1
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Robinson Brown DC, Webber TR, Casey TM, Franck J, Shell MS, Han S. Computation of Overhauser dynamic nuclear polarization processes reveals fundamental correlation between water dynamics, structure, and solvent restructuring entropy. Phys Chem Chem Phys 2024; 26:14637-14650. [PMID: 38742831 DOI: 10.1039/d4cp00030g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Hydration water dynamics, structure, and thermodynamics are crucially important to understand and predict water-mediated properties at molecular interfaces. Yet experimentally and directly quantifying water behavior locally near interfaces at the sub-nanometer scale is challenging, especially at interfaces submerged in biological solutions. Overhauser dynamic nuclear polarization (ODNP) experiments measure equilibrium hydration water dynamics within 8-15 angstroms of a nitroxide spin probe on instantaneous timescales (10 picoseconds to nanoseconds), making ODNP a powerful tool for probing local water dynamics in the vicinity of the spin probe. As with other spectroscopic techniques, concurrent computational analysis is necessary to gain access to detailed molecular level information about the dynamic, structural, and thermodynamic properties of water from experimental ODNP data. We chose a model system that can systematically tune the dynamics of water, a water-glycerol mixture with compositions ranging from 0 to 0.3 mole fraction glycerol. We demonstrate the ability of molecular dynamics (MD) simulations to compute ODNP spectroscopic quantities, and show that translational, rotational, and hydrogen bonding dynamics of hydration water align strongly with spectroscopic ODNP parameters. Moreover, MD simulations show tight correlations between the dynamic properties of water that ODNP captures and the structural and thermodynamic behavior of water. Hence, experimental ODNP readouts of varying water dynamics suggest changes in local structural and thermodynamic hydration water properties.
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Affiliation(s)
- Dennis C Robinson Brown
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - Thomas R Webber
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - Thomas M Casey
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
| | - John Franck
- Department of Chemistry, Syracuse University, Syracuse, NY, USA
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - Songi Han
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA.
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2
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Al-Mualem ZA, Lorenz-Ochoa KA, Pan L, Ren H, Baiz CR. Controlling Interfacial Hydrogen Bonding at a Gold Surface: The Effect of Organic Cosolvents. J Phys Chem Lett 2024; 15:4391-4399. [PMID: 38621259 DOI: 10.1021/acs.jpclett.4c00645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Water often serves as both a reactant and solvent in electrocatalytic reactions. Interfacial water networks can affect the transport and kinetics of these reactions, e.g., hydrogen evolution reaction and CO2 reduction reaction. Adding cosolvents that influence the hydrogen-bonding (H-bonding) environment, such as dimethyl sulfoxide (DMSO), has the potential to tune the reactivity of these important electrocatalytic reactions by regulating the interfacial local environment and water network. We investigate interfacial H-bonding networks in water-DMSO cosolvent mixtures on gold surfaces by using surface-enhanced infrared absorption spectroscopy and molecular dynamics simulations. Experiments and simulations show that the gold surface is enriched with dehydrated DMSO molecules and the mixture phase-separates to form water clusters. Simulations show a "buckled" water conformation at the surface, further constraining interfacial H-bonding. The small size of these water clusters and the energetically unfavorable H-bond conformations might inhibit H-bonding with bulk water, suppressing the proton diffusion required for efficient hydrogen evolution reaction processes.
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Affiliation(s)
- Ziareena A Al-Mualem
- Department of Chemistry, University of Texas at Austin, 105 E 24th St. A5300, Austin, Texas 78712, United States
| | - Keegan A Lorenz-Ochoa
- Department of Chemistry, University of Texas at Austin, 105 E 24th St. A5300, Austin, Texas 78712, United States
| | - Lei Pan
- Department of Chemistry, University of Texas at Austin, 105 E 24th St. A5300, Austin, Texas 78712, United States
| | - Hang Ren
- Department of Chemistry, University of Texas at Austin, 105 E 24th St. A5300, Austin, Texas 78712, United States
| | - Carlos R Baiz
- Department of Chemistry, University of Texas at Austin, 105 E 24th St. A5300, Austin, Texas 78712, United States
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3
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LeMessurier N, Salzmann H, Leversee R, Weber JM, Eaves JD. Water-Hydrocarbon Interactions in Anionic Pyrene Monohydrate. J Phys Chem B 2024; 128:3200-3210. [PMID: 38526297 DOI: 10.1021/acs.jpcb.3c07777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Interactions between water and polycyclic aromatic hydrocarbons are essential in many aspects of chemistry, from interstellar and atmospheric processes to interfacial hydrophobicity and wetting phenomena. Despite their growing importance, the intermolecular potentials of the water-hydrocarbon interactions are underdeveloped compared to the water-water potentials, and there are similarly few experimental probes that are sensitive to the details of the water-hydrocarbon potential. We present a combined experimental and computational study of anionic pyrene monohydrate, one of the simplest water/hydrocarbon clusters. The action spectrum in the OH region of the mass-selected cluster ion provides a rigorous benchmark for intermolecular potentials and computational methodologies. We identify missing intermolecular interactions and shortcomings in conventional dynamics calculations by comparing experimental data to density functional theory and classical molecular dynamics calculations. Kinetic trapping is prevalent, even for one water molecule and one pyrene molecule, leading to slow equilibration in conventional molecular dynamics calculations, even on nanosecond time scales and at low temperatures (50 K). At constant energy, temperature fluctuations for the pair of molecules are substantial. Immersing the system in a bath of soft spheres and employing parallel tempering alleviates kinetic trapping and dampens temperature fluctuations, bringing the system closer to the thermodynamic limit. With such augmented sampling, a simple, flexible water model reproduces the line width and the asymmetric broadening of the symmetric OH stretching mode, which we assign to spectral diffusion. In the OH stretching region, dynamics calculations predict a more intense antisymmetric peak than experiments observe but do not predict the bimodal split symmetric peak that the experiments show. Our work suggests that electronic polarization, missing in the empirical force field, is responsible for the first discrepancy and that quantum nuclear effects, captured neither in density functional theory nor in classical dynamics, may be responsible for the second.
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Affiliation(s)
- Natalie LeMessurier
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309-0215, United States
| | - Heinrich Salzmann
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309-0215, United States
- JILA, University of Colorado, Boulder, Colorado 80309-0440, United States
| | - River Leversee
- JILA, University of Colorado, Boulder, Colorado 80309-0440, United States
- Department of Physics, University of Colorado, Boulder, Colorado 80309-0215, United States
| | - J Mathias Weber
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309-0215, United States
- JILA, University of Colorado, Boulder, Colorado 80309-0440, United States
| | - Joel D Eaves
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309-0215, United States
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4
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Montero de Hijes P, Dellago C, Jinnouchi R, Schmiedmayer B, Kresse G. Comparing machine learning potentials for water: Kernel-based regression and Behler-Parrinello neural networks. J Chem Phys 2024; 160:114107. [PMID: 38506284 DOI: 10.1063/5.0197105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/03/2024] [Indexed: 03/21/2024] Open
Abstract
In this paper, we investigate the performance of different machine learning potentials (MLPs) in predicting key thermodynamic properties of water using RPBE + D3. Specifically, we scrutinize kernel-based regression and high-dimensional neural networks trained on a highly accurate dataset consisting of about 1500 structures, as well as a smaller dataset, about half the size, obtained using only on-the-fly learning. This study reveals that despite minor differences between the MLPs, their agreement on observables such as the diffusion constant and pair-correlation functions is excellent, especially for the large training dataset. Variations in the predicted density isobars, albeit somewhat larger, are also acceptable, particularly given the errors inherent to approximate density functional theory. Overall, this study emphasizes the relevance of the database over the fitting method. Finally, this study underscores the limitations of root mean square errors and the need for comprehensive testing, advocating the use of multiple MLPs for enhanced certainty, particularly when simulating complex thermodynamic properties that may not be fully captured by simpler tests.
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Affiliation(s)
- Pablo Montero de Hijes
- University of Vienna, Faculty of Physics, Kolingasse 14, A-1090 Vienna, Austria
- University of Vienna, Faculty of Earth Sciences, Geography and Astronomy, Josef-Holaubuek-Platz 2, 1090 Vienna, Austria
| | - Christoph Dellago
- University of Vienna, Faculty of Physics, Kolingasse 14, A-1090 Vienna, Austria
| | - Ryosuke Jinnouchi
- Toyota Central R&D Labs., Inc., 41-1 Yokomichi, Nagakute, Aichi 480-1192, Japan
| | | | - Georg Kresse
- University of Vienna, Faculty of Physics, Kolingasse 14, A-1090 Vienna, Austria
- VASP Software GmbH, Berggasse 21, A-1090 Vienna, Austria
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5
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Guo C, Yang K, Qin H, Zhu Y, Chen M, Lü Y. Abnormal condensation of water vapour at ambient temperature. Phys Chem Chem Phys 2024; 26:8784-8793. [PMID: 38420852 DOI: 10.1039/d3cp05628g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
The homogeneous condensation of water vapor at ambient temperature is studied using molecular dynamics simulation. We reveal that there is a droplet size at the nanoscale where water droplets can be stabilized in the condensation process. Our simulations show that the growth of water droplets is dominated by collision and coagulation between small water droplets after nucleation. This process is found to be accompanied by exceptionally fast evaporation such that droplet growth is balanced by evaporation when water droplets grow to a critical size, approximately 12.5 Å in radius, reaching a stable size distribution. The extremely high evaporation rate is attributed to the curvature dependence of surface tension. Surface tension shows a significant decrease with decreasing droplet size below 20 Å, which causes the total free energy of nanoscaled water droplets to rise after collision and coagulation. Consequently, water droplets have to shrink via fast evaporation. The curvature dependence of surface tension is related to the dielectric ordering of water molecules near the surface of water droplets. Owing to fast evaporation, secondary condensation occurs, and many small water clusters form, ultimately exhibiting a bimodal distribution of water-droplet size.
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Affiliation(s)
- Chenchen Guo
- School of Physics, Beijing Institute of Technology, Beijing 100081, China.
- Changping School Attached to Beijing Normal University, Beijing 102206, China
| | - Kun Yang
- School of Physics, Beijing Institute of Technology, Beijing 100081, China.
| | - Hairong Qin
- School of Physics, Beijing Institute of Technology, Beijing 100081, China.
| | - Yong Zhu
- Science and Technology on Electromagnetic Scattering Laboratory, Beijing 100854, China
| | - Min Chen
- Department of Engineering Mechanics, Center for Nano and Micro Mechanics, Tsinghua University, Beijing 100084, China
| | - Yongjun Lü
- School of Physics, Beijing Institute of Technology, Beijing 100081, China.
