1
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Blazquez S, de Lucas M, Vega C, Troncoso J, Gámez F. The temperature of maximum in density of aqueous solutions of nitrate and ammonium salts: Testing the Madrid-2019 force field. J Chem Phys 2024; 161:046103. [PMID: 39056391 DOI: 10.1063/5.0217827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
The shift in the temperature of maximum in density (TMD) at room pressure of aqueous solutions of a set of five salts containing NO3- and/or NH4+ groups is studied both through experiments and through molecular dynamics simulations using the Madrid-2019 force field for ions and the TIP4P/2005 model for water. The experiments demonstrate the potential transferability and limitations of the Madrid-2019 force field for nitrate and ammonium ions recently developed by our group at different temperatures and add updated information to the reported datasets of TMDs for strong electrolytes. By using the Despretz law, individual ion contributions are extracted for predictive purposes from the experimental values of the shift in the TMD. Interesting findings for the behavior of the shift in the TMD in nitrate salts expose that this property might be particularly challenging for modelization approaches when dealing with polyatomic species.
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Affiliation(s)
- S Blazquez
- Departamento de Química Física, Fac. Ciencias Químicas, Universidad Complutense de Madrid, E 28040 Madrid, Spain
| | - M de Lucas
- Departamento de Química Física, Fac. Ciencias Químicas, Universidad Complutense de Madrid, E 28040 Madrid, Spain
| | - C Vega
- Departamento de Química Física, Fac. Ciencias Químicas, Universidad Complutense de Madrid, E 28040 Madrid, Spain
| | - J Troncoso
- Departamento de Física Aplicada, Universidade de Vigo, Escola de Enxeñaría Aeronaútica e do Espazo, E 32004 Ourense, Spain
| | - F Gámez
- Departamento de Química Física, Fac. Ciencias Químicas, Universidad Complutense de Madrid, E 28040 Madrid, Spain
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2
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Sedano LF, Blazquez S, Vega C. Accuracy limit of non-polarizable four-point water models: TIP4P/2005 vs OPC. Should water models reproduce the experimental dielectric constant? J Chem Phys 2024; 161:044505. [PMID: 39046346 DOI: 10.1063/5.0211871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 06/30/2024] [Indexed: 07/25/2024] Open
Abstract
The last generation of four center non-polarizable models of water can be divided into two groups: those reproducing the dielectric constant of water, as OPC, and those significantly underestimating its value, as TIP4P/2005. To evaluate the global performance of OPC and TIP4P/2005, we shall follow the test proposed by Vega and Abascal in 2011 evaluating about 40 properties to fairly address this comparison. The liquid-vapor and liquid-solid equilibria are computed, as well as the heat capacities, isothermal compressibilities, surface tensions, densities of different ice polymorphs, the density maximum, equations of state at high pressures, and transport properties. General aspects of the phase diagram are considered by comparing the ratios of different temperatures (namely, the temperature of maximum density, the melting temperature of hexagonal ice, and the critical temperature). The final scores are 7.2 for TIP4P/2005 and 6.3 for OPC. The results of this work strongly suggest that we have reached the limit of what can be achieved with non-polarizable models of water and that the attempt to reproduce the experimental dielectric constant deteriorates the global performance of the water force field. The reason is that the dielectric constant depends on two surfaces (potential energy and dipole moment surfaces), whereas in the absence of an electric field, all properties can be determined simply from just one surface (the potential energy surface). The consequences of the choice of the water model in the modeling of electrolytes in water are also discussed.
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Affiliation(s)
- L F Sedano
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - S Blazquez
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - C Vega
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
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3
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Ho CH, Paesani F. Entropy of Liquid Water as Predicted by the Two-Phase Thermodynamic Model and Data-Driven Many-Body Potentials. J Phys Chem B 2024; 128:6885-6891. [PMID: 38970462 DOI: 10.1021/acs.jpcb.4c03245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2024]
Abstract
We investigate the entropy of liquid water at ambient conditions using the two-phase thermodynamic (2PT) model, applied to both common pairwise-additive water models and the MB-pol and MB-pol(2023) data-driven many-body potentials. Our simulations demonstrate that the 2PT model yields entropy values in semiquantitative agreement with experimental data when using MB-pol and MB-pol(2023). Additionally, our analyses indicate that the entropy values predicted by pairwise-additive water models may benefit from error compensation between the inherent approximations of the 2PT model and the known limitations of these water models in describing many-body interactions. Despite its approximate nature, the simplicity of the 2PT model makes it a valuable tool for estimating relative entropy changes of liquid water across various environments, especially when combined with water models that provide a consistently robust representation of the structural, thermodynamic, and dynamical properties of liquid water.
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Affiliation(s)
- Ching-Hwa Ho
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
- Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
- Halicioğlu Data Science Institute, University of California San Diego, La Jolla, California 92093, United States
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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4
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Kulkarni A, Bortz M, Küfer KH, Kohns M, Hasse H. Hierarchical Multicriteria Optimization of Molecular Models of Water. J Chem Inf Model 2024; 64:5077-5089. [PMID: 38888988 DOI: 10.1021/acs.jcim.4c00404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Many widely used molecular models of water are built from a single Lennard-Jones site on which three point charges are positioned, one negative and two positive ones. Models from that class, denoted LJ3PC here, are computationally efficient, but it is well known that they cannot represent all relevant properties of water simultaneously with good accuracy. Despite the importance of the LJ3PC water model class, its inherent limitations in simultaneously describing different properties of water have never been studied systematically. This task can only be solved by multicriteria optimization (MCO). However, due to its computational cost, applying MCO to molecular models is a formidable task. We have recently introduced the reduced units method (RUM) to cope with this problem. In the present work, we apply the RUM in a hierarchical scheme to optimize LJ3PC water models taking into account five objectives: the representation of vapor pressure, saturated liquid density, self-diffusion coefficient, shear viscosity, and relative permittivity. Of the six parameters of the LJ3PC models, five were varied; only the H-O-H bond angle, which is usually chosen based on physical arguments, was kept constant. Our hierarchical RUM-based approach yields a Pareto set that contains attractive new water models. Furthermore, the results give an idea of what can be achieved by molecular modeling of water with models from the LJ3PC class.
