1
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Gao Y, Wu J, Feng Y, Han J, Fang H. Structural effects of water clusters on viscosity at high shear rates. J Chem Phys 2024; 160:104502. [PMID: 38456533 DOI: 10.1063/5.0187906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/19/2024] [Indexed: 03/09/2024] Open
Abstract
In this study, we use molecular dynamics simulations of liquid water to investigate how shear thinning affects the viscosity of liquid water by structural changes of the hydrogen bond network. The effect of shear on viscosity can be divided into two parts: shear-induced destruction of the hydrogen bond network and the influence of the water structure on shear viscosity. First, strong shear destroys tetrahedral structures and thus reduces the connectivity of the hydrogen bond network. It is mainly because shear deformation, characterized by compression and expansion axes, respectively, triggers the destruction and formation of hydrogen bonds, resulting in anisotropic effects on water structures. At the same time, shear destroys large clusters and enhances the formation of small ones, resulting in a decrease in average cluster sizes. Second, the change of viscosity obeys a power law relationship with the change of hydrogen bond structures, highlighting a one-to-one correspondence between structure and property. Meanwhile, in order to explain why the structure affects viscosity, we define hydrogen-bond viscosity and find that the cooperative motion of the water structures can promote momentum transfer in the form of aggregations. Hydrogen-bond viscosity accounts for 5%-50% of the total viscosity. Our results elucidate that water structures are the important structural units to explain the change of water properties.
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Affiliation(s)
- Yitian Gao
- State Key Laboratory of Hydro-science and Engineering, Department of Hydraulic Engineering, Tsinghua University, Beijing 100084, China
| | - Jian Wu
- Department of Physics, Tsinghua University, Beijing 100084, China
| | - Yixuan Feng
- State Key Laboratory of Hydro-science and Engineering, Department of Hydraulic Engineering, Tsinghua University, Beijing 100084, China
| | - Jiale Han
- State Key Laboratory of Hydro-science and Engineering, Department of Hydraulic Engineering, Tsinghua University, Beijing 100084, China
| | - Hongwei Fang
- State Key Laboratory of Hydro-science and Engineering, Department of Hydraulic Engineering, Tsinghua University, Beijing 100084, China
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2
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Li XY, Wang T, Cai YC, Meng ZD, Nan JW, Ye JY, Yi J, Zhan DP, Tian N, Zhou ZY, Sun SG. Mechanism of Cations Suppressing Proton Diffusion Kinetics for Electrocatalysis. Angew Chem Int Ed Engl 2023; 62:e202218669. [PMID: 36762956 DOI: 10.1002/anie.202218669] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/07/2023] [Accepted: 02/10/2023] [Indexed: 02/11/2023]
Abstract
Proton transfer is crucial for electrocatalysis. Accumulating cations at electrochemical interfaces can alter the proton transfer rate and then tune electrocatalytic performance. However, the mechanism for regulating proton transfer remains ambiguous. Here, we quantify the cation effect on proton diffusion in solution by hydrogen evolution on microelectrodes, revealing the rate can be suppressed by more than 10 times. Different from the prevalent opinions that proton transport is slowed down by modified electric field, we found water structure imposes a more evident effect on kinetics. FTIR test and path integral molecular dynamics simulation indicate that proton prefers to wander within the hydration shell of cations rather than to hop rapidly along water wires. Low connectivity of water networks disrupted by cations corrupts the fast-moving path in bulk water. This study highlights the promising way for regulating proton kinetics via a modified water structure.
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Affiliation(s)
- Xiao-Yu Li
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Tan Kah Kee Innovation Laboratory, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Tao Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Tan Kah Kee Innovation Laboratory, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Yu-Chen Cai
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Tan Kah Kee Innovation Laboratory, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Zhao-Dong Meng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Tan Kah Kee Innovation Laboratory, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Jing-Wen Nan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Tan Kah Kee Innovation Laboratory, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Jin-Yu Ye
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Tan Kah Kee Innovation Laboratory, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Jun Yi
- School of Electronic Science and Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Dong-Ping Zhan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Tan Kah Kee Innovation Laboratory, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Na Tian
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Tan Kah Kee Innovation Laboratory, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Zhi-You Zhou
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Tan Kah Kee Innovation Laboratory, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Shi-Gang Sun
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Tan Kah Kee Innovation Laboratory, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
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3
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de Oliveira PMC, de Souza JIR, da Silva JAB, Longo RL. Temperature Dependence of Hydrogen Bond Networks of Liquid Water: Thermodynamic Properties and Structural Heterogeneity from Topological Descriptors. J Phys Chem B 2023; 127:2250-2257. [PMID: 36877152 DOI: 10.1021/acs.jpcb.2c08873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Topological analyses of hydrogen bond networks were performed based on the complex network and island statistics of liquid water at different temperatures. The influence of temperature on the liquid water structures and the topological properties of the hydrogen bond networks was investigated by Metropolis Monte Carlo simulations with the TIP4P/2005 potential model. The bilinear behavior of the second peak in the radial distribution function with the temperature was properly reproduced by these simulations. The average connectivity also displayed a bilinear behavior consistent with being a local descriptor. The semiglobal average path length (or geodesic distance) descriptor showed an unprecedented trimodal distribution, whose areas were dependent on the temperature. Considering equilibrium between these three sets of networks, standard enthalpy and entropy of equilibrium were determined for the first time, providing new insights into the structural heterogeneities of liquid water with interesting perspectives for modeling these quantitative properties of hydrogen bond networks.
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Affiliation(s)
- Paulo M C de Oliveira
- Núcleo Interdisciplinar de Ciências Exatas e da Natureza, Campus do Agreste. Universidade Federal de Pernambuco, 55.014-900 Caruaru, Pernambuco, Brazil
| | - Jéssica I R de Souza
- Programa de Pós-Graduação em Ciência de Materiais, Universidade Federal de Pernambuco, 50740-560 Recife, Pernambuco, Brazil
| | - Juliana A B da Silva
- Núcleo Interdisciplinar de Ciências Exatas e da Natureza, Campus do Agreste. Universidade Federal de Pernambuco, 55.014-900 Caruaru, Pernambuco, Brazil.,Programa de Pós-Graduação em Química, Universidade Federal Rural de Pernambuco, 52.171-900 Recife, Pernambuco, Brazil
| | - Ricardo L Longo
- Programa de Pós-Graduação em Ciência de Materiais, Universidade Federal de Pernambuco, 50740-560 Recife, Pernambuco, Brazil.,Departamento de Química Fundamental, Universidade Federal de Pernambuco, 50740-540 Recife, Pernambuco, Brazil
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4
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Gao Y, Fang H, Ni K, Feng Y. Water clusters and density fluctuations in liquid water based on extended hierarchical clustering methods. Sci Rep 2022; 12:8036. [PMID: 35577839 PMCID: PMC9110331 DOI: 10.1038/s41598-022-11947-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/25/2022] [Indexed: 11/29/2022] Open
Abstract
The microscopic structures of liquid water at ambient temperatures remain a hot debate, which relates with structural and density fluctuations in the hydrogen bond network. Here, we use molecular dynamics simulations of liquid water to study the properties of three-dimensional cage-like water clusters, which we investigate using extended graph-based hierarchical clustering methods. The water clusters can cover over 95% of hydrogen bond network, among which some clusters maximally encompass thousands of molecules extending beyond 3.0 nm. The clusters imply fractal behaviors forming percolating networks and the morphologies of small and large clusters show different scaling rules. The local favored clusters and the preferred connections between adjacent clusters correspond to lower energy and conformational entropy depending on cluster topologies. Temperature can destroy large clusters into small ones. We show further that the interior of clusters favors high-density patches. The water molecules in the small clusters, inside which are the void regarded as hydrophobic objects, have a preference for being more tetrahedral. Our results highlight the properties and changes of water clusters as the fundamental building blocks of hydrogen bond networks. In addition, the water clusters can elucidate structural and density fluctuations on different length scales in liquid water.
