. Calculated energies, bond lengths, and dipole moments under pressure fall within the range of established computational methods for high-pressure chemistry. A Diels-Alder reaction and the cyclotrimerization of acetylene showcase the ability of GOSTSHYP to model pressure-induced chemical reactions. The connection to mechanochemistry is pointed out.
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Affiliation(s)
- Maximilian Scheurer
- Interdisciplinary Center for Scientific Computing, Heidelberg University, D-69120 Heidelberg, Germany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Heidelberg University, D-69120 Heidelberg, Germany
| | - Evgeny Epifanovsky
- Q-Chem Inc., 6601 Owens Dr, Suite 105, Pleasanton, California 94588, United States
| | - Martin Head-Gordon
- Pitzer Center for Theoretical Chemistry, University of California, Berkeley, South Dr, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, California 94720, United States
| | - Tim Stauch
- Institute for Physical and Theoretical Chemistry, University of Bremen, Leobener Str. NW2, D-28359 Bremen, Germany.,Bremen Center for Computational Materials Science, University of Bremen, Am Fallturm 1, D-28359 Bremen, Germany.,MAPEX Center for Materials and Processes, University of Bremen, Bibliothekstr. 1, D-28359 Bremen, Germany
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9
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Wexler AD, Fuchs EC, Woisetschläger J, Vitiello G. Electrically induced liquid-liquid phase transition in water at room temperature. Phys Chem Chem Phys 2019; 21:18541-18550. [PMID: 31397450 DOI: 10.1039/c9cp03192h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this work we expand on findings previously reported [Wexler et al., Phys. Chem. Chem. Phys., 2016, 18, 16281] on the experimental observation of a phase transition in a hydrogen bonded liquid manifesting in long range dipole-dipole interactions. The studied system, liquid water stressed by an electric field, exhibits collective oscillations brought about through spontaneous breakdown of symmetry. Raman spectroscopy identifies the primary excitation of the emergent phase as transverse optically active phonon-like sidebands that appear on the hydrogen bonded asymmetric stretch mode. The phase transition is observed throughout the entire volume of liquid. The system also exhibits a self-similarity relation between the scattered Raman intensity and the electric field strength which further supports the conclusion that collective behavior persists against thermal disruption. The experimental findings are discussed in terms of a quantum field theory for macroscopic quantum systems.
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Affiliation(s)
- Adam D Wexler
- Arie Zwijnenburg Laboratory for Advanced Microscopy and Optical Metrology, Wetsus - European Center of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911MA Leeuwarden, The Netherlands.
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10
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Kang D, Dai J. Dynamic electron-ion collisions and nuclear quantum effects in quantum simulation of warm dense matter. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:073002. [PMID: 29186001 DOI: 10.1088/1361-648x/aa9e29] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The structural, thermodynamic and transport properties of warm dense matter (WDM) are crucial to the fields of astrophysics and planet science, as well as inertial confinement fusion. WDM refers to the states of matter in a regime of temperature and density between cold condensed matter and hot ideal plasmas, where the density is from near-solid up to ten times solid density, and the temperature between 0.1 and 100 eV. In the WDM regime, matter exhibits moderately or strongly coupled, partially degenerate properties. Therefore, the methods used to deal with condensed matter and isolated atoms need to be properly validated for WDM. It is therefore a big challenge to understand WDM within a unified theoretical description with reliable accuracy. Here, we review the progress in the theoretical study of WDM with state-of-the-art simulations, i.e. quantum Langevin molecular dynamics and first principles path integral molecular dynamics. The related applications for WDM are also included.
