1
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Tanaka H, Matsumoto M, Yagasaki T, Takeuchi M, Mori Y, Kono T. Stability mechanism of crystalline CO2 and Xe. J Chem Phys 2024; 161:084501. [PMID: 39177089 DOI: 10.1063/5.0223879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 08/08/2024] [Indexed: 08/24/2024] Open
Abstract
We explore the phase behaviors of simple molecular crystals in order to investigate the molecular basis of the stability mechanism relative to their liquid counterparts. The free energies of the face centered cubic crystals of Xe and CO2 are calculated as a collection of oscillators, and those of the liquids are from an equation of state via molecular dynamics simulations. The vibrational free energy in the solid is separated into the harmonic and anharmonic terms. The harmonic free energies decrease harshly with the expansion of the volume manifested as the large positive Grüneisen parameters, but the anharmonic free energies are positive and increase with volume, both of which originate from the deviation of the potential surface from the parabolic curve. The anharmonic free energies, though less significant in magnitude and destabilize the solids thermodynamically, serve to enhance their mechanical stability. The solid-liquid phase boundaries cannot be settled correctly without the exquisite balance between the two opposing contributions. A sharp contrast regarding the solid free energy is found in low-pressure ice, where the harmonic free energy does not decrease monotonically with volume and its anharmonic free energy is negative.
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Affiliation(s)
- Hideki Tanaka
- Toyota Physical and Chemical Research Institute, Nagakute 480-1192, Japan
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
| | - Masakazu Matsumoto
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
| | - Takuma Yagasaki
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Osaka 560-8531, Japan
| | - Munetaka Takeuchi
- Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Yoshihito Mori
- Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Takumi Kono
- Engineering Advancement Association of Japan, 1-11-9 Azabudai, Minato-ku, Tokyo 105-0001, Japan
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2
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Sedano LF, Blazquez S, Vega C. Accuracy limit of non-polarizable four-point water models: TIP4P/2005 vs OPC. Should water models reproduce the experimental dielectric constant? J Chem Phys 2024; 161:044505. [PMID: 39046346 DOI: 10.1063/5.0211871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 06/30/2024] [Indexed: 07/25/2024] Open
Abstract
The last generation of four center non-polarizable models of water can be divided into two groups: those reproducing the dielectric constant of water, as OPC, and those significantly underestimating its value, as TIP4P/2005. To evaluate the global performance of OPC and TIP4P/2005, we shall follow the test proposed by Vega and Abascal in 2011 evaluating about 40 properties to fairly address this comparison. The liquid-vapor and liquid-solid equilibria are computed, as well as the heat capacities, isothermal compressibilities, surface tensions, densities of different ice polymorphs, the density maximum, equations of state at high pressures, and transport properties. General aspects of the phase diagram are considered by comparing the ratios of different temperatures (namely, the temperature of maximum density, the melting temperature of hexagonal ice, and the critical temperature). The final scores are 7.2 for TIP4P/2005 and 6.3 for OPC. The results of this work strongly suggest that we have reached the limit of what can be achieved with non-polarizable models of water and that the attempt to reproduce the experimental dielectric constant deteriorates the global performance of the water force field. The reason is that the dielectric constant depends on two surfaces (potential energy and dipole moment surfaces), whereas in the absence of an electric field, all properties can be determined simply from just one surface (the potential energy surface). The consequences of the choice of the water model in the modeling of electrolytes in water are also discussed.
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Affiliation(s)
- L F Sedano
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - S Blazquez
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - C Vega
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
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3
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Cui X, Yang C, Sun Q, Zhang W, Wang X. Investigating Shear Stress of Ice Accumulated on Surfaces with Various Roughnesses: Effects of a Quasi-Water Layer. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:14214-14223. [PMID: 38954504 PMCID: PMC11256739 DOI: 10.1021/acs.langmuir.4c00617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 06/16/2024] [Accepted: 06/19/2024] [Indexed: 07/04/2024]
Abstract
The investigation of the anti-icing/deicing is essential because the icing phenomenon deteriorates the natural environment and various projects. By conducting molecular dynamics simulation, this work analyzes the effect of the quasi-water layer on the ice shear stress over smooth and rough surfaces, along with the underlying physics of the quasi-water layer. The results indicate that the thickness of the quasi-water layer monotonically increases with temperature, resulting in a monotonic decrease in the ice shear stress on the smooth surface. Due to the joint effects of the smooth surface wettability and the quasi-water layer, the ice shear stress increases and then decreases to almost a constant value when the surface changes from a hydrophobic to a hydrophilic one. For rough surfaces with stripe nanostructures, when the width of the bump for one case equals the depression for the other case, the variations of shear stress with height for these two cases are almost the same. The rough surface is effective in reducing the ice shear stress compared to the smooth surface due to the thickening of the quasi-water layer. Each molecule in the quasi-water layer and its four nearest neighboring molecules gradually form a tetrahedral ice-like structure along the direction away from the surface. The radial distribution function also shows that the quasi-water layer resembles the liquid water rather than the ice structure. These findings shed light on developing anti-icing and deicing techniques.
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Affiliation(s)
- Xinjiao Cui
- Institute
of Thermal Science and Technology, Shandong
University, Jinan 250061, China
- Institute
for Advanced Technology, Shandong University, Jinan 250061, China
| | - Chao Yang
- Institute
of Thermal Science and Technology, Shandong
University, Jinan 250061, China
| | - Qiangqiang Sun
- Faculty
of Engineering, University of Nottingham, Nottingham NG7 2RD, U.K.
| | - Wenqiang Zhang
- School
of Mechatronical Engineering, Beijing Institute
of Technology, Beijing 100081, China
| | - Xinyu Wang
- Institute
of Thermal Science and Technology, Shandong
University, Jinan 250061, China
- Shenzhen
Research Institute of Shandong University, Shenzhen 518057, China
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4
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Yasuda I, Endo K, Arai N, Yasuoka K. In-layer inhomogeneity of molecular dynamics in quasi-liquid layers of ice. Commun Chem 2024; 7:117. [PMID: 38811834 PMCID: PMC11136980 DOI: 10.1038/s42004-024-01197-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 05/02/2024] [Indexed: 05/31/2024] Open
Abstract
Quasi-liquid layers (QLLs) are present on the surface of ice and play a significant role in its distinctive chemical and physical properties. These layers exhibit considerable heterogeneity across different scales ranging from nanometers to millimeters. Although the formation of partially ice-like structures has been proposed, the molecular-level understanding of this heterogeneity remains unclear. Here, we examined the heterogeneity of molecular dynamics on QLLs based on molecular dynamics simulations and machine learning analysis of the simulation data. We demonstrated that the molecular dynamics of QLLs do not comprise a mixture of solid- and liquid water molecules. Rather, molecules having similar behaviors form dynamical domains that are associated with the dynamical heterogeneity of supercooled water. Nonetheless, molecules in the domains frequently switch their dynamical state. Furthermore, while there is no observable characteristic domain size, the long-range ordering strongly depends on the temperature and crystal face. Instead of a mixture of static solid- and liquid-like regions, our results indicate the presence of heterogeneous molecular dynamics in QLLs, which offers molecular-level insights into the surface properties of ice.
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Affiliation(s)
- Ikki Yasuda
- Department of Mechanical Engineering, Keio University, Yokohama, Japan
| | - Katsuhiro Endo
- Department of Mechanical Engineering, Keio University, Yokohama, Japan
| | - Noriyoshi Arai
- Department of Mechanical Engineering, Keio University, Yokohama, Japan
| | - Kenji Yasuoka
- Department of Mechanical Engineering, Keio University, Yokohama, Japan.
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5
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Algaba J, Blazquez S, Feria E, Míguez JM, Conde MM, Blas FJ. Three-phase equilibria of hydrates from computer simulation. II. Finite-size effects in the carbon dioxide hydrate. J Chem Phys 2024; 160:164722. [PMID: 38687000 DOI: 10.1063/5.0201306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024] Open
Abstract
In this work, the effects of finite size on the determination of the three-phase coexistence temperature (T3) of the carbon dioxide (CO2) hydrate have been studied by molecular dynamic simulations and using the direct coexistence technique. According to this technique, the three phases involved (hydrate-aqueous solution-liquid CO2) are placed together in the same simulation box. By varying the number of molecules of each phase, it is possible to analyze the effect of simulation size and stoichiometry on the T3 determination. In this work, we have determined the T3 value at 8 different pressures (from 100 to 6000 bar) and using 6 different simulation boxes with different numbers of molecules and sizes. In two of these configurations, the ratio of the number of water and CO2 molecules in the aqueous solution and the liquid CO2 phase is the same as in the hydrate (stoichiometric configuration). In both stoichiometric configurations, the formation of a liquid drop of CO2 in the aqueous phase is observed. This drop, which has a cylindrical geometry, increases the amount of CO2 available in the aqueous solution and can in some cases lead to the crystallization of the hydrate at temperatures above T3, overestimating the T3 value obtained from direct coexistence simulations. The simulation results obtained for the CO2 hydrate confirm the sensitivity of T3 depending on the size and composition of the system, explaining the discrepancies observed in the original work by Míguez et al. [J. Chem Phys. 142, 124505 (2015)]. Non-stoichiometric configurations with larger unit cells show a convergence of T3 values, suggesting that finite-size effects for these system sizes, regardless of drop formation, can be safely neglected. The results obtained in this work highlight that the choice of a correct initial configuration is essential to accurately estimate the three-phase coexistence temperature of hydrates by direct coexistence simulations.
