201
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Tanaka H, Yagasaki T, Matsumoto M. On the role of intermolecular vibrational motions for ice polymorphs. III. Mode characteristics associated with negative thermal expansion. J Chem Phys 2021; 155:214502. [PMID: 34879657 DOI: 10.1063/5.0068560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Low-pressure ice forms, such as hexagonal and cubic ice, expand on cooling below temperature 60 K. This negative thermal expansivity has been explored in terms of phonon frequency modulation with varying volume and attributed to the negative Grüneisen parameters unique mostly to tetrahedrally coordinated substances. However, an underlying mechanism for the negative Grüneisen parameters has not been known except some schematic analyses. We investigate in this study the characteristics of the intermolecular vibrational modes whose Grüneisen parameters are negative by examining the individual vibrational modes rigorously. It is found that the low frequency modes below 100 cm-1, which we explicitly show are mostly bending motions of three hydrogen-bonded molecules, necessarily accompany elongation of the hydrogen bond length at peak amplitudes compared with that at the equilibrium position in executing the vibrational motions. The elongation gives rise to a decrease in the repulsive interaction while an increase in the Coulombic one. The decrease in the repulsive interaction is relaxed substantially by expansion due to its steep slope against molecular separation compared with the sluggish increase in the Coulombic one, and therefore, the negative Grüneisen parameters are obtainable. This scenario is tested against some variants of cubic ice with various water potential models. It is demonstrated that four interaction-site models are suitable to describe the intermolecular vibrations and the thermal expansivity because of the moderate tendency to favor the tetrahedral coordination.
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Affiliation(s)
- Hideki Tanaka
- Toyota Physical and Chemical Research Institute, Nagakute 480-1192, Japan
| | - Takuma Yagasaki
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Osaka 560-8531, Japan
| | - Masakazu Matsumoto
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
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202
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Study the effect of Ag nanoparticles on the kinetics of CO2 hydrate growth by molecular dynamics simulation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117668] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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203
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Long FQ, Jin T, Han KL, Zhuang W. Impact of borate on structure of antifreeze glycoproteins. CHINESE J CHEM PHYS 2021. [DOI: 10.1063/1674-0068/cjcp2107120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Feng-qin Long
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tan Jin
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Ke-li Han
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
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204
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Gallo P, Bachler J, Bove LE, Böhmer R, Camisasca G, Coronas LE, Corti HR, de Almeida Ribeiro I, de Koning M, Franzese G, Fuentes-Landete V, Gainaru C, Loerting T, de Oca JMM, Poole PH, Rovere M, Sciortino F, Tonauer CM, Appignanesi GA. Advances in the study of supercooled water. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2021; 44:143. [PMID: 34825973 DOI: 10.1140/epje/s10189-021-00139-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/17/2021] [Indexed: 06/13/2023]
Abstract
In this review, we report recent progress in the field of supercooled water. Due to its uniqueness, water presents numerous anomalies with respect to most simple liquids, showing polyamorphism both in the liquid and in the glassy state. We first describe the thermodynamic scenarios hypothesized for the supercooled region and in particular among them the liquid-liquid critical point scenario that has so far received more experimental evidence. We then review the most recent structural indicators, the two-state model picture of water, and the importance of cooperative effects related to the fact that water is a hydrogen-bonded network liquid. We show throughout the review that water's peculiar properties come into play also when water is in solution, confined, and close to biological molecules. Concerning dynamics, upon mild supercooling water behaves as a fragile glass former following the mode coupling theory, and it turns into a strong glass former upon further cooling. Connections between the slow dynamics and the thermodynamics are discussed. The translational relaxation times of density fluctuations show in fact the fragile-to-strong crossover connected to the thermodynamics arising from the existence of two liquids. When considering also rotations, additional crossovers come to play. Mobility-viscosity decoupling is also discussed in supercooled water and aqueous solutions. Finally, the polyamorphism of glassy water is considered through experimental and simulation results both in bulk and in salty aqueous solutions. Grains and grain boundaries are also discussed.
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Affiliation(s)
- Paola Gallo
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, Via della Vasca Navale 84, 00146, Roma, Italy.
| | - Johannes Bachler
- Institute of Physical Chemistry, University of Innsbruck, Innrain 52c, A-6020, Innsbruck, Austria
| | - Livia E Bove
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185, Roma, Italy
- Sorbonne Université, CNRS UMR 7590, IMPMC, 75005, Paris, France
| | - Roland Böhmer
- Fakultät Physik, Technische Universität Dortmund, 44221, Dortmund, Germany
| | - Gaia Camisasca
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, Via della Vasca Navale 84, 00146, Roma, Italy
| | - Luis E Coronas
- Secció de Física Estadística i Interdisciplinària-Departament de Física de la Matèria Condensada, Universitat de Barcelona, & Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, C. Martí i Franquès 1, 08028, Barcelona, Spain
| | - Horacio R Corti
- Departamento de Física de la Materia Condensada, Centro Atómico Constituyentes, Comisión Nacional de Energía Atómica, B1650LWP, Buenos Aires, Argentina
| | - Ingrid de Almeida Ribeiro
- Instituto de Física "Gleb Wataghin", Universidade Estadual de Campinas, UNICAMP, 13083-859, Campinas, São Paulo, Brazil
| | - Maurice de Koning
- Instituto de Física "Gleb Wataghin", Universidade Estadual de Campinas, UNICAMP, 13083-859, Campinas, São Paulo, Brazil
- Center for Computing in Engineering & Sciences, Universidade Estadual de Campinas, UNICAMP, 13083-861, Campinas, São Paulo, Brazil
| | - Giancarlo Franzese
- Secció de Física Estadística i Interdisciplinària-Departament de Física de la Matèria Condensada, Universitat de Barcelona, & Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, C. Martí i Franquès 1, 08028, Barcelona, Spain
| | - Violeta Fuentes-Landete
- Institute of Physical Chemistry, University of Innsbruck, Innrain 52c, A-6020, Innsbruck, Austria
| | - Catalin Gainaru
- Fakultät Physik, Technische Universität Dortmund, 44221, Dortmund, Germany
| | - Thomas Loerting
- Institute of Physical Chemistry, University of Innsbruck, Innrain 52c, A-6020, Innsbruck, Austria
| | | | - Peter H Poole
- Department of Physics, St. Francis Xavier University, Antigonish, NS, B2G 2W5, Canada
| | - Mauro Rovere
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, Via della Vasca Navale 84, 00146, Roma, Italy
| | - Francesco Sciortino
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185, Roma, Italy
| | - Christina M Tonauer
- Institute of Physical Chemistry, University of Innsbruck, Innrain 52c, A-6020, Innsbruck, Austria
| | - Gustavo A Appignanesi
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000, Bahía Blanca, Argentina
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205
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Xu J, Du S, Hao Y, Yang X, Zhang J. Molecular simulation study of methane hydrate formation mechanism in NaCl solutions with different concentrations. Chem Phys 2021. [DOI: 10.1016/j.chemphys.2021.111323] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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206
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Cui S, Zhang W, Shao X, Cai W. Hyperactive Antifreeze Proteins Promote Ice Growth before Binding to It. J Chem Inf Model 2021; 62:5165-5174. [PMID: 34711054 DOI: 10.1021/acs.jcim.1c00915] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The antifreeze mechanism of antifreeze proteins (AFPs) evolved by organisms has been widely studied. However, detailed knowledge of the synergy between AFPs and ice crystals still remains fragmentary. In the present contribution, the cooperative effect of the hyperactive insect antifreeze protein TmAFP and ice crystals on the interfacial water during the entire process of inhibiting ice growth is systematically investigated at the atomic level and compared with its low activity mutant and a nonantifreeze protein. The results indicate a significant synergy between TmAFP and ice crystals, which enables the TmAFP to promote the ice growth before adsorbing on the surfaces of the ice crystals, while the mutant and the nonantifreeze protein cannot promote the ice growth due to the lack of this synergy. When TmAFP approaches the ice surface, the interfacial water is induced by both the AFP and the ice crystals to form the anchored clathrate motif, which binds TmAFP to the ice surface, resulting in a local increase in the curvature of the ice surface, thereby inhibiting the growth of ice. In this study, three stages, namely, promotion, adsorption, and inhibition, are observed in the complete process of TmAFP inhibiting ice growth, and the synergistic mechanism between protein and ice crystals is revealed. The results are helpful for the design of antifreeze proteins and bioinspired antifreeze materials with superior performance.
