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Zhong S, Shi Z, Zhang B, Wen Z, Chen L. Homogeneous water vapor condensation with a deep neural network potential model. J Chem Phys 2024; 160:124303. [PMID: 38516980 DOI: 10.1063/5.0189448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/03/2024] [Indexed: 03/23/2024] Open
Abstract
Molecular-level nucleation has not been clearly understood due to the complexity of multi-body potentials and the stochastic, rare nature of the process. This work utilizes molecular dynamics (MD) simulations, incorporating a first-principles-based deep neural network (DNN) potential model, to investigate homogeneous water vapor condensation. The nucleation rates and critical nucleus sizes predicted by the DNN model are compared against commonly used semi-empirical models, namely extended simple point charge (SPC/E), TIP4P, and OPC, in addition to classical nucleation theory (CNT). The nucleation rates from the DNN model are comparable with those from the OPC model yet surpass the rates from the SPC/E and TIP4P models, a discrepancy that could mainly arise from the overestimated bulk free energy by SPC/E and TIP4P. The surface free energy predicted by CNT is lower than that in MD simulations, while its bulk free energy is higher than that in MD simulations, irrespective of the potential model used. Further analysis of cluster properties with the DNN model unveils pronounced variations of O-H bond length and H-O-H bond angle, along with averaged bond lengths and angles that are enlarged during embryonic cluster formation. Properties such as cluster surface free energy and liquid-to-vapor density transition profiles exhibit significant deviations from CNT assumptions.
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Affiliation(s)
- Shenghui Zhong
- International Innovation Institute, Beihang University, Hangzhou 311115, China
| | - Zheyu Shi
- International Innovation Institute, Beihang University, Hangzhou 311115, China
- College of Science, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Bin Zhang
- International Innovation Institute, Beihang University, Hangzhou 311115, China
| | - Zhengcheng Wen
- College of Science, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Longfei Chen
- International Innovation Institute, Beihang University, Hangzhou 311115, China
- School of Energy and Power Engineering, Beihang University, Beijing 100191, China
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2
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Massahud E, Ahmed H, Babarao R, Ehrnst Y, Alijani H, Darmanin C, Murdoch BJ, Rezk AR, Yeo LY. Acoustomicrofluidic Defect Engineering and Ligand Exchange in ZIF-8 Metal-Organic Frameworks. SMALL METHODS 2023; 7:e2201170. [PMID: 36855216 DOI: 10.1002/smtd.202201170] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 01/19/2023] [Indexed: 06/09/2023]
Abstract
A way through which the properties of metal-organic frameworks (MOFs) can be tuned is by engineering defects into the crystal structure. Given its intrinsic stability and rigidity, however, it is difficult to introduce defects into zeolitic imidazolate frameworks (ZIFs)-and ZIF-8, in particular-without compromising crystal integrity. In this work, it is shown that the acoustic radiation pressure as well as the hydrodynamic stresses arising from the oscillatory flow generated by coupling high frequency (MHz-order) hybrid surface and bulk acoustic waves into a suspension of ZIF-8 crystals in a liquid pressure transmitting medium is capable of driving permanent structural changes in their crystal lattice structure. Over time, the enhancement in the diffusive transport of guest molecules into the material's pores as a consequence is shown to lead to expansion of the pore framework, and subsequently, the creation of dangling-linker and missing-linker defects, therefore offering the possibility of tuning the type and extent of defects engineered into the MOF through the acoustic exposure time. Additionally, the practical utility of the technology is demonstrated for one-pot, simultaneous solvent-assisted ligand exchange under ambient conditions, for sub-micron-dimension ZIF-8 crystals and relatively large ligands-more specifically 2-aminobenzimidazole-without compromising the framework porosity or overall crystal structure.