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Affiliation(s)
- J Algaba
- Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Ciencias Integradas, Universidad de Huelva, 21007 Huelva, Spain
| | - S Blazquez
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - E Feria
- Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Ciencias Integradas, Universidad de Huelva, 21007 Huelva, Spain
| | - J M Míguez
- Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Ciencias Integradas, Universidad de Huelva, 21007 Huelva, Spain
| | - M M Conde
- Departamento de Ingeniería Química Industrial y del Medio Ambiente, Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid, 28006 Madrid, Spain
| | - F J Blas
- Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Ciencias Integradas, Universidad de Huelva, 21007 Huelva, Spain
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6
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Blazquez S, Algaba J, Míguez JM, Vega C, Blas FJ, Conde MM. Three-phase equilibria of hydrates from computer simulation. I. Finite-size effects in the methane hydrate. J Chem Phys 2024; 160:164721. [PMID: 38686998 DOI: 10.1063/5.0201295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/01/2024] [Indexed: 05/02/2024] Open
Abstract
Clathrate hydrates are vital in energy research and environmental applications. Understanding their stability is crucial for harnessing their potential. In this work, we employ direct coexistence simulations to study finite-size effects in the determination of the three-phase equilibrium temperature (T3) for methane hydrates. Two popular water models, TIP4P/Ice and TIP4P/2005, are employed, exploring various system sizes by varying the number of molecules in the hydrate, liquid, and gas phases. The results reveal that finite-size effects play a crucial role in determining T3. The study includes nine configurations with varying system sizes, demonstrating that smaller systems, particularly those leading to stoichiometric conditions and bubble formation, may yield inaccurate T3 values. The emergence of methane bubbles within the liquid phase, observed in smaller configurations, significantly influences the behavior of the system and can lead to erroneous temperature estimations. Our findings reveal finite-size effects on the calculation of T3 by direct coexistence simulations and clarify the system size convergence for both models, shedding light on discrepancies found in the literature. The results contribute to a deeper understanding of the phase equilibrium of gas hydrates and offer valuable information for future research in this field.
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Affiliation(s)
- S Blazquez
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - J Algaba
- Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Ciencias Integradas, Universidad de Huelva, 21006 Huelva, Spain
| | - J M Míguez
- Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Ciencias Integradas, Universidad de Huelva, 21006 Huelva, Spain
| | - C Vega
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - F J Blas
- Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Ciencias Integradas, Universidad de Huelva, 21006 Huelva, Spain
| | - M M Conde
- Departamento de Ingeniería Química Industrial y del Medio Ambiente, Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid, 28006 Madrid, Spain
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7
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Algaba J, Blazquez S, Míguez JM, Conde MM, Blas FJ. Three-phase equilibria of hydrates from computer simulation. III. Effect of dispersive interactions in the methane and carbon dioxide hydrates. J Chem Phys 2024; 160:164723. [PMID: 38686999 DOI: 10.1063/5.0201309] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/02/2024] [Indexed: 05/02/2024] Open
Abstract
In this work, the effect of the range of dispersive interactions in determining the three-phase coexistence line of the CO2 and CH4 hydrates has been studied. In particular, the temperature (T3) at which solid hydrate, water, and liquid CO2/gas CH4 coexist has been determined through molecular dynamics simulations using different cutoff values (from 0.9 to 1.6 nm) for dispersive interactions. The T3 of both hydrates has been determined using the direct coexistence simulation technique. Following this method, the three phases in equilibrium are put together in the same simulation box, the pressure is fixed, and simulations are performed at different temperatures T. If the hydrate melts, then T > T3. Conversely, if the hydrate grows, then T < T3. The effect of the cutoff distance on the dissociation temperature has been analyzed at three different pressures for CO2 hydrate: 100, 400, and 1000 bar. Then, we have changed the guest and studied the effect of the cutoff distance on the dissociation temperature of the CH4 hydrate at 400 bar. Moreover, the effect of long-range corrections for dispersive interactions has been analyzed by running simulations with homo- and inhomogeneous corrections and a cutoff value of 0.9 nm. The results obtained in this work highlight that the cutoff distance for the dispersive interactions affects the stability conditions of these hydrates. This effect is enhanced when the pressure is decreased, displacing the T3 about 2-4 K depending on the system and the pressure.
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Affiliation(s)
- J Algaba
- Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Ciencias Integradas, Universidad de Huelva, 21006 Huelva, Spain
| | - S Blazquez
- Dpto. Química Física I, Fac. Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - J M Míguez
- Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Ciencias Integradas, Universidad de Huelva, 21006 Huelva, Spain
| | - M M Conde
- Departamento de Ingeniería Química Industrial y del Medio Ambiente, Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid, 28006 Madrid, Spain
| | - F J Blas
- Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Ciencias Integradas, Universidad de Huelva, 21006 Huelva, Spain
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8
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Ishiai S, Yasuda I, Endo K, Yasuoka K. Graph-Neural-Network-Based Unsupervised Learning of the Temporal Similarity of Structural Features Observed in Molecular Dynamics Simulations. J Chem Theory Comput 2024; 20:819-831. [PMID: 38190503 DOI: 10.1021/acs.jctc.3c00995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Classification of molecular structures is a crucial step in molecular dynamics (MD) simulations to detect various structures and phases within systems. Molecular structures, which are commonly identified using order parameters, were recently identified using machine learning (ML), that is, the ML models acquire structural features using labeled crystals or phases via supervised learning. However, these approaches may not identify unlabeled or unknown structures, such as the imperfect crystal structures observed in nonequilibrium systems and interfaces. In this study, we proposed the use of a novel unsupervised learning framework, denoted temporal self-supervised learning (TSSL), to learn structural features and design their parameters. In TSSL, the ML models learn that the structural similarity is learned via contrastive learning based on minor short-term variations caused by perturbations in MD simulations. This learning framework is applied to a sophisticated architecture of graph neural network models that use bond angle and length data of the neighboring atoms. TSSL successfully classifies water and ice crystals based on high local ordering, and furthermore, it detects imperfect structures typical of interfaces such as the water-ice and ice-vapor interfaces.
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Affiliation(s)
- Satoki Ishiai
- Department of Mechanical Engineering, Keio University, Yokohama 223-8522, Japan
| | - Ikki Yasuda
- Department of Mechanical Engineering, Keio University, Yokohama 223-8522, Japan
| | - Katsuhiro Endo
- Department of Mechanical Engineering, Keio University, Yokohama 223-8522, Japan
- National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki 305-8568, Japan
| | - Kenji Yasuoka
- Department of Mechanical Engineering, Keio University, Yokohama 223-8522, Japan
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9
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Ji S, Yang Z, Lei L, Galindo Torres SA, Li L. Estimation of the ice melting point in molecular dynamics simulations based on the finite-size effects. Phys Rev E 2024; 109:014108. [PMID: 38366460 DOI: 10.1103/physreve.109.014108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/22/2023] [Indexed: 02/18/2024]
Abstract
Predicting the ice melting point using molecular dynamics (MD) simulations is nontrivial due to uncertainty associated with the stochastic nature of the simulation and effect of finite domain sizes on the simulated ice-water phase transition. We developed a method based on the percolation theory to make use of the finite size effects to allow determination of a unique critical phase transition temperature as the melting point. The method involves construction of melting/freezing probability curves from multiple simulations with varying temperatures for different domain sizes. While the domain sizes affect the apparent melting/freezing probability and hence generate different curves with a wider probability distribution for a smaller size, the intersection of these curves is unique and locates the melting point. Based on MD simulations using the Tip4p/Ice water model, we tested and demonstrated the effectiveness of this method in locating the critical ice-water phase transition at a melting temperature of 268.78 K. Our analysis also showed that the apparent melting probability at this critical point is ∼0.69, not 0.5 assumed in the ad hoc method used previously. Our method, making no assumption about the system size, may provide a generic framework for analyzing phase transitions influenced by the finite size effects in MD simulations.
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Affiliation(s)
- Shuting Ji
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
- School of Engineering, Westlake University, Hangzhou 310030, Zhejiang Province, China
| | - Zhenlei Yang
- School of Engineering, Westlake University, Hangzhou 310030, Zhejiang Province, China
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, Westlake University, Hangzhou 310030, Zhejiang Province, China
| | - Liang Lei
- School of Engineering, Westlake University, Hangzhou 310030, Zhejiang Province, China
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, Westlake University, Hangzhou 310030, Zhejiang Province, China
| | - Sergio Andres Galindo Torres
- School of Engineering, Westlake University, Hangzhou 310030, Zhejiang Province, China
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, Westlake University, Hangzhou 310030, Zhejiang Province, China
| | - Ling Li
- School of Engineering, Westlake University, Hangzhou 310030, Zhejiang Province, China
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, Westlake University, Hangzhou 310030, Zhejiang Province, China
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10
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Joliat J, Picaud S, Jedlovszky P. Competitive Adsorption of Trace Gases on Ice at Tropospheric Temperatures: A Grand Canonical Monte Carlo Simulation Study. J Phys Chem A 2023; 127:10223-10232. [PMID: 38000079 DOI: 10.1021/acs.jpca.3c04789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2023]
Abstract
The coadsorption of two atmospheric trace gases on ice is characterized by using, for the first time, grand canonical Monte Carlo (GCMC) simulations performed in conditions similar to those of the corresponding experiments. Adsorption isotherms are simulated at tropospheric temperatures by considering two different gas mixtures of 1-butanol and acetic acid molecules, and selectivity of the ice surface with respect to these species is interpreted at the molecular scale as resulting from a competition process between these molecules for being adsorbed at the ice surface. It is thus shown that the trapping of acetic acid molecules on ice is always favored with respect to that of 1-butanol at low pressures, corresponding to low coverage of the surface, whereas the adsorption of the acid species is significantly modified by the presence of the alcohol molecules in the saturated portion of the adsorption isotherm, in accordance with the experimental observations. The present GCMC simulations thus confirm that competitive adsorption effects have to be taken into consideration in real situations when gas mixtures present in the troposphere interact with the surface of ice particles.