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6
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Rapallo A. Fractional Extended Diffusion Theory to capture anomalous relaxation from biased/accelerated molecular simulations. J Chem Phys 2024; 160:084114. [PMID: 38421066 DOI: 10.1063/5.0189518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/06/2024] [Indexed: 03/02/2024] Open
Abstract
Biased and accelerated molecular simulations (BAMS) are widely used tools to observe relevant molecular phenomena occurring on time scales inaccessible to standard molecular dynamics, but evaluation of the physical time scales involved in the processes is not directly possible from them. For this reason, the problem of recovering dynamics from such kinds of simulations is the object of very active research due to the relevant theoretical and practical implications of dynamics on the properties of both natural and synthetic molecular systems. In a recent paper [A. Rapallo et al., J. Comput. Chem. 42, 586-599 (2021)], it has been shown how the coupling of BAMS (which destroys the dynamics but allows to calculate average properties) with Extended Diffusion Theory (EDT) (which requires input appropriate equilibrium averages calculated over the BAMS trajectories) allows to effectively use the Smoluchowski equation to calculate the orientational time correlation function of the head-tail unit vector defined over a peptide in water solution. Orientational relaxation of this vector is the result of the coupling of internal molecular motions with overall molecular rotation, and it was very well described by correlation functions expressed in terms of weighted sums of suitable time-exponentially decaying functions, in agreement with a Brownian diffusive regime. However, situations occur where exponentially decaying functions are no longer appropriate to capture the actual dynamical behavior, which exhibits persistent long time correlations, compatible with the so called subdiffusive regimes. In this paper, a generalization of EDT will be given, exploiting a fractional Smoluchowski equation (FEDT) to capture the non-exponential character observed in the relaxation of intramolecular distances and molecular radius of gyration, whose dynamics depend on internal molecular motions only. The calculation methods, proper to EDT, are adapted to implement the generalization of the theory, and the resulting algorithm confirms FEDT as a tool of practical value in recovering dynamics from BAMS, to be used in general situations, involving both regular and anomalous diffusion regimes.
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Affiliation(s)
- Arnaldo Rapallo
- CNR - Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), via A. Corti 12, I-20133 Milano, Italy
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7
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Silva RS, Souza LMP, Costa RKM, Souza FR, Pimentel AS. Absolute binding free energies of the antiviral peptide ATN-161 with protein targets of SARS-CoV-2. J Biomol Struct Dyn 2023; 41:10546-10557. [PMID: 36476274 DOI: 10.1080/07391102.2022.2154848] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022]
Abstract
The interactions of the antiviral pentapeptide ATN-161 with the closed and open conformations of the α5β1 integrin, the SARS-CoV-2 major protease, and the omicron variant spike protein complexed with hACE2 were studied using molecular docking and molecular dynamics simulation. Molecular docking was performed to obtain ATN-161 binding poses with these studied protein targets. Subsequently, molecular dynamics simulations were performed to verify the ligand stability at the binding site of each protein target. Pulling simulations, umbrella sampling, and weighted histogram analysis method were used to obtain the potential of mean force of each system and calculate the Gibbs free energy of binding for the ATN-161 peptide in each binding site of these protein targets. The results showed that ATN-161 binds to α5β1 integrin in its active and inactive form, binds weakly to the omicron variant spike protein complexed with hACE2, and strongly binds to the main protease target.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rudielson Santos Silva
- Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Felipe Rodrigues Souza
- Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, Brazil
| | - André Silva Pimentel
- Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, Brazil
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8
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Mendonça BHS, de Moraes EE, Kirch A, Batista RJC, de Oliveira AB, Barbosa MC, Chacham H. Flow through Deformed Carbon Nanotubes Predicted by Rigid and Flexible Water Models. J Phys Chem B 2023; 127:8634-8643. [PMID: 37754781 DOI: 10.1021/acs.jpcb.3c02889] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
In this study, using nonequilibrium molecular dynamics simulation, the flow of water in deformed carbon nanotubes is studied for two water models TIP4P/2005 and simple point charge/FH (SPC/FH). The results demonstrated a nonuniform dependence of the flow on the tube deformation and the flexibility imposed on the water molecules, leading to an unexpected increase in the flow in some cases. The effects of the tube diameter and pressure gradient are investigated to explain the abnormal flow behavior with different degrees of structural deformation.
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Affiliation(s)
- Bruno H S Mendonça
- Departamento de Física, ICEX, Universidade Federal de Minas Gerais, CP 702, Belo Horizonte 30123-970, MG, Brazil
| | - Elizane E de Moraes
- Instituto de Física, Universidade Federal da Bahia, Campus Universitário de Ondina, Salvador 40210-340, BA, Brazil
| | - Alexsandro Kirch
- Instituto de Física, Universidade de São Paulo, CP 66318, São Paulo 05315-970, SP, Brazil
| | - Ronaldo J C Batista
- Departamento de Física, Universidade Federal de Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto 35400-000, MG, Brazil
| | - Alan B de Oliveira
- Departamento de Física, Universidade Federal de Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto 35400-000, MG, Brazil
| | - Marcia C Barbosa
- Instituto de Física, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, RS, Brazil
| | - Hélio Chacham
- Departamento de Física, ICEX, Universidade Federal de Minas Gerais, CP 702, Belo Horizonte 30123-970, MG, Brazil
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9
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Moreira LS, de Vargas DD, Köhler MH. Modeling water transport properties in carbon nanotubes: Interplay between force-field flexibility and geometrical parameters. Phys Rev E 2023; 108:034116. [PMID: 37849113 DOI: 10.1103/physreve.108.034116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 08/29/2023] [Indexed: 10/19/2023]
Abstract
Modeling water and other liquids in computational simulations requires a large set of parameters. Many works have been devoted to finding new, improved water models, with almost all of them designed for bulk systems. Here, we use carbon nanotubes as a play model to investigate the effects of introducing flexibility in water force fields during molecular dynamics simulations of nanoconfined water. We explore six different models to show that viscosity, diffusion, and dipole orientation are vastly influenced by the flexibility and the family of force fields used. Particularly, we found the level of confinement (decreasing the nanotube's diameter) to increase discrepancies in the description of the dipole alignment. In smaller (10,10) nanotubes, the flexible version of the transferable intermolecular potential with three points (TIP3P/Fs) features a high directionality, while its rigid counterpart shows a more distributed dipole orientation. Both viscosity and diffusion are also extremely dependent on the force-field family, with the flexible version of the simple point charge (SPC/Fw) featuring the lower confidence interval.
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Affiliation(s)
- Luana S Moreira
- Departamento de Física, Universidade Federal de Santa Maria, 97105-900 Santa Maria, Brazil
| | - Douglas D de Vargas
- Departamento de Física, Universidade Federal de Santa Maria, 97105-900 Santa Maria, Brazil
| | - Mateus H Köhler
- Departamento de Física, Universidade Federal de Santa Maria, 97105-900 Santa Maria, Brazil
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10
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Hossain M, Chowdhury N, Atahar A, Susan MABH. Water structure modification by d-(+)-glucose at different concentrations and temperatures-effect of mutarotation. RSC Adv 2023; 13:19195-19206. [PMID: 37362346 PMCID: PMC10289138 DOI: 10.1039/d3ra03081d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/19/2023] [Indexed: 06/28/2023] Open
Abstract
Water structure modification by carbohydrates is essential both in chemistry and life processes and in particular, molecular level interaction of glucose with water is very important. With a view to developing a fundamental knowledge base, thermodynamic parameters derived from measurements of density, viscosity, and refractive index have been analyzed to investigate how d-(+)-glucose alters the structure of water at various concentrations and temperatures. The nature and extent of the interactions have been investigated using apparent molar volume, Jones-Dole constants, changes in free energy (ΔG), changes in entropy (ΔS), and changes in enthalpy (ΔH) for viscous flow. Using measurements from dynamic light scattering (DLS), the sizes of the aggregates were studied. The kinetics of mutarotation have been investigated using polarimetry and the structural effect on water during mutarotation between α-d-glucose and β-d-glucose with time has been explored by near-infrared (NIR) spectroscopy. The spectroscopic results were examined using difference spectroscopy and two-dimensional correlation spectroscopy (2DCOS). The absorption bands of water shift to a higher wavenumber irrespective of the concentration of the solution with time due to the enhancement of the cleavage of hydrogen bonding in water. At high temperatures, three bands in the region 7100-7350 cm-1 are attributed to the first overtones of the hydrogen-bonded -O-H stretching vibration. Refractive index values indicate an increase in the density of the anomer solutions with time, suggesting an increase in free water concentration. These results provide evidence for more than one water molecule being involved in the mechanism of mutarotation and propose a concerted mechanism for proton transfer.
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Affiliation(s)
- Mohammad Hossain
- Department of Chemistry, University of Dhaka Dhaka 1000 Bangladesh
| | | | - Amiya Atahar
- Department of Chemistry, University of Dhaka Dhaka 1000 Bangladesh
| | - Md Abu Bin Hasan Susan
- Department of Chemistry, University of Dhaka Dhaka 1000 Bangladesh
- Dhaka University Nanotechnology Center (DUNC), University of Dhaka Dhaka 1000 Bangladesh
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11
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Gullbrekken Ø, Røe IT, Selbach SM, Schnell SK. Charge Transport in Water-NaCl Electrolytes with Molecular Dynamics Simulations. J Phys Chem B 2023; 127:2729-2738. [PMID: 36921121 PMCID: PMC10068734 DOI: 10.1021/acs.jpcb.2c08047] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
A systematic description of microscopic mechanisms is necessary to understand mass transport in solid and liquid electrolytes. From Molecular Dynamics (MD) simulations, transport properties can be computed and provide a detailed view of the molecular and ionic motions. In this work, ionic conductivity and transport numbers in electrolyte systems are computed from equilibrium and nonequilibrium MD simulations. Results from the two methods are compared with experimental results, and we discuss the significance of the frame of reference when determining and comparing transport numbers. Two ways of computing ionic conductivity from equilibrium simulations are presented: the Nernst-Einstein approximation or the Onsager coefficients. The Onsager coefficients take ionic correlations into account and are found to be more suitable for concentrated electrolytes. Main features and differences between equilibrium and nonequilibrium simulations are discussed, and some potential anomalies and critical pitfalls of using nonequilibrium molecular dynamics to determine transport properties are highlighted.