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5
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Kang DW, Lee W, Ahn YH, Lee JW. Exploring tuning phenomena of THF-H2 hydrates via molecular dynamics simulations. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118490] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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6
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Kainai D, Bai D. Effect of Cage Occupancy on Stability and Decomposition of Methane Hydrate. J Phys Chem B 2022; 126:492-502. [PMID: 34985263 DOI: 10.1021/acs.jpcb.1c07582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gas hydrates usually contain a certain number of empty cages that will both affect the hydrate stability and reduce the gas storage capacity. In this work, by MD simulations, we found that the hydrate stability is related to the cage occupancy, the empty cage types, and especially the distribution of empty cages. With the decrease of overall occupancy, the stability of hydrate becomes worse. Under the same overall occupancy, the more concentrated the empty cages are, the more unstable the hydrate is and hence the faster it decomposes. The methane molecules may migrate between distorted cages during the decomposition, resulting in a temporary increase in the stability of hydrate. Hydrates with different empty cage distributions show different decomposition mechanisms: when empty cages are concentrated, the melting rate is fast first due to the rapid decomposition of empty cages, but the remaining filled cages will reduce the melting rate; when empty cages are separated on the contrary, the early melting is slow because of the high local occupancy, and the following melting will be accelerated because of the high melting surface area. It indicates that the empty cage distribution plays a controlling role in hydrate decomposition kinetics at different stages.
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Affiliation(s)
- Dilare Kainai
- Department of Chemistry, College of Chemistry and Materials Engineering/Key Laboratory of Cosmetic, China National Light Industry, Beijing Technology and Business University, Beijing 100048, P. R. China
| | - Dongsheng Bai
- Department of Chemistry, College of Chemistry and Materials Engineering/Key Laboratory of Cosmetic, China National Light Industry, Beijing Technology and Business University, Beijing 100048, P. R. China
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7
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Huang J, Huang G, Li S. A Machine Learning Model to Classify Dynamic Processes in Liquid Water*. Chemphyschem 2021; 23:e202100599. [PMID: 34661956 DOI: 10.1002/cphc.202100599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/16/2021] [Indexed: 11/07/2022]
Abstract
The dynamics of water molecules plays a vital role in understanding water. We combined computer simulation and deep learning to study the dynamics of H-bonds between water molecules. Based on ab initio molecular dynamics simulations and a newly defined directed Hydrogen (H-) bond population operator, we studied a typical dynamic process in bulk water: interchange, in which the H-bond donor reverses roles with the acceptor. By designing a recurrent neural network-based model, we have successfully classified the interchange and breakage processes in water. We have found that the ratio between them is approximately 1 : 4, and it hardly depends on temperatures from 280 to 360 K. This work implies that deep learning has the great potential to help distinguish complex dynamic processes containing H-bonds in other systems.
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Affiliation(s)
- Jie Huang
- Department of Physics, Wenzhou University, Wenzhou, Zhejiang, 325035, China
| | - Gang Huang
- Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Shiben Li
- Department of Physics, Wenzhou University, Wenzhou, Zhejiang, 325035, China
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8
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Abstract
Water and methane can stay together under low temperature and high pressure in the forms of liquid solutions and crystalline solids. From liquid and gaseous states to crystalline solids or the contrary processes, amorphous methane hydrates can occur in these evolution scenarios. Herein, mechanical properties of amorphous methane hydrates are explored for the first time to bridge the gap between mechanical responses of monocrystalline and polycrystalline methane hydrates. Our results demonstrate that mechanical properties of amorphous methane hydrates are strongly governed by our original proposed order parameter, namely, normalized hydrogen-bond directional order parameter. Followed by this important achievement, a multistep deformation mechanism core is proposed to explain mechanical properties of amorphous methane hydrates. Through an extensive detailed analysis of amorphous methane hydrates, our simulation results not only greatly enlarge our fundamental understanding for mechanical responses of amorphous methane hydrates in geological systems but also offer a fresh perspective in structure-property topics of solid materials in future science and technology.
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Affiliation(s)
- Pinqiang Cao
- School of Resource and Environmental Engineering, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
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9
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D’Ambrosio F, Barkema J, Barkema GT. Efficient Structural Relaxation of Polycrystalline Graphene Models. NANOMATERIALS 2021; 11:nano11051242. [PMID: 34066793 PMCID: PMC8151425 DOI: 10.3390/nano11051242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 11/16/2022]
Abstract
Large samples of experimentally produced graphene are polycrystalline. For the study of this material, it helps to have realistic computer samples that are also polycrystalline. A common approach to produce such samples in computer simulations is based on the method of Wooten, Winer, and Weaire, originally introduced for the simulation of amorphous silicon. We introduce an early rejection variation of their method, applied to graphene, which exploits the local nature of the structural changes to achieve a significant speed-up in the relaxation of the material, without compromising the dynamics. We test it on a 3200 atoms sample, obtaining a speed-up between one and two orders of magnitude. We also introduce a further variation called early decision specifically for relaxing large samples even faster, and we test it on two samples of 10,024 and 20,000 atoms, obtaining a further speed-up of an order of magnitude. Furthermore, we provide a graphical manipulation tool to remove unwanted artifacts in a sample, such as bond crossings.
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Affiliation(s)
- Federico D’Ambrosio
- Department of Information and Computing Sciences, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands;
- Correspondence:
| | - Joris Barkema
- Informatics Institute, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands;
| | - Gerard T. Barkema
- Department of Information and Computing Sciences, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands;
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10
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Gao Y, Fang H, Ni K. A hierarchical clustering method of hydrogen bond networks in liquid water undergoing shear flow. Sci Rep 2021; 11:9542. [PMID: 33953246 PMCID: PMC8100111 DOI: 10.1038/s41598-021-88810-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 04/14/2021] [Indexed: 02/02/2023] Open
Abstract
Many properties of water, such as turbulent flow, are closely related to water clusters, whereas how water clusters form and transform in bulk water remains unclear. A hierarchical clustering method is introduced to search out water clusters in hydrogen bonded network based on modified Louvain algorithm of graph community. Hydrogen bonds, rings and fragments are considered as 1st-, 2nd-, and 3rd-level structures, respectively. The distribution, dynamics and structural characteristics of 4th- and 5th-level clusters undergoing non-shear- and shear-driven flow are also analyzed at various temperatures. At low temperatures, nearly 50% of water molecules are included in clusters. Over 60% of clusters remain unchanged between neighboring configurations. Obvious collective translational motion of clusters is observed. The topological difference for clusters is elucidated between the inner layer, which favors 6-membered rings, and the external surface layer, which contains more 5-membered rings. Temperature and shearing can not only accelerate the transformation or destruction of clusters at all levels but also change cluster structures. The assembly of large clusters can be used to discretize continuous liquid water to elucidate the properties of liquid water.