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Affiliation(s)
- Emily Massahud
- Micro/Nanophysics Research Laboratory, RMIT University, Melbourne, VIC, 3000, Australia
| | - Heba Ahmed
- Micro/Nanophysics Research Laboratory, RMIT University, Melbourne, VIC, 3000, Australia
| | - Ravichandar Babarao
- Manufacturing Business Unit, Commonwealth Scientific and Industrial Research Organization (CSIRO) Manufacturing, Clayton, VIC, 3168, Australia
- Centre for Advanced Materials and Industrial Chemistry, School of Science, RMIT University, Melbourne, VIC, 3000, Australia
| | - Yemima Ehrnst
- Micro/Nanophysics Research Laboratory, RMIT University, Melbourne, VIC, 3000, Australia
| | - Hossein Alijani
- Micro/Nanophysics Research Laboratory, RMIT University, Melbourne, VIC, 3000, Australia
| | - Connie Darmanin
- Department of Mathematical and Physical Sciences, School of Engineering, Computing and Mathematical Sciences, La Trobe University, Melbourne, VIC, 3086, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Billy J Murdoch
- RMIT Microscopy and Microanalysis Facility, STEM College, RMIT University, Melbourne, VIC, 3000, Australia
| | - Amgad R Rezk
- Micro/Nanophysics Research Laboratory, RMIT University, Melbourne, VIC, 3000, Australia
| | - Leslie Y Yeo
- Micro/Nanophysics Research Laboratory, RMIT University, Melbourne, VIC, 3000, Australia
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3
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Goel H, Ling S, Ellis BN, Taconi A, Slater B, Rai N. Predicting vapor liquid equilibria using density functional theory: A case study of argon. J Chem Phys 2018; 148:224501. [PMID: 29907054 DOI: 10.1063/1.5025726] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Predicting vapor liquid equilibria (VLE) of molecules governed by weak van der Waals (vdW) interactions using the first principles approach is a significant challenge. Due to the poor scaling of the post Hartree-Fock wave function theory with system size/basis functions, the Kohn-Sham density functional theory (DFT) is preferred for systems with a large number of molecules. However, traditional DFT cannot adequately account for medium to long range correlations which are necessary for modeling vdW interactions. Recent developments in DFT such as dispersion corrected models and nonlocal van der Waals functionals have attempted to address this weakness with a varying degree of success. In this work, we predict the VLE of argon and assess the performance of several density functionals and the second order Møller-Plesset perturbation theory (MP2) by determining critical and structural properties via first principles Monte Carlo simulations. PBE-D3, BLYP-D3, and rVV10 functionals were used to compute vapor liquid coexistence curves, while PBE0-D3, M06-2X-D3, and MP2 were used for computing liquid density at a single state point. The performance of the PBE-D3 functional for VLE is superior to other functionals (BLYP-D3 and rVV10). At T = 85 K and P = 1 bar, MP2 performs well for the density and structural features of the first solvation shell in the liquid phase.
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Affiliation(s)
- Himanshu Goel
- Dave C. Swalm School of Chemical Engineering, and Center for Advanced Vehicular Systems, Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - Sanliang Ling
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Breanna Nicole Ellis
- Dave C. Swalm School of Chemical Engineering, and Center for Advanced Vehicular Systems, Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - Anna Taconi
- Dave C. Swalm School of Chemical Engineering, and Center for Advanced Vehicular Systems, Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - Ben Slater
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Neeraj Rai
- Dave C. Swalm School of Chemical Engineering, and Center for Advanced Vehicular Systems, Mississippi State University, Mississippi State, Mississippi 39762, USA
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Understanding the adsorption process in ZIF-8 using high pressure crystallography and computational modelling. Nat Commun 2018; 9:1429. [PMID: 29650966 PMCID: PMC5897325 DOI: 10.1038/s41467-018-03878-6] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 03/20/2018] [Indexed: 11/08/2022] Open
Abstract
Some porous crystalline solids change their structure upon guest inclusion. Unlocking the potential of these solids for a wide variety of applications requires full characterisation of the response to adsorption and the underlying framework–guest interactions. Here, we introduce an approach to understanding gas uptake in porous metal-organic frameworks (MOFs) by loading liquefied gases at GPa pressures inside the Zn-based framework ZIF-8. An integrated experimental and computational study using high-pressure crystallography, grand canonical Monte Carlo (GCMC) and periodic DFT simulations has revealed six symmetry-independent adsorption sites within the framework and a transition to a high-pressure phase. The cryogenic high-pressure loading method offers a different approach to obtaining atomistic detail on guest molecules. The GCMC simulations provide information on interaction energies of the adsorption sites allowing to classify the sites by energy. DFT calculations reveal the energy barrier of the transition to the high-pressure phase. This combination of techniques provides a holistic approach to understanding both structural and energetic changes upon adsorption in MOFs. Understanding host–guest interactions and structural changes within porous materials is crucial for enhancing gas storage properties. Here, the authors combine cryogenic loading of gases with high pressure crystallography and computational techniques to obtain atomistic detail of adsorption-induced structural and energetic changes in ZIF-8.