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Affiliation(s)
- Øystein Gullbrekken
- Department of Materials Science and Engineering, Norwegian University of Science and Technology, NTNU, Trondheim NO-7491, Norway
| | - Ingeborg Treu Røe
- Department of Materials Science and Engineering, Norwegian University of Science and Technology, NTNU, Trondheim NO-7491, Norway
| | - Sverre Magnus Selbach
- Department of Materials Science and Engineering, Norwegian University of Science and Technology, NTNU, Trondheim NO-7491, Norway
| | - Sondre Kvalvåg Schnell
- Department of Materials Science and Engineering, Norwegian University of Science and Technology, NTNU, Trondheim NO-7491, Norway
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12
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Shin S, Willard AP. Quantifying the Molecular Polarization Response of Liquid Water Interfaces at Heterogeneously Charged Surfaces. J Chem Theory Comput 2023; 19:1843-1852. [PMID: 36866865 DOI: 10.1021/acs.jctc.2c01256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
The hydration shells of proteins mediate interactions, such as small molecule binding, that are vital to their biological function or in some cases their dysfunction. However, even when the structure of a protein is known, the properties of its hydration environment cannot be easily predicted due to the complex interplay between protein surface heterogeneity and the collective structure of water's hydrogen bonding network. This manuscript presents a theoretical study of the influence of surface charge heterogeneity on the polarization response of the liquid water interface. We focus our attention on classical point charge models of water, where the polarization response is limited to molecular reorientation. We introduce a new computational method for analyzing simulation data that is capable of quantifying water's collective polarization response and determining the effective surface charge distribution of hydrated surfaces over atomistic length scales. To illustrate the utility of this method, we present the results of molecular dynamics simulations of liquid water in contact with a heterogeneous model surface and the CheY protein.
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Affiliation(s)
- Sucheol Shin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Adam P Willard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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13
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Iwamoto O, Iwamoto N, Kunieda S, Minato F, Nakayama S, Abe Y, Tsubakihara K, Okumura S, Ishizuka C, Yoshida T, Chiba S, Otuka N, Sublet JC, Iwamoto H, Yamamoto K, Nagaya Y, Tada K, Konno C, Matsuda N, Yokoyama K, Taninaka H, Oizumi A, Fukushima M, Okita S, Chiba G, Sato S, Ohta M, Kwon S. Japanese evaluated nuclear data library version 5: JENDL-5. J NUCL SCI TECHNOL 2023. [DOI: 10.1080/00223131.2022.2141903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Go Chiba
- Hokkaido University, Sapporo, Japan
| | - Satoshi Sato
- National Institutes for Quantum Science and Technology, Rokkasho-mura, Japan
| | - Masayuki Ohta
- National Institutes for Quantum Science and Technology, Rokkasho-mura, Japan
| | - Saerom Kwon
- National Institutes for Quantum Science and Technology, Rokkasho-mura, Japan
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14
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Kumar R, Parashar A. Atomistic simulations of pristine and nanoparticle reinforced hydrogels: A review. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2023. [DOI: 10.1002/wcms.1655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Raju Kumar
- Department of Mechanical and Industrial Engineering Indian Institute of Technology Roorkee Uttarakhand India
| | - Avinash Parashar
- Department of Mechanical and Industrial Engineering Indian Institute of Technology Roorkee Uttarakhand India
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15
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Cuppen HM, Noble JA, Coussan S, Redlich B, Ioppolo S. Energy Transfer and Restructuring in Amorphous Solid Water upon Consecutive Irradiation. J Phys Chem A 2022; 126:8859-8870. [DOI: 10.1021/acs.jpca.2c06314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Herma M. Cuppen
- Institute for Molecules and Materials, Radboud University, Nijmegen 6525 AJ, The Netherlands
- Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam 1098 XH, The Netherlands
| | - Jennifer A. Noble
- PIIM, Aix-Marseille Université, CNRS, Marseille 13397, France
- School of Physical Sciences, University of Kent, Canterbury CT2 7NH, U.K
| | | | - Britta Redlich
- FELIX Laboratory, Radboud University, Nijmegen 6525 ED, The Netherlands
| | - Sergio Ioppolo
- Center for Interstellar Catalysis, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, Aarhus C 8000, Denmark
- School of Electronic Engineering and Computer Science, Queen Mary University of London, London E1 4NS, U.K
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16
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Deogratias G, Shadrack DM, Munissi JJE, Kinunda GA, Jacob FR, Mtei RP, Masalu RJ, Mwakyula I, Kiruri LW, Nyandoro SS. Hydrophobic π-π stacking interactions and hydrogen bonds drive self-aggregation of luteolin in water. J Mol Graph Model 2022; 116:108243. [PMID: 35777224 DOI: 10.1016/j.jmgm.2022.108243] [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: 12/01/2021] [Revised: 05/12/2022] [Accepted: 06/05/2022] [Indexed: 12/14/2022]
Abstract
Luteolin is a flavonoid obtained from different plant species. It is known for its versatile biological activities. However, the beneficial effects of luteolin have been limited to small concentrations as a result of poor water solubility. This study aimed at investigating the hydrophobic interaction and hydration of luteolin towards the improvement of its solubility when used as a drug. We report the aggregation properties of luteolin in water by varying the number of monomers using atomistic molecular dynamics simulation. Results show that the equilibrium structure of luteolin occurs in an aggregated state with different structural arrangements. As the monomers size increase, the antiparallel flipped conformation dominates over T-shaped antiparallel, T-shaped parallel, and antiparallel conformations. The formation of intramolecular hydrogen bonding of 0.19 nm between the keto-enol groups results in hydrophobic characteristics. A larger cluster exhibits slow hydrogen bond dynamics for luteolin-luteolin than luteolin-water interaction. Water structure at large cluster size exhibited slow dynamics and low self-diffusion of luteolin. The existence of hydrophobic π-π and hydrogen bonds between luteolin molecules drives strong self-aggregation resulting in poor water solubility. Breakage of these established interactions would result in increased solubility of luteolin in water.
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Affiliation(s)
- Geradius Deogratias
- Chemistry Department, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 35061, Dar es Salaam, Tanzania.
| | - Daniel M Shadrack
- Department of Chemistry, Faculty of Natural and Applied Sciences, St. John's University of Tanzania, P.O. Box 47, Dodoma, Tanzania
| | - Joan J E Munissi
- Chemistry Department, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 35061, Dar es Salaam, Tanzania
| | - Grace A Kinunda
- Chemistry Department, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 35061, Dar es Salaam, Tanzania
| | - Fortunatus R Jacob
- Chemistry Department, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 35061, Dar es Salaam, Tanzania
| | - Regina P Mtei
- Chemistry Department, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 35061, Dar es Salaam, Tanzania
| | - Rose J Masalu
- Department of Molecular Biology and Biotechnology, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 25179, Dar es Salaam, Tanzania
| | - Issakwisa Mwakyula
- Mbeya College of Health and Allied Sciences, University of Dar es Salaam, P.O. Box 608, Mbeya, Tanzania
| | - Lucy W Kiruri
- Department of Chemistry, Kenyatta University, P.O.Box, 43844-00100, Nairobi, Kenya
| | - Stephen S Nyandoro
- Chemistry Department, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 35061, Dar es Salaam, Tanzania
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17
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Sub-optical-cycle light-matter energy transfer in molecular vibrational spectroscopy. Nat Commun 2022; 13:5897. [PMID: 36202801 PMCID: PMC9537163 DOI: 10.1038/s41467-022-33477-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 09/19/2022] [Indexed: 11/18/2022] Open
Abstract
The evolution of ultrafast-laser technology has steadily advanced the level of detail in studies of light-matter interactions. Here, we employ electric-field-resolved spectroscopy and quantum-chemical modelling to precisely measure and describe the complete coherent energy transfer between octave-spanning mid-infrared waveforms and vibrating molecules in aqueous solution. The sub-optical-cycle temporal resolution of our technique reveals alternating absorption and (stimulated) emission on a few-femtosecond time scale. This behaviour can only be captured when effects beyond the rotating wave approximation are considered. At a femtosecond-to-picosecond timescale, optical-phase-dependent coherent transients and the dephasing of the vibrations of resonantly excited methylsulfonylmethane (DMSO2) are observed. Ab initio modelling using density functional theory traces these dynamics back to molecular-scale sample properties, in particular vibrational frequencies and transition dipoles, as well as their fluctuation due to the motion of DMSO2 through varying solvent environments. Future extension of our study to nonlinear interrogation of higher-order susceptibilities is fathomable with state-of-the-art lasers. Energy transfer between the electromagnetic field and atoms or molecules is fundamentally interesting. Here the authors demonstrate stepwise energy transfer between broadband mid-infrared optical pulses and vibrating methylsulfonylmethane molecules in aqueous solution.
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18
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19
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Abstract
Molecular simulations have provided valuable insight into the microscopic mechanisms underlying homogeneous ice nucleation. While empirical models have been used extensively to study this phenomenon, simulations based on first-principles calculations have so far proven prohibitively expensive. Here, we circumvent this difficulty by using an efficient machine-learning model trained on density-functional theory energies and forces. We compute nucleation rates at atmospheric pressure, over a broad range of supercoolings, using the seeding technique and systems of up to hundreds of thousands of atoms simulated with ab initio accuracy. The key quantity provided by the seeding technique is the size of the critical cluster (i.e., a size such that the cluster has equal probabilities of growing or melting at the given supersaturation), which is used together with the equations of classical nucleation theory to compute nucleation rates. We find that nucleation rates for our model at moderate supercoolings are in good agreement with experimental measurements within the error of our calculation. We also study the impact of properties such as the thermodynamic driving force, interfacial free energy, and stacking disorder on the calculated rates.
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20
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Xu S, Noguere G. Generation of thermal scattering files with the CINEL code. EPJ NUCLEAR SCIENCES & TECHNOLOGIES 2022. [DOI: 10.1051/epjn/2022004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The CINEL code dedicated to generate the thermal neutron scattering files in ENDF-6 format for solid crystalline, free gas materials and liquid water is presented. Compared to the LEAPR module of the NJOY code, CINEL is able to calculate the coherent and incoherent elastic scattering cross sections for any solid crystalline materials. Specific material properties such as anharmonicity and texture can be taken into account in CINEL. The calculation of the thermal scattering laws can be accelerated by using graphics processing unit (GPU), which enables to remove the short collision time approximation for large values of momentum transfer. CINEL is able to generate automatically the grids of dimensionless momentum and energy transfers. The Sampling the Velocity of the Target nucleus (SVT) algorithm capable of determining the scattered neutron distributions is implemented in CINEL. The obtained distributions for free target nuclei such as hydrogen and oxygen are in good agreement with analytical results and Monte-Carlo simulations when incident neutron energies are above a few eV. The introduction of the effective temperature and the rejection step to the SVT algorithm shows improvements to the neutron up-scattering treatment of hydrogen bound in liquid water.