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Affiliation(s)
- Shaoli Cui
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, China
| | - Weijia Zhang
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, China
| | - Xueguang Shao
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, China
| | - Wensheng Cai
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, China
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207
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Matsumoto M, Yagasaki T, Tanaka H. On the anomalous homogeneity of hydrogen-disordered ice and its origin. J Chem Phys 2021; 155:164502. [PMID: 34717348 DOI: 10.1063/5.0065215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Pauling's successful estimation of the residual entropy of hydrogen-disordered ice was based on the homogeneity of the binding energy of individual water molecules in ice. However, it has not been explained why the binding energies are homogeneous although the pair interaction energy of hydrogen-bonded dimers distributes widely. Here, we provide a rationale for this phenomenon. The topological constraints imposed by the ice rules, in which water molecules form directed cyclic paths of hydrogen bonds, cancel out the variability of local interactions. We also show that the cancellation mechanism does not work due to some imperfect cyclic paths on the surface of ice. Such water molecules do not enjoy homogeneity in the bulk state and suffer from a wide spectrum in the binding energy.
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Affiliation(s)
- 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
| | - Hideki Tanaka
- Toyota Physical and Chemical Research Institute, Nagakute 480-1192, Japan
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208
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Foffi R, Sciortino F. Structure of High-Pressure Supercooled and Glassy Water. PHYSICAL REVIEW LETTERS 2021; 127:175502. [PMID: 34739286 DOI: 10.1103/physrevlett.127.175502] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/09/2021] [Indexed: 06/13/2023]
Abstract
We numerically investigate the structure of deep supercooled and glassy water under pressure, covering the range of densities corresponding to the experimentally produced high- and very-high-density amorphous phases. At T=188 K, a continuous increase in density is observed on varying pressure from 2.5 to 13 kbar, with no signs of first-order transitions. Exploiting a recently proposed approach to the analysis of the radial distribution function-based on topological properties of the hydrogen-bond network-we are able to identify well-defined local geometries that involve pairs of molecules separated by multiple hydrogen bonds, specific to the high- and very-high-density structures.
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Affiliation(s)
- Riccardo Foffi
- Department of Physics, Sapienza Università di Roma, Piazzale Aldo Moro, 2, 00185 Rome, Italy
| | - Francesco Sciortino
- Department of Physics, Sapienza Università di Roma, Piazzale Aldo Moro, 2, 00185 Rome, Italy
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209
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Seal A, Govind Rajan A. Modulating Water Slip Using Atomic-Scale Defects: Friction on Realistic Hexagonal Boron Nitride Surfaces. NANO LETTERS 2021; 21:8008-8016. [PMID: 34606287 DOI: 10.1021/acs.nanolett.1c02208] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Atomic-scale defects are ubiquitous in nanomaterials, yet their role in modulating fluid flow is inadequately understood. Hexagonal boron nitride (hBN) is an important two-dimensional material with applications in desalination and osmotic power. Although pristine hBN offers higher friction to the flow of water than graphene, we show here that certain defects can enhance water slippage on hBN. Using classical molecular dynamics simulations assisted by quantum-mechanical density functional theory, we compute the friction coefficient of water on hBN containing various vacancies (B, N, BN, B2N, and B3N) and the Stone-Wales defect. By investigating two defect concentrations, we obtain friction coefficients ranging from 0.4 to 2.6 times that of pristine hBN, leading to a maximum water slip length of 18.1 nm on hBN with a N vacancy or a Stone-Wales defect. Our work informs the use of defects to tune water flow and reveals defective hBN as an alternative high-slip surface to graphene.
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Affiliation(s)
- Aniruddha Seal
- School of Chemical Sciences, National Institute of Science Education and Research Bhubaneswar, Khurda, Odisha 752050, India
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Ananth Govind Rajan
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, Karnataka 560012, India
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210
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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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211
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Mileo PGM, Rogge SMJ, Houlleberghs M, Breynaert E, Martens JA, Van Speybroeck V. Interfacial study of clathrates confined in reversed silica pores. JOURNAL OF MATERIALS CHEMISTRY. A 2021; 9:21835-21844. [PMID: 34707871 PMCID: PMC8491980 DOI: 10.1039/d1ta03105h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/22/2021] [Indexed: 05/08/2023]
Abstract
Storing methane in clathrates is one of the most promising alternatives for transporting natural gas (NG) as it offers similar gas densities to liquefied and compressed NG while offering lower safety risks. However, the practical use of clathrates is limited given the extremely low temperatures and high pressures necessary to form these structures. Therefore, it has been suggested to confine clathrates in nanoporous materials, as this can facilitate clathrate's formation conditions while preserving its CH4 volumetric storage. Yet, the choice of nanoporous materials to be employed as the clathrate growing platform is still rather arbitrary. Herein, we tackle this challenge in a systematic way by computationally exploring the stability of clathrates confined in alkyl-grafted silica materials with different pore sizes, ligand densities and ligand types. Based on our findings, we are able to propose key design criteria for nanoporous materials favoring the stability of a neighbouring clathrate phase, namely large pore sizes, high ligand densities, and smooth pore walls. We hope that the atomistic insight provided in this work will guide and facilitate the development of new nanomaterials designed to promote the formation of clathrates.
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Affiliation(s)
- Paulo G M Mileo
- Center for Molecular Modeling (CMM), Ghent University Technologiepark 46 B-9052 Zwijnaarde Belgium
| | - Sven M J Rogge
- Center for Molecular Modeling (CMM), Ghent University Technologiepark 46 B-9052 Zwijnaarde Belgium
| | - Maarten Houlleberghs
- Center for Surface Chemistry and Catalysis, Katholieke Universiteit Leuven Celestijnenlaan 200F 3001 Heverlee Belgium
| | - Eric Breynaert
- Center for Surface Chemistry and Catalysis, Katholieke Universiteit Leuven Celestijnenlaan 200F 3001 Heverlee Belgium
| | - Johan A Martens
- Center for Surface Chemistry and Catalysis, Katholieke Universiteit Leuven Celestijnenlaan 200F 3001 Heverlee Belgium
| | - Veronique Van Speybroeck
- Center for Molecular Modeling (CMM), Ghent University Technologiepark 46 B-9052 Zwijnaarde Belgium
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212
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Fernández-Fernández ÁM, Pérez-Rodríguez M, Piñeiro MM. Molecular dynamics of fluoromethane type I hydrates. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116720] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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213
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Cao P, Li T, Ning F, Wu J. Mechanical Instability of Methane Hydrate-Mineral Interface Systems. ACS APPLIED MATERIALS & INTERFACES 2021; 13:46043-46054. [PMID: 34520161 DOI: 10.1021/acsami.1c08114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Massive methane hydrates occur on sediment matrices in nature. Therefore, sediment-based methane hydrate systems play an essential role in the society and hydrate community, including energy resources, global climate changes, and geohazards. However, a fundamental understanding of mechanical properties of methane hydrate-mineral interface systems is largely limited due to insufficient experimental techniques. Herein, by using large-scale molecular simulations, we show that the mechanical properties of methane hydrate-mineral (silica, kaolinite, and Wyoming-type montmorillonite) interface systems are strongly dictated by the chemical components of sedimentary minerals that determine interfacial microstructures between methane hydrates and minerals. The tensile strengths of hydrate-mineral systems are found to decrease following the order of Wyoming-type montmorillonite- > silica- > kaolinite-based methane hydrate systems, all of which show a brittle failure at the interface between methane hydrates and minerals under tension. In contrast, upon compression, methane hydrates decompose into water and methane molecules, resulting from a large strain-induced mechanical instability. In particular, the failure of Wyoming-type montmorillonite-based methane hydrate systems under compression is characterized by a sudden decrease in the compressive stress at a strain of around 0.23, distinguishing it from those of silica- and kaolinite-based methane hydrate systems under compression. Our findings thus provide a molecular insight into the potential mechanisms of mechanical instability of gas hydrate-bearing sediment systems on Earth.