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Affiliation(s)
- Dongdong Kang
- Department of Physics, National University of Defense Technology, Changsha, Hunan 410073, People's Republic of China
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11
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Bejagam KK, Singh S, An Y, Berry C, Deshmukh SA. PSO-Assisted Development of New Transferable Coarse-Grained Water Models. J Phys Chem B 2018; 122:1958-1971. [DOI: 10.1021/acs.jpcb.7b10542] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Karteek K. Bejagam
- Department
of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Samrendra Singh
- CNH Industrial, Burr Ridge, Chicago, Illinois 60527, United States
| | - Yaxin An
- Department
of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Carter Berry
- Department
of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Sanket A. Deshmukh
- Department
of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
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12
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Skinner LB, Galib M, Fulton JL, Mundy CJ, Parise JB, Pham VT, Schenter GK, Benmore CJ. The structure of liquid water up to 360 MPa from x-ray diffraction measurements using a high Q-range and from molecular simulation. J Chem Phys 2016; 144:134504. [DOI: 10.1063/1.4944935] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- L. B. Skinner
- X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, USA
- Mineral Physics Institute, Stony Brook University, Stony Brook, New York, New York 11794-2100, USA
| | - M. Galib
- Physical and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - J. L. Fulton
- Physical and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - C. J. Mundy
- Physical and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - J. B. Parise
- Mineral Physics Institute, Stony Brook University, Stony Brook, New York, New York 11794-2100, USA
- Department of Geosciences, Stony Brook University, Stony Brook, New York, New York 11794-2100, USA
- Photon Sciences Division, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - V.-T. Pham
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, BP48, 91192 Gif-sur-Yvette, France
- Center for Quantum Electronics, Institute of Physics, Vietnam Academy of Science and Technology, P.O. Box 429, Boho, Hanoi 10000, Viet Nam
| | - G. K. Schenter
- Physical and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - C. J. Benmore
- X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, USA
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13
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Shevkunov SV. Hydration of Cl– ion in a planar nanopore with hydrophilic walls. 1. Molecular structure. COLLOID JOURNAL 2016. [DOI: 10.1134/s1061933x15060186] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Sridhar A, Srikanth B, Kumar A, Dasmahapatra AK. Coarse-grain molecular dynamics study of fullerene transport across a cell membrane. J Chem Phys 2015; 143:024907. [DOI: 10.1063/1.4926668] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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15
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16
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Ou SC, Patel S. Electrostatic contribution from solvent in modulating single-walled carbon nanotube association. J Chem Phys 2014; 141:114906. [PMID: 25240371 PMCID: PMC4187323 DOI: 10.1063/1.4892566] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 07/28/2014] [Indexed: 11/14/2022] Open
Abstract
We perform all-atom molecular dynamics simulations to compute the potential of mean force (PMF) between two (10,10) single-walled carbon nanotubes solvated in pure nonpolarizable SPC/E and polarizable TIP4P-FQ water, at various temperatures. In general, the reversible work required to bring two nanotubes from a dissociated state (free energy reference) to contact state (free energy minimum) is more favorable and less temperature-dependent in TIP4P-FQ than in SPC/E water models. In contrast, molecular properties and behavior of water such as the spatially-resolved water number density (intertube, intratube, or outer regions), for TIP4P-FQ are more sensitive to temperature than SPC/E. Decomposition of the solvent-induced PMF into different spatial regions suggests that TIP4P-FQ has stronger temperature dependence; the opposing destabilizing/stabilizing contributions from intertube water and more distal water balance each other and suppress the temperature dependence of total association free energy. Further investigation of hydrogen bonding network in intertube water reveals that TIP4P-FQ retains fewer hydrogen bonds than SPC/E, which correlates with the lower water number density in this region. This reduction of hydrogen bonds affects the intertube water dipoles. As the intertube volume decreases, TIP4P-FQ dipole moment approaches the gas phase value; the distribution of dipole magnitude also becomes narrower due to less average polarization/perturbation from other water molecules. Our results imply that the reduction of water under confinement may seem trivial, but underlying effects to structure and free energetics are non-negligible.