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Affiliation(s)
- Yitian Gao
- grid.12527.330000 0001 0662 3178State Key Laboratory of Hydro-Science and Engineering, Department of Hydraulic Engineering, Tsinghua University, Beijing, 100084 China
| | - Hongwei Fang
- grid.12527.330000 0001 0662 3178State Key Laboratory of Hydro-Science and Engineering, Department of Hydraulic Engineering, Tsinghua University, Beijing, 100084 China
| | - Ke Ni
- grid.12527.330000 0001 0662 3178State Key Laboratory of Hydro-Science and Engineering, Department of Hydraulic Engineering, Tsinghua University, Beijing, 100084 China
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11
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Sachar HS, Chava BS, Pial TH, Das S. Hydrogen Bonding and Its Effect on the Orientational Dynamics of Water Molecules inside Polyelectrolyte Brush-Induced Soft and Active Nanoconfinement. Macromolecules 2021. [DOI: 10.1021/acs.macromol.0c02813] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Harnoor Singh Sachar
- Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Bhargav Sai Chava
- Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Turash Haque Pial
- Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Siddhartha Das
- Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742, United States
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12
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Hao Y, Xu Z, Du S, Yang X, Ding T, Wang B, Xu J, Zhang J, Yin H. Iterative Cup Overlapping: An Efficient Identification Algorithm for Cage Structures of Amorphous Phase Hydrates. J Phys Chem B 2021; 125:1282-1292. [PMID: 33481597 DOI: 10.1021/acs.jpcb.0c08964] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular dynamics studies have revealed that the nucleation pathway of clathrate hydrates involves the evolution from amorphous to crystalline hydrates. In this study, complete cages are further classified into the standard edge-saturated cages (SECs) and nonstandard edge-saturated cages (non-SECs). Centered on studying the structure and evolution of non-SECs and SECs, we propose a novel and efficient algorithm, iterative cup overlapping (ICO), to monitor hydrate nucleation and growth in molecular simulations by identifying SECs and discuss possible causes of the instability of non-SECs. Manipulation of topological information makes it possible for ICO to avoid the repeated searches for identified cages and deduce all SECs with low time costs, improving the efficiency of identification significantly. The accuracy and efficiency of ICO were verified by comparing the identification results with other well-proven algorithms. Furthermore, it was found that non-SECs have short lifetimes and eventually decompose or reorganize into more stable structures. Some evidence suggests that the instability of non-SECs is closely related to the hydrogen-bonding configuration of water-ring aggregations that they contain. The spontaneous evolution of the hydrogen-bonding network into the tetrahedral network may be the main factor that causes the conversion of QWRAs and the evolution of non-SECs.
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Affiliation(s)
- Yongchao Hao
- School of Petroleum Engineering, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Zhe Xu
- School of Petroleum Engineering, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Shuai Du
- School of Petroleum Engineering, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Xuefeng Yang
- School of Petroleum Engineering, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Tingji Ding
- School of Petroleum Engineering, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Bowen Wang
- School of Petroleum Engineering, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Jiafang Xu
- School of Petroleum Engineering, China University of Petroleum (East China), Qingdao 266580, P. R. China.,Key Laboratory of Unconventional Oil & Gas Development (China University of Petroleum (East China)), Ministry of Education, Qingdao 266580, P. R. China
| | - Jun Zhang
- School of Material Science & Engineering, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Haiqing Yin
- School of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
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13
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Li L, Zhong J, Yan Y, Zhang J, Xu J, Francisco JS, Zeng XC. Unraveling nucleation pathway in methane clathrate formation. Proc Natl Acad Sci U S A 2020; 117:24701-24708. [PMID: 32958648 PMCID: PMC7547213 DOI: 10.1073/pnas.2011755117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Methane clathrates are widespread on the ocean floor of the Earth. A better understanding of methane clathrate formation has important implications for natural-gas exploitation, storage, and transportation. A key step toward understanding clathrate formation is hydrate nucleation, which has been suggested to involve multiple evolution pathways. Herein, a unique nucleation/growth pathway for methane clathrate formation has been identified by analyzing the trajectories of large-scale molecular dynamics (MD) simulations. In particular, ternary water-ring aggregations (TWRAs) have been identified as fundamental structures for characterizing the nucleation pathway. Based on this nucleation pathway, the critical nucleus size and nucleation timescale can be quantitatively determined. Specifically, a methane hydration layer compression/shedding process is observed to be the critical step in (and driving) the nucleation/growth pathway, which is manifested through overlapping/compression of the surrounding hydration layers of the methane molecules, followed by detachment (shedding) of the hydration layer. As such, an effective way to control methane hydrate nucleation is to alter the hydration layer compression/shedding process during the course of nucleation.
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Affiliation(s)
- Liwen Li
- School of Materials Science and Engineering, China University of Petroleum (East China), 266580 Qingdao, China
| | - Jie Zhong
- Department of Earth and Environmental Science, University of Pennsylvania, Philadelphia, PA 19104-6316
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6316
| | - Youguo Yan
- School of Materials Science and Engineering, China University of Petroleum (East China), 266580 Qingdao, China
| | - Jun Zhang
- School of Materials Science and Engineering, China University of Petroleum (East China), 266580 Qingdao, China;
| | - Jiafang Xu
- School of Petroleum Engineering, China University of Petroleum (East China), 266580 Qingdao, China;
- Key Laboratory of Unconventional Oil & Gas Development, China University of Petroleum (East China), Ministry of Education, 266580 Qingdao, China
| | - Joseph S Francisco
- Department of Earth and Environmental Science, University of Pennsylvania, Philadelphia, PA 19104-6316;
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6316
| | - Xiao Cheng Zeng
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588;
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588
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14
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Yagasaki T, Matsumoto M, Tanaka H. Molecular dynamics study of grain boundaries and triple junctions in ice. J Chem Phys 2020; 153:124502. [DOI: 10.1063/5.0021635] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Takuma Yagasaki
- Research Institute for Interdisciplinary Science and Department of Chemistry, Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Masakazu Matsumoto
- Research Institute for Interdisciplinary Science and Department of Chemistry, Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Hideki Tanaka
- Research Institute for Interdisciplinary Science and Department of Chemistry, Faculty of Science, Okayama University, Okayama 700-8530, Japan
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15
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Abstract
The chordless cycle sizes of spatially embedded networks are demonstrated to follow an exponential growth law similar to random graphs if the number of nodes [Formula: see text] is below a critical value [Formula: see text] For covalent polymer networks, increasing the network size, as measured by the number of cross-link nodes, beyond [Formula: see text] results in a crossover to a new regime in which the characteristic size of the chordless cycles [Formula: see text] no longer increases. From this result, the onset and intensity of finite-size effects can be predicted from measurement of [Formula: see text] in large networks. Although such information is largely inaccessible with experiments, the agreement of simulation results from molecular dynamics, Metropolis Monte Carlo, and kinetic Monte Carlo suggests the crossover is a fundamental physical feature which is insensitive to the details of the network generation. These results show random graphs as a promising model to capture structural differences in confined physical networks.