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21
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Miyanishi K, Mizukami W, Motoyama M, Ichijo N, Kagawa A, Negoro M, Kitagawa M. Prediction of 1H Singlet Relaxation via Intermolecular Dipolar Couplings Using the Molecular Dynamics Method. J Phys Chem B 2022; 126:3530-3538. [PMID: 35538043 DOI: 10.1021/acs.jpcb.1c10799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dissolution dynamic nuclear polarization has been applied in various fields, including chemistry, biology, and medical science. To expand the scope of these applications, the nuclear singlet state, which is decoherence-free against dipolar relaxation between spin pairs, has been studied experimentally, theoretically, and numerically. The singlet state composed of proton spins is used in several applications, such as enhanced polarization preservation, molecular tagging to probe slow dynamic processes, and detection of ligand-protein complexes. In this study, we predict the lifetimes of the nuclear spin states composed of proton spin pairs using the molecular dynamics method and quantum chemistry simulations. We consider intramolecular dipolar, intermolecular dipolar between solvent and solute, chemical shift anisotropy, and spin-rotation interactions. In particular, the relaxation rate of intermolecular dipolar interactions is calculated using the molecular dynamics method for various solvents. The calculated values and the experimental values are of the same order of magnitude. Our program would provide insight into the molecular design of several NMR applications and would be helpful in predicting the nuclear spin relaxation time of synthetic molecules in advance.
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Affiliation(s)
- K Miyanishi
- Division of Advanced Electronics and Optical Science, Department of Systems Innovation, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.,Center for Quantum Information and Quantum Biology, Osaka University, 1-2 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - W Mizukami
- Center for Quantum Information and Quantum Biology, Osaka University, 1-2 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.,JST, PRESTO, Kawaguchi, Saitama 332-0012, Japan
| | - M Motoyama
- Division of Advanced Electronics and Optical Science, Department of Systems Innovation, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - N Ichijo
- Division of Advanced Electronics and Optical Science, Department of Systems Innovation, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - A Kagawa
- Division of Advanced Electronics and Optical Science, Department of Systems Innovation, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.,Center for Quantum Information and Quantum Biology, Osaka University, 1-2 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.,JST, PRESTO, Kawaguchi, Saitama 332-0012, Japan
| | - M Negoro
- Center for Quantum Information and Quantum Biology, Osaka University, 1-2 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.,Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 4-9-1, Anagawa, Inage-Ku, Chiba 263-8555, Japan
| | - M Kitagawa
- Division of Advanced Electronics and Optical Science, Department of Systems Innovation, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.,Center for Quantum Information and Quantum Biology, Osaka University, 1-2 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
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22
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Prasad D, Mitra N. High-temperature and high-pressure plastic phase of ice at the boundary of liquid water and ice VII. Proc Math Phys Eng Sci 2022. [DOI: 10.1098/rspa.2021.0958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Simultaneous high-temperature and high-pressure studies reveal phase transformation of bulk liquid water to an ice-VII-like structure having an eight coordination. It was demonstrated through this numerical study that the observed high-temperature and high-pressure phase of water obtained upon shock compression and equilibration has high rotational diffusion and thereby the hydrogen dynamics of these crystal structures are significantly complex compared with ice VII. The current work provides new characterization methods for the numerically observed plastic crystal phase of ice at the boundary of the liquid water and ice VII phases in which the molecules have a defined lattice position but rotate freely. It is anticipated that the present work will provide important data and guide new theoretical and experimental investigations in the search for plastic crystal phases of water. The power spectra plots of bulk liquid water subjected to different temperature and pressure conditions have also been presented in this numerical study, demonstrating significant differences between these high-temperature and high-pressure shock-equilibrated phases and those of pure ice VII at 10 GPa and liquid water at ambient temperature and pressure, as well as at elevated pressures and temperatures.
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Affiliation(s)
- Dipak Prasad
- Department of Civil Engineering, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Nilanjan Mitra
- Hopkins Extreme Materials Institute, Johns Hopkins University, Baltimore 21218, MD, USA
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23
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Hartling K, Li G, Bentoumi G, Yamani Z. Molecular Dynamics of Supercritical Water for Nuclear Data Development. JOURNAL OF NUCLEAR ENGINEERING AND RADIATION SCIENCE 2022. [DOI: 10.1115/1.4051790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Abstract
The Canadian supercritical water-cooled reactor was selected as one of the Generation IV International Forum initiatives for reactor design. It uses supercritical light water as a coolant under operating conditions of 25 MPa (250 bar) and 623–898 K. However, the simulation codes used to assess the performance and safety of such a design depend upon the accuracy of available nuclear data parametrizations, which currently do not include models of light water in the supercritical regime. In this paper, we present a study of supercritical water (SCW) through molecular dynamics simulations. Flexible variants of the TIP4P/2005 and simple point charge models for H2O are assessed to determine their ability to reproduce experimental measurements of SCW properties, and their suitability for the future development of nuclear data parametrizations for thermal neutron scattering from SCW. Planned experiments measuring thermal neutron scattering from SCW to inform nuclear data development are also summarized.
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Affiliation(s)
- Katy Hartling
- Canadian Nuclear Laboratories, Chalk River, ON K0J 1J0, Canada
| | - Gang Li
- Canadian Nuclear Laboratories, Chalk River, ON K0J 1J0, Canada
| | | | - Zahra Yamani
- Canadian Nuclear Laboratories, Chalk River, ON K0J 1J0, Canada
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24
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González-Salgado D, Troncoso J, Lomba E. The increment of the temperature of maximum density of water by addition of small amounts of tert-butanol: Experimental data and microscopic description revisited. J Chem Phys 2022; 156:104502. [DOI: 10.1063/5.0083355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The temperature of maximum density, TMD, of aqueous solutions of tert-butanol has been experimentally determined in the pressure range of 0–300 bars and up to 0.025 tert-butanol mole fraction. At atmospheric pressure, this quantity increases for low alcohol mole fractions, reaches a maximum at intermediate concentrations, and then quickly falls. The new experimental results are basically in agreement with previous data in the literature by Wada and Umeda [G. Wada and S. Umeda, Bull. Chem. Soc. Jpn. 35, 646 (1962)], except at very low mole fractions, where these authors reported a stronger density anomaly. Our measurements also confirm the known effect of pressure, p, on the variation in the temperature of maximum density with respect to that of pure water, Δ TMD: this quantity increases with p over the whole composition range. In addition, molecular dynamics simulations were performed between 0 and 2000 bars and from 238 to 328 K using a recently proposed model for the tert-butanol/water system. It has been found that our model reproduces qualitatively the experimental behavior of the Δ TMD, but for pressures above 1000 bars. A detailed structural analysis showed that the addition of tert-butanol promotes the low density water structure, and this promotion is somewhat hampered as the temperature increases at high pressure (Δ TMD > 0) and mostly independent of temperature at low pressures (Δ TMD < 0). Our analysis shows that the ultimate factor determining changes in the TMD is the temperature dependence of the low density water structure enhancement. We have also carried out a local structure analysis in which in addition to solid-like structures, low density liquid water ones have also been considered.
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Affiliation(s)
- D. González-Salgado
- Departamento de Física Aplicada, Universidad de Vigo, Campus del Agua, Edificio Manuel Martínez-Risco, E 32004 Ourense, Spain
| | - J. Troncoso
- Departamento de Física Aplicada, Universidad de Vigo, Campus del Agua, Edificio Manuel Martínez-Risco, E 32004 Ourense, Spain
| | - E. Lomba
- Consejo Superior de Investigaciones Científicas, Instituto de Química Física Rocasolano, Serrano 119, E 28006 Madrid, Spain
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25
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A Molecular Investigation of the Solvent Influence on Inter- and Intra-Molecular Hydrogen Bond Interaction of Linamarin. Processes (Basel) 2022. [DOI: 10.3390/pr10020352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022] Open
Abstract
Linamarin has been reported to have anticancer activities; however, its extraction and isolation using different solvents yield a low amount. Therefore, understanding the physical properties, such as solvents’ solubility, membrane permeability and lipophilicity and how they are associated with different solvents, is a paramount topic for discussion, especially for its potential as a drug. Linamarin has a sugar moiety with many polar groups responsible for its physical properties. Following current trends, a molecular dynamics simulation is performed to investigate its physical properties and how different solvents, such as water, methanol (MeOH), dimethyl sulfoxide (DMSO) and dichloromethane (DCM), affect such properties. In this work, we have investigated the influence of intermolecular and intramolecular hydrogen bonding and the influence of polar and non-polar solvents on the physical properties of linamarin. Furthermore, solvation free-energy and electronic structure analysis are performed. The structural analysis results show that the polar groups of linamarin have strong interactions with all solvents except the etheric oxygen groups. A detailed analysis shows intermolecular hydrogen bonding between polar solvents (water, MeOH and DMSO) and the hydroxyl oxygens of linamarin. Water exhibits the strongest interaction with linamarin’s functional groups among the investigated solvents. The findings show that within the first solvation shell, the number of water molecules is greatest, while MeOH has the fewest. Centrally to the structural analysis, solvation free energy confirms DMSO to be the best solvent since it prefers to interact with linamarin over itself, while water prefers to interact with itself. While the solute–solvent interactions are strongest between linamarin and water, the solvent–solvent interactions are strongest in water. As a result, the solvation free-energy calculations reveal that linamarin solvation is most favourable in DMSO.
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26
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Hande V, Chakrabarty S. Size-Dependent Order-Disorder Crossover in Hydrophobic Hydration: Comparison between Spherical Solutes and Linear Alcohols. ACS OMEGA 2022; 7:2671-2678. [PMID: 35097265 PMCID: PMC8793046 DOI: 10.1021/acsomega.1c05064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/31/2021] [Indexed: 05/03/2023]
Abstract
Theory and computer simulation studies have predicted that water molecules around hydrophobic molecules should undergo an order-disorder transition with increasing solute size around a 1 nm length scale. Some theories predict the formation of a clathrate-like ordered structure around smaller hydrophobic solutes (<1 nm) and the formation of disordered vapor-liquid interfaces around larger solutes (>1 nm) and surfaces. Experimental validation of these predictions has often been elusive and contradictory. High-resolution Raman spectroscopy has detected that water around small hydrophobic solutes shows a signature similar to that of bulk water at lower temperature (increased ordering and a stronger hydrogen-bonded network). Similarly, water around larger solutes shows an increasing population of dangling OH bonds very similar to higher temperature bulk water. Thus, the solute size dependence of the structure and dynamics of water around hydrophobic molecules seems to have an analogy with the temperature dependence in bulk water. In this work, using atomistic classical molecular dynamics (MD) simulations, we have systematically investigated this aspect and characterized this interesting analogy. Structural order parameters including the tetrahedral order parameter (Q), hydrogen bond distribution, and vibrational power spectrum highlight this similarity. However, in contrast to the experimental observations, we do not observe any length-dependent crossover for linear hydrophobic alcohols (n-alkanols) using classical MD simulations. This is in agreement with earlier findings that linear alkane chains do not demonstrate the length-dependent order-disorder transition due to the presence of a sub-nanometer length scale along the cross section of the chain. Moreover, the collapsed state of linear hydrocarbon chains is not significantly populated for smaller chains (number of carbons below 20). In the context of our computational results, we raise several pertinent questions related to the sensitivity of various structural and dynamical parameters toward capturing these complex phenomena of hydrophobic hydration.