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Affiliation(s)
- Pinqiang Cao
- Faculty of Engineering, China University of Geosciences, Wuhan, Hubei 430074, China
- Department of Civil & Environmental Engineering, The George Washington University, Washington, District of Columbia 20052, United States
- Department of Physics, Jiujiang Research Institute, Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen, Fujian 361005, China
- School of Resource and Environmental Engineering, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
| | - Tianshu Li
- Department of Civil & Environmental Engineering, The George Washington University, Washington, District of Columbia 20052, United States
| | - Fulong Ning
- Faculty of Engineering, China University of Geosciences, Wuhan, Hubei 430074, China
| | - Jianyang Wu
- Department of Physics, Jiujiang Research Institute, Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen, Fujian 361005, China
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214
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Yagasaki T, Matubayasi N. Crystallization of Polyethylene Brushes and Its Effect on Interactions with Water. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c01145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Takuma Yagasaki
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka 560-8531, Japan
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215
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Moritz C, Geissler PL, Dellago C. The microscopic mechanism of bulk melting of ice. J Chem Phys 2021; 155:124501. [PMID: 34598556 DOI: 10.1063/5.0064380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We study the initial stages of homogeneous melting of a hexagonal ice crystal at coexistence and at moderate superheating. Our trajectory-based computer simulation approach provides a comprehensive picture of the events that lead to melting, from the initial accumulation of 5+7 defects, via the formation of L-D and interstitial-vacancy pairs, to the formation of a liquid nucleus. Of the different types of defects that we observe to be involved in melting, a particular kind of 5+7 type defect (type 5) plays a prominent role as it often forms prior to the formation of the initial liquid nucleus and close to the site where the nucleus forms. Hence, like other solids, ice homogeneously melts via the prior accumulation of defects.
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Affiliation(s)
- Clemens Moritz
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Phillip L Geissler
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Christoph Dellago
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
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216
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Kadaoluwa Pathirannahalage SP, Meftahi N, Elbourne A, Weiss ACG, McConville CF, Padua A, Winkler DA, Costa Gomes M, Greaves TL, Le TC, Besford QA, Christofferson AJ. Systematic Comparison of the Structural and Dynamic Properties of Commonly Used Water Models for Molecular Dynamics Simulations. J Chem Inf Model 2021; 61:4521-4536. [PMID: 34406000 DOI: 10.1021/acs.jcim.1c00794] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Water is a unique solvent that is ubiquitous in biology and present in a variety of solutions, mixtures, and materials settings. It therefore forms the basis for all molecular dynamics simulations of biological phenomena, as well as for many chemical, industrial, and materials investigations. Over the years, many water models have been developed, and it remains a challenge to find a single water model that accurately reproduces all experimental properties of water simultaneously. Here, we report a comprehensive comparison of structural and dynamic properties of 30 commonly used 3-point, 4-point, 5-point, and polarizable water models simulated using consistent settings and analysis methods. For the properties of density, coordination number, surface tension, dielectric constant, self-diffusion coefficient, and solvation free energy of methane, models published within the past two decades consistently show better agreement with experimental values compared to models published earlier, albeit with some notable exceptions. However, no single model reproduced all experimental values exactly, highlighting the need to carefully choose a water model for a particular study, depending on the phenomena of interest. Finally, machine learning algorithms quantified the relationship between the water model force field parameters and the resulting bulk properties, providing insight into the parameter-property relationship and illustrating the challenges of developing a water model that can accurately reproduce all properties of water simultaneously.
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Affiliation(s)
- Sachini P Kadaoluwa Pathirannahalage
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia.,Laboratoire de Chimie, Ecole Normale Supérieure de Lyon, CNRS, Lyon 69342, France
| | - Nastaran Meftahi
- ARC Centre of Excellence in Exciton Science, School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Aaron Elbourne
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Alessia C G Weiss
- Leibniz-Institut für Polymerforschung e.V., Hohe Straße 6, 01069 Dresden, Germany
| | - Chris F McConville
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia.,Institute for Frontier Materials, Deakin University, Geelong, Victoria 3220, Australia
| | - Agilio Padua
- Laboratoire de Chimie, Ecole Normale Supérieure de Lyon, CNRS, Lyon 69342, France
| | - David A Winkler
- School of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia.,Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia.,School of Pharmacy, University of Nottingham, Nottingham NG7 2QL, U.K
| | | | - Tamar L Greaves
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Tu C Le
- School of Engineering, RMIT University, Melbourne, Victoria 3001, Australia
| | - Quinn A Besford
- Leibniz-Institut für Polymerforschung e.V., Hohe Straße 6, 01069 Dresden, Germany
| | - Andrew J Christofferson
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia.,ARC Centre of Excellence in Exciton Science, School of Science, RMIT University, Melbourne, Victoria 3000, Australia
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217
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Smolyanitsky A, Luant B. Nanopores in Atomically Thin 2D Nanosheets Limit Aqueous Single-Stranded DNA Transport. PHYSICAL REVIEW LETTERS 2021; 127:138103. [PMID: 34623840 PMCID: PMC10932591 DOI: 10.1103/physrevlett.127.138103] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
Nanopores in 2D materials are highly desirable for DNA sequencing, yet achieving single-stranded DNA (ssDNA) transport through them is challenging. Using density functional theory calculations and molecular dynamics simulations we show that ssDNA transport through a pore in monolayer hexagonal boron nitride (h-BN) is marked by a basic nanomechanical conflict. It arises from the notably inhomogeneous flexural rigidity of ssDNA and causes high friction via transient DNA desorption costs exacerbated by solvation effects. For a similarly sized pore in bilayer h-BN, its self-passivated atomically smooth edge enables continuous ssDNA transport. Our findings shed light on the fundamental physics of biopolymer transport through pores in 2D materials.
