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Ray D, Parrinello M. Kinetics from Metadynamics: Principles, Applications, and Outlook. J Chem Theory Comput 2023; 19:5649-5670. [PMID: 37585703 DOI: 10.1021/acs.jctc.3c00660] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Metadynamics is a popular enhanced sampling algorithm for computing the free energy landscape of rare events by using molecular dynamics simulation. Ten years ago, Tiwary and Parrinello introduced the infrequent metadynamics approach for calculating the kinetics of transitions across free energy barriers. Since then, metadynamics-based methods for obtaining rate constants have attracted significant attention in computational molecular science. Such methods have been applied to study a wide range of problems, including protein-ligand binding, protein folding, conformational transitions, chemical reactions, catalysis, and nucleation. Here, we review the principles of elucidating kinetics from metadynamics-like approaches, subsequent methodological developments in this area, and successful applications on chemical, biological, and material systems. We also highlight the challenges of reconstructing accurate kinetics from enhanced sampling simulations and the scope of future developments.
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Affiliation(s)
- Dhiman Ray
- Atomistic Simulations, Italian Institute of Technology, Via Enrico Melen 83, 16152 Genova, Italy
| | - Michele Parrinello
- Atomistic Simulations, Italian Institute of Technology, Via Enrico Melen 83, 16152 Genova, Italy
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2
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Sicard F, Yazaydin AO. Biohybrid Membrane Formation by Directed Insertion of Aquaporin into a Solid-State Nanopore. ACS APPLIED MATERIALS & INTERFACES 2022; 14:48029-48036. [PMID: 36244033 PMCID: PMC9614727 DOI: 10.1021/acsami.2c14250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Biohybrid nanopores combine the durability of solid-state nanopores with the precise structure and function of biological nanopores. Particular care must be taken to control how biological nanopores adapt to their surroundings once they come into contact with the solid-state nanopores. Two major challenges are to precisely control this adaptability under dynamic conditions and provide predesigned functionalities that can be manipulated for engineering applications. In this work, we report on the computational design of a distinctive class of biohybrid active membrane layers, built from the directed-insertion of an aquaporin-incorporated lipid nanodisc into a model alkyl-functionalized silica pore. We show that in an aqueous environment when a pressure difference exists between the two sides of the solid-state nanopore, the preferential interactions between the hydrocarbon tail of the lipid molecules that surround the aquaporin protein and the alkyl group functionalizing the interior surface of the silica nanopore enable the insertion of the aquaporin-incorporated lipid shell into the nanopore by forcing out the water molecules. The same preferential interactions are responsible for the structural stability of the inserted aquaporin-incorporated lipid shell as well as the water sealing properties of the lipid-alkyl interface. We further show that the aquaporin protein stabilized in the alkyl-functionalized silica nanopore preserves its biological structure and function in both pure and saline water, and, remarkably, its water permeability is equal to the one measured in the biological environment. The designed biohybrid membrane could pave the way for the development of durable transformative devices for water filtration.
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Mohr S, Pétuya R, Sarria J, Purkayastha N, Bodnar S, Wylde J, Tsimpanogiannis IN. Assessing the effect of a liquid water layer on the adsorption of hydrate anti-agglomerants using molecular simulations. J Chem Phys 2022; 157:094703. [DOI: 10.1063/5.0100260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We have performed Molecular Dynamics simulations to study the adsorption of ten hydrate anti-agglomerants onto a mixed methane-propane sII hydrate surface covered by layers of liquid water of various thickness. As a general trend, we found that the more liquid water is present on the hydrate surface the less favorable the adsorption becomes, even though there are considerable differences between the individual molecules, indicating that the presence and thickness of this liquid water layer is a crucial parameter for anti-agglomerant adsorption studies. Additionally, we found that there exists an optimal thickness of the liquid water layer favoring hydrate growth due to the presence of both liquid water and hydrate-forming guest molecules. For all other cases of liquid water layer thickness, hydrate growth is slower due to the limited availability of hydrate-forming guests close to the hydrate formation front. Finally, we investigated the connection between the thickness of the liquid water layer and the degree of subcooling, and found a very good agreement between our Molecular Dynamics simulations and theoretical predictions.
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Affiliation(s)
| | | | | | | | - Scot Bodnar
- Clariant Oil Services, United States of America
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4
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Surface morphology effects on clathrate hydrate wettability. J Colloid Interface Sci 2021; 611:421-431. [PMID: 34968961 DOI: 10.1016/j.jcis.2021.12.083] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/08/2021] [Accepted: 12/13/2021] [Indexed: 11/23/2022]
Abstract
HYPOTHESIS Clathrate hydrates preferentially form at interfaces; hence, wetting properties play an important role in their formation, growth, and agglomeration. Experimental evidence suggests that the hydrate preparation process can strongly affect contact angle measurements, leading to the different results reported in the literature. These differences hamper technological progress. We hypothesize that changes in hydrate surface morphologies are responsible for the wide variation of contact angles reported in the literature. EXPERIMENTS Experimental testing of our hypothesis is problematic due to the preparation history of hydrates on their surface properties, and the difficulties in advanced surface characterization. Thus, we employ molecular dynamics simulations, which allow us to systematically change the interfacial features and the system composition. Implementing advanced algorithms, we quantify fundamental thermodynamic properties to validate our observations. FINDINGS We achieve excellent agreement with experimental observations for both atomically smooth and rough hydrate surfaces. Our results suggest that contact line pinning forces, enhanced by surface heterogeneity, are accountable for altering water contact angles, thus explaining the differences among reported experimental data. Our analysis and molecular level insights help interpret adhesion force measurements and yield a better understanding of the agglomeration between hydrate particles, providing a microscopic tool for advancing flow assurance applications.