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Calculating free energy profiles using entropy as a reaction coordinate: Application to water nucleation. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.02.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Planková B, Vinš V, Hrubý J. Predictions of homogeneous nucleation rates for n-alkanes accounting for the diffuse phase interface and capillary waves. J Chem Phys 2017; 147:164702. [PMID: 29096481 DOI: 10.1063/1.5008612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Homogeneous droplet nucleation has been studied for almost a century but has not yet been fully understood. In this work, we used the density gradient theory (DGT) and considered the influence of capillary waves (CWs) on the predicted size-dependent surface tensions and nucleation rates for selected n-alkanes. The DGT model was completed by an equation of state (EoS) based on the perturbed-chain statistical associating fluid theory and compared to the classical nucleation theory and the Peng-Robinson EoS. It was found that the critical clusters are practically free of CWs because they are so small that even the smallest wavelengths of CWs do not fit into their finite dimensions. The CWs contribute to the entropy of the system and thus decrease the surface tension. A correction for the effect of CWs on the surface tension is presented. The effect of the different EoSs is relatively small because by a fortuitous coincidence their predictions are similar in the relevant range of critical cluster sizes. The difference of the DGT predictions to the classical nucleation theory computations is important but not decisive. Of the effects investigated, the most pronounced is the suppression of CWs which causes a sizable decrease of the predicted nucleation rates. The major difference between experimental nucleation rate data and theoretical predictions remains in the temperature dependence. For normal alkanes, this discrepancy is much stronger than observed, e.g., for water. Theoretical corrections developed here have a minor influence on the temperature dependency. We provide empirical equations correcting the predicted nucleation rates to values comparable with experiments.
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Affiliation(s)
- Barbora Planková
- Institute of Thermomechanics of the Czech Academy of Sciences, v. v. i., Dolejškova 5, 182 00 Prague, Czech Republic
| | - Václav Vinš
- Institute of Thermomechanics of the Czech Academy of Sciences, v. v. i., Dolejškova 5, 182 00 Prague, Czech Republic
| | - Jan Hrubý
- Institute of Thermomechanics of the Czech Academy of Sciences, v. v. i., Dolejškova 5, 182 00 Prague, Czech Republic
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Van Vleet MJ, Misquitta AJ, Stone AJ, Schmidt JR. Beyond Born-Mayer: Improved Models for Short-Range Repulsion in ab Initio Force Fields. J Chem Theory Comput 2016; 12:3851-70. [PMID: 27337546 DOI: 10.1021/acs.jctc.6b00209] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Short-range repulsion within intermolecular force fields is conventionally described by either Lennard-Jones (A/r(12)) or Born-Mayer (A exp(-Br)) forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of intermolecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, and robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Finally, we show how this methodology can be adapted to yield the standard Born-Mayer functional form while still retaining many of the advantages of the Slater-ISA approach.
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Affiliation(s)
- Mary J Van Vleet
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Alston J Misquitta
- Department of Physics and Astronomy, Queen Mary University of London , London E1 4NS, United Kingdom
| | - Anthony J Stone
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, United Kingdom
| | - J R Schmidt
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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Abstract
We introduce grand and semigrand canonical global optimization approaches using basin-hopping with an acceptance criterion based on the local contribution of each potential energy minimum to the (semi)grand potential. The method is tested using local harmonic vibrational densities of states for atomic clusters as a function of temperature and chemical potential. The predicted global minima switch from dissociated states to clusters for larger values of the chemical potential and lower temperatures, in agreement with the predictions of a model fitted to heat capacity data for selected clusters. Semigrand canonical optimization allows us to identify particularly stable compositions in multicomponent nanoalloys as a function of increasing temperature, whereas the grand canonical potential can produce a useful survey of favorable structures as a byproduct of the global optimization search.
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Affiliation(s)
- F Calvo
- Université Grenoble Alpes , LIPHY, F-38000 Grenoble, France.,CNRS , LIPHY, F-38000 Grenoble, France
| | - D Schebarchov
- University Chemical Laboratories , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - D J Wales
- University Chemical Laboratories , Lensfield Road, Cambridge CB2 1EW, United Kingdom
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Papadimitriou NI, Tsimpanogiannis IN, Economou IG, Stubos AK. Influence of combining rules on the cavity occupancy of clathrate hydrates by Monte Carlo simulations. Mol Phys 2014. [DOI: 10.1080/00268976.2014.902136] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Palmer JC, Coasne B, Śliwinska-Bartkowiak M, Jackson G, Müller EA, Gubbins KE. On the molecular origin of high-pressure effects in nanoconfinement: The role of surface chemistry and roughness. J Chem Phys 2013; 139:144701. [DOI: 10.1063/1.4824125] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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Diemand J, Angélil R, Tanaka KK, Tanaka H. Large scale molecular dynamics simulations of homogeneous nucleation. J Chem Phys 2013; 139:074309. [DOI: 10.1063/1.4818639] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Loeffler TD, Henderson DE, Chen B. Vapor–liquid nucleation in two dimensions: On the intriguing sign switch of the errors of the classical nucleation theory. J Chem Phys 2012. [DOI: 10.1063/1.4766328] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Pérez A, Rubio A. A molecular dynamics study of water nucleation using the TIP4P/2005 model. J Chem Phys 2012; 135:244505. [PMID: 22225167 DOI: 10.1063/1.3672063] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Extensive molecular dynamics simulations were conducted using the TIP4P/2005 water model of Abascal and Vega [J. Chem. Phys. 123, 234505 (2005)] to investigate its condensation from supersaturated vapor to liquid at 330 K. The mean first passage time method [J. Wedekind, R. Strey, and D. Reguera, J. Chem. Phys. 126, 134103 (2007); L. S. Bartell and D. T. Wu, 125, 194503 (2006)] was used to analyze the influence of finite size effects, thermostats, and charged species on the nucleation dynamics. We find that the Nosé-Hoover thermostat and the one proposed by Bussi et al. [J. Chem. Phys. 126, 014101 (2007)] give essentially the same averages. We identify the maximum thermostat coupling time to guarantee proper thermostating for these simulations. The presence of charged species has a dramatic impact on the dynamics, inducing a marked change towards a pure growth regime, which highlights the importance of ions in the formation of liquid droplets in the atmosphere. It was found a small but noticeable sign preference at intermediate cluster sizes (between 5 and 30 water molecules) corresponding mostly to the formation of the second solvation shell around the ion. The TIP4P/2005 water model predicts that anions induce faster formation of water clusters than cations of the same magnitude of charge.