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Affiliation(s)
- Julien Joliat
- Institut UTINAM─UMR 6213, CNRS/Université de Franche-Comté, 25000 Besançon, France
| | - Sylvain Picaud
- Institut UTINAM─UMR 6213, CNRS/Université de Franche-Comté, 25000 Besançon, France
| | - Pál Jedlovszky
- Department of Chemistry, Eszterházy Károly Catholic University, Leányka U. 6, H-3300 Eger, Hungary
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11
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Lupi L, Gallo P. Glassy dynamics of water in TIP4P/Ice aqueous solutions of trehalose in comparison with the bulk phase. J Chem Phys 2023; 159:154504. [PMID: 37850697 DOI: 10.1063/5.0168933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/25/2023] [Indexed: 10/19/2023] Open
Abstract
We perform molecular dynamics simulations of TIP4P/Ice water in solution with trehalose for 3.65 and 18.57 wt. % concentrations and of bulk TIP4P/Ice water at ambient pressure, to characterize the structure and dynamics of water in a sugar aqueous solution in the supercooled region. We find here that TIP4P/Ice water in solution with trehalose molecules follows the Mode Coupling Theory and undergoes a fragile to strong transition up to the highest concentration investigated, similar to the bulk. Moreover, we perform a Mode Coupling Theory test, showing that the Time Temperature Superposition principle holds for both bulk TIP4P/Ice water and for TIP4P/Ice water in the solutions and we calculate the exponents of the theory. The direct comparison of the dynamical results for bulk water and water in the solutions shows upon cooling along the isobar a fastening of water dynamics for lower temperatures, T < 240 K. We found that the counter-intuitive behavior for the low temperature solutions can be explained with the diffusion anomaly of water leading us to the conclusion that the fastening observed below T = 240 K in water dynamics is only fictitious, due to the fact that the density of water molecules in the solutions is higher than the density of the bulk at the same temperature and pressure. This result should be taken into account in experimental investigations which are often carried out at constant pressure.
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Affiliation(s)
- Laura Lupi
- Dipartimento di Matematica e Fisica, Università Roma Tre, Via della Vasca Navale 84, 00146 Rome, Italy
| | - Paola Gallo
- Dipartimento di Matematica e Fisica, Università Roma Tre, Via della Vasca Navale 84, 00146 Rome, Italy
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12
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Bore SL, Paesani F. Realistic phase diagram of water from "first principles" data-driven quantum simulations. Nat Commun 2023; 14:3349. [PMID: 37291095 DOI: 10.1038/s41467-023-38855-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 05/12/2023] [Indexed: 06/10/2023] Open
Abstract
Since the experimental characterization of the low-pressure region of water's phase diagram in the early 1900s, scientists have been on a quest to understand the thermodynamic stability of ice polymorphs on the molecular level. In this study, we demonstrate that combining the MB-pol data-driven many-body potential for water, which was rigorously derived from "first principles" and exhibits chemical accuracy, with advanced enhanced-sampling algorithms, which correctly describe the quantum nature of molecular motion and thermodynamic equilibria, enables computer simulations of water's phase diagram with an unprecedented level of realism. Besides providing fundamental insights into how enthalpic, entropic, and nuclear quantum effects shape the free-energy landscape of water, we demonstrate that recent progress in "first principles" data-driven simulations, which rigorously encode many-body molecular interactions, has opened the door to realistic computational studies of complex molecular systems, bridging the gap between experiments and simulations.
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Affiliation(s)
- Sigbjørn Løland Bore
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA.
- Materials Science and Engineering, University of California San Diego, La Jolla, CA, 92093, USA.
- Halicioğlu Data Science Institute, University of California San Diego, La Jolla, CA, 92093, USA.
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, 92093, USA.
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13
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Algaba J, Zerón IM, Míguez JM, Grabowska J, Blazquez S, Sanz E, Vega C, Blas FJ. Solubility of carbon dioxide in water: Some useful results for hydrate nucleation. J Chem Phys 2023; 158:2889490. [PMID: 37158326 DOI: 10.1063/5.0146618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/18/2023] [Indexed: 05/10/2023] Open
Abstract
In this paper, the solubility of carbon dioxide (CO2) in water along the isobar of 400 bar is determined by computer simulations using the well-known TIP4P/Ice force field for water and the TraPPE model for CO2. In particular, the solubility of CO2 in water when in contact with the CO2 liquid phase and the solubility of CO2 in water when in contact with the hydrate have been determined. The solubility of CO2 in a liquid-liquid system decreases as the temperature increases. The solubility of CO2 in a hydrate-liquid system increases with temperature. The two curves intersect at a certain temperature that determines the dissociation temperature of the hydrate at 400 bar (T3). We compare the predictions with T3 obtained using the direct coexistence technique in a previous work. The results of both methods agree, and we suggest 290(2) K as the value of T3 for this system using the same cutoff distance for dispersive interactions. We also propose a novel and alternative route to evaluate the change in chemical potential for the formation of hydrates along the isobar. The new approach is based on the use of the solubility curve of CO2 when the aqueous solution is in contact with the hydrate phase. It considers rigorously the non-ideality of the aqueous solution of CO2, providing reliable values for the driving force for nucleation of hydrates in good agreement with other thermodynamic routes used. It is shown that the driving force for hydrate nucleation at 400 bar is larger for the methane hydrate than for the carbon dioxide hydrate when compared at the same supercooling. We have also analyzed and discussed the effect of the cutoff distance of dispersive interactions and the occupancy of CO2 on the driving force for nucleation of the hydrate.
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Affiliation(s)
- Jesús Algaba
- Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Ciencias Integradas, Universidad de Huelva, 21006 Huelva, Spain
| | - Iván M Zerón
- Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Ciencias Integradas, Universidad de Huelva, 21006 Huelva, Spain
| | - José Manuel Míguez
- Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Ciencias Integradas, Universidad de Huelva, 21006 Huelva, Spain
| | - Joanna Grabowska
- Department of Physical Chemistry, Faculty of Chemistry and BioTechMed Center, Gdansk University of Technology, ul. Narutowicza 11/12, 80-233 Gdansk, Poland
- Dpto. Química Física, Fac. Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Samuel Blazquez
- Dpto. Química Física, Fac. Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Eduardo Sanz
- Dpto. Química Física, Fac. Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Carlos Vega
- Dpto. Química Física, Fac. Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Felipe J Blas
- Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Ciencias Integradas, Universidad de Huelva, 21006 Huelva, Spain
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14
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Weldon R, Wang F. Simulating a flexible water model as rigid: Best practices and lessons learned. J Chem Phys 2023; 158:134506. [PMID: 37031157 PMCID: PMC10076064 DOI: 10.1063/5.0143836] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
Two ways to create rigid versions of flexible models are explored. The rigid model can assume the Model's Geometry (MG) as if the molecule is not interacting with any other molecules or the ensemble averaged geometry (EG) under a particular thermodynamic condition. Although the MG model is more straightforward to create, it leads to relatively poor performance. The EG model behaves similarly to the corresponding flexible model (the FL model) and, in some cases, agrees even better with experiments. While the difference between the EG and the FL models is mostly a result of flexibility, the MG and EG models have different dipole moments as a result of an effective induction in the condensed phase. For the three water models studied, the property that shows the most difference is the temperature dependence of density. The MG version of the water model by adaptive force matching for ice and liquid does not possess a temperature of maximum density, which is attributed to a downshift of the putative liquid-liquid phase transition line, leading to the hypothesized second critical point of liquid water to manifest at negative pressure. A new three-phase coexistence method for determining the melting temperature of ice is also presented.
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Affiliation(s)
- Raymond Weldon
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Feng Wang
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA
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15
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Belosludov RV, Gets KV, Zhdanov RK, Bozhko YY, Belosludov VR, Chen LJ, Kawazoe Y. Molecular Dynamics Study of Clathrate-like Ordering of Water in Supersaturated Methane Solution at Low Pressure. Molecules 2023; 28:molecules28072960. [PMID: 37049727 PMCID: PMC10095827 DOI: 10.3390/molecules28072960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Using molecular dynamics, the evolution of a metastable solution for “methane + water” was studied for concentrations of 3.36, 6.5, 9.45, 12.2, and 14.8 mol% methane at 270 K and 1 bar during 100 ns. We have found the intriguing behavior of the system containing over 10,000 water molecules: the formation of hydrate-like structures is observed at 6.5 and 9.45 mol% concentrations throughout the entire solution volume. This formation of “blobs” and the following amorphous hydrate were studied. The creation of a metastable methane solution through supersaturation is the key to triggering the collective process of hydrate formation under low pressure. Even the first stage (0–1 ns), before the first fluctuating cavities appear, is a collective process of H-bond network reorganization. The formation of fluctuation cavities appears before steady hydrate growth begins and is associated with a preceding uniform increase in the water molecule’s tetrahedrality. Later, the constantly presented hydrate cavities become the foundation for a few independent hydrate nucleation centers, this evolution is consistent with the labile cluster and local structure hypotheses. This new mechanism of hydrogen-bond network reorganization depends on the entropy of the cavity arrangement of the guest molecules in the hydrate lattice and leads to hydrate growth.