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Affiliation(s)
- Aditya Kulkarni
- Laboratory of Engineering Thermodynamics (LTD), RPTU Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Michael Bortz
- Fraunhofer Institute for Industrial Mathematics (ITWM), 67663 Kaiserslautern, Germany
| | - Karl-Heinz Küfer
- Fraunhofer Institute for Industrial Mathematics (ITWM), 67663 Kaiserslautern, Germany
| | - Maximilian Kohns
- Laboratory of Engineering Thermodynamics (LTD), RPTU Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Hans Hasse
- Laboratory of Engineering Thermodynamics (LTD), RPTU Kaiserslautern, 67663 Kaiserslautern, Germany
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5
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Tóth Ugyonka H, Hantal G, Szilágyi I, Idrissi A, Jorge M, Jedlovszky P. Spatial organization of the ions at the free surface of imidazolium-based ionic liquids. J Colloid Interface Sci 2024; 676:989-1000. [PMID: 39068842 DOI: 10.1016/j.jcis.2024.07.041] [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: 04/08/2024] [Revised: 07/02/2024] [Accepted: 07/05/2024] [Indexed: 07/30/2024]
Abstract
HYPOTHESIS Experimental information on the molecular scale structure of ionic liquid interfaces is controversial, giving rise to two competing scenarios, namely the double layer-like and "chessboard"-like structures. This issue can be resolved by computer simulation methods, at least for the underlying molecular model. Systematically changing the anion type can elucidate the relative roles of electrostatic interactions, hydrophobic (or, strictly speaking, apolar) effects and steric restrictions on the interfacial properties. SIMULATIONS Molecular dynamics simulation is combined with intrinsic analysis methods both at the molecular and atomic levels, supplemented by Voronoi analysis of self-association. FINDINGS We see no evidence for the existence of a double-layer-type arrangement of the ions, or for their self-association at the surface of the liquid. Instead, our results show that cation chains associate into apolar domains that protrude into the vapour phase, while charged groups form domains that are embedded in this apolar environment at the surface. However, the apolar chains largely obscure the cation groups, to which they are bound, while the smaller and more mobile anions can more easily access the free surface, leading to a somewhat counterintuitive net excess of negative charge at the interface. Importantly, this excess charge could only be identified by applying intrinsic analysis.
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Affiliation(s)
- Helga Tóth Ugyonka
- Department of Chemistry, Eszterházy Károly Catholic University, Leányka utca 12, H-3300 Eger, Hungary
| | - György Hantal
- PULS Group, Department of Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstr. 3, D-91058 Erlangen, Germany
| | - István Szilágyi
- MTA-SZTE Lendület Biocolloids Research Group, Department of Physical Chemistry and Materials Science, Interdisciplinary Excellence Center, University of Szeged, H-6720 Szeged, Hungary
| | - Abdenacer Idrissi
- University of Lille, CNRS UMR 8516 -LASIRe - Laboratoire Avancé de Spectroscopie pour les Interactions la Réactivité et l'environnement, 59000 Lille, France
| | - Miguel Jorge
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow G1 1XJ, United Kingdom
| | - Pál Jedlovszky
- Department of Chemistry, Eszterházy Károly Catholic University, Leányka utca 12, H-3300 Eger, Hungary.
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6
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Oliveira AC, Filipe HAL, Geraldes CF, Voth GA, Moreno MJ, Loura LMS. Interaction of MRI Contrast Agent [Gd(DOTA)] - with Lipid Membranes: A Molecular Dynamics Study. Inorg Chem 2024; 63:10897-10914. [PMID: 38795015 PMCID: PMC11186012 DOI: 10.1021/acs.inorgchem.4c00972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/16/2024] [Accepted: 04/30/2024] [Indexed: 05/27/2024]
Abstract
Contrast agents are important imaging probes in clinical MRI, allowing the identification of anatomic changes that otherwise would not be possible. Intensive research on the development of new contrast agents is being made to image specific pathological markers or sense local biochemical changes. The most widely used MRI contrast agents are based on gadolinium(III) complexes. Due to their very high charge density, they have low permeability through tight biological barriers such as the blood-brain barrier, hampering their application in the diagnosis of neurological disorders. In this study, we explore the interaction between the widely used contrast agent [Gd(DOTA)]- (Dotarem) and POPC lipid bilayers by means of molecular dynamics simulations. This metal complex is a standard reference where several chemical modifications have been introduced to improve key properties such as bioavailability and targeting. The simulations unveil detailed insights into the agent's interaction with the lipid bilayer, offering perspectives beyond experimental methods. Various properties, including the impact on global and local bilayer properties, were analyzed. As expected, the results indicate a low partition coefficient (KP) and high permeation barrier for this reference compound. Nevertheless, favorable interactions are established with the membrane leading to moderately long residence times. While coordination of one inner-sphere water molecule is maintained for the membrane-associated chelate, the physical-chemical attributes of [Gd(DOTA)]- as a MRI contrast agent are affected. Namely, increases in the rotational correlation times and in the residence time of the inner-sphere water are observed, with the former expected to significantly increase the water proton relaxivity. This work establishes a reference framework for the use of simulations to guide the rational design of new contrast agents with improved relaxivity and bioavailability and for the development of liposome-based formulations for use as imaging probes or theranostic agents.
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Affiliation(s)
- Alexandre C. Oliveira
- Coimbra
Chemistry Centre, Institute of Molecular
Sciences (CQC-IMS), 3004-535 Coimbra, Portugal
- Department
of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Hugo A. L. Filipe
- Coimbra
Chemistry Centre, Institute of Molecular
Sciences (CQC-IMS), 3004-535 Coimbra, Portugal
- CPIRN-IPG—Center
of Potential and Innovation of Natural Resources, Polytechnic Institute of Guarda, 6300-559 Guarda, Portugal
| | - Carlos F.G.C. Geraldes
- Coimbra
Chemistry Centre, Institute of Molecular
Sciences (CQC-IMS), 3004-535 Coimbra, Portugal
- Department
of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-393 Coimbra, Portugal
- CIBIT/ICNAS
- Instituto de Ciências Nucleares Aplicadas à Saúde, Pólo das Ciências
da Saúde, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal
| | - Gregory A. Voth
- Department
of Chemistry, Chicago Center for Theoretical Chemistry, James Franck
Institute, and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, United States
| | - Maria João Moreno
- Coimbra
Chemistry Centre, Institute of Molecular
Sciences (CQC-IMS), 3004-535 Coimbra, Portugal
- Department
of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
- CNC−Center
for Neuroscience and Cell Biology, University
of Coimbra, 3004-517 Coimbra, Portugal
| | - Luís M. S. Loura
- Coimbra
Chemistry Centre, Institute of Molecular
Sciences (CQC-IMS), 3004-535 Coimbra, Portugal
- Faculty
of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
- CNC−Center
for Neuroscience and Cell Biology, University
of Coimbra, 3004-517 Coimbra, Portugal
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7
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Hartke B. On the brink of self-hydration: the water heptadecamer. Phys Chem Chem Phys 2024; 26:15445-15451. [PMID: 38747364 DOI: 10.1039/d4cp00816b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
For pure, neutral, isolated molecular clusters, (H2O)17 marks the transition from structures with all water molecules on the cluster surface to water self-hydration, i.e., cluster structures around one central water molecule. Getting this right with water model potentials turns out to be challenging. Even the best water potentials currently available, which reproduce collective properties very well, still deliver contradicting results for (H2O)17, when different low-energy isomers from global structure optimizations are examined. Interestingly, ab initio quantum chemistry also struggles with the only seemingly simple question if (H2O)17 is all-surface or water-centered. Hence, although the long history of water potential development may be entering its final phase, it is not quite finished yet.