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Affiliation(s)
- Alex Smolyanitsky
- Applied Chemicals and Materials Division, National Institute of Standards and Technology, Boulder, Colorado 80305, USA
| | - Binquan Luant
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA
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218
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Brant Carvalho PHB, Moraes PIR, Leitão AA, Andersson O, Tulk CA, Molaison J, Lyubartsev AP, Häussermann U. Structural investigation of three distinct amorphous forms of Ar hydrate. RSC Adv 2021; 11:30744-30754. [PMID: 35479871 PMCID: PMC9041099 DOI: 10.1039/d1ra05697b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/03/2021] [Indexed: 11/21/2022] Open
Abstract
Three amorphous forms of Ar hydrate were produced using the crystalline clathrate hydrate Ar·6.5H2O (structure II, Fd3̄m, a ≈ 17.1 Å) as a precursor and structurally characterized by a combination of isotope substitution (36Ar) neutron diffraction and molecular dynamics (MD) simulations. The first form followed from the pressure-induced amorphization of the precursor at 1.5 GPa at 95 K and the second from isobaric annealing at 2 GPa and subsequent cooling back to 95 K. In analogy to amorphous ice, these amorphs are termed high-density amorphous (HDA) and very-high-density amorphous (VHDA), respectively. The third amorph (recovered amorphous, RA) was obtained when recovering VHDA to ambient pressure (at 95 K). The three amorphs have distinctly different structures. In HDA the distinction of the original two crystallographically different Ar guests is maintained as differently dense Ar–water hydration structures, which expresses itself in a split first diffraction peak in the neutron structure factor function. Relaxation of the local water structure during annealing produces a homogeneous hydration environment around Ar, which is accompanied with a densification by about 3%. Upon pressure release the homogeneous amorphous structure undergoes expansion by about 21%. Both VHDA and RA can be considered frozen solutions of immiscible Ar and water in which in average 15 and 11 water molecules, respectively, coordinate Ar out to 4 Å. The local water structures of HDA and VHDA Ar hydrates show some analogy to those of the corresponding amorphous ices, featuring H2O molecules in 5- and 6-fold coordination with neighboring molecules. However, they are considerably less dense. Most similarity is seen between RA and low density amorphous ice (LDA), which both feature strictly 4-coordinated H2O networks. It is inferred that, depending on the kind of clathrate structure and occupancy of cages, amorphous states produced from clathrate hydrates display variable local water structures. Three amorphous forms of Ar clathrate hydrate (pressure-amorphized, annealed and recovered) were characterized by isotope substitution (36Ar) neutron diffraction and molecular dynamics and their local coordinations analyzed and compared to pure ice.![]()
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Affiliation(s)
- Paulo H B Brant Carvalho
- Department of Materials and Environmental Chemistry, Stockholm University SE-10691 Stockholm Sweden
| | - Pedro Ivo R Moraes
- Department of Chemistry, Federal University of Juiz de Fora Juiz de Fora MG 36036-900 Brazil
| | - Alexandre A Leitão
- Department of Chemistry, Federal University of Juiz de Fora Juiz de Fora MG 36036-900 Brazil
| | - Ove Andersson
- Department of Physics, Umeå University Umeå SE-90187 Sweden
| | - Chris A Tulk
- Neutron Scattering Division, Oak Ridge National Laboratory Oak Ridge Tennessee 37831 USA
| | - Jamie Molaison
- Neutron Scattering Division, Oak Ridge National Laboratory Oak Ridge Tennessee 37831 USA
| | - Alexander P Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm University SE-10691 Stockholm Sweden
| | - Ulrich Häussermann
- Department of Materials and Environmental Chemistry, Stockholm University SE-10691 Stockholm Sweden
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219
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Castillo-Borja F, Bravo-Sánchez UI. Molecular Dynamics simulation study of the performance of different inhibitors for methane hydrate growth. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116510] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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220
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Phan A, Stamatakis M, Koh CA, Striolo A. Correlating Antiagglomerant Performance with Gas Hydrate Cohesion. ACS APPLIED MATERIALS & INTERFACES 2021; 13:40002-40012. [PMID: 34382786 DOI: 10.1021/acsami.1c06309] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Although inhibiting hydrate formation in hydrocarbon-water systems is paramount in preventing pipe blockage in hydrocarbon transport systems, the molecular mechanisms responsible for antiagglomerant (AA) performance are not completely understood. To better understand why macroscopic performance is affected by apparently small changes in the AA molecular structure, we perform molecular dynamics simulations. We quantify the cohesion energy between two gas hydrate nanoparticles dispersed in liquid hydrocarbons in the presence of different AAs, and we achieve excellent agreement against experimental data obtained at high pressure using the micromechanical force apparatus. This suggests that the proposed simulation approach could provide a screening method for predicting, in silico, the performance of new molecules designed to manage hydrates in flow assurance. Our results suggest that entropy and free energy of solvation of AAs, combined in some cases with the molecular orientation at hydrate-oil interfaces, are descriptors that could be used to predict performance, should the results presented here be reproduced for other systems as well. These insights could help speed up the design of new AAs and guide future experiments.
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Affiliation(s)
- Anh Phan
- Department of Chemical Engineering, University College London, London WC1E 7JE, U.K
| | - Michail Stamatakis
- Department of Chemical Engineering, University College London, London WC1E 7JE, U.K
| | - Carolyn A Koh
- Center for Hydrate Research, Chemical & Biological Engineering Department, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Alberto Striolo
- Department of Chemical Engineering, University College London, London WC1E 7JE, U.K
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221
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Li C, Liu Z, Goonetilleke EC, Huang X. Temperature-dependent kinetic pathways of heterogeneous ice nucleation competing between classical and non-classical nucleation. Nat Commun 2021; 12:4954. [PMID: 34400646 PMCID: PMC8367957 DOI: 10.1038/s41467-021-25267-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 07/26/2021] [Indexed: 12/04/2022] Open
Abstract
Ice nucleation on the surface plays a vital role in diverse areas, ranging from physics and cryobiology to atmospheric science. Compared to ice nucleation in the bulk, the water-surface interactions present in heterogeneous ice nucleation complicate the nucleation process, making heterogeneous ice nucleation less comprehended, especially the relationship between the kinetics and the structures of the critical ice nucleus. Here we combine Markov State Models and transition path theory to elucidate the ensemble pathways of heterogeneous ice nucleation. Our Markov State Models reveal that the classical one-step and non-classical two-step nucleation pathways can surprisingly co-exist with comparable fluxes at T = 230 K. Interestingly, we find that the disordered mixing of rhombic and hexagonal ice leads to a favorable configurational entropy that stabilizes the critical nucleus, facilitating the non-classical pathway. In contrast, the favorable energetics promotes the formation of hexagonal ice, resulting in the classical pathway. Furthermore, we discover that, at elevated temperatures, the nucleation process prefers to proceed via the classical pathway, as opposed to the non-classical pathway, since the potential energy contributions override the configurational entropy compensation. This study provides insights into the mechanisms of heterogeneous ice nucleation and sheds light on the rational designs to control crystallization processes.
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Affiliation(s)
- Chu Li
- Department of Chemistry, Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Zhuo Liu
- Department of Chemistry, Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
- Institute for Advanced Study, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Eshani C Goonetilleke
- Department of Chemistry, Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Xuhui Huang
- Department of Chemistry, Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong.
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222
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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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223
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Kim J, Lee B, Shin K, Kang SP, Park KH, Cha M, Alavi S, Ripmeester JA. Incorporation of Ammonium Fluoride and Methanol in Carbon Dioxide Clathrate Hydrates and Their Significance for Hydrate-Based Gas Separation. Ind Eng Chem Res 2021. [DOI: 10.1021/acs.iecr.1c01423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jeongtak Kim
- Department of Applied Chemistry, Kyungpook National University, Daegu 41566, Republic of Korea
- Climate Change Research Division, Korea Institute of Energy Research, Daejeon 34129, Republic of Korea
| | - Byeonggwan Lee
- Department of Hydrogen & Renewable Energy, Kyungpook National University, Daegu 41566, Republic of Korea
- Radioactive Waste Treatment Research Team, Korea Atomic Energy Research Institute, Daejeon 34057, Republic of Korea
| | - Kyuchul Shin
- Department of Applied Chemistry, Kyungpook National University, Daegu 41566, Republic of Korea
- Department of Hydrogen & Renewable Energy, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Seong-Pil Kang
- Climate Change Research Division, Korea Institute of Energy Research, Daejeon 34129, Republic of Korea
| | - Ki Hun Park
- Department of Energy and Resources Engineering, Kangwon National University, Gangwon-do 24341, Republic of Korea
| | - Minjun Cha
- Department of Energy and Resources Engineering, Kangwon National University, Gangwon-do 24341, Republic of Korea
| | - Saman Alavi
- National Research Council of Canada, 100 Sussex Dr., Ottawa, Ontario K1A 0R6, Canada
| | - John A. Ripmeester
- National Research Council of Canada, 100 Sussex Dr., Ottawa, Ontario K1A 0R6, Canada
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224
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Liu Y, Zhu W, Jiang J, Zhu C, Liu C, Slater B, Ojamäe L, Francisco JS, Zeng XC. Formation of porous ice frameworks at room temperature. Proc Natl Acad Sci U S A 2021; 118:e2104442118. [PMID: 34326263 PMCID: PMC8346885 DOI: 10.1073/pnas.2104442118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bulk crystalline ices with ultralow densities have been demonstrated to be thermodynamically metastable at negative pressures. However, the direct formation of these bulk porous ices from liquid water at negative pressures is extremely challenging. Inspired by approaches toward porous media based on host-guest chemistry, such as metal-organic frameworks and covalent organic frameworks, we herein demonstrate via molecular dynamics simulations that a class of ultralow-density porous ices with upright channels can be formed spontaneously from liquid water at 300 K with the assistance of carbon nanotube arrays. We refer to these porous ice polymorphs as water oxygen-vertex frameworks (WOFs). Notably, our simulations revealed that the liquid-WOF phase transition is first-order and occurs at room temperature. All the WOFs exhibited the unique structural feature that they can be regarded as assemblies of nanoribbons of hexagonal bilayer ice (2D ice I) at their armchair or zigzag edges. Based on density functional theory calculations, a comprehensive phase diagram of the WOFs was constructed considering both the thermodynamic and thermal stabilities of the porous ices at negative pressures. Like other types of porous media, these WOFs may be applicable to gas storage, purification, and separation. Moreover, these biocompatible porous ice networks may be exploited as medical-related carriers.