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Affiliation(s)
| | - Kirill V. Gets
- Nikolaev Institute of Inorganic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Ravil K. Zhdanov
- Nikolaev Institute of Inorganic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Yulia Y. Bozhko
- Nikolaev Institute of Inorganic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Vladimir R. Belosludov
- Nikolaev Institute of Inorganic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
| | - Li-Jen Chen
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Yoshiyuki Kawazoe
- New Industry Creation Hatchery Center, Tohoku University, Sendai 980-8579, Japan
- Department of Physics and Nanotechnology, SRM Institute of Science and Technology, Kattankurathur 603203, India
- School of Physics, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
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16
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Baran Ł, Rżysko W, MacDowell LG. Self-diffusion and shear viscosity for the TIP4P/Ice water model. J Chem Phys 2023; 158:064503. [PMID: 36792509 DOI: 10.1063/5.0134932] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
With an ever-increasing interest in water properties, many intermolecular force fields have been proposed to describe the behavior of water. Unfortunately, good models for liquid water usually cannot provide simultaneously an accurate melting point for ice. For this reason, the TIP4P/Ice model was developed for targeting the melting point and has become the preferred choice for simulating ice at coexistence. Unfortunately, available data for its dynamic properties in the liquid state are scarce. Therefore, we demonstrate a series of simulations aimed at the calculation of transport coefficients for the TIP4P/Ice model over a large range of thermodynamic conditions, ranging from T = 245 K to T = 350 K, for the temperature, and from p = 0 to p = 500 MPa, for the pressure. We have found that the self-diffusion (shear viscosity) exhibits smaller (increased) values than TIP4P/2005 and experiments. However, rescaling the temperature with respect to the triple point temperature, as in a corresponding states plot, we find that TIP4P/Ice compares very well with TIP4P/2005 and experiment. Such observations allow us to infer that despite the different original purposes of these two models examined here, one can benefit from a vast number of reports regarding the behavior of transport coefficients for the TIP4P/2005 model and utilize them following the routine described in this paper.
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Affiliation(s)
- Łukasz Baran
- Department of Theoretical Chemistry, Institute of Chemical Sciences, Faculty of Chemistry, Maria-Curie-Sklodowska University in Lublin, Pl. M Curie-Sklodowskiej 3, 20-031 Lublin, Poland
| | - Wojciech Rżysko
- Department of Theoretical Chemistry, Institute of Chemical Sciences, Faculty of Chemistry, Maria-Curie-Sklodowska University in Lublin, Pl. M Curie-Sklodowskiej 3, 20-031 Lublin, Poland
| | - Luis G MacDowell
- Departamento de Química-Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
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17
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Jedrecy A, Saitta AM, Pietrucci F. Free energy calculations and unbiased molecular dynamics targeting the liquid-liquid transition in water no man's land. J Chem Phys 2023; 158:014502. [PMID: 36610960 DOI: 10.1063/5.0120789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The existence of a first-order phase transition between a low-density liquid (LDL) and a high-density liquid (HDL) form of supercooled water has been a central and highly debated issue of physics and chemistry for the last three decades. We present a computational study that allows us to determine the free-energy landscapes of supercooled water over a wide range of pressure and temperature conditions using the TIP4P/2005 force field. Our approach combines topology-based structural transformation coordinates, state-of-the-art free-energy calculation methods, and extensive unbiased molecular dynamics. All our diverse simulations cannot detect any barrier within the investigated timescales and system size, for a discontinuous transition between the LDL and HDL forms throughout the so-called "no man's land," until the onset of the solid, non-diffusive amorphous forms.
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Affiliation(s)
- Alexandre Jedrecy
- Insitut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, CNRS, MNHN, UMR 7590, Paris, France
| | - A Marco Saitta
- Insitut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, CNRS, MNHN, UMR 7590, Paris, France
| | - Fabio Pietrucci
- Insitut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, CNRS, MNHN, UMR 7590, Paris, France
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18
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Michalis VK, Economou IG, Stubos AK, Tsimpanogiannis IN. Phase equilibria molecular simulations of hydrogen hydrates via the direct phase coexistence approach. J Chem Phys 2022; 157:154501. [PMID: 36272800 DOI: 10.1063/5.0108738] [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
We report the three-phase (hydrate-liquid water-vapor) equilibrium conditions of the hydrogen-water binary system calculated with molecular dynamics simulations via the direct phase coexistence approach. A significant improvement of ∼10.5 K is obtained in the current study, over earlier simulation attempts, by using a combination of modifications related to the hydrogen model that include (i) hydrogen Lennard-Jones parameters that are a function of temperature and (ii) the water-guest energy interaction parameters optimized further by using the Lorentz-Berthelot combining rules, based on an improved description of the solubility of hydrogen in water.
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Affiliation(s)
| | - Ioannis G Economou
- Chemical Engineering Program, Texas A&M University at Qatar, P.O. Box 23874, Doha, Qatar
| | - Athanasios K Stubos
- Environmental Research Laboratory, National Center for Scientific Research "Demokritos," 15310 Aghia Paraskevi Attikis, Greece
| | - Ioannis N Tsimpanogiannis
- Chemical Process and Energy Resources Institute (CPERI), Centre for Research & Technology Hellas (CERTH), 57001 Thermi-Thessaloniki, Greece
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19
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Li M, Zhang J, Niu H, Lei YK, Han X, Yang L, Ye Z, Yang YI, Gao YQ. Phase Transition between Crystalline Variants of Ordinary Ice. J Phys Chem Lett 2022; 13:8601-8606. [PMID: 36073968 DOI: 10.1021/acs.jpclett.2c02176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Water is one of the most abundant molecules on Earth. However, this common and "simple" material has more than 18 different phases, which poses a great challenge to theoretically study the nature of water and ice. We designed two reaction coordinates that can distinguish between water and various ice states and used them to efficiently sample all possible states of the system in all-atom molecular dynamics simulation at ambient temperature and pressure. Various structural and thermodynamics properties, including the water-ice phase diagrams, can thus be calculated. We also present a simple model that successfully explains the thermodynamic stability of different ice states. Our work provides effective methods and data for theoretical studies of different phases of water and ice.
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Affiliation(s)
- Maodong Li
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Institute of Systems and Physical Biology, Shenzhen 518132, China
| | - Jun Zhang
- Institute of Systems and Physical Biology, Shenzhen 518132, China
| | - Haiyang Niu
- State Key Laboratory of Solidification Processing, International Centre for Materials Discovery, School of Materials Science and Engineering, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Yao-Kun Lei
- Institute of Systems and Physical Biology, Shenzhen 518132, China
| | - Xu Han
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Lijiang Yang
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhiqiang Ye
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Institute of Systems and Physical Biology, Shenzhen 518132, China
| | - Yi Isaac Yang
- Institute of Systems and Physical Biology, Shenzhen 518132, China
| | - Yi Qin Gao
- Institute of Systems and Physical Biology, Shenzhen 518132, China
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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20
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Berrens ML, Bononi FC, Donadio D. Effect of sodium chloride adsorption on the surface premelting of ice. Phys Chem Chem Phys 2022; 24:20932-20940. [PMID: 36040383 DOI: 10.1039/d2cp02277j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We characterise the structural properties of the quasi-liquid layer (QLL) at two low-index ice surfaces in the presence of sodium chloride (Na+/Cl-) ions by molecular dynamics simulations. We find that the presence of a high surface density of Na+/Cl- pairs changes the surface melting behaviour from step-wise to gradual melting. The ions lead to an overall increase of the thickness and the disorder of the QLL, and to a low-temperature roughening transition of the air-ice interface. The local molecular structure of the QLL is similar to that of liquid water, and the differences between the basal and primary prismatic surface are attenuated by the presence of Na+/Cl- pairs. These changes modify the crystal growth rates of different facets and the solvation environment at the surface of sea-water ice with a potential impact on light scattering and environmental chemical reactions.
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Affiliation(s)
- Margaret L Berrens
- Department of Chemistry, University of California Davis, Davis, CA, 95616, USA.
| | - Fernanda C Bononi
- Department of Chemistry, University of California Davis, Davis, CA, 95616, USA.
| | - Davide Donadio
- Department of Chemistry, University of California Davis, Davis, CA, 95616, USA.
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21
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Martínez-Jiménez M, Benavides AL. The liquidus temperature curve of aqueous methanol mixtures: a numerical simulation study. J Chem Phys 2022; 157:104502. [DOI: 10.1063/5.0099751] [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 liquidus temperature curve that characterizes the boundary between the liquid methanol/water mixture and its coexistence with ice Ih is determined using the direct-coexistence method. Several methanol concentrations and pressures of 0.1 MPa, 50 MPa, and 100 MPa are considered. In this study, we used the TIP4P/Ice model for water and two different models for methanol: OPLS and OPLS/2016, using the geometric rule for the Lennard-Jones cross interactions. We compared our simulation results with available experimental data and found that this combination of models reproduces reasonably well the liquidus curve for methanol mole fractions up to xm=0.3 at p=0.1 MPa. The freezing point depression of these mixtures is calculated and compared to experimental results. We also analyzed the effect of pressure on the liquidus curve, and we found that both models also reproduce qualitatively well the experimental decreasing of the liquidus temperatures as the pressure increases.