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Affiliation(s)
- Bernd Hartke
- Institute for Physical Chemistry, Kiel University, 24118 Kiel, Germany.
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8
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Akshat R, Bharti A, Padmanabhan P. Atomistic molecular dynamics simulation and COSMO-SAC approach for enhanced 1,3-propanediol extraction with imidazolium-based ionic liquids. J Mol Model 2024; 30:164. [PMID: 38733431 DOI: 10.1007/s00894-024-05964-7] [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: 01/11/2024] [Accepted: 05/03/2024] [Indexed: 05/13/2024]
Abstract
CONTEXT 1,3-Propanediol (1,3-PDO) is a key chemical in various industries, including pharmaceuticals and material sciences, and is projected to see significant market growth. However, the current challenges in its downstream processing, particularly in terms of cost and efficiency, highlight the need for innovative solutions. Our study delves into using ionic liquids (ILs) as a potential alternative, aiming to address these critical separation challenges more sustainably and efficiently. In this study, we utilized molecular dynamics (MD) simulations and the COSMO-SAC to examine 1,3-propanediol (1,3-PDO) extraction using four imidazolium-based ionic liquids with 1-butyl-3-methylimidazolium [Bmim] cation and with different anions bis(pentafluoroethanesulfonyl)imide [NPF2]-, bis(trifluoromethylsulfonyl)imide [NTF2]-, thiocyanate [SCN]-, and trifluoromethanesulfonate [TFO]-. Molecular dynamics simulations, incorporating analysis of radial distribution functions (RDF) and spatial distribution functions (SDF), revealed that [Bmim][SCN] and [Bmim][TFO] exhibit enhanced interactions with 1,3-PDO. Notably, [Bmim][SCN] formed the most hydrogen bonds, averaging 1.639 per molecule, due to its coordinating [SCN]- anion. This was in contrast to the fewer hydrogen bonds formed by non-coordinating anions in [Bmim][NPF2] and [Bmim][NTF2]. In ternary systems, [Bmim][SCN] and [Bmim][TFO] demonstrated superior selectivity for 1,3-PDO extraction compared to the other ionic liquids, with selectivity values around 29. These findings, supported by COSMO-SAC predictive modeling, highlight the potential of [Bmim][SCN] as a promising candidate for 1,3-PDO extraction, emphasizing the importance of anion selection in optimizing ionic liquid properties for this application. METHODS In our study, we employed MD simulations, incorporating the OPLS-AA force field, and COSMO-SAC to investigate the extraction of 1,3-PDO using imidazolium-based ionic liquids: [Bmim][NTF2], [Bmim][NPF2], [Bmim][SCN], and [Bmim][TFO]. The MD simulations were conducted using LAMMPS software, focusing on elucidating the RDF, SDF, and hydrogen bonding. Analysis of the distribution coefficient (β) and selectivity (S) for the ternary mixture was also conducted. These aspects of the simulation were analyzed using TRAVIS and VMD software. Additionally, the COSMO-SAC model was employed to determine the activity coefficients of 1,3-PDO in the ionic liquids, with molecular optimization conducted using Gaussian16 and sigma profile calculations performed using COSMO-SAC.
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Affiliation(s)
- Raj Akshat
- Department of Bioengineering and Biotechnology, Birla Institute of Technology Mesra, Ranchi, Jharkhand, 835215, India
| | - Anand Bharti
- Department of Chemical Engineering, Birla Institute of Technology, Ranchi, Jharkhand, 835215, India.
| | - Padmini Padmanabhan
- Department of Bioengineering and Biotechnology, Birla Institute of Technology Mesra, Ranchi, Jharkhand, 835215, India.
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9
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Habibi P, Polat HM, Blazquez S, Vega C, Dey P, Vlugt TJH, Moultos OA. Accurate Free Energies of Aqueous Electrolyte Solutions from Molecular Simulations with Non-polarizable Force Fields. J Phys Chem Lett 2024; 15:4477-4485. [PMID: 38634502 PMCID: PMC11057036 DOI: 10.1021/acs.jpclett.4c00428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 04/19/2024]
Abstract
Non-polarizable force fields fail to accurately predict free energies of aqueous electrolytes without compromising the predictive ability for densities and transport properties. A new approach is presented in which (1) TIP4P/2005 water and scaled charge force fields are used to describe the interactions in the liquid phase and (2) an additional Effective Charge Surface (ECS) is used to compute free energies at zero additional computational expense. The ECS is obtained using a single temperature-independent charge scaling parameter per species. Thereby, the chemical potential of water and the free energies of hydration of various aqueous salts (e.g., NaCl and LiCl) are accurately described (deviations less than 5% from experiments), in sharp contrast to calculations where the ECS is omitted (deviations larger than 20%). This approach enables accurate predictions of free energies of aqueous electrolyte solutions using non-polarizable force fields, without compromising liquid-phase properties.
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Affiliation(s)
- Parsa Habibi
- Engineering
Thermodynamics, Process & Energy Department, Faculty of Mechanical
Engineering, Delft University of Technology, Leeghwaterstraat 39, 2628 CB Delft, Netherlands
- Department
of Materials Science and Engineering, Faculty of Mechanical Engineering, Delft University of Technology, Mekelweg 2, 2628 CD Delft, Netherlands
| | - H. Mert Polat
- Engineering
Thermodynamics, Process & Energy Department, Faculty of Mechanical
Engineering, Delft University of Technology, Leeghwaterstraat 39, 2628 CB Delft, Netherlands
| | - Samuel Blazquez
- Departamento
de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Carlos Vega
- Departamento
de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Poulumi Dey
- Department
of Materials Science and Engineering, Faculty of Mechanical Engineering, Delft University of Technology, Mekelweg 2, 2628 CD Delft, Netherlands
| | - Thijs J. H. Vlugt
- Engineering
Thermodynamics, Process & Energy Department, Faculty of Mechanical
Engineering, Delft University of Technology, Leeghwaterstraat 39, 2628 CB Delft, Netherlands
| | - Othonas A. Moultos
- Engineering
Thermodynamics, Process & Energy Department, Faculty of Mechanical
Engineering, Delft University of Technology, Leeghwaterstraat 39, 2628 CB Delft, Netherlands
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10
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Muthachikavil AV, Sun G, Peng B, Tanaka H, Kontogeorgis GM, Liang X. Unraveling thermodynamic anomalies of water: A molecular simulation approach to probe the two-state theory with atomistic and coarse-grained water models. J Chem Phys 2024; 160:154505. [PMID: 38624123 DOI: 10.1063/5.0194036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/19/2024] [Indexed: 04/17/2024] Open
Abstract
Thermodynamic and dynamic anomalies of water play a crucial role in supporting life on our planet. The two-state theory attributes these anomalies to a dynamic equilibrium between locally favored tetrahedral structures (LFTSs) and disordered normal liquid structures. This theory provides a straightforward, phenomenological explanation for water's unique thermodynamic and dynamic characteristics. To validate this two-state feature, it is critical to unequivocally identify these structural motifs in a dynamically fluctuating disordered liquid. In this study, we employ a recently introduced structural parameter (θavg) that characterizes the local angular order within the first coordination shell to identify these LFTSs through molecular dynamics simulations. We employ both realistic water models with a liquid-liquid critical point (LLCP) and a coarse-grained water model without an LLCP to study water's anomalies in low-pressure regions below 2 kbar. The two-state theory consistently describes water's thermodynamic anomalies in these models, both with and without an LLCP. This suggests that the anomalies predominantly result from the two-state features rather than criticality, particularly within experimentally accessible temperature-pressure regions.