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Affiliation(s)
- Timothy W Sirk
- Polymers Branch, US Army Research Laboratory, Aberdeen Proving Ground, MD 21005
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16
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Inhibition Effect of Kinetic Hydrate Inhibitors on the Growth of Methane Hydrate in Gas–Liquid Phase Separation State. ENERGIES 2019. [DOI: 10.3390/en12234482] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The effect of kinetic hydrate inhibitors (KHIs) on the growth of methane hydrate in the gas–liquid phase separation state is studied at the molecular level. The simulation results show that the kinetic inhibitors, named PVP and PVP-A, show good inhibitory effects on the growth of methane hydrate under the gas–liquid phase separation state, and the initial position of the kinetic hydrate inhibitors has a major effect on the growth of methane hydrates. In addition, inhibitors at different locations exhibit different inhibition performances. When the inhibitor molecules are located at the gas–liquid phase interface, increasing the contact area between the groups of the inhibitor molecules and methane is beneficial to enhance the inhibitory performance of the inhibitors. When inhibitor molecules are located at the solid–liquid phase interface, the inhibitor molecules adsorbed on the surface of the hydrate nucleus and decreased the direct contact of hydrate nucleus with the surrounding water and methane molecules, which would delay the growth of hydrate nucleus. Moreover, the increase of hydrate surface curvature and the Gibbs–Thomson effect caused by inhibitors can also reduce the growth rate of methane hydrate.
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17
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Nakate P, Ghosh B, Das S, Roy S, Kumar R. Molecular dynamics study on growth of carbon dioxide and methane hydrate from a seed crystal. Chin J Chem Eng 2019. [DOI: 10.1016/j.cjche.2019.02.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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18
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Leoni F, Shi R, Tanaka H, Russo J. Crystalline clusters in mW water: Stability, growth, and grain boundaries. J Chem Phys 2019; 151:044505. [DOI: 10.1063/1.5100812] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Fabio Leoni
- School of Mathematics, University of Bristol, Bristol BS8 1TW, United Kingdom
| | - Rui Shi
- Department of Fundamental Engineering, Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Hajime Tanaka
- Department of Fundamental Engineering, Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - John Russo
- School of Mathematics, University of Bristol, Bristol BS8 1TW, United Kingdom
- Department of Fundamental Engineering, Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
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19
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Choi KE, Chae E, Balupuri A, Yoon HR, Kang NS. Topological Water Network Analysis Around Amino Acids. Molecules 2019; 24:molecules24142653. [PMID: 31336667 PMCID: PMC6681432 DOI: 10.3390/molecules24142653] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/20/2019] [Accepted: 07/22/2019] [Indexed: 02/07/2023] Open
Abstract
Water molecules play a key role in protein stability, folding, function and ligand binding. Protein hydration has been studied using free energy perturbation algorithms. However, the study of protein hydration without free energy calculation is also an active field of research. Accordingly, topological water network (TWN) analysis has been carried out instead of free energy calculation in the present work to investigate hydration of proteins. Water networks around 20 amino acids in the aqueous solution were explored through molecular dynamics (MD) simulations. These simulation results were compared with experimental observations. Water molecules from the protein data bank structures showed TWN patterns similar to MD simulations. This work revealed that TWNs are effected by the surrounding environment. TWNs could provide valuable clues about the environment around amino acid residues in the proteins. The findings from this study could be exploited for TWN-based drug discovery and development.
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Affiliation(s)
- Kwang-Eun Choi
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Eunkyoung Chae
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Anand Balupuri
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Hye Ree Yoon
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Nam Sook Kang
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea.
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20
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Matsumoto M, Yagasaki T, Tanaka H. A Bayesian approach for identification of ice Ih, ice Ic, high density, and low density liquid water with a torsional order parameter. J Chem Phys 2019; 150:214504. [DOI: 10.1063/1.5096556] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Masakazu Matsumoto
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
| | - Takuma Yagasaki
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
| | - Hideki Tanaka
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
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21
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Functional Hydration Behavior: Interrelation between Hydration and Molecular Properties at Lipid Membrane Interfaces. J CHEM-NY 2019. [DOI: 10.1155/2019/4867327] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Water is an abundant commodity and has various important functions. It stabilizes the structure of biological macromolecules, controls biochemical activities, and regulates interfacial/intermolecular interactions. Common aspects of interfacial water can be obtained by overviewing fundamental functions and properties at different temporal and spatial scales. It is important to understand the hydrogen bonding and structural properties of water and to evaluate the individual molecular species having different hydration properties. Water molecules form hydrogen bonds with biomolecules and contribute to the adjustment of their properties, such as surface charge, hydrophilicity, and structural flexibility. In this review, the fundamental properties of water molecules and the methods used for the analyses of water dynamics are summarized. In particular, the interrelation between the hydration properties, determined by molecules, and the properties of molecules, determined by their hydration properties, are discussed using the lipid membrane as an example. Accordingly, interesting water functions are introduced that provide beneficial information in the fields of biochemistry, medicine, and food chemistry.
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22
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23
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Parui S, Jana B. Molecular Insights into the Unusual Structure of an Antifreeze Protein with a Hydrated Core. J Phys Chem B 2018; 122:9827-9839. [PMID: 30286600 DOI: 10.1021/acs.jpcb.8b05350] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The primary driving force for protein folding is the formation of a well-packed, anhydrous core. However, recently, the crystal structure of an antifreeze protein, maxi, has been resolved where the core of the protein is filled with water, which apparently contradicts the existing notion of protein folding. Here, we have performed standard molecular dynamics (MD) simulation, replica exchange MD (REMD) simulation, and umbrella sampling using TIP4P water at various temperatures (300, 260, and 240 K) to explore the origin of this unusual structural feature. It is evident from standard MD and REMD simulations that the protein is found to be stable at 240 K in its unusual state. The core of protein has two layers of semi-clathrate water separating the methyl groups of alanine residues from different helical strands. However, with increasing temperature (260 and 300 K), the stability decreases as the core becomes dehydrated, and methyl groups of alanine are tightly packed driven by hydrophobic interactions. Calculation of the potential of mean force by an umbrella sampling technique between a pair of model hydrophobes resembling maxi protein at 240 K shows the stabilization of second solvent-separated minima (SSM), which provides a thermodynamic rationale of the unusual structural feature in terms of weakening of the hydrophobic interaction. Because the stabilization of SSMs is implicated for cold denaturation, it suggests that the maxi protein is so designed by nature where the cold denatured-like state becomes the biologically active form as it works near or below the freezing point of water.
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Affiliation(s)
- Sridip Parui
- Department of Physical Chemistry , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
| | - Biman Jana
- Department of Physical Chemistry , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
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24
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Kumar A, Nguyen AH, Okumu R, Shepherd TD, Molinero V. Could Mesophases Play a Role in the Nucleation and Polymorph Selection of Zeolites? J Am Chem Soc 2018; 140:16071-16086. [DOI: 10.1021/jacs.8b06664] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Abhinaw Kumar
- Department of Chemistry, The University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Andrew H. Nguyen
- Department of Chemistry, The University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Rita Okumu
- Department of Chemistry, Westminster College, 1840 South 1300 East, Salt Lake City, Utah 84105, United States
| | - Tricia D. Shepherd
- Department of Chemistry, Westminster College, 1840 South 1300 East, Salt Lake City, Utah 84105, United States
| | - Valeria Molinero
- Department of Chemistry, The University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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25
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Hou J, Bai D, Zhou W. Methane Hydrate Nucleation within Elastic Confined Spaces: Suitable Spacing and Elasticity Can Accelerate the Nucleation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:10889-10896. [PMID: 30157653 DOI: 10.1021/acs.langmuir.8b02387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Elastic materials are candidates for process intensification of gas storage by forming gas hydrate. In this work, molecular dynamics simulations of hydrate nucleation in elastic silica double layers were performed to study the effect of elastic confined spaces on hydrate formation. It is found that in narrow confined spaces, hexagonal rings dominated the hydrogen bond network of water molecules established rapidly by a multisite nucleation mechanism. With molecules added, a bilayer water structure was formed finally because elastic space can adapt the volume expansion. In medium and wide confined spaces, hydrates were formed from a series of "pseudo cages" which are considered as precursors of complete hydrate cages. Moreover, the induction time for nucleation was a minimum when the elasticity of the silica layer changes: nucleation is fastest in the weak-elastic system. When the elasticity increases, it becomes hard to adapt the volume expansion during nucleation and also difficult to nucleate in very weak-elastic systems because of the fluctuation of the layers.