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Affiliation(s)
| | - Ana Laura Benavides
- Ingeniería Física, Universidad de Guanajuato División de Ciencias e Ingenierías Campus León, Mexico
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22
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Abstract
By using the direct coexistence method, we have calculated the melting points of ice I h at normal pressure for three recently proposed water models, namely, TIP3P-FB, TIP4P-FB, and TIP4P-D. We obtained T m = 216 K for TIP3P-FB, T m = 242 K for TIP4P-FB, and T m = 247 K for TIP4P-D. We revisited the melting point of TIP4P/2005 and TIP5P obtaining T m = 250 and 274 K, respectively. We summarize the current situation of the melting point of ice I h for a number of water models and conclude that no model is yet able to simultaneously reproduce the melting temperature of ice I h and the temperature of the maximum in density at room pressure. This probably points toward our both still incomplete knowledge of the potential energy surface of water and the necessity of incorporating nuclear quantum effects to describe both properties simultaneously.
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Affiliation(s)
- S. Blazquez
- Dpto. Química Física I, Fac. Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - C. Vega
- Dpto. Química Física I, Fac. Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
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23
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Joliat J, Picaud S, Patt A, Jedlovszky P. Adsorption of C2-C5 alcohols on ice. A grand canonical Monte Carlo simulation study. J Chem Phys 2022; 156:224702. [DOI: 10.1063/5.0096013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this paper, we report Grand Canonical Monte Carlo simulations performed to characterize the adsorption of four linear alcohol molecules, comprising between 2 and 5 carbon atoms (namely, ethanol, n-propanol, n-butanol, and n-pentanol) on crystalline ice in a temperature range typical of the Earth's troposphere.The adsorption details analysed at 228 K show that, at low coverage of the ice surface, the polar head of the adsorbed molecules tend to optimize its hydrogen bonding with the surrounding water, whereas the aliphatic chain lie more or less parallel to the ice surface. With increasing coverage, the lateral interactions between the adsorbed alcohol molecules lead to the reorientation of the aliphatic chains which tend to become perpendicular to the surface, the adsorbed molecules pointing thus their terminal methyl group up to the gas phase. When compared to the experimental data, the simulated and measured isotherms show a very good agreement, although a small temperature shift between simulations and experiments could be inferred from simulations at various temperatures. In addition, this agreement appears to be better for ethanol and n-propanol than for n-butanol and n-pentanol, especially at the highest pressures investigated, pointing to a possible slight underestimation of the lateral interactions between the largest alcohol molecules by the interaction potential model used. Nevertheless, the global accuracy of the approach used, as tested in tropospheric conditions, opens the way for its use in modeling studies also relevant to another (e.g., astrophysical) context.
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Affiliation(s)
| | - Sylvain Picaud
- U.F.R. des Sciences et des techniques, Institut UTINAM, France
| | | | - Pál Jedlovszky
- Department of Chemistry, Eszterhazy Karoly University, Hungary
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24
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Lamas CP, Vega C, Noya EG. Freezing point depression of salt aqueous solutions using the Madrid-2019 model. J Chem Phys 2022; 156:134503. [PMID: 35395902 DOI: 10.1063/5.0085051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Salt aqueous solutions are relevant in many fields, ranging from biological systems to seawater. Thus, the availability of a force-field that is able to reproduce the thermodynamic and dynamic behavior of salt aqueous solutions would be of great interest. Unfortunately, this has been proven challenging, and most of the existing force-fields fail to reproduce much of their behavior. In particular, the diffusion of water or the salt solubility are often not well reproduced by most of the existing force-fields. Recently, the Madrid-2019 model was proposed, and it was shown that this force-field, which uses the TIP4P/2005 model for water and non-integer charges for the ions, provides a good description of a large number of properties, including the solution densities, viscosities, and the diffusion of water. In this work, we assess the performance of this force-field on the evaluation of the freezing point depression. Although the freezing point depression is a colligative property that at low salt concentrations depends solely on properties of pure water, a good model for the electrolytes is needed to accurately predict the freezing point depression at moderate and high salt concentrations. The coexistence line between ice and several salt aqueous solutions (NaCl, KCl, LiCl, MgCl2, and Li2SO4) up to the eutectic point is estimated from direct coexistence molecular dynamics simulations. Our results show that this force-field reproduces fairly well the experimentally measured freezing point depression with respect to pure water freezing for all the salts and at all the compositions considered.
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Affiliation(s)
- Cintia P Lamas
- Departamento de Química-Física I (Unidad de I+D+i Asociada al CSIC), Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Carlos Vega
- Departamento de Química-Física I (Unidad de I+D+i Asociada al CSIC), Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Eva G Noya
- Instituto de Química Física Rocasolano, CSIC, C/ Serrano 119, 28006 Madrid, Spain
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25
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Gasparotto P, Fitzner M, Cox SJ, Sosso GC, Michaelides A. How do interfaces alter the dynamics of supercooled water? NANOSCALE 2022; 14:4254-4262. [PMID: 35244128 DOI: 10.1039/d2nr00387b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The structure of liquid water in the proximity of an interface can deviate significantly from that of bulk water, with surface-induced structural perturbations typically converging to bulk values at about ∼1 nm from the interface. While these structural changes are well established it is, in contrast, less clear how an interface perturbs the dynamics of water molecules within the liquid. Here, through an extensive set of molecular dynamics simulations of supercooled bulk and interfacial water films and nano-droplets, we observe the formation of persistent, spatially extended dynamical domains in which the average mobility varies as a function of the distance from the interface. This is in stark contrast with the dynamical heterogeneity observed in bulk water, where these domains average out spatially over time. We also find that the dynamical response of water to an interface depends critically on the nature of the interface and on the choice of interface definition. Overall these results reveal a richness in the dynamics of interfacial water that opens up the prospect of tuning the dynamical response of water through specific modifications of the interface structure or confining material.
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Affiliation(s)
- Piero Gasparotto
- Scientific Computing Division, Paul Scherrer Institute, Villigen 5232, Switzerland.
| | - Martin Fitzner
- Thomas Young Centre, London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, London WC1E 6BT, UK
| | - Stephen James Cox
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Gabriele Cesare Sosso
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Angelos Michaelides
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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26
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Bianco V, Conde MM, Lamas CP, Noya EG, Sanz E. Phase diagram of the NaCl–water system from computer simulations. J Chem Phys 2022; 156:064505. [DOI: 10.1063/5.0083371] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- V. Bianco
- Departamento de Química Física (Unidad de I+D+i asociada al CSIC), Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - M. M. Conde
- Departamento de Ingeniería Química Industrial y Medio Ambiente, Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid, 28006 Madrid, Spain
| | - C. P. Lamas
- Departamento de Química Física (Unidad de I+D+i asociada al CSIC), Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, CSIC, Calle Serrano 119, 28006 Madrid, Spain
| | - E. G. Noya
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, CSIC, Calle Serrano 119, 28006 Madrid, Spain
| | - E. Sanz
- Departamento de Química Física (Unidad de I+D+i asociada al CSIC), Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
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27
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Shen L, Gai W, Qin L, Zhou R, Li S. Research of seawater freezing based on TIP4P/ICE potential: A new algorithm for generating proton disordered ice Ih. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2021.139182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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28
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Leoni F, Calero C, Franzese G. Nanoconfined Fluids: Uniqueness of Water Compared to Other Liquids. ACS NANO 2021; 15:19864-19876. [PMID: 34807577 PMCID: PMC8717635 DOI: 10.1021/acsnano.1c07381] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/18/2021] [Indexed: 05/27/2023]
Abstract
Nanoconfinement can drastically change the behavior of liquids, puzzling us with counterintuitive properties. It is relevant in applications, including decontamination and crystallization control. However, it still lacks a systematic analysis for fluids with different bulk properties. Here we address this gap. We compare, by molecular dynamics simulations, three different liquids in a graphene slit pore: (1) A simple fluid, such as argon, described by a Lennard-Jones potential; (2) an anomalous fluid, such as a liquid metal, modeled with an isotropic core-softened potential; and (3) water, the prototypical anomalous liquid, with directional HBs. We study how the slit-pore width affects the structure, thermodynamics, and dynamics of the fluids. All the fluids show similar oscillating properties by changing the pore size. However, their free-energy minima are quite different in nature: (i) are energy-driven for the simple liquid; (ii) are entropy-driven for the isotropic core-softened potential; and (iii) have a changing nature for water. Indeed, for water, the monolayer minimum is entropy driven, at variance with the simple liquid, while the bilayer minimum is energy driven, at variance with the other anomalous liquid. Also, water has a large increase in diffusion for subnm slit pores, becoming faster than bulk. Instead, the other two fluids have diffusion oscillations much smaller than water, slowing down for decreasing slit-pore width. Our results, clarifying that water confined at the subnm scale behaves differently from other (simple or anomalous) fluids under similar confinement, are possibly relevant in nanopores applications, for example, in water purification from contaminants.