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Affiliation(s)
- Aswin V Muthachikavil
- Department of Chemical and Biochemical Engineering, Center for Energy Resources Engineering, Technical University of Denmark, Building 229, Lyngby DK-2800, Denmark
| | - Gang Sun
- Department of Physics, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
| | - Baoliang Peng
- Research Institute of Petroleum Exploration & Development (RIPED), PetroChina, Beijing 100083, China
| | - Hajime Tanaka
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Georgios M Kontogeorgis
- Department of Chemical and Biochemical Engineering, Center for Energy Resources Engineering, Technical University of Denmark, Building 229, Lyngby DK-2800, Denmark
| | - Xiaodong Liang
- Department of Chemical and Biochemical Engineering, Center for Energy Resources Engineering, Technical University of Denmark, Building 229, Lyngby DK-2800, Denmark
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11
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Zhai Y, Rashmi R, Palos E, Paesani F. Many-body interactions and deep neural network potentials for water. J Chem Phys 2024; 160:144501. [PMID: 38587225 DOI: 10.1063/5.0203682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 03/23/2024] [Indexed: 04/09/2024] Open
Abstract
We present a detailed assessment of deep neural network potentials developed within the Deep Potential Molecular Dynamics (DeePMD) framework and trained on the MB-pol data-driven many-body potential energy function. Specific focus is directed at the ability of DeePMD-based potentials to correctly reproduce the accuracy of MB-pol across various water systems. Analyses of bulk and interfacial properties as well as many-body interactions characteristic of water elucidate inherent limitations in the transferability and predictive accuracy of DeePMD-based potentials. These limitations can be traced back to an incomplete implementation of the "nearsightedness of electronic matter" principle, which may be common throughout machine learning potentials that do not include a proper representation of self-consistently determined long-range electric fields. These findings provide further support for the "short-blanket dilemma" faced by DeePMD-based potentials, highlighting the challenges in achieving a balance between computational efficiency and a rigorous, physics-based representation of the properties of water. Finally, we believe that our study contributes to the ongoing discourse on the development and application of machine learning models in simulating water systems, offering insights that could guide future improvements in the field.
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Affiliation(s)
- Yaoguang Zhai
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA
| | - Richa Rashmi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Etienne Palos
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
- Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, USA
- Halicioğlu Data Science Institute, University of California San Diego, La Jolla, California 92093, USA
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, USA
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12
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Frischknecht AL, Stevens MJ. Force Fields for High Concentration Aqueous KOH Solutions and Zincate Ions. J Phys Chem B 2024; 128:3475-3484. [PMID: 38547112 DOI: 10.1021/acs.jpcb.3c08302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Motivated by increasing interest in electrochemical devices that include highly alkaline electrolytes, we investigated two force fields for potassium hydroxide (KOH) at high concentrations in water. The "FNB" model uses the SPC/E water model, while the "FHM" model uses the TIP4P/2005 water model. We also developed parameters to describe zincate ions in these solutions. The density and viscosity of KOH using the FHM model are in better agreement with experiment than the values from the FNB model. Comparing the properties of the zincate solutions to the available experimental data, we find that both force fields agree reasonably well, although the FHM parameters give a better prediction of the viscosity. The developed force field parameters can be used in future simulations of zincate/KOH solutions in combination with other species of interest.
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Affiliation(s)
- Amalie L Frischknecht
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
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13
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Mortara L, Mukhina T, Chaimovich H, Brezesinski G, van der Vegt NFA, Schneck E. Anion Competition at Positively Charged Surfactant Monolayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:6949-6961. [PMID: 38502024 DOI: 10.1021/acs.langmuir.3c04003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Interactions of anions with hydrophobic surfaces of proteins and water-soluble polymers depend on the ability of the ions to shed their hydration shells. At positively charged surfactant monolayers, the interactions of anions are less well understood. Due to the interplay of electrostatic surface forces, hydration effects, and ion-ion interactions in the electrostatic double layer, a comprehensive microscopic picture remains elusive. Herein, we study the interactions of chloride, bromide, and a mixture of these two anions at the aqueous interface of dihexadecyldimethylammonium (DHDA+) and dioctadecyldimethylammonium (DODA+) cationic monolayers. Using molecular dynamics simulations and three surface-sensitive X-ray scattering techniques, we demonstrate that bromide interacts preferentially over chloride with both monolayers. The structure of the two monolayers and their interfacial electron density profiles obtained from the simulations quantitatively reproduce the experimental data. We observe that chloride and bromide form contact ion pairs with the quaternary ammonium groups on both monolayers. However, ion pairing with bromide leads to a greater reduction in the number of water molecules hydrating the anion, resulting in more energetically stable ion pairs. This leads to long-range (>3 nm) lateral correlations between bromide ions on the structured DODA+ monolayer. These observations indicate that ion hydration is the dominant factor determining the interfacial electrolyte structure.