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Affiliation(s)
- Yuan Liu
- School of Chemical Engineering and Technology, Sun Yat-sen University, Zhuhai 519082, China;
| | - Weiduo Zhu
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588
| | - Jian Jiang
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588
| | - Chongqin Zhu
- Department of Earth and Environmental Science, University of Pennsylvania, Philadelphia, PA 19104
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Chang Liu
- College of Physics, Liaoning University, Shenyang 110036, China
| | - Ben Slater
- Department of Chemistry, University College London, London WC1H 0AJ, United Kingdom
| | - Lars Ojamäe
- Department of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Joseph S Francisco
- Department of Earth and Environmental Science, University of Pennsylvania, Philadelphia, PA 19104;
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Xiao Cheng Zeng
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588;
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225
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Zhou H, Feng YJ, Wang C, Huang T, Liu YR, Jiang S, Wang CY, Huang W. A high-accuracy machine-learning water model for exploring water nanocluster structures. NANOSCALE 2021; 13:12212-12222. [PMID: 34231634 DOI: 10.1039/d1nr03128g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Water, the most important molecule on the Earth, possesses many essential and unique physical properties that are far from completely understood, partly due to serious difficulties in identifying the precise microscopic structures of water. Hence, identifying the structures of water nanoclusters is a fundamental and challenging issue for studies on the relationship between the macroscopic physical properties of water and its microscopic structures. For large-scale simulations (at the level of nm and ns) of water nanoclusters, a calculation method with simultaneous accuracy at the level of quantum chemistry and efficiency at the level of an empirical potential method is in great demand. Herein, a machine-learning (ML) water model was utilized to explore the microscopic structural features at different length scales for water nanoclusters with a size up to several nm. The ML water model can be employed to efficiently predict the structures of water nanoclusters with a similar accuracy to that of density functional theory and with substantially lower computational resource demands. To validate the low-lying structure search results with experimental spectral results, an ML water model combined with velocity autocorrelation function analysis was used to simulate the vibrational spectra of water nanoclusters with up to thousands of water molecules. By comparing the simulated and experimentally recorded vibrational spectra, the atomic structures determined by a simulation based on the ML water model are all verified. To demonstrate its ability to represent water's structural evolution at large length and time scales, the ML water model was employed to model the structural evolution during the crystal-liquid transition, and the phase transition temperatures of water clusters with different sizes were precisely predicted. The ML water model provides an efficient theoretical calculation tool for exploring the structures and physical properties of water and their relationships, especially for clusters with relatively large sizes and processes with relatively long durations.
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Affiliation(s)
- Hao Zhou
- School of Information Science and Technology, University of Science and Technology of China, Hefei, Anhui 230026, China.
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226
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Lu H, Xu Q, Wu J, Hong R, Zhang Z. Effect of interfacial dipole on heterogeneous ice nucleation. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:375001. [PMID: 34181589 DOI: 10.1088/1361-648x/ac0f2c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 06/28/2021] [Indexed: 06/13/2023]
Abstract
In this work, we performed molecular dynamics simulations of ice nucleation on a rigid surface model of cubic zinc blende structure with different surface dipole strength and orientation. Our results show that, although substrates are excellently lattice-matched to cubic ice, ice nucleation merely occurred as the interfacial water molecules (IWs) show identical or similar orientations to that of water molecules in cubic ice. Free energy landscapes revealed that, as substrates have non-suitable dipole strength/orientation, there exist large free energy barriers for rotating dipole IWs to the right orientation to trigger ice formation. This study stresses that, beyond the traditional view of lattice match and the similarity of lattice length between the substrate and new-formed crystal, the similarity between molecular orientations of interfacial component and component in the specific new-formed crystalline face is also critical for promoting ice nucleation.
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Affiliation(s)
- Hao Lu
- Department of Physics, Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Laboratory for Soft Functional Materials Research, Jiujiang Research Institute, Xiamen University, Xiamen, Fujian 361005, People's Republic of China
| | - Quanming Xu
- Department of Physics, Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Laboratory for Soft Functional Materials Research, Jiujiang Research Institute, Xiamen University, Xiamen, Fujian 361005, People's Republic of China
| | - Jianyang Wu
- Department of Physics, Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Laboratory for Soft Functional Materials Research, Jiujiang Research Institute, Xiamen University, Xiamen, Fujian 361005, People's Republic of China
| | - Rongdun Hong
- Department of Physics, Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Laboratory for Soft Functional Materials Research, Jiujiang Research Institute, Xiamen University, Xiamen, Fujian 361005, People's Republic of China
| | - Zhisen Zhang
- Department of Physics, Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Laboratory for Soft Functional Materials Research, Jiujiang Research Institute, Xiamen University, Xiamen, Fujian 361005, People's Republic of China
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227
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Tsimpanogiannis IN. A novel hybrid method for the calculation of methane hydrate-water interfacial tension along the three-phase (hydrate-liquid water-vapor) equilibrium line. J Chem Phys 2021; 155:024702. [PMID: 34266278 DOI: 10.1063/5.0051383] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
We use a novel hybrid method to explore the temperature dependence of the solid-liquid interfacial tension of a system that consists of solid methane hydrate and liquid water. The calculated values along the three-phase (hydrate-liquid water-vapor) equilibrium line are obtained through the combination of available experimental measurements and computational results that are based on approaches at the atomistic scale, including molecular dynamics and Monte Carlo. An extensive comparison with available experimental and computational studies is performed, and a critical assessment and re-evaluation of previously reported data is presented.
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Affiliation(s)
- Ioannis N Tsimpanogiannis
- Chemical Process & Energy Resources Institute (CPERI), Centre for Research & Technology Hellas (CERTH), 57001 Thermi-Thessaloniki, Greece
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228
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Barabash M, Gibby WAT, Guardiani C, Luchinsky DG, Luan B, Smolyanitsky A, McClintock PVE. Field-Dependent Dehydration and Optimal Ionic Escape Paths for C 2N Membranes. J Phys Chem B 2021; 125:7044-7059. [PMID: 34115497 PMCID: PMC8279548 DOI: 10.1021/acs.jpcb.1c03255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/29/2021] [Indexed: 11/28/2022]
Abstract
Most analytic theories describing electrostatically driven ion transport through water-filled nanopores assume that the corresponding permeation barriers are bias-independent. While this assumption may hold for sufficiently wide pores under infinitely small bias, transport through subnanometer pores under finite bias is difficult to interpret analytically. Given recent advances in subnanometer pore fabrication and the rapid progress in detailed computer simulations, it is important to identify and understand the specific field-induced phenomena arising during ion transport. Here we consider an atomistic model of electrostatically driven ion permeation through subnanoporous C2N membranes. We analyze probability distributions of ionic escape trajectories and show that the optimal escape path switches between two different configurations depending on the bias magnitude. We identify two distinct mechanisms contributing to field-induced changes in transport-opposing barriers: a weak one arising from field-induced ion dehydration and a strong one due to the field-induced asymmetry of the hydration shells. The simulated current-voltage characteristics are compared with the solution of the 1D Nernst-Planck model. Finally, we show that the deviation of simulated currents from analytic estimates for large fields is consistent with the field-induced barriers and the observed changes in the optimal ion escape path.