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Affiliation(s)
- Fabio Leoni
- Department
of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Carles Calero
- Secció
de Física Estadística i Interdisciplinària-Departament
de Física de la Matèria Condensada, Institut de Nanociència i Nanotecnologia (IN2UB), Universitat
de Barcelona, Carrer Martí i Franquès 1, 08028 Barcelona, Spain
| | - Giancarlo Franzese
- Secció
de Física Estadística i Interdisciplinària-Departament
de Física de la Matèria Condensada, Institut de Nanociència i Nanotecnologia (IN2UB), Universitat
de Barcelona, Carrer Martí i Franquès 1, 08028 Barcelona, Spain
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29
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Conde MM, Rovere M, Gallo P. Spontaneous NaCl-doped ices I h, I c, III, V and VI. Understanding the mechanism of ion inclusion and its dependence on the crystalline structure of ice. Phys Chem Chem Phys 2021; 23:22897-22911. [PMID: 34533147 DOI: 10.1039/d1cp02638k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Direct coexistence simulations on a microsecond time scale have been performed for different types of ice (Ih, Ic, III, V, and VI) in contact with a NaCl aqueous solution at different pressures. In line with the previous results obtained for ice Ih [Conde et al., Phys. Chem. Chem. Phys., 2017, 19, 9566-9574], our results reveal the spontaneous growth of a new ice doped phase and the formation of a brine rejection phase in all ices studied. However, both the preferential incorporation of ions into the ice lattice and the inclusion mechanisms depend on the crystalline structure of each ice. This work shows the inclusion of Cl- and Na+ ions in ice from salt using molecular dynamics simulation, in agreement with the experimental evidence found in the literature. The model used for water is TIP4P/2005. For NaCl we employ a set of potential parameters that uses unit charges for the ions.
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Affiliation(s)
- M M Conde
- Departamento de Ingeniería Química Industrial y Medio Ambiente, Escuela Técnica Superior de Ingenieros Industriales, Universidad Politecnica de Madrid, 28006 Madrid, Spain.
| | - M Rovere
- Dipartimento di Matematica e Fisica, Università Roma Tre, Via della Vasca Navale 84, 00146 Roma, Italy.
| | - P Gallo
- Dipartimento di Matematica e Fisica, Università Roma Tre, Via della Vasca Navale 84, 00146 Roma, Italy.
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30
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Gerhäuser J, Gaukel V. Detailed Analysis of the Ice Surface after Binding of an Insect Antifreeze Protein and Correlation with the Gibbs-Thomson Equation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:11716-11725. [PMID: 34585573 DOI: 10.1021/acs.langmuir.1c01620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Antifreeze proteins (AFPs) are able to influence the ice crystal growth and the recrystallization process due to the Gibbs-Thomson effect. The binding of the AFP leads to the formation of a curved ice surface and it is generally assumed that there is a critical radius between the proteins on the ice surface that determines the maximal thermal hysteresis. Up to now, this critical radius has not yet been proven beyond doubt or only in poor agreement with the Gibbs-Thomson equation. Using molecular dynamics (MD) simulations, the resulting three-dimensional surface structure is analyzed and the location of the critical radius is identified. Our results demonstrate that the correct analysis of the geometry of the ice surface is extremely important and cannot be guessed upfront a simulation. In contrary to earlier expectations from the literature, we could show that the critical radius is not located directly between the adsorbed proteins. In addition, we showed that the minimum temperature at which the system does not freeze is in very good agreement with the value calculated with the Gibbs-Thomson equation at the critical radius, as long as dynamic system conditions are taken into account. This proves on the one hand that the Gibbs-Thomson effect is the basis of thermal hysteresis and that MD simulations are suitable for the prediction of the melting point depression.
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Affiliation(s)
- Julian Gerhäuser
- Section I: Food Process Engineering, KIT (Karlsruhe Institute of Technology), Institute of Process Engineering in Life Sciences, Kaiserstraße 12, Karlsruhe 76131, Germany
| | - Volker Gaukel
- Section I: Food Process Engineering, KIT (Karlsruhe Institute of Technology), Institute of Process Engineering in Life Sciences, Kaiserstraße 12, Karlsruhe 76131, Germany
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31
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Lupi L, Vázquez Ramírez B, Gallo P. Dynamical crossover and its connection to the Widom line in supercooled TIP4P/Ice water. J Chem Phys 2021; 155:054502. [PMID: 34364341 DOI: 10.1063/5.0059190] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We perform molecular dynamics simulations with the TIP4P/Ice water model to characterize the relationship between dynamics and thermodynamics of liquid water in the supercooled region. We calculate the relevant properties of the phase diagram, and we find that TIP4P/Ice presents a retracing line of density maxima, similar to what was previously found for atomistic water models and models of other tetrahedral liquids. For this model, a liquid-liquid critical point between a high-density liquid and a low-density liquid was recently found. We compute the lines of the maxima of isothermal compressibility and the minima of the coefficient of thermal expansion in the one phase region, and we show that these lines point to the liquid-liquid critical point while collapsing on the Widom line. This line is the line of the maxima of correlation length that emanates from a second order critical point in the one phase region. Supercooled water was found to follow mode coupling theory and to undergo a transition from a fragile to a strong behavior right at the crossing of the Widom line. We find here that this phenomenology also happens for TIP4P/Ice. Our results appear, therefore, to be a general characteristic of supercooled water, which does not depend on the interaction potential used, and they reinforce the idea that the dynamical crossover from a region where the relaxation mechanism is dominated by cage relaxation to a region where cages are frozen and hopping dominates is correlated in water to a phase transition between a high-density liquid and a low-density liquid.
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Affiliation(s)
- Laura Lupi
- Dipartimento di Matematica e Fisica, Università Roma Tre, Via della Vasca Navale 84, 00146 Rome, Italy
| | - Benjamín Vázquez Ramírez
- Dipartimento di Matematica e Fisica, Università Roma Tre, Via della Vasca Navale 84, 00146 Rome, Italy
| | - Paola Gallo
- Dipartimento di Matematica e Fisica, Università Roma Tre, Via della Vasca Navale 84, 00146 Rome, Italy
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32
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Wang C, Wu J, Wang H, Zhang Z. Classical nucleation theory of ice nucleation: Second-order corrections to thermodynamic parameters. J Chem Phys 2021; 154:234503. [PMID: 34241278 DOI: 10.1063/5.0049570] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Accurately estimating the nucleation rate is crucial in studying ice nucleation and ice-promoting and anti-freeze strategies. In classical nucleation theory, estimates of the ice nucleation rate are very sensitive to thermodynamic parameters, such as the chemical potential difference between water and ice Δμ and the ice-water interfacial free energy γ. However, even today, there are still many contradictions and approximations when estimating these thermodynamic parameters, introducing a large uncertainty in any estimate of the ice nucleation rate. Starting from basic concepts for a general solid-liquid crystallization system, we expand the Gibbs-Thomson equation to second order and derive second-order analytical formulas for Δμ, γ, and the nucleation barrier ΔG*, which are used in molecular dynamics simulations. These formulas describe well the temperature dependence of these thermodynamic parameters. This may be a new method of estimating Δμ, γ, and ΔG*.
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Affiliation(s)
- Chaohong Wang
- Department of Physics, Research Institute for Biomimetics and Soft Matter and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen 361005, People's Republic of China
| | - Jianyang Wu
- Department of Physics, Research Institute for Biomimetics and Soft Matter and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen 361005, People's Republic of China
| | - Hao Wang
- Department of Physics, Research Institute for Biomimetics and Soft Matter and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen 361005, People's Republic of China
| | - Zhisen Zhang
- Department of Physics, Research Institute for Biomimetics and Soft Matter and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen 361005, People's Republic of China
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33
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Piaggi PM, Panagiotopoulos AZ, Debenedetti PG, Car R. Phase Equilibrium of Water with Hexagonal and Cubic Ice Using the SCAN Functional. J Chem Theory Comput 2021; 17:3065-3077. [PMID: 33835819 DOI: 10.1021/acs.jctc.1c00041] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Machine learning models are rapidly becoming widely used to simulate complex physicochemical phenomena with ab initio accuracy. Here, we use one such model as well as direct density functional theory (DFT) calculations to investigate the phase equilibrium of water, hexagonal ice (Ih), and cubic ice (Ic), with an eye toward studying ice nucleation. The machine learning model is based on deep neural networks and has been trained on DFT data obtained using the SCAN exchange and correlation functional. We use this model to drive enhanced sampling simulations aimed at calculating a number of complex properties that are out of reach of DFT-driven simulations and then employ an appropriate reweighting procedure to compute the corresponding properties for the SCAN functional. This approach allows us to calculate the melting temperature of both ice polymorphs, the driving force for nucleation, the heat of fusion, the densities at the melting temperature, the relative stability of ices Ih and Ic, and other properties. We find a correct qualitative prediction of all properties of interest. In some cases, quantitative agreement with experiment is better than for state-of-the-art semiempirical potentials for water. Our results also show that SCAN correctly predicts that ice Ih is more stable than ice Ic.
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Affiliation(s)
- Pablo M Piaggi
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Athanassios Z Panagiotopoulos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States.,Princeton Institute for the Science and Technology of Materials, Princeton University, Princeton, New Jersey 08544, United States
| | - Pablo G Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States.,Princeton Institute for the Science and Technology of Materials, Princeton University, Princeton, New Jersey 08544, United States
| | - Roberto Car
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States.,Princeton Institute for the Science and Technology of Materials, Princeton University, Princeton, New Jersey 08544, United States.,Department of Physics, Princeton University, Princeton, New Jersey 08544, United States.,Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544, United States
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34
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Su Z, Alavi S, Ripmeester JA, Wolosh G, Dias CL. Methane Clathrate Formation is Catalyzed and Kinetically Inhibited by the Same Molecule: Two Facets of Methanol. J Phys Chem B 2021; 125:4162-4168. [PMID: 33861613 DOI: 10.1021/acs.jpcb.1c01274] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here, we perform molecular dynamics simulations to provide atomic-level insights into the dual roles of methanol in enhancing and delaying the rate of methane clathrate hydrate nucleation. Consistent with experiments, we find that methanol slows clathrate hydrate nucleation above 250 K but promotes clathrate formation at temperatures below 250 K. We show that this behavior can be rationalized by the unusual temperature dependence of the methane-methanol interaction in an aqueous solution, which emerges due to the hydrophobic effect. In addition to its antifreeze properties at temperatures above 250 K, methanol competes with water to interact with methane prior to the formation of clathrate nuclei. Below 250 K, methanol encourages water to occupy the space between methane molecules favoring clathrate formation and it may additionally promote water mobility.