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Affiliation(s)
- Shu-Ching Ou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Sandeep Patel
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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17
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Sun Q, Wang Q, Ding D. Hydrogen Bonded Networks in Supercritical Water. J Phys Chem B 2014; 118:11253-8. [DOI: 10.1021/jp503474s] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Qiang Sun
- Key Laboratory of Orogenic
Belts and Crustal Evolution, Ministry of Education, The School of
Earth and Planetary Sciences, Peking University, Beijing 100871, China
| | - Qianqian Wang
- Key Laboratory of Orogenic
Belts and Crustal Evolution, Ministry of Education, The School of
Earth and Planetary Sciences, Peking University, Beijing 100871, China
| | - Dongye Ding
- School of Resources and Environmental
Engineering, Shandong University of Technology, Zibo 255049, China
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18
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Alfè D, Bartók AP, Csányi G, Gillan MJ. Analyzing the errors of DFT approximations for compressed water systems. J Chem Phys 2014; 141:014104. [DOI: 10.1063/1.4885440] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- D. Alfè
- Department of Earth Sciences, UCL, London WC1E 6BT, United Kingdom
- London Centre for Nanotechnology, UCL, London WC1H 0AH, United Kingdom
- Thomas Young Centre, UCL, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, UCL, London WC1E 6BT, United Kingdom
| | - A. P. Bartók
- Department of Engineering, University of Cambridge, Cambridge CB2 1PZ, United Kingdom
| | - G. Csányi
- Department of Engineering, University of Cambridge, Cambridge CB2 1PZ, United Kingdom
| | - M. J. Gillan
- London Centre for Nanotechnology, UCL, London WC1H 0AH, United Kingdom
- Thomas Young Centre, UCL, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, UCL, London WC1E 6BT, United Kingdom
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19
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Sun H, Kang D, Dai J, Zeng J, Yuan J. Quantum molecular dynamics study on the structures and dc conductivity of warm dense silane. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:022128. [PMID: 25353443 DOI: 10.1103/physreve.89.022128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Indexed: 06/04/2023]
Abstract
The ionic and electronic structures of warm dense silane at the densities of 1.795, 2.260, 3.382, and 3.844 g/cm(3) have been studied with temperatures from 1000 K to 3 eV using quantum molecular dynamics simulations. At all densities, the structures are melted above 1000 K. The matter states are characterized as polymeric from 1000 to 4000 K and become dense plasma states with further increasing temperature to 1 eV. At two lower densities of 1.795 and 2.260 g/cm(3), silane first dissociates and then becomes the polymeric state via a chain state from the initial crystalline structure. At higher densities, however, no dissociation stage was found. These findings can help us understand how the warm dense matter forms. A rise is found for the direct current electric conductivity at T ∼ 1000 K, indicating the nonmetal-to-metal transition. The conductivity decreases slightly with the increase of temperature, which is due to the more disordered structures at higher temperatures.
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Affiliation(s)
- Huayang Sun
- Department of Physics, College of Science, National University of Defense Technology, Changsha 410073, People's Republic of China
| | - Dongdong Kang
- Department of Physics, College of Science, National University of Defense Technology, Changsha 410073, People's Republic of China
| | - Jiayu Dai
- Department of Physics, College of Science, National University of Defense Technology, Changsha 410073, People's Republic of China
| | - Jiaolong Zeng
- Department of Physics, College of Science, National University of Defense Technology, Changsha 410073, People's Republic of China
| | - Jianmin Yuan
- Department of Physics, College of Science, National University of Defense Technology, Changsha 410073, People's Republic of China and State Key Laboratory of High Performance Computing, National University of Defense Technology, Changsha 410073, People's Republic of China
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20
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Shvab I, Sadus RJ. Intermolecular potentials and the accurate prediction of the thermodynamic properties of water. J Chem Phys 2013; 139:194505. [DOI: 10.1063/1.4832381] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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21
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Dai J, Kang D, Zhao Z, Wu Y, Yuan J. Dynamic ionic clusters with flowing electron bubbles from warm to hot dense iron along the Hugoniot curve. PHYSICAL REVIEW LETTERS 2012; 109:175701. [PMID: 23215202 DOI: 10.1103/physrevlett.109.175701] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2012] [Indexed: 06/01/2023]
Abstract
Complex structures of warm and hot dense matter are essential to understanding the behavior of materials in high energy density processes and provide new features of matter constitutions. Here, around a new unified first-principles determined Hugoniot curve of iron from the normal condensed condition up to 1 Gbar, the novel structures characterized by the ionic clusters with electron bubbles are found using quantum Langevin molecular dynamics. Subsistence of complex clusters can persist in the time scale of 50 fs dynamically with quantum flowing bubbles, which are produced by the interplay of Fermi electron degeneracy, the ionic coupling, and the dynamical nature. With the inclusion of those complicated features in quantum Langevin molecular dynamics, the present equation of states could serve as a first-principles based database in a wide range of temperatures and densities.