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Affiliation(s)
- Laura Mortara
- Chemistry Institute, University of São Paulo, São Paulo, SP 05508-000, Brazil
- Physics Department, Technical University of Darmstadt, Darmstadt 64289, Germany
| | - Tetiana Mukhina
- Physics Department, Technical University of Darmstadt, Darmstadt 64289, Germany
| | - Hernan Chaimovich
- Chemistry Institute, University of São Paulo, São Paulo, SP 05508-000, Brazil
| | - Gerald Brezesinski
- Physics Department, Technical University of Darmstadt, Darmstadt 64289, Germany
| | | | - Emanuel Schneck
- Physics Department, Technical University of Darmstadt, Darmstadt 64289, Germany
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14
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Villard J, Bircher MP, Rothlisberger U. Structure and dynamics of liquid water from ab initio simulations: adding Minnesota density functionals to Jacob's ladder. Chem Sci 2024; 15:4434-4451. [PMID: 38516095 PMCID: PMC10952088 DOI: 10.1039/d3sc05828j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/12/2024] [Indexed: 03/23/2024] Open
Abstract
The accurate representation of the structural and dynamical properties of water is essential for simulating the unique behavior of this ubiquitous solvent. Here we assess the current status of describing liquid water using ab initio molecular dynamics, with a special focus on the performance of all the later generation Minnesota functionals. Findings are contextualized within the current knowledge on DFT for describing bulk water under ambient conditions and compared to experimental data. We find that, contrary to the prevalent idea that local and semilocal functionals overstructure water and underestimate dynamical properties, M06-L, revM06-L, and M11-L understructure water, while MN12-L and MN15-L overdistance water molecules due to weak cohesive effects. This can be attributed to a weakening of the hydrogen bond network, which leads to dynamical fingerprints that are over fast. While most of the hybrid Minnesota functionals (M06, M08-HX, M08-SO, M11, MN12-SX, and MN15) also yield understructured water, their dynamical properties generally improve over their semilocal counterparts. It emerges that exact exchange is a crucial component for accurately describing hydrogen bonds, which ultimately leads to corrections in both the dynamical and structural properties. However, an excessive amount of exact exchange strengthens hydrogen bonds and causes overstructuring and slow dynamics (M06-HF). As a compromise, M06-2X is the best performing Minnesota functional for water, and its D3 corrected variant shows very good structural agreement. From previous studies considering nuclear quantum effects (NQEs), the hybrid revPBE0-D3, and the rung-5 RPA (RPA@PBE) have been identified as the only two approximations that closely agree with experiments. Our results suggest that the M06-2X(-D3) functionals have the potential to further improve the reproduction of experimental properties when incorporating NQEs through path integral approaches. This work provides further proof that accurate modeling of water interactions requires the inclusion of both exact exchange and balanced (non-local) correlation, highlighting the need for higher rungs on Jacob's ladder to achieve predictive simulations of complex biological systems in aqueous environments.
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Affiliation(s)
- Justin Villard
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL) Lausanne CH-1015 Switzerland
| | - Martin P Bircher
- Computational and Soft Matter Physics, Universität Wien Wien A-1090 Austria
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL) Lausanne CH-1015 Switzerland
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15
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Cruces Chamorro V, Jungwirth P, Martinez-Seara H. Building Water Models Compatible with Charge Scaling Molecular Dynamics. J Phys Chem Lett 2024; 15:2922-2928. [PMID: 38451169 PMCID: PMC10945568 DOI: 10.1021/acs.jpclett.4c00344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 02/29/2024] [Accepted: 03/04/2024] [Indexed: 03/08/2024]
Abstract
Charge scaling has proven to be an efficient way to account in a mean-field manner for electronic polarization by aqueous ions in force field molecular dynamics simulations. However, commonly used water models with dielectric constants over 50 are not consistent with this approach leading to "overscaling", i.e., generally too weak ion-ion interactions. Here, we build water models fully compatible with charge scaling, i.e., having the correct low-frequency dielectric constant of about 45. To this end, we employ advanced optimization and machine learning schemes in order to explore the vast parameter space of four-site water models efficiently. As an a priori unwarranted positive result, we find a sizable range of force field parameters that satisfy the above dielectric constant constraint providing at the same time accuracy with respect to experimental data comparable with the best existing four-site water models such as TIP4P/2005, TIP4P-FB, or OPC. The present results thus open the way to the development of a consistent charge scaling force field for modeling ions in aqueous solutions.
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Affiliation(s)
- Victor Cruces Chamorro
- Institute of Organic Chemistry and
Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and
Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and
Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
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16
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Takayama T, Otosu T, Yamaguchi S. Theoretical and experimental OD-stretch vibrational spectroscopy of heavy water. J Chem Phys 2024; 160:104504. [PMID: 38465684 DOI: 10.1063/5.0200623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 02/22/2024] [Indexed: 03/12/2024] Open
Abstract
In view of the current situation in which the OD-stretch vibrational spectra have been scarcely computed with non-polarizable rigid D2O models, we investigate the IR and Raman spectra of D2O by using a newly-reported model TIP4P/2005-HW. From the comparison between the calculations and experimental data, we find the excellent performance of TIP4P/2005-HW for vibrational spectroscopy of D2O in the same manner as TIP4P/2005 for H2O, although one may still conveniently employ an alternative method that regards OH as putative OD to calculate the OD-stretch spectra with similar quality from TIP4P/2005 trajectories. We also demonstrate that the appropriate setting for the spectral simulation of D2O under the time-averaging approximation reflects the slower dynamics (i.e., slower motion of translation and rotation due to the heavier mass and stronger hydrogen bond) of D2O than H2O. Moreover, we show from the theoretical calculations that the established interpretation of the OH-stretch spectra of H2O is finely applicable to the OD-stretch of D2O.
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Affiliation(s)
- Tetsuyuki Takayama
- Department of Applied Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura, Saitama 338-8570, Japan
| | - Takuhiro Otosu
- Department of Applied Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura, Saitama 338-8570, Japan
| | - Shoichi Yamaguchi
- Department of Applied Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura, Saitama 338-8570, Japan
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17
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Quoika PK, Zacharias M. Liquid-Vapor Coexistence and Spontaneous Evaporation at Atmospheric Pressure of Common Rigid Three-Point Water Models in Molecular Simulations. J Phys Chem B 2024; 128:2457-2468. [PMID: 38427971 PMCID: PMC10945489 DOI: 10.1021/acs.jpcb.3c08183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/03/2024]
Abstract
Molecular dynamics (MD) simulations are widely used to investigate molecular systems at atomic resolution including biomolecular structures, drug-receptor interactions, and novel materials. Frequently, MD simulations are performed in an aqueous solution with explicit models of water molecules. Commonly, such models are parameterized to reproduce the liquid phase of water under ambient conditions. However, often, simulations at significantly higher temperatures are also of interest. Hence, it is important to investigate the equilibrium of the liquid and vapor phases of molecular models of water at elevated temperatures. Here, we evaluate the behavior of 11 common rigid three-point water models over a wide range of temperatures. From liquid-vapor coexistence simulations, we estimated the critical points and studied the spontaneous evaporation of these water models. Moreover, we investigated the influence of the system size, choice of the pressure-coupling algorithm, and rate of heating on the process and compared them with the experimental data. We found that modern rigid three-point water models reproduce the critical point surprisingly well. Furthermore, we discovered that the critical temperature correlates with the quadrupole moment of the respective water model. This indicates that the spatial arrangement of the partial charges is important for reproducing the liquid-vapor phase transition. Our findings may guide the selection of water models for simulations conducted at high temperatures.