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Affiliation(s)
- Jingpeng Hou
- Department of Chemistry, School of Science/Key Laboratory of Cosmetic, China National Light Industry , Beijing Technology and Business University , Beijing 100048 , PR China
| | - Dongsheng Bai
- Department of Chemistry, School of Science/Key Laboratory of Cosmetic, China National Light Industry , Beijing Technology and Business University , Beijing 100048 , PR China
| | - Wei Zhou
- Department of Chemistry, School of Science/Key Laboratory of Cosmetic, China National Light Industry , Beijing Technology and Business University , Beijing 100048 , PR China
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26
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Zheng L, Chen M, Sun Z, Ko HY, Santra B, Dhuvad P, Wu X. Structural, electronic, and dynamical properties of liquid water by ab initio molecular dynamics based on SCAN functional within the canonical ensemble. J Chem Phys 2018; 148:164505. [DOI: 10.1063/1.5023611] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Lixin Zheng
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Mohan Chen
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Zhaoru Sun
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Hsin-Yu Ko
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Biswajit Santra
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Pratikkumar Dhuvad
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Xifan Wu
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, USA
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27
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Kaur SP, Sujith KS, Ramachandran CN. Formation of a nanobubble and its effect on the structural ordering of water in a CH 4-N 2-CO 2-H 2O mixture. Phys Chem Chem Phys 2018; 20:9157-9166. [PMID: 29560970 DOI: 10.1039/c7cp07934f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The replacement of methane (CH4) from its hydrate by a mixture of nitrogen (N2) and carbon dioxide (CO2) involves the dissociation of methane hydrate leading to the formation of a CH4-N2-CO2-H2O mixture that can significantly influence the subsequent steps of the replacement process. In the present work, we study the evolution of dissolved gas molecules in this mixture by applying classical molecular dynamics simulations. Our study shows that a higher CO2 : N2 ratio in the mixture enhances the formation of nanobubbles composed of N2, CH4 and CO2 molecules. To understand how the CO2 : N2 ratio affects nanobubble nucleation, the distribution of molecules in the bubble formed is examined. It is observed that unlike N2 and CH4, the density of CO2 in the bubble reaches a maximum at the surface of the bubble. The accumulation of CO2 molecules at the surface makes the bubble more stable by decreasing the excess pressure inside the bubble as well as surface tension at its interface with water. It is found that a frequent exchange of gas molecules takes place between the bubble and the surrounding liquid and an increase in concentration of CO2 in the mixture leads to a decrease in the number of such exchanges. The effect of nanobubbles on the structural ordering of water molecules is examined by determining the number of water rings formed per unit volume in the mixture. The role of nanobubbles in water structuring is correlated to the dynamic nature of the bubble arising from the exchange of gas molecules between the bubble and the liquid.
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Affiliation(s)
- Surinder Pal Kaur
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, 247667, India.
| | - K S Sujith
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, 247667, India.
| | - C N Ramachandran
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, 247667, India.
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28
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Hölzl C, Horinek D. Pressure increases the ice-like order of water at hydrophobic interfaces. Phys Chem Chem Phys 2018; 20:21257-21261. [DOI: 10.1039/c8cp03057j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Ice-like order of water at hydrophobic interfaces is quantified on different length scales based on molecular dynamics simulations.
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Affiliation(s)
- Christoph Hölzl
- Institut für Physikalische und Theoretische Chemie
- Universität Regensburg
- 93040 Regensburg
- Germany
| | - Dominik Horinek
- Institut für Physikalische und Theoretische Chemie
- Universität Regensburg
- 93040 Regensburg
- Germany
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29
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Enhanced heterogeneous ice nucleation by special surface geometry. Nat Commun 2017; 8:15372. [PMID: 28513603 PMCID: PMC5442314 DOI: 10.1038/ncomms15372] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 03/23/2017] [Indexed: 12/01/2022] Open
Abstract
The freezing of water typically proceeds through impurity-mediated heterogeneous nucleation. Although non-planar geometry generically exists on the surfaces of ice nucleation centres, its role in nucleation remains poorly understood. Here we show that an atomically sharp, concave wedge can further promote ice nucleation with special wedge geometries. Our molecular analysis shows that significant enhancements of ice nucleation can emerge both when the geometry of a wedge matches the ice lattice and when such lattice match does not exist. In particular, a 45° wedge is found to greatly enhance ice nucleation by facilitating the formation of special topological defects that consequently catalyse the growth of regular ice. Our study not only highlights the active role of defects in nucleation but also suggests that the traditional concept of lattice match between a nucleation centre and crystalline lattice should be extended to include a broader match with metastable, non-crystalline structural motifs. Understanding ice nucleation is important for the development of accurate cloud models. Here Bi et al. show that sharp wedges can enhance ice nucleation both when the wedge geometry matches the ice lattice and when such matching is absent, in which case nucleation is promoted by topological defects.
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30
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Kanemaru H, Yukita S, Namiki H, Nosaka Y, Kobayashi T, Tokunaga E. Giant Pockels effect of polar organic solvents and water in the electric double layer on a transparent electrode. RSC Adv 2017. [DOI: 10.1039/c7ra05875f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The Pockels effect of polar organic solvents and water within the electric double layer on an ITO electrode is studied to find that water has the largest Pockels coefficient, followed in order by methanol, ethanol, and dimethyl sulfoxide.
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Affiliation(s)
- Hironori Kanemaru
- Department of Physics
- Faculty of Science
- Tokyo University of Science
- Tokyo 162-8601
- Japan
| | - Shunpei Yukita
- Department of Physics
- Faculty of Science
- Tokyo University of Science
- Tokyo 162-8601
- Japan
| | - Hajime Namiki
- Department of Physics
- Faculty of Science
- Tokyo University of Science
- Tokyo 162-8601
- Japan
| | - Yugo Nosaka
- Department of Physics
- Faculty of Science
- Tokyo University of Science
- Tokyo 162-8601
- Japan
| | - Takayoshi Kobayashi
- Advanced Ultrafast Laser Research Center
- Brain Science Inspired Life Support Research Center
- The University of Electro-Communications
- Tokyo 182-8585
- Japan
| | - Eiji Tokunaga
- Department of Physics
- Faculty of Science
- Tokyo University of Science
- Tokyo 162-8601
- Japan
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31
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Toda M, Kajimoto S, Toyouchi S, Kawakatsu T, Akama Y, Kotani M, Fukumura H. Phase behavior of a binary fluid mixture of quadrupolar molecules. Phys Rev E 2016; 94:052601. [PMID: 27967026 DOI: 10.1103/physreve.94.052601] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Indexed: 06/06/2023]
Abstract
We propose a model molecule to investigate microscopic properties of a binary mixture with a closed-loop coexistence region. The molecule is comprised of a Lennard-Jones particle and a uniaxial quadrupole. Gibbs ensemble Monte Carlo simulations demonstrate that the high-density binary fluid of the molecules with the quadrupoles of the same magnitude but of the opposite signs can show closed-loop immiscibility. We find that an increase in the magnitude of the quadrupoles causes a shrinkage of the coexistence region. Molecular dynamics simulations also reveal that aggregates with two types of molecules arranged alternatively are formed in the stable one-phase region both above and below the coexistence region. String structures are dominant below the lower critical solution temperature, while branched aggregates are observed above the upper critical solution temperature. We conclude that the anisotropic interaction between the quadrupoles of the opposite signs plays a crucial role in controlling these properties of the phase behavior.