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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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6
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Sicard F, Koskin V, Annibale A, Rosta E. Position-Dependent Diffusion from Biased Simulations and Markov State Model Analysis. J Chem Theory Comput 2021; 17:2022-2033. [DOI: 10.1021/acs.jctc.0c01151] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- François Sicard
- Department of Chemistry, King’s College London, SE1 1DB London, U.K
- Department of Physics and Astronomy, University College London, WC1E 6BT London, U.K
| | - Vladimir Koskin
- Department of Chemistry, King’s College London, SE1 1DB London, U.K
- Department of Physics and Astronomy, University College London, WC1E 6BT London, U.K
| | - Alessia Annibale
- Department of Mathematics, King’s College London, SE11 6NJ London, U.K
| | - Edina Rosta
- Department of Chemistry, King’s College London, SE1 1DB London, U.K
- Department of Physics and Astronomy, University College London, WC1E 6BT London, U.K
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7
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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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Bui T, Monteiro D, Vo L, Striolo A. Synergistic and Antagonistic Effects of Aromatics on the Agglomeration of Gas Hydrates. Sci Rep 2020; 10:5496. [PMID: 32218443 PMCID: PMC7098976 DOI: 10.1038/s41598-020-62060-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 03/02/2020] [Indexed: 11/15/2022] Open
Abstract
Surfactants are often used to stabilize aqueous dispersions. For example, surfactants can be used to prevent hydrate particles from forming large plugs that can clog, and sometimes rupture pipelines. Changes in oil composition, however dramatically affect the performance of said surfactants. In this work we demonstrate that aromatic compounds, dissolved in the hydrocarbon phase, can have both synergistic and antagonistic effects, depending on their molecular structure, with respect to surfactants developed to prevent hydrate agglomerations. While monocyclic aromatics such as benzene were found to disrupt the structure of surfactant films at low surfactant density, they are expelled from the interfacial film at high surfactant density. On the other hand, polycyclic aromatics, in particular pyrene, are found to induce order and stabilize the surfactant films both at low and high surfactant density. Based on our simulation results, polycyclic aromatics could behave as natural anti-agglomerants and enhance the performance of the specific surfactants considered here, while monocyclic aromatics could, in some cases, negatively affect performance. Although limited to the conditions chosen for the present simulations, the results, explained in terms of molecular features, could be valuable for better understanding synergistic and antagonistic effects relevant for stabilizing aqueous dispersions used in diverse applications, ranging from foodstuff to processing of nanomaterials and advanced manufacturing.
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Affiliation(s)
- Tai Bui
- Department of Chemical Engineering, University College London, WC1 E7JE, London, UK
| | | | - Loan Vo
- Halliburton, Houston, Texas, USA
| | - Alberto Striolo
- Department of Chemical Engineering, University College London, WC1 E7JE, London, UK.
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Hassanpouryouzband A, Joonaki E, Vasheghani Farahani M, Takeya S, Ruppel C, Yang J, English NJ, Schicks JM, Edlmann K, Mehrabian H, Aman ZM, Tohidi B. Gas hydrates in sustainable chemistry. Chem Soc Rev 2020; 49:5225-5309. [DOI: 10.1039/c8cs00989a] [Citation(s) in RCA: 247] [Impact Index Per Article: 61.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
This review includes the current state of the art understanding and advances in technical developments about various fields of gas hydrates, which are combined with expert perspectives and analyses.