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Affiliation(s)
- Alejandro Pérez
- Nano-bio Spectroscopy Group and ETSF Scientific Development Center, Department of Materials Science, Faculty of Chemistry, University of the Basque Country (UPV/EHU), Donostia-San Sebastián, Spain.
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Horsch M, Hasse H, Shchekin AK, Agarwal A, Eckelsbach S, Vrabec J, Müller EA, Jackson G. Excess equimolar radius of liquid drops. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:031605. [PMID: 22587106 DOI: 10.1103/physreve.85.031605] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Indexed: 05/31/2023]
Abstract
The curvature dependence of the surface tension is related to the excess equimolar radius of liquid drops, i.e., the deviation of the equimolar radius from the radius defined by the macroscopic capillarity approximation. Based on the Tolman [J. Chem. Phys. 17, 333 (1949)] approach and its interpretation by Nijmeijer et al. [J. Chem. Phys. 96, 565 (1991)], the surface tension of spherical interfaces is analyzed in terms of the pressure difference due to curvature. In the present study, the excess equimolar radius, which can be obtained directly from the density profile, is used instead of the Tolman length. Liquid drops of the truncated and shifted Lennard-Jones fluid are investigated by molecular dynamics simulation in the canonical ensemble, with equimolar radii ranging from 4 to 33 times the Lennard-Jones size parameter σ. In these simulations, the magnitude of the excess equimolar radius is shown to be smaller than σ/2. This suggests that the surface tension of liquid drops at the nanometer length scale is much closer to that of the planar vapor-liquid interface than reported in studies based on the mechanical route.
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Affiliation(s)
- Martin Horsch
- Lehrstuhl für Thermodynamik, Fachbereich Maschinenbau und Verfahrenstechnik, Technische Universität Kaiserslautern, Kaiserslautern, Germany.
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Bhabhe A, Wyslouzil B. Nitrogen nucleation in a cryogenic supersonic nozzle. J Chem Phys 2011; 135:244311. [DOI: 10.1063/1.3671453] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Das Arulsamy A, Kregar Z, Eleršič K, Modic M, Subramani US. Polarization induced water molecule dissociation below the first-order electronic-phase transition temperature. Phys Chem Chem Phys 2011; 13:15175-81. [PMID: 21776515 DOI: 10.1039/c1cp20138g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrogen produced from the photocatalytic splitting of water is one of the reliable alternatives to replace the polluting fossil and the radioactive nuclear fuels. Here, we provide unequivocal evidence for the existence of blue- and red-shifting O-H covalent bonds within a single water molecule adsorbed on the MgO surface as a result of asymmetric displacement polarizabilities. The adsorbed H-O-H on MgO gives rise to one weaker H-O bond, while the other O-H covalent bond from the same adsorbed water molecule compensates this effect with a stronger bond. The weaker bond (nearest to the surface), the interlayer tunneling electrons and the silver substrate are shown to be the causes for the smallest dissociative activation energy on the MgO monolayer. The origin that is responsible to initiate the splitting mechanism is proven to be due to the changes in the polarizability of an adsorbed water molecule, which are further supported by the temperature-dependent static dielectric constant measurements for water below the first-order electronic-phase transition temperature.
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Affiliation(s)
- Andrew Das Arulsamy
- Condensed Matter Group, Division of Interdisciplinary Science, D403 Puteri Court, No. 1, Jalan 28, Taman Putra, 68000 Ampang, Selangor DE, Malaysia.
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