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Affiliation(s)
- Masatoshi Toda
- Department of Chemistry, Tohoku University, Sendai, 980-8578, Japan
| | - Shinji Kajimoto
- Department of Chemistry, Tohoku University, Sendai, 980-8578, Japan
| | - Shuichi Toyouchi
- Department of Chemistry, Tohoku University, Sendai, 980-8578, Japan
| | | | - Yohji Akama
- Mathematical Institute, Tohoku University, Sendai, 980-8578, Japan
| | - Motoko Kotani
- Mathematical Institute, Tohoku University, Sendai, 980-8578, Japan
- WPI-AIMR, Tohoku University, Sendai, 980-8577, Japan
| | - Hiroshi Fukumura
- Department of Chemistry, Tohoku University, Sendai, 980-8578, Japan
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32
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Pathak AK, Bandyopadhyay T. Solvation of arsenate anion: combined quantum mechanics and molecular dynamics based investigation. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1177219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Arup Kumar Pathak
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai, India
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33
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Małolepsza E, Keyes T. Pathways through Equilibrated States with Coexisting Phases for Gas Hydrate Formation. J Phys Chem B 2015; 119:15857-65. [DOI: 10.1021/acs.jpcb.5b06832] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Edyta Małolepsza
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215-2521, United States
| | - Tom Keyes
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215-2521, United States
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34
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Matsumoto M, Yagasaki T, Tanaka H. Chiral Ordering in Supercooled Liquid Water and Amorphous Ice. PHYSICAL REVIEW LETTERS 2015; 115:197801. [PMID: 26588416 DOI: 10.1103/physrevlett.115.197801] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Indexed: 06/05/2023]
Abstract
The emergence of homochiral domains in supercooled liquid water is presented using molecular dynamics simulations. An individual water molecule possesses neither a chiral center nor a twisted conformation that can cause spontaneous chiral resolution. However, an aggregation of water molecules will naturally give rise to a collective chirality. Such homochiral domains possess obvious topological and geometrical orders and are energetically more stable than the average. However, homochiral domains cannot grow into macroscopic homogeneous structures due to geometrical frustrations arising from their icosahedral local order. Homochiral domains are the major constituent of supercooled liquid water and the origin of heterogeneity in that substance, and are expected to be enhanced in low-density amorphous ice at lower temperatures.
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Affiliation(s)
- Masakazu Matsumoto
- Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima, Okayama 700-8530, Japan
| | - Takuma Yagasaki
- Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima, Okayama 700-8530, Japan
| | - Hideki Tanaka
- Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima, Okayama 700-8530, Japan
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35
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Bai D, Zhang D, Zhang X, Chen G. Origin of Self-preservation Effect for Hydrate Decomposition: Coupling of Mass and Heat Transfer Resistances. Sci Rep 2015; 5:14599. [PMID: 26423519 PMCID: PMC4589738 DOI: 10.1038/srep14599] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 08/27/2015] [Indexed: 12/28/2022] Open
Abstract
Gas hydrates could show an unexpected high stability at conditions out of thermodynamic equilibrium, which is called the self-preservation effect. The mechanism of the effect for methane hydrates is here investigated via molecular dynamics simulations, in which an NVT/E method is introduced to represent different levels of heat transfer resistance. Our simulations suggest a coupling between the mass transfer resistance and heat transfer resistance as the driving mechanism for self-preservation effect. We found that the hydrate is initially melted from the interface, and then a solid-like water layer with temperature-dependent structures is formed next to the hydrate interface that exhibits fractal feature, followed by an increase of mass transfer resistance for the diffusion of methane from hydrate region. Furthermore, our results indicate that heat transfer resistance is a more fundamental factor, since it facilitates the formation of the solid-like layer and hence inhibits the further dissociation of the hydrates. The self-preservation effect is found to be enhanced with the increase of pressure and particularly the decrease of temperature. Kinetic equations based on heat balance calculations is also developed to describe the self-preservation effect, which reproduces our simulation results well and provides an association between microscopic and macroscopic properties.
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Affiliation(s)
- Dongsheng Bai
- Department of Chemistry, School of Science, Beijing Technology and Business University, Beijing, 100048, P.R. China.,State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing, 100029, P.R. China
| | - Diwei Zhang
- Department of Chemistry, School of Science, Beijing Technology and Business University, Beijing, 100048, P.R. China
| | - Xianren Zhang
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing, 100029, P.R. China
| | - Guangjin Chen
- State Key Laboratory of Heavy Oil Processing, School of Chemical Engineering, China University of Petroleum, Beijing, 102249, P.R. China
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36
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Bai D, Chen G, Zhang X, Sum AK, Wang W. How Properties of Solid Surfaces Modulate the Nucleation of Gas Hydrate. Sci Rep 2015; 5:12747. [PMID: 26227239 PMCID: PMC4521183 DOI: 10.1038/srep12747] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 07/07/2015] [Indexed: 11/09/2022] Open
Abstract
Molecular dynamics simulations were performed for CO2 dissolved in water near silica surfaces to investigate how the hydrophilicity and crystallinity of solid surfaces modulate the local structure of adjacent molecules and the nucleation of CO2 hydrates. Our simulations reveal that the hydrophilicity of solid surfaces can change the local structure of water molecules and gas distribution near liquid-solid interfaces, and thus alter the mechanism and dynamics of gas hydrate nucleation. Interestingly, we find that hydrate nucleation tends to occur more easily on relatively less hydrophilic surfaces. Different from surface hydrophilicity, surface crystallinity shows a weak effect on the local structure of adjacent water molecules and on gas hydrate nucleation. At the initial stage of gas hydrate growth, however, the structuring of molecules induced by crystalline surfaces are more ordered than that induced by amorphous solid surfaces.