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Affiliation(s)
| | - William A. T. Gibby
- Department
of Physics, Lancaster University, Lancaster LA1 4YB, United Kingdom
| | - Carlo Guardiani
- Department
of Physics, Lancaster University, Lancaster LA1 4YB, United Kingdom
- Department
of Mechanical and Aerospace Engineering, Sapienza University, 00184 Rome, Italy
| | - Dmitry G. Luchinsky
- Department
of Physics, Lancaster University, Lancaster LA1 4YB, United Kingdom
- Ames
Research Center, KBR, Inc., Moffett Field, California 94035, United States
| | - Binquan Luan
- Computational
Biological Center, IBM Thomas J. Watson
Research, Yorktown
Heights, New York 10598, United States
| | - Alex Smolyanitsky
- Applied
Chemicals and Materials Division, National
Institute of Standards and Technology, Boulder, Colorado 80305, United States
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229
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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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230
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Zhang L, Wang H, Car R, E W. Phase Diagram of a Deep Potential Water Model. PHYSICAL REVIEW LETTERS 2021; 126:236001. [PMID: 34170175 DOI: 10.1103/physrevlett.126.236001] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/28/2021] [Indexed: 06/13/2023]
Abstract
Using the Deep Potential methodology, we construct a model that reproduces accurately the potential energy surface of the SCAN approximation of density functional theory for water, from low temperature and pressure to about 2400 K and 50 GPa, excluding the vapor stability region. The computational efficiency of the model makes it possible to predict its phase diagram using molecular dynamics. Satisfactory overall agreement with experimental results is obtained. The fluid phases, molecular and ionic, and all the stable ice polymorphs, ordered and disordered, are predicted correctly, with the exception of ice III and XV that are stable in experiments, but metastable in the model. The evolution of the atomic dynamics upon heating, as ice VII transforms first into ice VII^{''} and then into an ionic fluid, reveals that molecular dissociation and breaking of the ice rules coexist with strong covalent fluctuations, explaining why only partial ionization was inferred in experiments.
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Affiliation(s)
- Linfeng Zhang
- Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544, USA
| | - Han Wang
- Laboratory of Computational Physics, Institute of Applied Physics and Computational Mathematics, Fenghao East Road 2, Beijing 100094, People's Republic of China
| | - Roberto Car
- Department of Chemistry, Department of Physics, Program in Applied and Computational Mathematics, Princeton Institute for the Science and Technology of Materials, Princeton University, Princeton, New Jersey 08544, USA
| | - Weinan E
- Department of Mathematics and Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544, USA and Beijing Institute of Big Data Research, Beijing 100871, People's Republic of China
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231
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Sizova AA, Grintsevich SA, Kochurin MA, Sizov VV, Brodskaya EN. Molecular Simulations of CO2/CH4, CO2/N2 and N2/CH4 Binary Mixed Hydrates. COLLOID JOURNAL 2021. [DOI: 10.1134/s1061933x21030145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract
Grand canonical Monte Carlo simulations were performed to study the occupancy of structure I multicomponent gas hydrates by CO2/CH4, CO2/N2, and N2/CH4 binary gas mixtures with various compositions at a temperature of 270 K and pressures up to 70 atm. The presence of nitrogen in the gas mixture allows for an increase of both the hydrate framework selectivity to CO2 and the amount of carbon dioxide encapsulated in hydrate cages, as compared to the CO2/CH4 hydrate. Despite the selectivity to CH4 molecules demonstrated by N2/CH4 hydrate, nitrogen can compete with methane if the gas mixture contains at least 70% of N2.
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232
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Guo Q, Hu W, Zhang Y, Zhang K, Dong B, Qin Y, Li W. Molecular dynamics simulation of the interfacial properties of methane-water and methane-brine systems. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1929969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Qiuyi Guo
- Key Laboratory of Ocean Energy Utilization and Energy Conservation of Ministry of Education, Dalian, People’s Republic of China
| | - Wenfeng Hu
- Key Laboratory of Ocean Energy Utilization and Energy Conservation of Ministry of Education, Dalian, People’s Republic of China
| | - Yue Zhang
- Key Laboratory of Ocean Energy Utilization and Energy Conservation of Ministry of Education, Dalian, People’s Republic of China
| | - Kun Zhang
- School of Ocean and Civil Engineering, Dalian Ocean University, Dalian, People’s Republic of China
| | - Bo Dong
- Key Laboratory of Ocean Energy Utilization and Energy Conservation of Ministry of Education, Dalian, People’s Republic of China
- School of Energy and Power Engineering, Dalian University of Technology, Dalian, People’s Republic of China
| | - Yan Qin
- Key Laboratory of Ocean Energy Utilization and Energy Conservation of Ministry of Education, Dalian, People’s Republic of China
- School of Energy and Power Engineering, Dalian University of Technology, Dalian, People’s Republic of China
| | - Weizhong Li
- Key Laboratory of Ocean Energy Utilization and Energy Conservation of Ministry of Education, Dalian, People’s Republic of China
- School of Energy and Power Engineering, Dalian University of Technology, Dalian, People’s Republic of China
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233
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Mukherjee S, Bagchi B. Theoretical analyses of pressure induced glass transition in water: Signatures of surprising diffusion-entropy scaling across the transition. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1930222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Saumyak Mukherjee
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, India
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234
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Goswami A, Dalal IS, Singh JK. Universal Nucleation Behavior of Sheared Systems. PHYSICAL REVIEW LETTERS 2021; 126:195702. [PMID: 34047572 DOI: 10.1103/physrevlett.126.195702] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 04/15/2021] [Indexed: 06/12/2023]
Abstract
Using molecular simulations and a modified classical nucleation theory, we study the nucleation, under flow, of a variety of liquids: different water models, Lennard-Jones, and hard sphere colloids. Our approach enables us to analyze a wide range of shear rates inaccessible to brute-force simulations. Our results reveal that the variation of the nucleation rate with shear is universal. A simplified version of the theory successfully captures the nonmonotonic temperature dependence of the nucleation behavior, which is shown to originate from the violation of the Stokes-Einstein relation.
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Affiliation(s)
- Amrita Goswami
- Department of Chemical Engineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Indranil Saha Dalal
- Department of Chemical Engineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Jayant K Singh
- Department of Chemical Engineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
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235
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Foffi R, Russo J, Sciortino F. Structural and topological changes across the liquid-liquid transition in water. J Chem Phys 2021; 154:184506. [PMID: 34241034 DOI: 10.1063/5.0049299] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
It has recently been shown that the TIP4P/Ice model of water can be studied numerically in metastable equilibrium at and below its liquid-liquid critical temperature. We report here simulations along a subcritical isotherm, for which two liquid states with the same pressure and temperature but different density can be equilibrated. This allows for a clear visualization of the structural changes taking place across the transition. We specifically focus on how the topological properties of the H-bond network change across the liquid-liquid transition. Our results demonstrate that the structure of the high-density liquid, characterized by the existence of interstitial molecules and commonly explained in terms of the collapse of the second neighbor shell, actually originates from the folding back of long rings, bringing pairs of molecules separated by several hydrogen-bonds close by in space.
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Affiliation(s)
- Riccardo Foffi
- Department of Physics, Sapienza Università di Roma, Piazzale Aldo Moro, 2, 00185 Rome, Italy
| | - John Russo
- Department of Physics, Sapienza Università di Roma, Piazzale Aldo Moro, 2, 00185 Rome, Italy
| | - Francesco Sciortino
- Department of Physics, Sapienza Università di Roma, Piazzale Aldo Moro, 2, 00185 Rome, Italy
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236
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Stevens CA, Bachtiger F, Kong XD, Abriata LA, Sosso GC, Gibson MI, Klok HA. A minimalistic cyclic ice-binding peptide from phage display. Nat Commun 2021; 12:2675. [PMID: 33976148 PMCID: PMC8113477 DOI: 10.1038/s41467-021-22883-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 04/01/2021] [Indexed: 11/09/2022] Open
Abstract
Developing molecules that emulate the properties of naturally occurring ice-binding proteins (IBPs) is a daunting challenge. Rather than relying on the (limited) existing structure-property relationships that have been established for IBPs, here we report the use of phage display for the identification of short peptide mimics of IBPs. To this end, an ice-affinity selection protocol is developed, which enables the selection of a cyclic ice-binding peptide containing just 14 amino acids. Mutational analysis identifies three residues, Asp8, Thr10 and Thr14, which are found to be essential for ice binding. Molecular dynamics simulations reveal that the side chain of Thr10 hydrophobically binds to ice revealing a potential mechanism. To demonstrate the biotechnological potential of this peptide, it is expressed as a fusion ('Ice-Tag') with mCherry and used to purify proteins directly from cell lysate.