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Affiliation(s)
- Vrushali Hande
- Physical
and Materials Chemistry Division, CSIR-National
Chemical Laboratory, Pune, Maharashtra 411008, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Suman Chakrabarty
- Department
of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700 106, India
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27
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Moid M, Finkelstein Y, Moreh R, Maiti PK. Anisotropy of the Proton Kinetic Energy as a Tool for Capturing Structural Transition in Water Confined in a Graphene Nanoslit Pore. J Phys Chem Lett 2022; 13:455-461. [PMID: 34995445 DOI: 10.1021/acs.jpclett.1c03086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The proton dynamics of a 2D water monolayer confined inside a graphene slit pore is studied in Cartesian and molecular frames of reference using molecular dynamics simulations. The vibrational density of states of the proton was calculated versus temperature and was further used to deduce the mean kinetic energy of the hydrogen atoms, Ke(H), in both frames of reference. The directional components of Ke(H) are in good agreement with experimental observations for bulk as well as nanoconfined water. Nonetheless, while in the molecular frame of reference the effect of temperature on the anisotropy ratios of Ke(H) (the ratio between its directional components) are practically invariant between the 2D and 3D cases, those in the Cartesian frame of reference reveal a rather notable reduction across 200 K, indicating the occurrence of an order-disorder transition. This result is further supported by the calculated entropy and enthalpy of the confined water molecules. Overall, it is shown that Ke(H) anisotropy ratios may serve as a valuable order parameter for detecting structural transformations in hydrogen bonds containing molecular systems.
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Affiliation(s)
- Mohd Moid
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | | | - Raymond Moreh
- Physics Department, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Prabal K Maiti
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
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28
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Chapman A, Bresme F. Polarisation of water under thermal fields: the effect of the molecular dipole and quadrupole moments. Phys Chem Chem Phys 2022; 24:14924-14936. [DOI: 10.1039/d2cp00756h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The investigation of the behaviour of water under thermal fields is important to understand thermoelectricity of solutions, aqueous suspensions, bioelectric effects or the properties of wet materials under spatially inhomogeneous...
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29
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Reich V, Majumdar A, Müller M, Busch S. Comparison of molecular dynamics simulations of water with neutron and X-ray scattering experiments. EPJ WEB OF CONFERENCES 2022. [DOI: 10.1051/epjconf/202227201015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The atomistic structure and dynamics obtained from molecular dynamics (MD) simulations with the example of TIP3P (rigid and flexible) and TIP4P/2005 (rigid) water is compared to neutron and X-ray scattering data at ambient conditions. Neutron and X-ray diffractograms are calculated from the simulations for four isotopic substitutions as well as the incoherent intermediate scattering function for neutrons. The resulting curves are compared to each other and to published experimental data. Differences between simulated and measured intermediate scattering functions are quantified by fitting an analytic model to the computed values. The sensitivity of the scattering curves to the parameters of the MD simulations is demonstrated on the example of two parameters, bond length and angle.
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30
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Lynch CI, Klesse G, Rao S, Tucker SJ, Sansom MSP. Water Nanoconfined in a Hydrophobic Pore: Molecular Dynamics Simulations of Transmembrane Protein 175 and the Influence of Water Models. ACS NANO 2021; 15:19098-19108. [PMID: 34784172 PMCID: PMC7612143 DOI: 10.1021/acsnano.1c06443] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Water molecules within biological ion channels are in a nanoconfined environment and therefore exhibit behaviors which differ from that of bulk water. Here, we investigate the phenomenon of hydrophobic gating, the process by which a nanopore may spontaneously dewet to form a "vapor lock" if the pore is sufficiently hydrophobic and/or narrow. This occurs without steric occlusion of the pore. Using molecular dynamics simulations with both rigid fixed-charge and polarizable (AMOEBA) force fields, we investigate this wetting/dewetting behavior in the transmembrane protein 175 ion channel. We examine how a range of rigid fixed-charge and polarizable water models affect wetting/dewetting in both the wild-type structure and in mutants chosen to cover a range of nanopore radii and pore-lining hydrophobicities. Crucially, we find that the rigid fixed-charge water models lead to similar wetting/dewetting behaviors, but that the polarizable water model resulted in an increased wettability of the hydrophobic gating region of the pore. This has significant implications for molecular simulations of nanoconfined water, as it implies that polarizability may need to be included if we are to gain detailed mechanistic insights into wetting/dewetting processes. These findings are of importance for the design of functionalized biomimetic nanopores (e.g., sensing or desalination) as well as for furthering our understanding of the mechanistic processes underlying biological ion channel function.
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Affiliation(s)
- Charlotte I. Lynch
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK, OX1 3QU
| | - Gianni Klesse
- Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, UK, OX1 3PU
| | - Shanlin Rao
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK, OX1 3QU
| | - Stephen J. Tucker
- Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, UK, OX1 3PU
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK, OX1 3QU
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31
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Mass action model of solution activity via speciation by solvation and ion pairing equilibria. Commun Chem 2021; 4:163. [PMID: 36697558 PMCID: PMC9814931 DOI: 10.1038/s42004-021-00599-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/25/2021] [Indexed: 01/28/2023] Open
Abstract
Solutes and their concentrations influence many natural and anthropogenic solution processes. Electrolyte and solution models are used to quantify and predict such behavior. Here we present a mechanistic solution model based on mass action equilibria. Solvation and ion pairing are used to model speciated solute and solvent concentrations such that they correlate to a solution's vapor pressure (solvent activity) according to Raoult's law from dilute conditions to saturation. This model introduces a hydration equilibrium constant (Kha) that is used with either an ion dissociation constant (Kid) or a hydration modifier (m) with an experimentally determined ion dissociation constant, as adjustable parameters to fit vapor-liquid equilibrium data. The modeled solvation equilibria are accompanied by molecular dynamics (MD) studies that support a decline in the observed degree of solvation with increased concentration. MD calculations indicate this finding is a combination of a solvent that solvates multiple solutes, and changes in a solute's solvation sphere, with the dominant factor changing with concentration. This speciation-based solution model is lateral to established electrostatics-based electrolyte theories. With its basis in mass action, the model can directly relate experimental data to the modeled solute and solvent speciated concentrations and structures.
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32
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Vuai SAH, Sahini MG, Onoka I, Kiruri LW, Shadrack DM. Cation-π interactions drive hydrophobic self-assembly and aggregation of niclosamide in water. RSC Adv 2021; 11:33136-33147. [PMID: 35493563 PMCID: PMC9042188 DOI: 10.1039/d1ra05358b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/13/2021] [Indexed: 12/15/2022] Open
Abstract
The beneficial medicinal effects of niclosamide have been reported to be hampered by poor aqueous solubility and so a higher concentration dosage is required. In this work, we have studied the aggregation properties of niclosamide in water by varying the number of monomers. We have employed all-atom classical molecular dynamics simulation in order to explore such properties. The equilibrium structure exists in an aggregated state with structural rearrangements of the stacking units. Niclosamide monomers tend to form clusters in an orderly manner and tend to aggregate in parallel and antiparallel orientations of the phenyl rings as the monomers are increased in number from 4 to 9. Upon increasing the size from 9 to 14, and from 49 to 150, a considerable dominance of the metastable parallel arrangement is observed, resulting in the formation of a closely packed cluster with hydrophobic contacts. The metastable conformation self-arranges to a T-shape before forming a stable planar antiparallel displaced conformation. The aggregated π–π parallel and cation–π antiparallel clusters in water exist in a β-conformer. We further observed that formation of a stable cluster aggregate entails the formation of an intermediate metastable cluster that disperses in solution forming a large stable cluster. We also discovered that movement of the water is faster in less aggregated clusters and as the cluster size increases, the mobility rate becomes much slower. In this work, we have studied the aggregation properties of niclosamide in water by varying the number of monomers.![]()
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Affiliation(s)
- Said A H Vuai
- Department of Chemistry, College of Natural and Mathematical Sciences, University of Dodoma P. O. Box 338 Dodoma Tanzania
| | - Mtabazi G Sahini
- Department of Chemistry, College of Natural and Mathematical Sciences, University of Dodoma P. O. Box 338 Dodoma Tanzania
| | - Isaac Onoka
- Department of Chemistry, College of Natural and Mathematical Sciences, University of Dodoma P. O. Box 338 Dodoma Tanzania
| | - Lucy W Kiruri
- Department of Chemistry, Kenyatta University P. O. Box 43844-00100 Nairobi Kenya
| | - Daniel M Shadrack
- Department of Chemistry, Faculty of Natural and Applied Sciences, St. John's University of Tanzania P. O. Box 47 Dodoma Tanzania
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33
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Kadaoluwa Pathirannahalage SP, Meftahi N, Elbourne A, Weiss ACG, McConville CF, Padua A, Winkler DA, Costa Gomes M, Greaves TL, Le TC, Besford QA, Christofferson AJ. Systematic Comparison of the Structural and Dynamic Properties of Commonly Used Water Models for Molecular Dynamics Simulations. J Chem Inf Model 2021; 61:4521-4536. [PMID: 34406000 DOI: 10.1021/acs.jcim.1c00794] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Water is a unique solvent that is ubiquitous in biology and present in a variety of solutions, mixtures, and materials settings. It therefore forms the basis for all molecular dynamics simulations of biological phenomena, as well as for many chemical, industrial, and materials investigations. Over the years, many water models have been developed, and it remains a challenge to find a single water model that accurately reproduces all experimental properties of water simultaneously. Here, we report a comprehensive comparison of structural and dynamic properties of 30 commonly used 3-point, 4-point, 5-point, and polarizable water models simulated using consistent settings and analysis methods. For the properties of density, coordination number, surface tension, dielectric constant, self-diffusion coefficient, and solvation free energy of methane, models published within the past two decades consistently show better agreement with experimental values compared to models published earlier, albeit with some notable exceptions. However, no single model reproduced all experimental values exactly, highlighting the need to carefully choose a water model for a particular study, depending on the phenomena of interest. Finally, machine learning algorithms quantified the relationship between the water model force field parameters and the resulting bulk properties, providing insight into the parameter-property relationship and illustrating the challenges of developing a water model that can accurately reproduce all properties of water simultaneously.