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Affiliation(s)
- Zhaoqian Su
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Saman Alavi
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - John A Ripmeester
- National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada
| | - Gedaliah Wolosh
- New Jersey Institute of Technology, Academic and Research Computing Systems, University Heights, Newark, New Jersey 07102, United States
| | - Cristiano L Dias
- New Jersey Institute of Technology, Department of Physics, University Heights, Newark, New Jersey 07102, United States
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35
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Influence of external static and alternating electric fields on self-diffusion of water from molecular dynamics. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114788] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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36
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Mohr S, Pétuya R, Wylde J, Sarria J, Purkayastha N, Ward Z, Bodnar S, Tsimpanogiannis IN. Size dependence of the dissociation process of spherical hydrate particles via microsecond molecular dynamics simulations. Phys Chem Chem Phys 2021; 23:11180-11185. [DOI: 10.1039/d1cp01223a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The dissociation process of spherical sII mixed methane–propane hydrate particles in liquid hydrocarbon was investigated via microsecond-long molecular dynamics simulations.
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Affiliation(s)
- Stephan Mohr
- Nextmol (Bytelab Solutions SL)
- Barcelona
- Spain
- Barcelona Supercomputing Center (BSC)
- Barcelona
| | - Rémi Pétuya
- Nextmol (Bytelab Solutions SL)
- Barcelona
- Spain
| | - Jonathan Wylde
- Clariant Oil Services, Clariant Corporation
- Houston
- USA
- Heriot Watt University
- Edinburgh
| | - Juan Sarria
- Clariant Produkte (Deutschland) GmbH
- Frankfurt
- Germany
| | | | - Zachary Ward
- Clariant Oil Services, Clariant Corporation
- Houston
- USA
| | - Scot Bodnar
- Clariant Oil Services, Clariant Corporation
- Houston
- USA
| | - Ioannis N. Tsimpanogiannis
- Chemical Process & Energy Resources Institute (CPERI)
- Centre for Research & Technology Hellas (CERTH)
- Thermi-Thessaloniki
- Greece
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37
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Xiong Y, Shabane PS, Onufriev AV. Melting Points of OPC and OPC3 Water Models. ACS OMEGA 2020; 5:25087-25094. [PMID: 33043187 PMCID: PMC7542584 DOI: 10.1021/acsomega.0c02638] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
A recently introduced family of globally optimal water models, OPC, has shown promise in a variety of biomolecular simulations, but properties of these water models outside of the liquid phase remain mostly unexplored. Here, we contribute to filling the gap by reporting melting temperatures of ice I h of OPC and OPC3 water models. Through the direct coexistence method, which we make available in the AMBER package, the melting points of OPC and OPC3 are estimated as 242 and 210 K, similar to TIP4P-Ew and SPC/E models, respectively, and appreciably below the experimental value of 273.15 K under 1 bar pressure. Water models of the OPC family were optimized to best reproduce water properties in the liquid phase where these models offer noteworthy accuracy advantages over many models of previous generations. It is not surprising that the accuracy of OPC models in describing the phase transition to the solid state does not appear to offer similar improvements. The new anisotropic barostat option implemented in AMBER may benefit system preparation and simulation outside of the direct coexistence applications, such as modeling of membranes or very long DNA strands.
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Affiliation(s)
- Yeyue Xiong
- Department
of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg 24061-0131, United States
| | | | - Alexey V. Onufriev
- Department
of Physics, Virginia Tech, Blacksburg 24061-0131, United States
- Department
of Computer Science, Virginia Tech Department of Physics, Virginia Tech, Blacksburg 24061-0131, United States
- Center
for Soft Matter and Biological Physics, Virginia Tech, Blacksburg 24061-0131, United States
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38
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Bianco V, Espinosa JR, Vega C. Antifreeze proteins and homogeneous nucleation: On the physical determinants impeding ice crystal growth. J Chem Phys 2020; 153:091102. [PMID: 32891082 DOI: 10.1063/5.0023211] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Antifreeze proteins (AFPs) are biopolymers capable of interfering with ice growth. Their antifreeze action is commonly understood considering that the AFPs, by pinning the ice surface, force the crystal-liquid interface to bend forming an ice meniscus, causing an increase in the surface free energy and resulting in a decrease in the freezing point ΔTmax. Here, we present an extensive computational study for a model protein adsorbed on a TIP4P/Ice crystal, computing ΔTmax as a function of the average distance d between AFPs, with simulations spanning over 1 µs. First, we show that the lower the d, the larger the ΔTmax. Then, we find that the water-ice-protein contact angle along the line ΔTmax(d) is always larger than 0°, and we provide a theoretical interpretation. We compute the curvature radius of the stable solid-liquid interface at a given supercooling ΔT ≤ ΔTmax, connecting it with the critical ice nucleus at ΔT. Finally, we discuss the antifreeze capability of AFPs in terms of the protein-water and protein-ice interactions. Our findings establish a unified description of the AFPs in the contest of homogeneous ice nucleation, elucidating key aspects of the antifreeze mechanisms and paving the way for the design of novel ice-controlling materials.
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Affiliation(s)
- Valentino Bianco
- Faculty of Chemistry, Chemical Physics Department, Universidad Complutense de Madrid, Plaza de las Ciencias, Ciudad Universitaria, Madrid 28040, Spain
| | - Jorge R Espinosa
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0H3, United Kingdom
| | - Carlos Vega
- Faculty of Chemistry, Chemical Physics Department, Universidad Complutense de Madrid, Plaza de las Ciencias, Ciudad Universitaria, Madrid 28040, Spain
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39
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Piaggi PM, Car R. Phase equilibrium of liquid water and hexagonal ice from enhanced sampling molecular dynamics simulations. J Chem Phys 2020; 152:204116. [DOI: 10.1063/5.0011140] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- Pablo M. Piaggi
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Roberto Car
- Department of Chemistry and Department of Physics, Princeton University, Princeton, New Jersey 08544, USA
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40
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Qiu H, Guo W. Phase Diagram of Nanoscale Water on Solid Surfaces with Various Wettabilities. J Phys Chem Lett 2019; 10:6316-6323. [PMID: 31566984 DOI: 10.1021/acs.jpclett.9b02512] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Understanding structural and dynamic properties of water in contact with solid surfaces is essential for diverse fields, including environmental sciences, nanofluidics, lubrication, and electrochemistry. Despite tremendous efforts, how interfacial water phase behaviors correlate with a surface's wettability remains elusive. Here, we investigate the structure and dynamics of nanoscale water droplets or adlayers on solid surfaces with wettabilities spanning from strongly hydrophobic to strongly hydrophilic using extensive molecular dynamics simulations. It is shown that liquid water drops on solid surfaces with contact angles greater than 42.6° transform into drops of ordinary hexagonal ice (Ih) upon cooling. In contrast, water forms a liquid disc on a completely wetted surface with a zero contact angle, which freezes into a hexagonal bilayer ice disc at low temperatures. Unexpectedly, on surfaces with a mild contact angle in the range of 21.9°-29.2°, the originally stable liquid drop at room temperature further wets the surface upon cooling and eventually transforms into a bilayer ice disc. These results establish a phase diagram of nanoscale water at the wettability versus temperature plane, which may expand our knowledge of water-surface interactions as well as enrich the complexity of water behaviors at interfaces.
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Affiliation(s)
- Hu Qiu
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science , Nanjing University of Aeronautics and Astronautics , Nanjing 210016 , China
| | - Wanlin Guo
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science , Nanjing University of Aeronautics and Astronautics , Nanjing 210016 , China
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41
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Zhuang L, Wang R, Lindberg GE, Hu H, Li XZ, Wang F. From a Liquid to a Crystal without Going through a First-Order Phase Transition: Determining the Free Energy of Melting with Glassy Intermediates. J Phys Chem B 2019; 123:7740-7747. [DOI: 10.1021/acs.jpcb.9b06840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lin Zhuang
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, and School of Physics, Peking University, Beijing 100871, People’s Republic of China
| | - Rui Wang
- International Center for Quantum Materials, School of Physics, Peking University, Beijing 100871, People’s Republic of China
| | - Gerrick E. Lindberg
- Department of Chemistry and Biochemistry, and Department of Applied Physics and Materials Science, Northern Arizona University, 700 South Osborne Drive, Flagstaff, Arizona 86011, United States
| | - Hongyi Hu
- Department of Chemistry and Biochemistry, University of Arkansas, 119 Chemistry Building, Fayetteville, Arkansas 72701, United States
| | - Xin-Zheng Li
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, and School of Physics, Peking University, Beijing 100871, People’s Republic of China
- Collaborative Innovation Center of Quantum Matter, Peking University, Beijing 100871, People’s Republic of China
| | - Feng Wang
- Department of Chemistry and Biochemistry, University of Arkansas, 119 Chemistry Building, Fayetteville, Arkansas 72701, United States
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42
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Zanetti-Polzi L, Biswas AD, Del Galdo S, Barone V, Daidone I. Hydration Shell of Antifreeze Proteins: Unveiling the Role of Non-Ice-Binding Surfaces. J Phys Chem B 2019; 123:6474-6480. [PMID: 31280567 DOI: 10.1021/acs.jpcb.9b06375] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Antifreeze proteins (AFPs) have the ability to inhibit ice growth by binding to ice nuclei. Their ice-binding mechanism is still unclear, yet the hydration layer is thought to play a fundamental role. Here, we use molecular dynamics simulations to characterize the hydration shell of two AFPs and two non-AFPs. The calculated shell thickness and density of the AFPs do not feature any relevant difference with respect to the non-AFPs. Moreover, the hydration shell density is always higher than the bulk density and, thus, no low-density, ice-like layer is detected at the ice-binding surface (IBS) of AFPs. Instead, we observe local water-density differences in AFPs between the IBS (lower density) and the non-IBS (higher density). The lower solvent density at the ice-binding site can pave the way to the protein binding to ice nuclei, while the higher solvent density at the non-ice-binding surfaces might provide protection against ice growth.