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Affiliation(s)
- Patrick K. Quoika
- Center for Functional Protein
Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, Garching 85748, Germany
| | - Martin Zacharias
- Center for Functional Protein
Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, Garching 85748, Germany
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18
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Frank HO, Paesani F. Molecular driving forces for water adsorption in MOF-808: A comparative analysis with UiO-66. J Chem Phys 2024; 160:094703. [PMID: 38426523 DOI: 10.1063/5.0189569] [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: 02/12/2024] [Indexed: 03/02/2024] Open
Abstract
Metal-organic frameworks (MOFs), with their unique porous structures and versatile functionality, have emerged as promising materials for the adsorption, separation, and storage of diverse molecular species. In this study, we investigate water adsorption in MOF-808, a prototypical MOF that shares the same secondary building unit (SBU) as UiO-66, and elucidate how differences in topology and connectivity between the two MOFs influence the adsorption mechanism. To this end, molecular dynamics simulations were performed to calculate several thermodynamic and dynamical properties of water in MOF-808 as a function of relative humidity (RH), from the initial adsorption step to full pore filling. At low RH, the μ3-OH groups of the SBUs form hydrogen bonds with the initial water molecules entering the pores, which triggers the filling of these pores before the μ3-OH groups in other pores become engaged in hydrogen bonding with water molecules. Our analyses indicate that the pores of MOF-808 become filled by water sequentially as the RH increases. A similar mechanism has been reported for water adsorption in UiO-66. Despite this similarity, our study highlights distinct thermodynamic properties and framework characteristics that influence the adsorption process differently in MOF-808 and UiO-66.
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Affiliation(s)
- Hilliary O Frank
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
- Materials Science and Engineering, University of California, San Diego, La Jolla, California 92093, USA
- Halicioğlu Data Science Institute, University of California, San Diego, La Jolla, California 92093, USA
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, California 92093, USA
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19
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Dohnalová H, Matoušková E, Lankaš F. Temperature-dependent elasticity of DNA, RNA, and hybrid double helices. Biophys J 2024; 123:572-583. [PMID: 38340722 PMCID: PMC10938081 DOI: 10.1016/j.bpj.2024.01.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 12/19/2023] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
Nucleic acid double helices in their DNA, RNA, and DNA-RNA hybrid form play a fundamental role in biology and are main building blocks of artificial nanostructures, but how their properties depend on temperature remains poorly understood. Here, we report thermal dependence of dynamic bending persistence length, twist rigidity, stretch modulus, and twist-stretch coupling for DNA, RNA, and hybrid duplexes between 7°C and 47°C. The results are based on all-atom molecular dynamics simulations using different force field parameterizations. We first demonstrate that unrestrained molecular dynamics can reproduce experimentally known mechanical properties of the duplexes at room temperature. Beyond experimentally known features, we also infer the twist rigidity and twist-stretch coupling of the hybrid duplex. As for the temperature dependence, we found that increasing temperature softens all the duplexes with respect to bending, twisting, and stretching. The relative decrease of the stretch moduli is 0.003-0.004/°C, similar for all the duplex variants despite their very different stretching stiffness, whereas RNA twist stiffness decreases by 0.003/°C, and smaller values are found for the other elastic moduli. The twist-stretch couplings are nearly unaffected by temperature. The stretching, bending, and twisting stiffness all include an important entropic component. Relation of our results to the two-state model of DNA flexibility is discussed. Our work provides temperature-dependent elasticity of nucleic acid duplexes at the microsecond scale relevant for initial stages of protein binding.
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Affiliation(s)
- Hana Dohnalová
- Department of Informatics and Chemistry, University of Chemistry and Technology Prague, Praha 6, Czech Republic
| | - Eva Matoušková
- Department of Informatics and Chemistry, University of Chemistry and Technology Prague, Praha 6, Czech Republic
| | - Filip Lankaš
- Department of Informatics and Chemistry, University of Chemistry and Technology Prague, Praha 6, Czech Republic.
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20
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Paschek D, Busch J, Mock E, Ludwig R, Strate A. Computing the frequency-dependent NMR relaxation of 1H nuclei in liquid water. J Chem Phys 2024; 160:074102. [PMID: 38364003 DOI: 10.1063/5.0191052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 01/23/2024] [Indexed: 02/18/2024] Open
Abstract
We present a computational framework for reliably determining the frequency-dependent intermolecular and intramolecular nuclear magnetic resonance (NMR) dipole-dipole relaxation rates of spin 1/2 nuclei from Molecular Dynamics (MD) simulations. This approach avoids the alterations caused by the well-known finite-size effects of translational diffusion. Moreover, a procedure is derived to control and correct for effects caused by fixed distance-sampling cutoffs and periodic boundary conditions. By construction, this approach is capable of accurately predicting the correct low-frequency scaling behavior of the intermolecular NMR dipole-dipole relaxation rate and thus allows for the reliable calculation of the frequency-dependent relaxation rate over many orders of magnitude. Our approach is based on the utilization of the theory of Hwang and Freed for the intermolecular dipole-dipole correlation function and its corresponding spectral density [L.-P. Hwang and J. H. Freed, J. Chem. Phys. 63, 4017-4025 (1975)] and its combination with data from MD simulations. The deviations from the Hwang and Freed theory caused by periodic boundary conditions and sampling distance cutoffs are quantified by means of random walker Monte Carlo simulations. An expression based on the Hwang and Freed theory is also suggested for correcting those effects. As a proof of principle, our approach is demonstrated by computing the frequency-dependent intermolecular and intramolecular dipolar NMR relaxation rates of 1H nuclei in liquid water at 273 and 298 K based on the simulations of the TIP4P/2005 model. Our calculations are suggesting that the intermolecular contribution to the 1H NMR relaxation rate of the TIP4P/2005 model in the extreme narrowing limit has previously been substantially underestimated.