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Affiliation(s)
- Sachini P Kadaoluwa Pathirannahalage
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia.,Laboratoire de Chimie, Ecole Normale Supérieure de Lyon, CNRS, Lyon 69342, France
| | - Nastaran Meftahi
- ARC Centre of Excellence in Exciton Science, School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Aaron Elbourne
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Alessia C G Weiss
- Leibniz-Institut für Polymerforschung e.V., Hohe Straße 6, 01069 Dresden, Germany
| | - Chris F McConville
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia.,Institute for Frontier Materials, Deakin University, Geelong, Victoria 3220, Australia
| | - Agilio Padua
- Laboratoire de Chimie, Ecole Normale Supérieure de Lyon, CNRS, Lyon 69342, France
| | - David A Winkler
- School of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia.,Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia.,School of Pharmacy, University of Nottingham, Nottingham NG7 2QL, U.K
| | | | - Tamar L Greaves
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Tu C Le
- School of Engineering, RMIT University, Melbourne, Victoria 3001, Australia
| | - Quinn A Besford
- Leibniz-Institut für Polymerforschung e.V., Hohe Straße 6, 01069 Dresden, Germany
| | - Andrew J Christofferson
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia.,ARC Centre of Excellence in Exciton Science, School of Science, RMIT University, Melbourne, Victoria 3000, Australia
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34
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Abstract
The thermodynamic stability of water next to graphitic surfaces is of fundamental interest, as it underlies several natural phenomena and important industrial processes. It is commonly assumed that water wets graphite more than graphene due to increased, favorable van der Waals interactions between the interfacial water molecules with multiple carbon sheets. Here, we employed extensive computer simulations and analysis of the molecular correlation functions to show that the interfacial water thermodynamics is in fact dominated by surface entropy. We show that on graphite, destabilization of the interfacial hydrogen bond network leads to an overcompensating increase in population of low frequency translational and librational modes, which is ultimately responsible for the increased interfacial stability compared to graphene. The spectroscopic signature of this effect is an enhancement of the modes near 100 and 300 cm-1. This subtle interplay between entropy and surface binding may have important consideration for interpretations of various phenomena, including the hydrophobic effect.
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Affiliation(s)
- Tod A Pascal
- ATLAS Materials Physics Laboratory, Department of NanoEngineering and Chemical Engineering, University of California San Diego, La Jolla, California 92093, United States
- Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
| | - William A Goddard
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, United States
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35
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Dubey V, Dueby S, Daschakraborty S. Breakdown of the Stokes-Einstein relation in supercooled water: the jump-diffusion perspective. Phys Chem Chem Phys 2021; 23:19964-19986. [PMID: 34515269 DOI: 10.1039/d1cp02202d] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Although water is the most ubiquitous liquid it shows many thermodynamic and dynamic anomalies. Some of the anomalies further intensify in the supercooled regime. While many experimental and theoretical studies have focused on the thermodynamic anomalies of supercooled water, fewer studies explored the dynamical anomalies very extensively. This is due to the intricacy of the experimental measurement of the dynamical properties of supercooled water. Violation of the Stokes-Einstein relation (SER), an important relation connecting the diffusion of particles with the viscosity of the medium, is one of the major dynamical anomalies. In absence of experimentally measured viscosity, researchers used to check the validity of SER indirectly using average translational relaxation time or α-relaxation time. Very recently, the viscosity of supercooled water was accurately measured at a wide range of temperatures and pressures. This allowed direct verification of the SER at different temperature-pressure thermodynamic state points. An increasing breakdown of the SER was observed with decreasing temperature. Increasing pressure reduces the extent of breakdown. Although some well-known theories explained the above breakdown, a detailed molecular mechanism was still elusive. Recently, a translational jump-diffusion (TJD) approach has been able to quantitatively explain the breakdown of the SER in pure supercooled water and an aqueous solution of methanol. The objective of this article is to present a detailed and state-of-the-art analysis of the past and present works on the breakdown of SER in supercooled water with a specific focus on the new TJD approach for explaining the breakdown of the SER.
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Affiliation(s)
- Vikas Dubey
- Department of Chemistry, Indian Institute of Technology Patna, Bihar 801106, India.
| | - Shivam Dueby
- Department of Chemistry, Indian Institute of Technology Patna, Bihar 801106, India.
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36
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Gittus OR, Bresme F. Thermophysical properties of water using reactive force fields. J Chem Phys 2021; 155:114501. [PMID: 34551553 DOI: 10.1063/5.0057868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The widescale importance and rich phenomenology of water continue to motivate the development of computational models. ReaxFF force fields incorporate many characteristics desirable for modeling aqueous systems: molecular flexibility, polarization, and chemical reactivity (bond formation and breaking). However, their ability to model the general properties of water has not been evaluated in detail. We present comprehensive benchmarks of the thermophysical properties of water for two ReaxFF models, the water-2017 and CHON-2017_weak force fields. These include structural, electrostatic, vibrational, thermodynamic, coexistence, and transport properties at ambient conditions (300 K and 0.997 g cm-3) and along the standard pressure (1 bar) isobar. Overall, CHON-2017_weak predicts more accurate thermophysical properties than the water-2017 force field. Based on our results, we recommend potential avenues for improvement: the dipole moment to quadrupole moment ratio, the self-diffusion coefficient, especially for water-2017, and the gas phase vibrational frequencies with the aim to improve the vibrational properties of liquid water.
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Affiliation(s)
- Oliver R Gittus
- Department of Chemistry, Molecular Sciences Research Hub Imperial College, London W12 0BZ, United Kingdom
| | - Fernando Bresme
- Department of Chemistry, Molecular Sciences Research Hub Imperial College, London W12 0BZ, United Kingdom
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37
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Vuai SAH, Onoka I, Sahini MG, Swai HS, Shadrack DM. Abrogating the nsp10–nsp16 switching mechanisms in SARS-CoV-2 by phytochemicals from Withania somnifera: a molecular dynamics study. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1974432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Said A. H. Vuai
- Department of Chemistry, College of Natural and Mathematical Sciences, University of Dodoma, Dodoma, Tanzania
| | - Isaac Onoka
- Department of Chemistry, College of Natural and Mathematical Sciences, University of Dodoma, Dodoma, Tanzania
| | - Mtabazi G. Sahini
- Department of Chemistry, College of Natural and Mathematical Sciences, University of Dodoma, Dodoma, Tanzania
| | - Hulda S. Swai
- School of Life Sciences and Bioengeering, The Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Daniel M. Shadrack
- Department of Chemistry, Faculty of Natural and Applied Sciences, St. John's University of Tanzania, Dodoma, Tanzania
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38
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Flexible model of water based on the dielectric and electromagnetic spectrum properties: TIP4P/∊Flex. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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39
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Noguere G, Scotta JP, Xu S, Farhi E, Ollivier J, Calzavarra Y, Rols S, Koza M, Marquez Damian JI. Temperature-dependent dynamic structure factors for liquid water inferred from inelastic neutron scattering measurements. J Chem Phys 2021; 155:024502. [PMID: 34266266 DOI: 10.1063/5.0055779] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Temperature-dependent dynamic structure factors S(Q, ω) for liquid water have been calculated using a composite model, which is based on the decoupling approximation of the mean square displacement of the water molecules into diffusion and solid-like vibrational parts. The solid-like vibrational part Svib(Q, ω) is calculated with the phonon expansion method established in the framework of the incoherent Gaussian approximation. The diffusion part Sdiff(Q, ω) relies on the Egelstaff-Schofield translational diffusion model corrected for jump diffusions and rotational diffusions with the Singwi-Sjölander random model and Sears expansion, respectively. Systematics of the model parameters as a function of temperature were deduced from quasi-elastic neutron scattering data analysis reported in the literature and from molecular dynamics (MD) simulations relying on the TIP4P/2005f model. The resulting S(Q, ω) values are confronted by means of Monte Carlo simulations to inelastic neutron scattering data measured with IN4, IN5, and IN6 time-of-flight spectrometers of the Institut Laue-Langevin (ILL) (Grenoble, France). A modest range of temperatures (283-494 K) has been investigated with neutron wavelengths corresponding to incident neutron energies ranging from 0.57 to 67.6 meV. The neutron-weighted multiphonon spectra deduced from the ILL data indicate a slight overestimation by the MD simulations of the frequency shift and broadening of the librational band. The descriptive power of the composite model was suited for improving the comparison to experiments via Bayesian updating of prior model parameters inferred from MD simulations. The reported posterior temperature-dependent densities of state of hydrogen in H2O would represent valuable insights for studying the collective coupling interactions in the water molecule between the inter- and intramolecular degrees of freedom.
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Affiliation(s)
- G Noguere
- CEA, DES, IRESNE, Cadarache, F-13108 Saint Paul Les Durance, France
| | - J P Scotta
- CEA, DES, IRESNE, Cadarache, F-13108 Saint Paul Les Durance, France
| | - S Xu
- CEA, DES, IRESNE, Cadarache, F-13108 Saint Paul Les Durance, France
| | - E Farhi
- Institut Laue-Langevin, F-38042 Grenoble, France
| | - J Ollivier
- Institut Laue-Langevin, F-38042 Grenoble, France
| | - Y Calzavarra
- Institut Laue-Langevin, F-38042 Grenoble, France
| | - S Rols
- Institut Laue-Langevin, F-38042 Grenoble, France
| | - M Koza
- Institut Laue-Langevin, F-38042 Grenoble, France
| | - J I Marquez Damian
- Neutron Physics Departement and Instituto Balseiro, Centro Atomico Bariloche, CNEA, Bariloche, Argentina
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40
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Sun Y, Rogge SMJ, Lamaire A, Vandenbrande S, Wieme J, Siviour CR, Van Speybroeck V, Tan JC. High-rate nanofluidic energy absorption in porous zeolitic frameworks. NATURE MATERIALS 2021; 20:1015-1023. [PMID: 33888902 DOI: 10.1038/s41563-021-00977-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 03/03/2021] [Indexed: 05/09/2023]
Abstract
Optimal mechanical impact absorbers are reusable and exhibit high specific energy absorption. The forced intrusion of liquid water in hydrophobic nanoporous materials, such as zeolitic imidazolate frameworks (ZIFs), presents an attractive pathway to engineer such systems. However, to harness their full potential, it is crucial to understand the underlying water intrusion and extrusion mechanisms under realistic, high-rate deformation conditions. Here, we report a critical increase of the energy absorption capacity of confined water-ZIF systems at elevated strain rates. Starting from ZIF-8 as proof-of-concept, we demonstrate that this attractive rate dependence is generally applicable to cage-type ZIFs but disappears for channel-containing zeolites. Molecular simulations reveal that this phenomenon originates from the intrinsic nanosecond timescale needed for critical-sized water clusters to nucleate inside the nanocages, expediting water transport through the framework. Harnessing this fundamental understanding, design rules are formulated to construct effective, tailorable and reusable impact energy absorbers for challenging new applications.
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Affiliation(s)
- Yueting Sun
- Department of Engineering Science, University of Oxford, Oxford, UK.
- School of Engineering, University of Birmingham, Edgbaston, Birmingham, UK.
| | - Sven M J Rogge
- Center for Molecular Modeling (CMM), Ghent University, Zwijnaarde, Belgium.
| | - Aran Lamaire
- Center for Molecular Modeling (CMM), Ghent University, Zwijnaarde, Belgium
| | | | - Jelle Wieme
- Center for Molecular Modeling (CMM), Ghent University, Zwijnaarde, Belgium
| | - Clive R Siviour
- Department of Engineering Science, University of Oxford, Oxford, UK
| | | | - Jin-Chong Tan
- Department of Engineering Science, University of Oxford, Oxford, UK.