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Affiliation(s)
- Laura Zanetti-Polzi
- Department of Physical and Chemical Sciences , University of L'Aquila , via Vetoio (Coppito 1) , 67010 L'Aquila , Italy
| | - Akash Deep Biswas
- Department of Physical and Chemical Sciences , University of L'Aquila , via Vetoio (Coppito 1) , 67010 L'Aquila , Italy.,Scuola Normale Superiore di Pisa , Piazza dei Cavalieri 7 , I-56126 Pisa , Italy
| | - Sara Del Galdo
- Scuola Normale Superiore di Pisa , Piazza dei Cavalieri 7 , I-56126 Pisa , Italy.,Institute for the Chemistry of Organometallic Compounds , Italian National Council for Research (ICCOMCNR) , Via G. Moruzzi 1 , I-6124 Pisa , Italy
| | - Vincenzo Barone
- Scuola Normale Superiore di Pisa , Piazza dei Cavalieri 7 , I-56126 Pisa , Italy.,National Institute for Nuclear Physics (INFN) Pisa Section , Largo BrunoPontecorvo 3 , 56127 Pisa , Italy
| | - Isabella Daidone
- Department of Physical and Chemical Sciences , University of L'Aquila , via Vetoio (Coppito 1) , 67010 L'Aquila , Italy
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43
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Montero de Hijes P, Espinosa JR, Vega C, Sanz E. Ice growth rate: Temperature dependence and effect of heat dissipation. J Chem Phys 2019; 151:044509. [DOI: 10.1063/1.5103273] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- P. Montero de Hijes
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - J. R. Espinosa
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, United Kingdom
| | - C. Vega
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - E. Sanz
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
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44
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Niu H, Yang YI, Parrinello M. Temperature Dependence of Homogeneous Nucleation in Ice. PHYSICAL REVIEW LETTERS 2019; 122:245501. [PMID: 31322390 DOI: 10.1103/physrevlett.122.245501] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/06/2019] [Indexed: 06/10/2023]
Abstract
Ice nucleation is a process of great relevance in physics, chemistry, technology, and environmental sciences; much theoretical effort has been devoted to its understanding, but it still remains a topic of intense research. We shed light on this phenomenon by performing atomistic based simulations. Using metadynamics and a carefully designed set of collective variables, reversible transitions between water and ice are able to be simulated. We find that water freezes into a stacking disordered structure with the all-atom transferable intermolecular potential with 4 points/ice (TIP4P/ice) model, and the features of the critical nucleus of nucleation at the microscopic level are revealed. We have also estimated the ice nucleation rates along with other nucleation parameters at different undercoolings. Our results are in agreement with recent experimental and other theoretical works, and they confirm that nucleation is preceded by a large increase in tetrahedrally coordinated water molecules.
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Affiliation(s)
- Haiyang Niu
- Department of Chemistry and Applied Biosciences, ETH Zurich c/o USI Campus, Via Giuseppe Buffi 13, 6900 Lugano, Switzerland
- Facoltà di Informatica, Instituto di Scienze Computationali, and National Center for Computational Design and Discovery of Novel Materials MARVEL, Università della Svizzera Italiana, Via Giuseppe Buffi 13, 6900 Lugano, Switzerland
| | - Yi Isaac Yang
- Department of Chemistry and Applied Biosciences, ETH Zurich c/o USI Campus, Via Giuseppe Buffi 13, 6900 Lugano, Switzerland
- Facoltà di Informatica, Instituto di Scienze Computationali, and National Center for Computational Design and Discovery of Novel Materials MARVEL, Università della Svizzera Italiana, Via Giuseppe Buffi 13, 6900 Lugano, Switzerland
| | - Michele Parrinello
- Department of Chemistry and Applied Biosciences, ETH Zurich c/o USI Campus, Via Giuseppe Buffi 13, 6900 Lugano, Switzerland
- Facoltà di Informatica, Instituto di Scienze Computationali, and National Center for Computational Design and Discovery of Novel Materials MARVEL, Università della Svizzera Italiana, Via Giuseppe Buffi 13, 6900 Lugano, Switzerland
- Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
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45
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Matsumoto M, Yagasaki T, Tanaka H. A Bayesian approach for identification of ice Ih, ice Ic, high density, and low density liquid water with a torsional order parameter. J Chem Phys 2019; 150:214504. [DOI: 10.1063/1.5096556] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Masakazu Matsumoto
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
| | - Takuma Yagasaki
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
| | - Hideki Tanaka
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
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46
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Benet J, Llombart P, Sanz E, MacDowell LG. Structure and fluctuations of the premelted liquid film of ice at the triple point. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1583388] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Jorge Benet
- Departamento de Química-Física (Unidad Asociada de I+D+i al CSIC), Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Pablo Llombart
- Departamento de Química-Física (Unidad Asociada de I+D+i al CSIC), Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid, Spain
- Instituto de Química Física Rocasolano, CSIC, Madrid, Spain
| | - Eduardo Sanz
- Departamento de Química-Física (Unidad Asociada de I+D+i al CSIC), Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Luis G. MacDowell
- Departamento de Química-Física (Unidad Asociada de I+D+i al CSIC), Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid, Spain
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47
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Matsui T, Yagasaki T, Matsumoto M, Tanaka H. Phase diagram of ice polymorphs under negative pressure considering the limits of mechanical stability. J Chem Phys 2019; 150:041102. [DOI: 10.1063/1.5083021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Takahiro Matsui
- Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - Takuma Yagasaki
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
| | - Masakazu Matsumoto
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
| | - Hideki Tanaka
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
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48
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Capponi S, White SH, Tobias DJ, Heyden M. Structural Relaxation Processes and Collective Dynamics of Water in Biomolecular Environments. J Phys Chem B 2019; 123:480-486. [PMID: 30566356 DOI: 10.1021/acs.jpcb.8b12052] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this simulation study, we investigate the influence of biomolecular confinement on dynamical processes in water. We compare water confined in a membrane protein nanopore at room temperature to pure liquid water at low temperatures with respect to structural relaxations, intermolecular vibrations, and the propagation of collective modes. We observe distinct potential energy landscapes experienced by water molecules in the two environments, which nevertheless result in comparable hydrogen bond lifetimes and sound propagation velocities. Hence, we show that a viscoelastic argument that links slow rearrangements of the water-hydrogen bond network to ice-like collective properties applies to both, the pure liquid and biologically confined water, irrespective of differences in the microscopic structure.
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Affiliation(s)
| | | | | | - Matthias Heyden
- School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287-1604 , United States
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49
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Fernández-Fernández A, Pérez-Rodríguez M, Comesaña A, Piñeiro M. Three-phase equilibrium curve shift for methane hydrate in oceanic conditions calculated from Molecular Dynamics simulations. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.10.146] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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50
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Guo Q, Ghaani MR, Nandi PK, English NJ. Pressure-Induced Densification of Ice I h under Triaxial Mechanical Compression: Dissociation versus Retention of Crystallinity for Intermediate States in Atomistic and Coarse-Grained Water Models. J Phys Chem Lett 2018; 9:5267-5274. [PMID: 30145899 DOI: 10.1021/acs.jpclett.8b02270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Molecular-dynamics (MD) simulation of triaxially pressurized ice Ih up to 30 kbar at 240 K (with sudden mechanical pressurization from its ambient-pressure structure) has been carried out with both the single-particle mW and atomistic TIP4P-Ice water potentials on systems of up to ∼1 million molecules, for times of the order of 100 ns. It was found that the TIP4P-Ice systems adopted a high-density liquid state above ∼7 kbar, while densification of the mW systems retained essentially crystalline order, owing to a failure for the tetrahedral network to break down appreciably from its ice Ih lattice structure. Both are intermediate states adopted along the path toward respective thermodynamically stable states (and with pressure removal show reversion to Ih for mW and to supercooled liquid for TIP4P-Ice), similar to recent ice electro-freezing simulations in "No Man's Land". Densification kinetics showed faster mW-system adaptation.
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Affiliation(s)
- Qiang Guo
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin Key Laboratory of Applied Catalysis Science and Technology, College of Chemical Engineering and Technology , Tianjin University , Tianjin 300072 , P.R. China
- School of Chemical and Bioprocess Engineering , University College Dublin , Belfield , Dublin 4 , Ireland
| | - Mohammad Reza Ghaani
- School of Chemical and Bioprocess Engineering , University College Dublin , Belfield , Dublin 4 , Ireland
| | - Prithwish K Nandi
- School of Chemical and Bioprocess Engineering , University College Dublin , Belfield , Dublin 4 , Ireland
- Irish Centre for High-End Computing , Grand Canal Quay , Dublin 2 , Ireland
| | - Niall J English
- School of Chemical and Bioprocess Engineering , University College Dublin , Belfield , Dublin 4 , Ireland
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