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Affiliation(s)
- Corey A Stevens
- Laboratoire des Polymères, Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Fabienne Bachtiger
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, UK
| | - Xu-Dong Kong
- Laboratory of Therapeutic Proteins and Peptides, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Luciano A Abriata
- Protein Production and Structure Core Facility and Laboratory for Biomolecular Modeling, École Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Gabriele C Sosso
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, UK
| | - Matthew I Gibson
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, UK.,Warwick Medical School, University of Warwick, Coventry, UK
| | - Harm-Anton Klok
- Laboratoire des Polymères, Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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237
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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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238
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239
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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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240
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Arjun A, Bolhuis PG. Homogenous nucleation rate of CO 2 hydrates using transition interface sampling. J Chem Phys 2021; 154:164507. [PMID: 33940852 DOI: 10.1063/5.0044883] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Carbon dioxide and water can form solid clathrate structures in which water cages encapsulate the gas molecules. Such hydrates have sparked much interest due to their possible application in CO2 sequestration. How the solid structure forms exactly from the liquid phase via a homogenous nucleation process is still poorly understood. This nucleation event is rare on the molecular timescale even under moderate undercooling or supersaturation conditions because of the large free energy barrier toward crystallization, rendering a brute force simulation of hydrate nucleation unfeasible for moderate undercooling or supersaturation. Here, we perform transition interface sampling simulations to quantify the homogenous nucleation rate for CO2 hydrate formation using accurate atomistic force fields at 500 bars for three different temperatures between 260 and 273 K. Collecting more than 100 000 pathways comprising roughly two milliseconds of simulation time, we computed a nucleation rate in the amorphous phase of ∼1021 nuclei s-1 cm-3 for a temperature of 260 K and a rate of ∼1012 nuclei s-1 cm-3 for a temperature of 265 K. For a temperature of 273 K, we find that the hydrate forms an sI crystalline phase with a rate of order of ∼101 nuclei s-1 cm-3. We compare these rates to classical nucleation theory estimates as well as experiments, and to nucleation rate estimates for methane hydrates and discuss possible causes of the observed differences. Our findings shed light on the kinetics of this important clathrate and should assist in future hydrate formation investigation.
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Affiliation(s)
- A Arjun
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Peter G Bolhuis
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
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241
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Roudsari G, Veshki FG, Reischl B, Pakarinen OH. Liquid Water and Interfacial, Cubic, and Hexagonal Ice Classification through Eclipsed and Staggered Conformation Template Matching. J Phys Chem B 2021; 125:3909-3917. [PMID: 33844543 DOI: 10.1021/acs.jpcb.1c01926] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We propose a novel method based on template matching for the recognition of liquid water, cubic ice (ice Ic), hexagonal ice (ice Ih), clathrate hydrates, and different interfacial structures in atomistic and coarse-grained simulations of water and ice. The two template matrices represent staggered and eclipsed conformations, which are the building blocks of hexagonal and cubic ice and clathrate crystals. The algorithm is rotationally invariant and highly robust against imperfections in the ice structure, and its sensitivity for recognizing ice-like structures can be tuned for different applications. Unlike most other algorithms, it can discriminate between cubic, hexagonal, clathrate, mixed, and other interfacial ice types and is therefore well suited to study complex systems and heterogeneous ice nucleation.
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Affiliation(s)
- Golnaz Roudsari
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki, P.O. Box 64, Helsinki FI-00014, Finland
| | - Farshad G Veshki
- Department of Signal Processing and Acoustics, School of Electrical Engineering, Aalto University, P.O. Box 11000, Espoo FI-00076, Finland
| | - Bernhard Reischl
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki, P.O. Box 64, Helsinki FI-00014, Finland
| | - Olli H Pakarinen
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki, P.O. Box 64, Helsinki FI-00014, Finland
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242
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Reduced phase stability and faster formation/dissociation kinetics in confined methane hydrate. Proc Natl Acad Sci U S A 2021; 118:2024025118. [PMID: 33850020 DOI: 10.1073/pnas.2024025118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The mechanisms involved in the formation/dissociation of methane hydrate confined at the nanometer scale are unraveled using advanced molecular modeling techniques combined with a mesoscale thermodynamic approach. Using atom-scale simulations probing coexistence upon confinement and free energy calculations, phase stability of confined methane hydrate is shown to be restricted to a narrower temperature and pressure domain than its bulk counterpart. The melting point depression at a given pressure, which is consistent with available experimental data, is shown to be quantitatively described using the Gibbs-Thomson formalism if used with accurate estimates for the pore/liquid and pore/hydrate interfacial tensions. The metastability barrier upon hydrate formation and dissociation is found to decrease upon confinement, therefore providing a molecular-scale picture for the faster kinetics observed in experiments on confined gas hydrates. By considering different formation mechanisms-bulk homogeneous nucleation, external surface nucleation, and confined nucleation within the porosity-we identify a cross-over in the nucleation process; the critical nucleus formed in the pore corresponds either to a hemispherical cap or to a bridge nucleus depending on temperature, contact angle, and pore size. Using the classical nucleation theory, for both mechanisms, the typical induction time is shown to scale with the pore volume to surface ratio and hence the pore size. These findings for the critical nucleus and nucleation rate associated with such complex transitions provide a means to rationalize and predict methane hydrate formation in any porous media from simple thermodynamic data.
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243
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Metya AK, Molinero V. Is Ice Nucleation by Organic Crystals Nonclassical? An Assessment of the Monolayer Hypothesis of Ice Nucleation. J Am Chem Soc 2021; 143:4607-4624. [PMID: 33729789 DOI: 10.1021/jacs.0c12012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Potent ice nucleating organic crystals display an increase in nucleation efficiency with pressure and memory effect after pressurization that set them apart from inorganic nucleants. These characteristics were proposed to arise from an ordered water monolayer at the organic-water interface. It was interpreted that ordering of the monolayer is the limiting step for ice nucleation on organic crystals, rendering their mechanism of nucleation nonclassical. Despite the importance of organics in atmospheric ice nucleation, that explanation has never been investigated. Here we elucidate the structure of interfacial water and its role in ice nucleation at ambient pressure on phloroglucinol dihydrate, the paradigmatic example of outstanding ice nucleating organic crystal, using molecular simulations. The simulations confirm the existence of an interfacial monolayer that orders on cooling and becomes fully ordered upon ice formation. The monolayer does not resemble any ice face but seamlessly connects the distinct hydrogen-bonding orders of ice and the organic surface. Although large ordered patches develop in the monolayer before ice nucleates, we find that the critical step is the formation of the ice crystallite, indicating that the mechanism is classical. We predict that the fully ordered, crystalline monolayer nucleates ice above -2 °C and could be responsible for the exceptional ice nucleation by the organic crystal at high pressures. The lifetime of the fully ordered monolayer around 0 °C, however, is too short to account for the memory effect reported in the experiments. The latter could arise from an increase in the melting temperature of ice confined by strongly ice-binding surfaces.
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Affiliation(s)
- Atanu K Metya
- Department of Chemistry, The University of Utah, Salt Lake City, Utah 84112-0850, United States
| | - Valeria Molinero
- Department of Chemistry, The University of Utah, Salt Lake City, Utah 84112-0850, United States
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244
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Tavagnacco L, Chiessi E, Zaccarelli E. Molecular insights on poly( N-isopropylacrylamide) coil-to-globule transition induced by pressure. Phys Chem Chem Phys 2021; 23:5984-5991. [PMID: 33666621 PMCID: PMC8247264 DOI: 10.1039/d0cp06452a] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/17/2021] [Indexed: 12/17/2022]
Abstract
By using extensive all-atom molecular dynamics simulations of an atactic linear polymer chain, we provide microscopic insights into poly(N-isopropylacrylamide) (PNIPAM) coil-to-globule transition addressing the roles played by both temperature and pressure. We detect a coil-to-globule transition up to large pressures, showing a reentrant behavior of the critical temperature with increasing pressure in agreement with experimental observations. Furthermore, again confirming the experimental findings, we report the existence at high pressures of a new kind of globular state. It is characterized by a more structured hydration shell that is closer to PNIPAM hydrophobic domains, as compared to the globular state observed at atmospheric pressure. Our results highlight that temperature and pressure induce a PNIPAM coil-to-globule transition through different molecular mechanisms, opening the way for a systematic use of both thermodynamic variables to tune the location of the transition and the properties of the associated swollen/collapsed states.