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Affiliation(s)
- Dietmar Paschek
- Institut für Chemie, Abteilung Physikalische und Theoretische Chemie, Universität Rostock, Albert-Einstein-Str. 27, D-18059 Rostock, Germany
| | - Johanna Busch
- Institut für Chemie, Abteilung Physikalische und Theoretische Chemie, Universität Rostock, Albert-Einstein-Str. 27, D-18059 Rostock, Germany
| | - Eduard Mock
- Institut für Chemie, Abteilung Physikalische und Theoretische Chemie, Universität Rostock, Albert-Einstein-Str. 27, D-18059 Rostock, Germany
| | - Ralf Ludwig
- Institut für Chemie, Abteilung Physikalische und Theoretische Chemie, Universität Rostock, Albert-Einstein-Str. 27, D-18059 Rostock, Germany
- Leibniz-Institut für Katalyse an der Universität Rostock e.V., Albert-Einstein-Str. 29a, D-18059 Rostock, Germany
- Department Life, Light & Matter, Universität Rostock, Albert-Einstein-Str. 25, D-18059 Rostock, Germany
| | - Anne Strate
- Institut für Chemie, Abteilung Physikalische und Theoretische Chemie, Universität Rostock, Albert-Einstein-Str. 27, D-18059 Rostock, Germany
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21
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van Rooijen WA, Habibi P, Xu K, Dey P, Vlugt TJH, Hajibeygi H, Moultos OA. Interfacial Tensions, Solubilities, and Transport Properties of the H 2/H 2O/NaCl System: A Molecular Simulation Study. JOURNAL OF CHEMICAL AND ENGINEERING DATA 2024; 69:307-319. [PMID: 38352074 PMCID: PMC10859954 DOI: 10.1021/acs.jced.2c00707] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 12/23/2022] [Indexed: 02/16/2024]
Abstract
Data for several key thermodynamic and transport properties needed for technologies using hydrogen (H2), such as underground H2 storage and H2O electrolysis are scarce or completely missing. Force field-based Molecular Dynamics (MD) and Continuous Fractional Component Monte Carlo (CFCMC) simulations are carried out in this work to cover this gap. Extensive new data sets are provided for (a) interfacial tensions of H2 gas in contact with aqueous NaCl solutions for temperatures of (298 to 523) K, pressures of (1 to 600) bar, and molalities of (0 to 6) mol NaCl/kg H2O, (b) self-diffusivities of infinitely diluted H2 in aqueous NaCl solutions for temperatures of (298 to 723) K, pressures of (1 to 1000) bar, and molalities of (0 to 6) mol NaCl/kg H2O, and (c) solubilities of H2 in aqueous NaCl solutions for temperatures of (298 to 363) K, pressures of (1 to 1000) bar, and molalities of (0 to 6) mol NaCl/kg H2O. The force fields used are the TIP4P/2005 for H2O, the Madrid-2019 and the Madrid-Transport for NaCl, and the Vrabec and Marx for H2. Excellent agreement between the simulation results and available experimental data is found with average deviations lower than 10%.
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Affiliation(s)
- W. A. van Rooijen
- Reservoir
Engineering, Geoscience and Engineering Department, Faculty of Civil
Engineering and Geosciences, Delft University
of Technology, Stevinweg 1, 2628CN, Delft, The Netherlands
| | - P. Habibi
- Engineering
Thermodynamics, Process and Energy Department, Faculty of Mechanical,
Maritime and Materials Engineering, Delft
University of Technology, Leeghwaterstraat 39, 2628CB, Delft, The Netherlands
- Department
of Materials Science and Engineering, Faculty of Mechanical, Maritime
and Materials Engineering, Delft University
of Technology, Mekelweg
2, 2628CD, Delft, The Netherlands
| | - K. Xu
- Department
of Materials Science and Engineering, Faculty of Mechanical, Maritime
and Materials Engineering, Delft University
of Technology, Mekelweg
2, 2628CD, Delft, The Netherlands
| | - P. Dey
- Department
of Materials Science and Engineering, Faculty of Mechanical, Maritime
and Materials Engineering, Delft University
of Technology, Mekelweg
2, 2628CD, Delft, The Netherlands
| | - T. J. H. Vlugt
- Engineering
Thermodynamics, Process and Energy Department, Faculty of Mechanical,
Maritime and Materials Engineering, Delft
University of Technology, Leeghwaterstraat 39, 2628CB, Delft, The Netherlands
| | - H. Hajibeygi
- Reservoir
Engineering, Geoscience and Engineering Department, Faculty of Civil
Engineering and Geosciences, Delft University
of Technology, Stevinweg 1, 2628CN, Delft, The Netherlands
| | - O. A. Moultos
- Engineering
Thermodynamics, Process and Energy Department, Faculty of Mechanical,
Maritime and Materials Engineering, Delft
University of Technology, Leeghwaterstraat 39, 2628CB, Delft, The Netherlands
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22
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Busch J, Paschek D. Computing Accurate True Self-Diffusion Coefficients and Shear Viscosities Using the OrthoBoXY Approach. J Phys Chem B 2024; 128:1040-1052. [PMID: 38240259 DOI: 10.1021/acs.jpcb.3c07540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
In a recent paper [Busch, J.; Paschek, D. J. Phys. Chem. B 2023, 127, 7983-7987], we have shown that for molecular dynamics (MD) simulations using orthorhombic periodic boundary conditions with "magic" box length ratios of Lz/Lx = Lz/Ly = 2.7933596497, the self-diffusion coefficients Dx and Dy in x- and y-directions are independent of the system size. They both represent the true self-diffusion coefficient D0 = (Dx + Dy)/2, while the shear viscosity can be calculated from diffusion coefficients in x-, y-, and z-directions, using η = kBT·8.1711245653/[3πLz(Dx + Dy - 2Dz)]. In this contribution, we test this "OrthoBoXY" approach by its application to a variety of different systems: liquid water, dimethyl ether, methanol, triglyme, water/methanol mixtures, water/triglyme mixtures, and imidazolium-based ionic liquids. The chosen systems range from small-sized molecular liquids to complex mixtures and ionic liquids, while spanning a viscosity range of almost 3 orders of magnitude. We assess the efficiency of the method for computing true self-diffusion and viscosity data and provide simple formulas for estimating the required MD simulation lengths and sizes for delivering reliable data with targeted uncertainty levels. Our analysis of the system size dependence of statistical uncertainties for both the viscosity and the self-diffusion coefficient leads us to the conclusion that it is preferable to extend the simulation length instead of increasing the system size. MD simulations consisting of 768 molecules or ion pairs seem to be perfectly adequate.
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Affiliation(s)
- Johanna Busch
- Institut für Chemie, Abteilung Physikalische und Theoretische Chemie, Universität Rostock, Albert-Einstein-Str. 27, D-18059 Rostock, Germany
| | - Dietmar Paschek
- Institut für Chemie, Abteilung Physikalische und Theoretische Chemie, Universität Rostock, Albert-Einstein-Str. 27, D-18059 Rostock, Germany
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23
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Blazquez S, Bourg IC, Vega C. Madrid-2019 force field: An extension to divalent cations Sr2+ and Ba2. J Chem Phys 2024; 160:046101. [PMID: 38270237 DOI: 10.1063/5.0186233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 12/27/2023] [Indexed: 01/26/2024] Open
Abstract
In this work, we present a parameterization of Sr2+ and Ba2+ cations, which expands the alkali earth set of cations of the Madrid-2019 force field. We have tested the model against the experimental densities of eight different salts, namely, SrCl2, SrBr2, SrI2, Sr(NO3)2, BaCl2, BaBr2, BaI2, and Ba(NO3)2. The force field is able to reproduce the experimental densities of all these salts up to their solubility limit. Furthermore, we have computed the viscosities for two selected salts, finding that the experimental values are overestimated, but the predictions are still reasonable. Finally, the structural properties for all the salts have been calculated with this model and align remarkably well with experimental observations.