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Affiliation(s)
- Dongsheng Bai
- 1] Department of Chemistry, School of Science, Beijing Technology and Business University, Beijing, 100048, P. R. China [2] Division of Molecular and Materials Simulation, State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Guangjin Chen
- State Key Laboratory of Heavy Oil Processing, School of Chemical Engineering, China University of Petroleum, Beijing, 102249, P. R. China
| | - Xianren Zhang
- Division of Molecular and Materials Simulation, State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Amadeu K Sum
- Center for Hydrate Research, Department of Chemical &Biological Engineering, Colorado School of Mines, Golden, CO 80401, U.S.A
| | - Wenchuan Wang
- Division of Molecular and Materials Simulation, State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
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37
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Lauricella M, Meloni S, Liang S, English NJ, Kusalik PG, Ciccotti G. Clathrate structure-type recognition: Application to hydrate nucleation and crystallisation. J Chem Phys 2015; 142:244503. [DOI: 10.1063/1.4922696] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Marco Lauricella
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland
- Instituto per le Applicazioni del Calcolo, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Simone Meloni
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fedérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Shuai Liang
- Deptartment of Chemistry, University of Calgary, Calgary, Alberta T2N 1N4, Canada
- Key Laboratory of Gas Hydrate, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, China
| | - Niall J. English
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Peter G. Kusalik
- Deptartment of Chemistry, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Giovanni Ciccotti
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland
- Dipartimento di Fisica and CNISM, Università La Sapienza, P. le A. Moro 5, 00185 Rome, Italy
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38
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Yuhara D, Barnes BC, Suh D, Knott BC, Beckham GT, Yasuoka K, Wu DT, Sum AK. Nucleation rate analysis of methane hydrate from molecular dynamics simulations. Faraday Discuss 2015; 179:463-74. [PMID: 25876773 DOI: 10.1039/c4fd00219a] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Clathrate hydrates are solid crystalline structures most commonly formed from solutions that have nucleated to form a mixed solid composed of water and gas. Understanding the mechanism of clathrate hydrate nucleation is essential to grasp the fundamental chemistry of these complex structures and their applications. Molecular dynamics (MD) simulation is an ideal method to study nucleation at the molecular level because the size of the critical nucleus and formation rate occur on the nano scale. Various analysis methods for nucleation have been developed through MD to analyze nucleation. In particular, the mean first-passage time (MFPT) and survival probability (SP) methods have proven to be effective in procuring the nucleation rate and critical nucleus size for monatomic systems. This study assesses the MFPT and SP methods, previously used for monatomic systems, when applied to analyzing clathrate hydrate nucleation. Because clathrate hydrate nucleation is relatively difficult to observe in MD simulations (due to its high free energy barrier), these methods have yet to be applied to clathrate hydrate systems. In this study, we have analyzed the nucleation rate and critical nucleus size of methane hydrate using MFPT and SP methods from data generated by MD simulations at 255 K and 50 MPa. MFPT was modified for clathrate hydrate from the original version by adding the maximum likelihood estimate and growth effect term. The nucleation rates calculated by MFPT and SP methods are within 5%, and the critical nucleus size estimated by the MFPT method was 50% higher, than values obtained through other more rigorous but computationally expensive estimates. These methods can also be extended to the analysis of other clathrate hydrates.
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Affiliation(s)
- Daisuke Yuhara
- Department of Mechanical Engineering, Keio University, Yokohama, Japan
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39
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Sæthre BS, Hoffmann AC, van der Spoel D. Order Parameters and Algorithmic Approaches for Detection and Demarcation of Interfaces in Hydrate-Fluid and Ice-Fluid Systems. J Chem Theory Comput 2014; 10:5606-15. [PMID: 26583243 DOI: 10.1021/ct500459x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Some aspects of the use of order parameter fields in molecular dynamics simulations to delimit solid phases containing water, namely ice and hydrate, in both hydrophilic and hydrophobic fluids are examined; this includes the influences of rectangular meshes and of filtering on the quality of these parameters. Three order parameters are studied: the mass density, ρ; an angular tetrahedrality measure, Sg (Chau and Hardwick, Mol. Phys. 1998, 93, 511); and the water-dimer dihedral angle, F4 (Rodger et al. Fluid Phase Equilib. 1996, 116, 326). The parameters are studied to find their ability to distinguish between bulk phases, their consistency in different environments, their noise susceptibility, and their ability to demarcate the interface region. Spatial sampling and filtering are covered in detail, and some temporal features are illustrated by using autocorrelation maps. The parameters are employed to determine the position of interfaces as functions of time and, with the capillary wave fluctuation method (Hoyt et al. Phys. Rev. Lett. 2001, 86, 5530; Math. Comput. Simul. 2010, 80, 1382), to estimate solid-fluid interfacial stiffnesses, with partial success for the hydrophilic/hydrophobic-type interfaces.
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Affiliation(s)
- Bjørn Steen Sæthre
- Institute of Physics & Technology, University of Bergen , 5007 Bergen, Norway
| | - Alex C Hoffmann
- Institute of Physics & Technology, University of Bergen , 5007 Bergen, Norway
| | - David van der Spoel
- Uppsala Centre for Computational Chemistry, Science for Life Laboratory, Department of Cell & Molecular Biology, University of Uppsala , SE-75124 Uppsala, Sweden
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40
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Lupi L, Kastelowitz N, Molinero V. Vapor deposition of water on graphitic surfaces: Formation of amorphous ice, bilayer ice, ice I, and liquid water. J Chem Phys 2014; 141:18C508. [DOI: 10.1063/1.4895543] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Laura Lupi
- Department of Chemistry, The University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, USA
| | - Noah Kastelowitz
- Department of Chemistry, The University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, USA
| | - Valeria Molinero
- Department of Chemistry, The University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, USA
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41
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Barnes BC, Knott BC, Beckham GT, Wu DT, Sum AK. Reaction coordinate of incipient methane clathrate hydrate nucleation. J Phys Chem B 2014; 118:13236-43. [PMID: 25347748 DOI: 10.1021/jp507959q] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Nucleation from solution is a ubiquitous phenomenon with relevance to myriad scientific disciplines, including pharmaceuticals, biomineralization, and disease. One prominent example is the nucleation of clathrate hydrates, multicomponent crystalline inclusion compounds relevant to the energy industry where they block pipelines and also constitute a potential vast energy resource. Despite their importance, the molecular mechanism of incipient hydrate formation remains unknown. Herein, we employ advanced molecular simulation tools (pB histogram, equilibrium path sampling) to provide a statistical-mechanical basis for extracting physical insight into the molecular steps by which clathrates form. Through testing the Mutually Coordinated Guest (MCG) order parameter, we demonstrate that both guest (methane) and host (water) structuring are crucial to accurately describe the nucleation of hydrates and determine a critical nucleus size of MCG-1 = 16 at 255 K and 500 bar. Equipped with a validated (and novel) reaction coordinate, subsequent equilibrium path sampling simulations yield the free energy barrier and nucleation rate. The resulting quantitative nucleation process is described by the MCG clustering mechanism. This constitutes a significant advance in the field of hydrates research, as the fitness of a molecular descriptor has never been statistically verified. More broadly, this work has significance to a wide range of multicomponent nucleation contexts wherein the formation mechanism depends on contributions from both solute and solvent.