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Affiliation(s)
- Letizia Tavagnacco
- CNR-ISC and Department of Physics, Sapienza University of Rome, Piazzale A. Moro 2, 00185, Rome, Italy.
| | - Ester Chiessi
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica I, 00133, Rome, Italy.
| | - Emanuela Zaccarelli
- CNR-ISC and Department of Physics, Sapienza University of Rome, Piazzale A. Moro 2, 00185, Rome, Italy.
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245
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Joliat J, Patt A, Simon JM, Picaud S. Adsorption of organic compounds at the surface of Enceladus’ ice grains. A grand canonical Monte Carlo simulation study. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1900571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Julien Joliat
- Institut UTINAM, UMR 6213, CNRS, Université Bourgogne Franche-Comté, Besançon, France
| | - Antoine Patt
- Institut UTINAM, UMR 6213, CNRS, Université Bourgogne Franche-Comté, Besançon, France
| | - Jean Marc Simon
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303, CNRS, Université de Bourgogne Franche-Comté, Cedex Dijon, France
| | - Sylvain Picaud
- Institut UTINAM, UMR 6213, CNRS, Université Bourgogne Franche-Comté, Besançon, France
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246
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Atakoohi SE, Naeiji P, Peyvandi K, Mollashahi Sanatgar S. The experimental study and molecular dynamic simulation of THF hydrate growth kinetics in the presence of Arabic and Guar gum: New approaches in promotion of THF hydrate formation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.115249] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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247
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Bachtiger F, Congdon TR, Stubbs C, Gibson MI, Sosso GC. The atomistic details of the ice recrystallisation inhibition activity of PVA. Nat Commun 2021; 12:1323. [PMID: 33637764 PMCID: PMC7910567 DOI: 10.1038/s41467-021-21717-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 02/05/2021] [Indexed: 01/31/2023] Open
Abstract
Understanding the ice recrystallisation inhibition (IRI) activity of antifreeze biomimetics is crucial to the development of the next generation of cryoprotectants. In this work, we bring together molecular dynamics simulations and quantitative experimental measurements to unravel the microscopic origins of the IRI activity of poly(vinyl)alcohol (PVA)-the most potent of biomimetic IRI agents. Contrary to the emerging consensus, we find that PVA does not require a "lattice matching" to ice in order to display IRI activity: instead, it is the effective volume of PVA and its contact area with the ice surface which dictates its IRI strength. We also find that entropic contributions may play a role in the ice-PVA interaction and we demonstrate that small block co-polymers (up to now thought to be IRI-inactive) might display significant IRI potential. This work clarifies the atomistic details of the IRI activity of PVA and provides novel guidelines for the rational design of cryoprotectants.
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Affiliation(s)
- Fabienne Bachtiger
- Department of Chemistry, University of Warwick, Coventry, UK
- Centre for Scientific Computing, University of Warwick, Coventry, UK
| | | | | | - Matthew I Gibson
- Department of Chemistry, University of Warwick, Coventry, UK
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Gabriele C Sosso
- Department of Chemistry, University of Warwick, Coventry, UK.
- Centre for Scientific Computing, University of Warwick, Coventry, UK.
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248
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Tarn MD, Sikora SNF, Porter GCE, Shim JU, Murray BJ. Homogeneous Freezing of Water Using Microfluidics. MICROMACHINES 2021; 12:223. [PMID: 33672200 PMCID: PMC7926757 DOI: 10.3390/mi12020223] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 01/17/2023]
Abstract
The homogeneous freezing of water is important in the formation of ice in clouds, but there remains a great deal of variability in the representation of the homogeneous freezing of water in the literature. The development of new instrumentation, such as droplet microfluidic platforms, may help to constrain our understanding of the kinetics of homogeneous freezing via the analysis of monodisperse, size-selected water droplets in temporally and spatially controlled environments. Here, we evaluate droplet freezing data obtained using the Lab-on-a-Chip Nucleation by Immersed Particle Instrument (LOC-NIPI), in which droplets are generated and frozen in continuous flow. This high-throughput method was used to analyse over 16,000 water droplets (86 μm diameter) across three experimental runs, generating data with high precision and reproducibility that has largely been unrepresented in the microfluidic literature. Using this data, a new LOC-NIPI parameterisation of the volume nucleation rate coefficient (JV(T)) was determined in the temperature region of -35.1 to -36.9 °C, covering a greater JV(T) compared to most other microfluidic techniques thanks to the number of droplets analysed. Comparison to recent theory suggests inconsistencies in the theoretical representation, further implying that microfluidics could be used to inform on changes to parameterisations. By applying classical nucleation theory (CNT) to our JV(T) data, we have gone a step further than other microfluidic homogeneous freezing examples by calculating the stacking-disordered ice-supercooled water interfacial energy, estimated to be 22.5 ± 0.7 mJ m-2, again finding inconsistencies when compared to theoretical predictions. Further, we briefly review and compile all available microfluidic homogeneous freezing data in the literature, finding that the LOC-NIPI and other microfluidically generated data compare well with commonly used non-microfluidic datasets, but have generally been obtained with greater ease and with higher numbers of monodisperse droplets.
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Affiliation(s)
- Mark D. Tarn
- School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK; (S.N.F.S.); (G.C.E.P.)
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK;
| | - Sebastien N. F. Sikora
- School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK; (S.N.F.S.); (G.C.E.P.)
| | - Grace C. E. Porter
- School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK; (S.N.F.S.); (G.C.E.P.)
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK;
| | - Jung-uk Shim
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK;
| | - Benjamin J. Murray
- School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK; (S.N.F.S.); (G.C.E.P.)
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249
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Gilmore RAJ, Misquitta AJ, Dove MT. Methane hydrate clathrates: effects in the simulation of melting arising from the assumption of simple combining rules in interatomic potentials. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2019.1572139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- R. A. J. Gilmore
- School of Physics and Astronomy, Queen Mary University of London, London UK
| | - A. J. Misquitta
- School of Physics and Astronomy, Queen Mary University of London, London UK
| | - M. T. Dove
- School of Physics and Astronomy, Queen Mary University of London, London UK
- Department of Physics, School of Sciences, Wuhan University of Technology, Wuhan, People's Republic of China
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Mohr S, Hoevelmann F, Wylde J, Schelero N, Sarria J, Purkayastha N, Ward Z, Navarro Acero P, Michalis VK. Ranking the Efficiency of Gas Hydrate Anti-agglomerants through Molecular Dynamic Simulations. J Phys Chem B 2021; 125:1487-1502. [PMID: 33529037 DOI: 10.1021/acs.jpcb.0c08969] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Using both computational and experimental methods, the capacity of four different surfactant molecules to inhibit the agglomeration of sII hydrate particles was assessed. The computational simulations were carried out using both steered and non-steered molecular dynamics (MD), simulating the coalescence process of a hydrate slab and a water droplet, both covered with surfactant molecules. The surfactants were ranked according to free energy calculations (steered MD) and the number of agglomeration events (non-steered MD). The experimental work was based on rocking cell measurements, determining the minimum effective dose necessary to inhibit agglomeration. Overall, good agreement was obtained between the performance predicted by the simulations and the experimental measurements. Moreover, the simulations allowed us to gain additional insights that are not directly accessible via experiments, such as an analysis of the mass density profiles, the diffusion coefficients, or the orientations of the long tails.
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Affiliation(s)
- Stephan Mohr
- Nextmol (Bytelab Solutions SL), Barcelona 08018, Spain.,Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | | | - Jonathan Wylde
- Clariant Oil Services, Clariant Corporation, Houston, Texas 77258, United States.,Heriot-Watt University, Edinburgh EH14 4AS, Scotland, U.K
| | | | - Juan Sarria
- Clariant Produkte (Deutschland) GmbH, Frankfurt 65933, Germany
| | | | - Zachary Ward
- Clariant Oil Services, Clariant Corporation, Houston, Texas 77258, United States
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