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Affiliation(s)
- Jiayu Dai
- Department of Physics, College of Science, National University of Defense Technology, Changsha 410073, People's Republic of China
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22
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Lin Y, Wynveen A, Halley JW, Curtiss LA, Redfern PC. Self consistent tight binding model for dissociable water. J Chem Phys 2012; 136:174507. [PMID: 22583249 DOI: 10.1063/1.4705667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We report results of development of a self consistent tight binding model for water. The model explicitly describes the electrons of the liquid self consistently, allows dissociation of the water and permits fast direct dynamics molecular dynamics calculations of the fluid properties. It is parameterized by fitting to first principles calculations on water monomers, dimers, and trimers. We report calculated radial distribution functions of the bulk liquid, a phase diagram and structure of solvated protons within the model as well as ac conductivity of a system of 96 water molecules of which one is dissociated. Structural properties and the phase diagram are in good agreement with experiment and first principles calculations. The estimated DC conductivity of a computational sample containing a dissociated water molecule was an order of magnitude larger than that reported from experiment though the calculated ratio of proton to hydroxyl contributions to the conductivity is very close to the experimental value. The conductivity results suggest a Grotthuss-like mechanism for the proton component of the conductivity.
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Affiliation(s)
- You Lin
- Brion Technologies Incorporated, 4211 Burton Drive, Santa Clara, California 95054, USA
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23
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Shvab I, Sadus RJ. Structure and polarization properties of water: molecular dynamics with a nonadditive intermolecular potential. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:051509. [PMID: 23004769 DOI: 10.1103/physreve.85.051509] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2012] [Revised: 04/23/2012] [Indexed: 06/01/2023]
Abstract
The temperature and density dependence of the structure and polarization properties of bulk water were systematically investigated using the ab initio MCYna potential [Li et al., J. Chem. Phys. 127, 154509 (2007)], which includes nonadditive contributions to intermolecular interactions. Molecular dynamics simulations were conducted for isochores of 1, 0.8, and 0.6 g/cm^{3} and temperatures from 278 to 750 K. Special attention was paid to the structural change of water in the range from the normal boiling point to supercritical temperatures. At temperatures below the normal boiling temperature, water exhibits a tetrahedral structure along the 0.8 and 0.6 g/cm^{3} isochores. A significant collapse of the hydrogen bonding network was observed at temperatures of 450, 550, and 650 K. The MCYna potential was able to successfully reproduce the experimental dielectric constant. The dielectric constant and average dipole moments decrease with increasing temperature and decreasing density due to weakened polarization. A comparison is also made with SPC-based models.
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Affiliation(s)
- I Shvab
- Centre for Molecular Simulation, Swinburne University of Technology, P.O. Box 218, Hawthorn, Victoria 3122, Australia
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Leverentz HR, Maerzke KA, Keasler SJ, Siepmann JI, Truhlar DG. Electrostatically embedded many-body method for dipole moments, partial atomic charges, and charge transfer. Phys Chem Chem Phys 2012; 14:7669-78. [DOI: 10.1039/c2cp24113g] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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