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41
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Majumdar J, Moid M, Dasgupta C, Maiti PK. Dielectric Profile and Electromelting of a Monolayer of Water Confined in Graphene Slit Pore. J Phys Chem B 2021; 125:6670-6680. [PMID: 34107687 DOI: 10.1021/acs.jpcb.1c02266] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A monolayer of water confined between two parallel graphene sheets exists in many different phases and exhibits fascinating dielectric properties that have been studied in experiments. In this work, we use molecular dynamics simulations to study how the dielectric properties of a confined monolayer of water is affected by its structure. We consider six of the popular nonpolarizable water models-SPC/E, SPC/Fw, TIP3P, TIP3P_M (modified), TIP4P-2005, and TIP4P-2005f-and find that the in-plane structure of the water molecules at ambient temperature and pressure is strongly dependent on the water model: all the 3-point water models considered here show square ice formation, whereas no such structural ordering is observed for the 4-point water models. This allows us to investigate the role of the in-plane structure of the water monolayer on its dielectric profile. Our simulations show an anomalous perpendicular dielectric constant compared to the bulk, and the models that do not exhibit ice formation show very different dielectric response along the channel width compared to models that exhibit square ice formation. We also demonstrate the occurrence of electromelting of the in-plane ordered water under the application of a perpendicular electric field and find that the critical field for electromelting strongly depends on the water model. Together, we have shown the dependence of confined water properties on the different water structures that it may take when sandwiched between bilayer graphene. These remarkable properties of confined water can be exploited in various nanofluidic devices, artificial ion channels, and molecular sieving.
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Affiliation(s)
- Jeet Majumdar
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Mohd Moid
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Chandan Dasgupta
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.,International Centre for Theoretical Sciences, Bangalore 560089, India
| | - Prabal K Maiti
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
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42
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Kuo AT, Urata S, Koguchi R, Sonoda T, Kobayashi S, Tanaka M. Effects of Side-Chain Spacing and Length on Hydration States of Poly(2-methoxyethyl acrylate) Analogues: A Molecular Dynamics Study. ACS Biomater Sci Eng 2021; 7:2383-2391. [PMID: 33979126 DOI: 10.1021/acsbiomaterials.1c00388] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydration states of polymers are known to directly influence the adsorption of biomolecules. Particularly, intermediate water (IW) has been found able to prevent protein adsorption. Experimental studies have examined the IW content and nonthrombogenicity of poly(2-methoxyethyl acrylate) analogues with different side-chain spacings and lengths, which are HPx (x is the number of backbone carbons in a monomer) and PMCyA (y is the number of carbons in-between ester and ether oxygens of the side-chain) series, respectively. HPx was reported to possess more IW content but lower nonthrombogenicity compared to PMCyA with analogous composition. To understand the reason for the conflict, molecular dynamics simulations were conducted to elucidate the difference in the properties between the HPx and PMCyA. Simulation results showed that the presence of more methylene groups in the side chain more effectively prohibits water penetration in the polymer than those in the polymer backbone, causing a lower IW content in the PMCyA. At a high water content, the methoxy oxygen in the shorter side chain of the HPx cannot effectively bind water compared to that in the PMCyA side chain. HPx side chains may have more room to contact with molecules other than water (e.g., proteins), causing experimentally less nonthrombogenicity of HPx than that of PMCyA. In summary, theoretical simulations successfully explained the difference in the effects of side-chain spacing and length in atomistic scale.
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Affiliation(s)
- An-Tsung Kuo
- Innovative Technology Laboratories, AGC Inc., Yokohama 230-0045, Japan
| | - Shingo Urata
- Innovative Technology Laboratories, AGC Inc., Yokohama 230-0045, Japan
| | - Ryohei Koguchi
- Materials Integration Laboratories, AGC Inc., Yokohama 230-0045, Japan
| | - Toshiki Sonoda
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Shingo Kobayashi
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Masaru Tanaka
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
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43
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Ortega-Guerrero A, Sahabudeen H, Croy A, Dianat A, Dong R, Feng X, Cuniberti G. Multiscale Modeling Strategy of 2D Covalent Organic Frameworks Confined at an Air-Water Interface. ACS APPLIED MATERIALS & INTERFACES 2021; 13:26411-26420. [PMID: 34034486 DOI: 10.1021/acsami.1c05967] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Two-dimensional covalent organic frameworks (2D COFs) have attracted attention as versatile active materials in many applications. Recent advances have demonstrated the synthesis of monolayer 2D COF via an air-water interface. However, the interfacial 2D polymerization mechanism has been elusive. In this work, we have used a multiscale modeling strategy to study dimethylmethylene-bridged triphenylamine building blocks confined at the air-water interface to form a 2D COF via Schiff-base reaction. A synergy between the computational investigations and experiments allowed the synthesis of a 2D-COF with one of the linkers considered. Our simulations complement the experimental characterization and show the preference of the building blocks to be at the interface with a favorable orientation for the polymerization. The air-water interface is shown to be a key factor to stabilize a flat conformation when a dimer molecule is considered. The structural and electronic properties of the monolayer COFs based on the two monomers are calculated and show a semiconducting nature with direct bandgaps. Our strategy provides a first step toward the in silico polymerization of 2D COFs at air-water interfaces capturing the initial steps of the synthesis up to the prediction of electronic properties of the 2D material.
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Affiliation(s)
- Andres Ortega-Guerrero
- Laboratory of Molecular Simulation (LSMO), Institut des Sciences et Ingénierie Chimiques, Valais Ecole Polytechnique Fédérale de Lausanne (EPFL), Rue de l'Industrie 17, CH-1951 Sion, Valais, Switzerland
| | - Hafeesudeen Sahabudeen
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, 01062 Dresden, Germany
- Center for Advancing Electronics Dresden (CFAED), Technische Universität Dresden, 01062 Dresden, Germany
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, Teltow 14513, Germany
| | - Alexander Croy
- Institute for Materials Science and Max Bergmann Center of Biomaterials, Technische Universität Dresden, 01062 Dresden, Germany
| | - Arezoo Dianat
- Institute for Materials Science and Max Bergmann Center of Biomaterials, Technische Universität Dresden, 01062 Dresden, Germany
| | - Renhao Dong
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, 01062 Dresden, Germany
- Center for Advancing Electronics Dresden (CFAED), Technische Universität Dresden, 01062 Dresden, Germany
| | - Xinliang Feng
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, 01062 Dresden, Germany
- Center for Advancing Electronics Dresden (CFAED), Technische Universität Dresden, 01062 Dresden, Germany
| | - Gianaurelio Cuniberti
- Institute for Materials Science and Max Bergmann Center of Biomaterials, Technische Universität Dresden, 01062 Dresden, Germany
- Dresden Center for Computational Materials Science (DCMS), Technische Universität Dresden, 01062 Dresden, Germany
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44
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45
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Moid M, Sastry S, Dasgupta C, Pascal TA, Maiti PK. Dimensionality dependence of the Kauzmann temperature: A case study using bulk and confined water. J Chem Phys 2021; 154:164510. [PMID: 33940812 DOI: 10.1063/5.0047656] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Kauzmann temperature (TK) of a supercooled liquid is defined as the temperature at which the liquid entropy becomes equal to that of the crystal. The excess entropy, the difference between liquid and crystal entropies, is routinely used as a measure of the configurational entropy, whose vanishing signals the thermodynamic glass transition. The existence of the thermodynamic glass transition is a widely studied subject, and of particular recent interest is the role of dimensionality in determining the presence of a glass transition at a finite temperature. The glass transition in water has been investigated intensely and is challenging as the experimental glass transition appears to occur at a temperature where the metastable liquid is strongly prone to crystallization and is not stable. To understand the dimensionality dependence of the Kauzmann temperature in water, we study computationally bulk water (three-dimensions), water confined in the slit pore of the graphene sheet (two-dimensions), and water confined in the pore of the carbon nanotube of chirality (11,11) having a diameter of 14.9 Å (one-dimension), which is the lowest diameter where amorphous water does not always crystallize into nanotube ice in the supercooled region. Using molecular dynamics simulations, we compute the entropy of water in bulk and under reduced dimensional nanoscale confinement to investigate the variation of the Kauzmann temperature with dimension. We obtain a value of TK (133 K) for bulk water in good agreement with experiments [136 K (C. A. Angell, Science 319, 582-587 (2008) and K. Amann-Winkel et al., Proc. Natl. Acad. Sci. U. S. A. 110, 17720-17725 (2013)]. However, for confined water, in two-dimensions and one-dimension, we find that there is no finite temperature Kauzmann point (in other words, the Kauzmann temperature is 0 K). Analysis of the fluidicity factor, a measure of anharmonicity in the oscillation of normal modes, reveals that the Kauzmann temperature can also be computed from the difference in the fluidicity factor between amorphous and ice phases.
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Affiliation(s)
- Mohd Moid
- Department of Physics, Centre for Condensed Matter Theory, Indian Institute of Science, Bangalore 560012, India
| | - Srikanth Sastry
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Chandan Dasgupta
- Department of Physics, Centre for Condensed Matter Theory, Indian Institute of Science, Bangalore 560012, India
| | - Tod A Pascal
- Department of Nanoengineering and Chemical Engineering, University of California San Diego, La Jolla, California 92023, USA
| | - Prabal K Maiti
- Department of Physics, Centre for Condensed Matter Theory, Indian Institute of Science, Bangalore 560012, India
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46
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Maxim F, Karalis K, Boillat P, Banuti DT, Marquez Damian JI, Niceno B, Ludwig C. Thermodynamics and Dynamics of Supercritical Water Pseudo-Boiling. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2002312. [PMID: 33552857 PMCID: PMC7856905 DOI: 10.1002/advs.202002312] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/12/2020] [Indexed: 06/12/2023]
Abstract
Supercritical fluid pseudo-boiling (PB), recently brought to the attention of the scientific community, is the phenomenon occurring when fluid changes its structure from liquid-like (LL) to gas-like (GL) states across the Widom line. This work provides the first quantitative analysis on the thermodynamics and the dynamics of water's PB, since the understanding of this phase transition is mandatory for the successful implementation of technologies using supercritical water (scH2O) for environmental, energy, and nanomaterial applications. The study combines computational techniques with in situ neutron imaging measurements. The results demonstrate that, during isobaric heating close to the critical point, while water density drops by a factor of three in the PB transitional region, the system needs >16 times less energy to increase its temperature by 1 K than to change its structure from LL to GL phase. Above the PB-Widom line, the structure of LL water consists mainly of tetramers and trimers, while below the line mostly dimers and monomers form in the GL phase. At atomic level, the PB dynamics are similar to those of the subcritical water vaporization. This fundamental knowledge has great impact on water science, as it helps to establish the structure-properties relationship of scH2O.