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Affiliation(s)
- Brian C Barnes
- Center for Hydrate Research, Chemical & Biological Engineering Department, Colorado School of Mines , Golden, Colorado 80401, United States
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42
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Saito M, D’Amico F, Bencivenga F, Cucini R, Gessini A, Principi E, Masciovecchio C. Spatial correlation between chemical and topological defects in vitreous silica: UV-resonance Raman study. J Chem Phys 2014; 140:244505. [DOI: 10.1063/1.4884155] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- M. Saito
- Elettra-Sincrotrone Trieste, S. S. 14 Km 163.5, I-34149 Trieste, Italy
| | - F. D’Amico
- Elettra-Sincrotrone Trieste, S. S. 14 Km 163.5, I-34149 Trieste, Italy
| | - F. Bencivenga
- Elettra-Sincrotrone Trieste, S. S. 14 Km 163.5, I-34149 Trieste, Italy
| | - R. Cucini
- Elettra-Sincrotrone Trieste, S. S. 14 Km 163.5, I-34149 Trieste, Italy
| | - A. Gessini
- Elettra-Sincrotrone Trieste, S. S. 14 Km 163.5, I-34149 Trieste, Italy
| | - E. Principi
- Elettra-Sincrotrone Trieste, S. S. 14 Km 163.5, I-34149 Trieste, Italy
| | - C. Masciovecchio
- Elettra-Sincrotrone Trieste, S. S. 14 Km 163.5, I-34149 Trieste, Italy
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Barnes BC, Beckham GT, Wu DT, Sum AK. Two-component order parameter for quantifying clathrate hydrate nucleation and growth. J Chem Phys 2014; 140:164506. [PMID: 24784286 DOI: 10.1063/1.4871898] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Methane clathrate hydrate nucleation and growth is investigated via analysis of molecular dynamics simulations using a new order parameter. This order parameter (OP), named the Mutually Coordinated Guest (MCG) OP, quantifies the appearance and connectivity of molecular clusters composed of guests separated by water clusters. It is the first two-component OP used for quantifying hydrate nucleation and growth. The algorithm for calculating the MCG OP is described in detail. Its physical motivation and advantages compared to existing methods are discussed.
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Affiliation(s)
- Brian C Barnes
- Center for Hydrate Research, Chemical and Biological Engineering Department, Colorado School of Mines, Golden, Colorado 80401, USA
| | - Gregg T Beckham
- National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - David T Wu
- Center for Hydrate Research, Chemical and Biological Engineering Department, Colorado School of Mines, Golden, Colorado 80401, USA
| | - Amadeu K Sum
- Center for Hydrate Research, Chemical and Biological Engineering Department, Colorado School of Mines, Golden, Colorado 80401, USA
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44
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Abstract
The diffusion of protons through water is understood within the framework of the Grotthuss mechanism, which requires that they undergo structural diffusion in a stepwise manner throughout the water network. Despite long study, this picture oversimplifies and neglects the complexity of the supramolecular structure of water. We use first-principles simulations and demonstrate that the currently accepted picture of proton diffusion is in need of revision. We show that proton and hydroxide diffusion occurs through periods of intense activity involving concerted proton hopping followed by periods of rest. The picture that emerges is that proton transfer is a multiscale and multidynamical process involving a broader distribution of pathways and timescales than currently assumed. To rationalize these phenomena, we look at the 3D water network as a distribution of closed directed rings, which reveals the presence of medium-range directional correlations in the liquid. One of the natural consequences of this feature is that both the hydronium and hydroxide ion are decorated with proton wires. These wires serve as conduits for long proton jumps over several hydrogen bonds.
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45
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Mochizuki K, Matsumoto M, Ohmine I. Defect pair separation as the controlling step in homogeneous ice melting. Nature 2013; 498:350-4. [DOI: 10.1038/nature12190] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 04/12/2013] [Indexed: 11/09/2022]
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46
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Cabral do Couto P, Chipman DM. Insights into the ultraviolet spectrum of liquid water from model calculations: the different roles of donor and acceptor hydrogen bonds in water pentamers. J Chem Phys 2013; 137:184301. [PMID: 23163365 DOI: 10.1063/1.4764044] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
With a view toward a better understanding of changes in the peak position and shape of the first absorption band of water with condensation or temperature, results from electronic structure calculations using high level wavefunction based and time-dependent density functional methods are reported for water pentamers. Excitation energies, oscillator strengths, and redistributions of electron density are determined for the quasitetrahedral water pentamer in its C(2v) equilibrium geometry and for many pentamer configurations sampled from molecular simulation of liquid water. Excitations associated with surface molecules are removed in order to focus on those states associated with the central molecule, which are the most representative of the liquid environment. The effect of hydrogen bonding on the lowest excited state associated with the central molecule is studied by adding acceptor or donor hydrogen bonds to tetramer and trimer substructures of the C(2v) pentamer, and by sampling liquid-like configurations having increasing number of acceptor or donor hydrogen bonds of the central molecule. Our results provide clear evidence that the blueshift of excitation energies upon condensation is essentially determined by acceptor hydrogen bonds, and the magnitudes of these shifts are determined by the number of such, whereas donor hydrogen bonds do not induce significant shifts in excitation energies. This qualitatively different role of donor and acceptor hydrogen bonds is understood in terms of the different roles of the 1b(1) monomer molecular orbitals, which establishes an intimate connection between the valence hole and excitation energy shifts. Since the valence hole of the lowest excitation associated with the central molecule is found to be well localized in all liquid-like hydrogen bonding environments, with an average radius of gyration of ~1.6 Å that is much lower than the nearest neighbor O-O distance, a clear and unambiguous connection between hydrogen bonding environments and excitation energy shifts can be established. Based on these results, it is concluded that peak position of the first absorption band is mainly determined by the relative distribution of single and double acceptor hydrogen bonding environments, whereas the shape of the first absorption band is mainly determined by the relative distribution of acceptor and broken acceptor hydrogen bonding environments. The temperature dependence of the peak position and shape of the first absorption band can be readily understood in terms of changes to these relative populations.
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Affiliation(s)
- Paulo Cabral do Couto
- Notre Dame Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556, USA
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47
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Bakó I, Bencsura Á, Hermannson K, Bálint S, Grósz T, Chihaia V, Oláh J. Hydrogen bond network topology in liquid water and methanol: a graph theory approach. Phys Chem Chem Phys 2013; 15:15163-71. [DOI: 10.1039/c3cp52271g] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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48
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Correlation between the local OH stretching vibration wavenumber and the hydrogen bonding pattern of water in a condensed phase: Quantum chemical approach to analyze the broad OH band. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2012.09.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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49
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Kozai T, Yamashita S, Hirochi K, Miyagawa H, Tsurumachi N, Koshiba S, Nakanishi S, Itoh H. Molecular vibrational dynamics in polyvinyl alcohol studied by femtosecond coherent anti-stokes Raman spectroscopy. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.09.057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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50
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Bai D, Chen G, Zhang X, Wang W. Nucleation of the CO2 hydrate from three-phase contact lines. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:7730-7736. [PMID: 22551251 DOI: 10.1021/la300647s] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Using molecular dynamics simulations on the microsecond time scale, we investigate the nucleation and growth mechanisms of CO(2) hydrates in a water/CO(2)/silica three-phase system. Our simulation results indicate that the CO(2) hydrate nucleates near the three-phase contact line rather than at the two-phase interfaces and then grows along the contact line to form an amorphous crystal. In the nucleation stage, the hydroxylated silica surface can be understand as a stabilizer to prolong the lifetime of adsorbed hydrate cages that interact with the silica surface by hydrogen bonding, and the adsorbed cages behave as the nucleation sites for the formation of an amorphous CO(2) hydrate. After nucleation, the nucleus grows along the three-phase contact line and prefers to develop toward the CO(2) phase as a result of the hydrophilic nature of the modified solid surface and the easy availability of CO(2) molecules. During the growth process, the population of sI cages in the formed amorphous crystal is found to increase much faster than that of sII cages, being in agreement with the fact that only the sI hydrate can be formed in nature for CO(2) molecules.
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Affiliation(s)
- Dongsheng Bai
- Division of Molecular and Materials Simulation, State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, China
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