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Affiliation(s)
- Aliakbar Hassanpouryouzband
- Hydrates, Flow Assurance & Phase Equilibria Research Group
- Institute of GeoEnergy Engineering
- School of Energy
- Geoscience, Infrastructure and Society
- Heriot-Watt University
| | - Edris Joonaki
- Hydrates, Flow Assurance & Phase Equilibria Research Group
- Institute of GeoEnergy Engineering
- School of Energy
- Geoscience, Infrastructure and Society
- Heriot-Watt University
| | - Mehrdad Vasheghani Farahani
- Hydrates, Flow Assurance & Phase Equilibria Research Group
- Institute of GeoEnergy Engineering
- School of Energy
- Geoscience, Infrastructure and Society
- Heriot-Watt University
| | - Satoshi Takeya
- National Institute of Advanced Industrial Science and Technology (AIST)
- Tsukuba 305-8565
- Japan
| | | | - Jinhai Yang
- Hydrates, Flow Assurance & Phase Equilibria Research Group
- Institute of GeoEnergy Engineering
- School of Energy
- Geoscience, Infrastructure and Society
- Heriot-Watt University
| | - Niall J. English
- School of Chemical and Bioprocess Engineering
- University College Dublin
- Dublin 4
- Ireland
| | | | - Katriona Edlmann
- School of Geosciences
- University of Edinburgh
- Grant Institute
- Edinburgh
- UK
| | - Hadi Mehrabian
- Department of Chemical Engineering
- Massachusetts Institute of Technology
- Cambridge
- USA
| | - Zachary M. Aman
- Fluid Science & Resources
- School of Engineering
- University of Western Australia
- Perth
- Australia
| | - Bahman Tohidi
- Hydrates, Flow Assurance & Phase Equilibria Research Group
- Institute of GeoEnergy Engineering
- School of Energy
- Geoscience, Infrastructure and Society
- Heriot-Watt University
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10
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Fang B, Ning F, Hu S, Guo D, Ou W, Wang C, Wen J, Sun J, Liu Z, Koh CA. The effect of surfactants on hydrate particle agglomeration in liquid hydrocarbon continuous systems: a molecular dynamics simulation study. RSC Adv 2020; 10:31027-31038. [PMID: 35520650 PMCID: PMC9056346 DOI: 10.1039/d0ra04088f] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/14/2020] [Indexed: 12/02/2022] Open
Abstract
Anti-agglomerants (AAs), both natural and commercial, are currently being considered for gas hydrate risk management of petroleum pipelines in offshore operations. However, the molecular mechanisms of the interaction between the AAs and gas hydrate surfaces and the prevention of hydrate agglomeration remain critical and complex questions that need to be addressed to advance this technology. Here, we use molecular dynamics (MD) simulations to investigate the effect of model surfactant molecules (polynuclear aromatic carboxylic acids) on the agglomeration behaviour of gas hydrate particles and disruption of the capillary liquid bridge between hydrate particles. The results show that the anti-agglomeration pathway can be divided into two processes: the spontaneous adsorption effect of surfactant molecules onto the hydrate surface and the weakening effect of the intensity of the liquid bridge between attracted hydrate particles. The MD simulation results also indicate that the anti-agglomeration effectiveness of surfactants is determined by the intrinsic nature of their molecular functional groups. Additionally, we find that surfactant molecules can affect hydrate growth, which decreases hydrate particle size and correspondingly lower the risk of hydrate agglomeration. This study provides molecular-level insights into the anti-agglomeration mechanism of surfactant molecules, which can aid in the ultimate application of natural or commercial AAs with optimal anti-agglomeration properties. Schematic of anti-agglomeration effect of surfactants promoting gas hydrate particle dispersion.![]()
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11
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Striolo A, Phan A, Walsh MR. Molecular properties of interfaces relevant for clathrate hydrate agglomeration. Curr Opin Chem Eng 2019. [DOI: 10.1016/j.coche.2019.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Striolo A. Clathrate hydrates: recent advances on CH4 and CO2 hydrates, and possible new frontiers. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1646436] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Alberto Striolo
- Department of Chemical Engineering, University College London, London, UK
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13
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Naullage P, Bertolazzo AA, Molinero V. How Do Surfactants Control the Agglomeration of Clathrate Hydrates? ACS CENTRAL SCIENCE 2019; 5:428-439. [PMID: 30937370 PMCID: PMC6439454 DOI: 10.1021/acscentsci.8b00755] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Indexed: 05/14/2023]
Abstract
Clathrate hydrates can spontaneously form under typical conditions found in oil and gas pipelines. The agglomeration of clathrates into large solid masses plugs the pipelines, posing adverse safety, economic, and environmental threats. Surfactants are customarily used to prevent the aggregation of clathrate particles and their coalescence with water droplets. It is generally assumed that a large contact angle between the surfactant-covered clathrate and water is a key predictor of the antiagglomerant performance of the surfactant. Here we use molecular dynamic simulations to investigate the structure and dynamics of surfactant films at the clathrate-oil interface, and their impact on the contact angle and coalescence between water droplets and hydrate particles. In agreement with the experiments, the simulations predict that surfactant-covered clathrate-oil interfaces are oil wet but super-hydrophobic to water. Although the water contact angle determines the driving force for coalescence, we find that a large contact angle is not sufficient to predict good antiagglomerant performance of a surfactant. We conclude that the length of the surfactant molecules, the density of the interfacial film, and the strength of binding of its molecules to the clathrate surface are the main factors in preventing the coalescence and agglomeration of clathrate particles with water droplets in oil. Our analysis provides a molecular foundation to guide the molecular design of effective clathrate antiagglomerants.
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Affiliation(s)
- Pavithra
M. Naullage
- Department
of Chemistry, The University of Utah, Salt Lake City, Utah 84112-0850, United States
| | - Andressa A. Bertolazzo
- Department
of Chemistry, The University of Utah, Salt Lake City, Utah 84112-0850, United States
- Departamento
de Ciências Exatas e Educação, Universidade Federal de Santa Catarina, Blumenau, Santa Catarina, Brazil
| | - Valeria Molinero
- Department
of Chemistry, The University of Utah, Salt Lake City, Utah 84112-0850, United States
- E-mail:
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