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Affiliation(s)
- Florentina Maxim
- Laboratory for Chemical Thermodynamics“Ilie Murgulescu” Institute of Physical ChemistrySplaiul Independentei 202Bucharest060021Romania
- Laboratory for Bioenergy and Catalysis (LBK)ENE DivisionPaul Scherrer InstituteVilligen PSI5232Switzerland
| | | | - Pierre Boillat
- Electrochemistry Laboratory (LEC)ENE DivisionPaul Scherrer InstituteVilligen PSI5232Switzerland
- Laboratory for Neutron Scattering and Imaging (LNS)NUM DivisionPaul Scherrer InstituteVilligen PSI5232Switzerland
| | - Daniel T. Banuti
- Department of Mechanical EngineeringThe University of New MexicoMSC01 1150AlbuquerqueNM87131USA
| | | | - Bojan Niceno
- Laboratory for Scientific Computing and Modelling (LSM)NES DivisionPaul Scherrer InstituteVilligen PSI5232Switzerland
- Eidgenössische Technische Hochschule Zürich (ETHZ)MAVT‐LKEZurich8092Switzerland
| | - Christian Ludwig
- Laboratory for Bioenergy and Catalysis (LBK)ENE DivisionPaul Scherrer InstituteVilligen PSI5232Switzerland
- École Polytechnique Fédérale de Lausanne (EPFL)ENAC IIE GR‐LUDLausanne1015Switzerland
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Rapallo A, Gaspari R, Grasso G, Danani A. Extended diffusion theory: Recovering dynamics from biased/accelerated molecular simulations. J Comput Chem 2020; 42:586-599. [PMID: 33351966 DOI: 10.1002/jcc.26474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/09/2020] [Accepted: 12/02/2020] [Indexed: 11/08/2022]
Abstract
Dynamical properties are of great importance in determining the behavior of synthetic and natural molecules, but capturing them by computational methods is a nontrivial task. Very often the time scales of the relevant phenomena are far beyond the typical time windows accessible by classical Molecular Dynamics (MD) simulations, currently limited to the order of microseconds on standard laboratory workstations. On the other hand, biased and accelerated simulations allow for fast and thorough exploration of the molecular conformational space, but they lose the dynamic information. The problem of recovering dynamics from biased/accelerated simulations is a very active field of research, but no totally robust/reliable solutions have been given yet. In this paper it is shown how the Smoluchowski equation, in the framework of Diffusion Theory (DT), can be used to bridge this gap, and dynamical properties, in the form of time correlation functions (TCFs), can be extracted also from such kind of simulations. DT is first extended (EDT) to express the mobility tensors entering the Smoluchowski operator in terms of a recently introduced unified and regularized Rotne-Prager-Yamakawa approximation, [P. J. Zuk, E. Wajnryb, K. A. Mizerski, P. Szymczak, J. Fluid. Mech. 2014, 741, R5, 1-13] also involving mixed rotation-translation contributions, and rotation-rotation terms beside the classical translation-translation ones, so far used in DT. Then, the method is applied to recover the dynamics of a nontrivial example of a peptide in explicit water from the first 200 ns of a Replica Exchange Molecular Dynamics simulation, which is a popular computational method that destroys the long time dynamics. EDT dynamics were found to favorably compare against those coming from a standard MD simulation of the same system, requiring a time window of 30 μs to converge. This result shows that EDT is a tool of practical value to recover the long time dynamics of systems in diffusive regimes from biased/accelerated simulations, to be exploited in those cases when direct evaluation by standard MD is unfeasible.
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Affiliation(s)
- Arnaldo Rapallo
- CNR - Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), Milano, Italy
| | - Roberto Gaspari
- CNR - Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), Milano, Italy
| | - Gianvito Grasso
- Dalle Molle Institute for Artificial Intelligence (IDSIA), Università della Svizzera italiana (USI), Scuola Universitaria Professionale della Svizzera italiana (SUPSI), Lugano-Viganello, Switzerland
| | - Andrea Danani
- Dalle Molle Institute for Artificial Intelligence (IDSIA), Università della Svizzera italiana (USI), Scuola Universitaria Professionale della Svizzera italiana (SUPSI), Lugano-Viganello, Switzerland
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48
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Kuo AT, Urata S, Koguchi R, Sonoda T, Kobayashi S, Tanaka M. Molecular Dynamics Study on the Water Mobility and Side-Chain Flexibility of Hydrated Poly(ω-methoxyalkyl acrylate)s. ACS Biomater Sci Eng 2020; 6:6690-6700. [PMID: 33320637 DOI: 10.1021/acsbiomaterials.0c01220] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Intermediate water (IW) is known to play an important role in the antifouling property of biocompatible polymers. However, how IW prevents protein adsorption is still unclear. To understand the role of IW in the antifouling mechanism, molecular dynamics simulation was used to investigate the dynamic properties of water and side-chains for hydrated poly(ω-methoxyalkyl acrylate)s (PMCxA, where x indicates the number of methylene carbons) with x = 1-6 and poly(n-butyl acrylate) (PBA) in this study. Since the polymers uptake more water than their equilibrium water content (EWC) at the polymer/water interface, we analyzed the hydrated polymers at a water content higher than that of EWC. It was found that the water molecules interacting with one polymer oxygen atom (BW1), of which most are IW molecules, in PMC2A exhibit the lowest mobility, while those in PBA and PMC1A show a higher mobility. The result was consistent with the expectation that the biocompatible polymer with a long-resident hydration layer possesses good antifouling property. Through the detailed analysis of side-chain binding with three different types of BW1 molecules, we found that the amount of side-chains simultaneously interacting with two BW1 molecules, which exhibit the highest flexibility among the three kinds of side-chains, is the lowest for PMC1A. The high mobility of BW1 is thus suggested as the main factor for the poor protein adsorption resistance of PMC1A even though it possesses enough IW content and relatively flexible side-chains. Contrarily, a maximum amount of side-chains simultaneously interacting with two BW1 molecules was found in the hydrated PMC3A. The moderate side-chain length of PMC3A allows side-chains to simultaneously interact with two BW1 molecules and minimizes the hydrophobic part attractively interacting with a protein at the polymer/water interface. The unique structure of PMC3A may be the reason causing the best protein adsorption resistance among the PMCxAs.
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Affiliation(s)
- An-Tsung Kuo
- Innovative Technology Laboratories, AGC Inc., Yokohama 230-0045, Japan
| | - Shingo Urata
- Innovative Technology Laboratories, AGC Inc., Yokohama 230-0045, Japan
| | - Ryohei Koguchi
- Materials Integration Laboratories, AGC Inc., Yokohama 230-0045, Japan
| | - Toshiki Sonoda
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Shingo Kobayashi
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Masaru Tanaka
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
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Lynch C, Rao S, Sansom MSP. Water in Nanopores and Biological Channels: A Molecular Simulation Perspective. Chem Rev 2020; 120:10298-10335. [PMID: 32841020 PMCID: PMC7517714 DOI: 10.1021/acs.chemrev.9b00830] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Indexed: 12/18/2022]
Abstract
This Review explores the dynamic behavior of water within nanopores and biological channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside selected structural and other experimental investigations. Structures of biological nanopores and channels are reviewed, emphasizing those high-resolution crystal structures, which reveal water molecules within the transmembrane pores, which can be used to aid the interpretation of simulation studies. Different levels of molecular simulations of water within nanopores are described, with a focus on molecular dynamics (MD). In particular, models of water for MD simulations are discussed in detail to provide an evaluation of their use in simulations of water in nanopores. Simulation studies of the behavior of water in idealized models of nanopores have revealed aspects of the organization and dynamics of nanoconfined water, including wetting/dewetting in narrow hydrophobic nanopores. A survey of simulation studies in a range of nonbiological nanopores is presented, including carbon nanotubes, synthetic nanopores, model peptide nanopores, track-etched nanopores in polymer membranes, and hydroxylated and functionalized nanoporous silica. These reveal a complex relationship between pore size/geometry, the nature of the pore lining, and rates of water transport. Wider nanopores with hydrophobic linings favor water flow whereas narrower hydrophobic pores may show dewetting. Simulation studies over the past decade of the behavior of water in a range of biological nanopores are described, including porins and β-barrel protein nanopores, aquaporins and related polar solute pores, and a number of different classes of ion channels. Water is shown to play a key role in proton transport in biological channels and in hydrophobic gating of ion channels. An overall picture emerges, whereby the behavior of water in a nanopore may be predicted as a function of its hydrophobicity and radius. This informs our understanding of the functions of diverse channel structures and will aid the design of novel nanopores. Thus, our current level of understanding allows for the design of a nanopore which promotes wetting over dewetting or vice versa. However, to design a novel nanopore, which enables fast, selective, and gated flow of water de novo would remain challenging, suggesting a need for further detailed simulations alongside experimental evaluation of more complex nanopore systems.
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Affiliation(s)
- Charlotte
I. Lynch
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Shanlin Rao
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
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50
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Chapman CW, Arbanas G, Kolesnikov AI, Leal L, Danon Y, Wendorff C, Ramić K, Liu L, Rahnema F. Methodology for Generating Covariance Data of Thermal Neutron Scattering Cross Sections. NUCL SCI ENG 2020. [DOI: 10.1080/00295639.2020.1792716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Chris W. Chapman
- Oak Ridge National Laboratory, Nuclear Data and Criticality Safety, Reactor and Nuclear Systems Division, Oak Ridge, Tennessee 37831
| | - Goran Arbanas
- Oak Ridge National Laboratory, Nuclear Data and Criticality Safety, Reactor and Nuclear Systems Division, Oak Ridge, Tennessee 37831
| | | | - Luiz Leal
- Institut de Radioprotection et de Sûréte Nucléaire, 31, avenue de la division Leclerc, Fontenay-aux-Roses 92260, France
| | - Yaron Danon
- Rensselaer Polytechnic Institute, Gaerttner LINAC Center, 3021 Tibbits Avenue, Troy, New York 12180
| | - Carl Wendorff
- Rensselaer Polytechnic Institute, Gaerttner LINAC Center, 3021 Tibbits Avenue, Troy, New York 12180
| | - Kemal Ramić
- Rensselaer Polytechnic Institute, Gaerttner LINAC Center, 3021 Tibbits Avenue, Troy, New York 12180
| | - Li Liu
- Rensselaer Polytechnic Institute, Gaerttner LINAC Center, 3021 Tibbits Avenue, Troy, New York 12180
| | - Farzad Rahnema
- Georgia Institute of Technology, Nuclear and Radiological Engineering Department, 770 State Street, Atlanta, Georgia 30332
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