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Affiliation(s)
- S Blazquez
- Dpto. Química Física I, Fac. Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Ian C Bourg
- Department of Civil and Environmental Engineering, Princeton University, Princeton, New Jersey 08544, USA
- High Meadows Environmental Institute, Princeton University, Princeton, New Jersey 08544, USA
| | - C Vega
- Dpto. Química Física I, Fac. Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
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24
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Busch J, Paschek D. An OrthoBoXY-method for various alternative box geometries. Phys Chem Chem Phys 2024; 26:2907-2914. [PMID: 38086638 DOI: 10.1039/d3cp04916g] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
We have shown in a recent contribution [Busch and Paschek, J. Phys. Chem. B, 2023 127, 7983-7987] that for molecular dynamics (MD) simulations of isotropic fluids based on orthorhombic periodic boundary conditions with "magical" box length ratios of Lz/Lx = Lz/Ly = 2.7933596497, the computed self-diffusion coefficients Dx and Dy in x- and y-direction become system size independent. They thus represent the true self-diffusion coefficient D0 = (Dx + Dy)/2, while the shear viscosity can be determined from diffusion coefficients in x-, y-, and z-direction, using the expression η = kBT·8.1711245653/[3πLz(Dx + Dy - 2Dz)]. Here we present a more generalized version of this "OrthoBoXY"-approach, which can be applied to any orthorhombic MD box of any shape. In particular, we would like to test, how the efficiency is affected by using a shape more akin to the cubic form, albeit with different box length ratios Lx/Lz ≠ Ly/Lz and Lx < Ly < Lz. We use NVT and NpT simulations of systems of 1536 TIP4P/2005 water molecules as a benchmark and explore different box geometries to determine the influence of the box shape on the computed statistical uncertainties for D0 and η. Moreover, another "magical" set of box length ratios is discovered with Ly/Lz = 0.57804765578 and Lx/Lz = 0.33413909235, where the self-diffusion coefficient in x-direction becomes system size independent, such that D0 = Dx.
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Affiliation(s)
- Johanna Busch
- Institut für Chemie, Abteilung Physikalische und Theoretische Chemie, Universität Rostock, Albert-Einstein-Straße 27, D-18059 Rostock, Germany.
| | - Dietmar Paschek
- Institut für Chemie, Abteilung Physikalische und Theoretische Chemie, Universität Rostock, Albert-Einstein-Straße 27, D-18059 Rostock, Germany.
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25
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Bass L, Elder LH, Folescu DE, Forouzesh N, Tolokh IS, Karpatne A, Onufriev AV. Improving the Accuracy of Physics-Based Hydration-Free Energy Predictions by Machine Learning the Remaining Error Relative to the Experiment. J Chem Theory Comput 2024; 20:396-410. [PMID: 38149593 PMCID: PMC10950260 DOI: 10.1021/acs.jctc.3c00981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
The accuracy of computational models of water is key to atomistic simulations of biomolecules. We propose a computationally efficient way to improve the accuracy of the prediction of hydration-free energies (HFEs) of small molecules: the remaining errors of the physics-based models relative to the experiment are predicted and mitigated by machine learning (ML) as a postprocessing step. Specifically, the trained graph convolutional neural network attempts to identify the "blind spots" in the physics-based model predictions, where the complex physics of aqueous solvation is poorly accounted for, and partially corrects for them. The strategy is explored for five classical solvent models representing various accuracy/speed trade-offs, from the fast analytical generalized Born (GB) to the popular TIP3P explicit solvent model; experimental HFEs of small neutral molecules from the FreeSolv set are used for the training and testing. For all of the models, the ML correction reduces the resulting root-mean-square error relative to the experiment for HFEs of small molecules, without significant overfitting and with negligible computational overhead. For example, on the test set, the relative accuracy improvement is 47% for the fast analytical GB, making it, after the ML correction, almost as accurate as uncorrected TIP3P. For the TIP3P model, the accuracy improvement is about 39%, bringing the ML-corrected model's accuracy below the 1 kcal/mol threshold. In general, the relative benefit of the ML corrections is smaller for more accurate physics-based models, reaching the lower limit of about 20% relative accuracy gain compared with that of the physics-based treatment alone. The proposed strategy of using ML to learn the remaining error of physics-based models offers a distinct advantage over training ML alone directly on reference HFEs: it preserves the correct overall trend, even well outside of the training set.
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Affiliation(s)
- Lewis Bass
- Department of Computer Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Luke H Elder
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Dan E Folescu
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, United States
- Department of Mathematics, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Negin Forouzesh
- Department of Computer Science, California State University, Los Angeles, California 90032, United States
| | - Igor S Tolokh
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Anuj Karpatne
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Alexey V Onufriev
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, United States
- Department of Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
- Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
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26
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Mejri A, Arroyo N, Herlem G, Palmeri J, Manghi M, Henn F, Picaud F. Impact of Single-Walled Carbon Nanotube Functionalization on Ion and Water Molecule Transport at the Nanoscale. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:117. [PMID: 38202572 PMCID: PMC10780950 DOI: 10.3390/nano14010117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/23/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024]
Abstract
Nanofluidics has a very promising future owing to its numerous applications in many domains. It remains, however, very difficult to understand the basic physico-chemical principles that control the behavior of solvents confined in nanometric channels. Here, water and ion transport in carbon nanotubes is investigated using classical force field molecular dynamics simulations. By combining one single walled carbon nanotube (uniformly charged or not) with two perforated graphene sheets, we mimic single nanopore devices similar to experimental ones. The graphitic edges delimit two reservoirs of water and ions in the simulation cell from which a voltage is imposed through the application of an external electric field. By analyzing the evolution of the electrolyte conductivity, the role of the carbon nanotube geometric parameters (radius and chirality) and of the functionalization of the carbon nanotube entrances with OH or COO- groups is investigated for different concentrations of group functions.
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Affiliation(s)
- Alia Mejri
- Unité de Recherche SINERGIES, UFR Sciences et Techniques, Centre Hospitalier, 16 Route de Gray, 25030 Besançon, France (N.A.); (G.H.)
| | - Nicolas Arroyo
- Unité de Recherche SINERGIES, UFR Sciences et Techniques, Centre Hospitalier, 16 Route de Gray, 25030 Besançon, France (N.A.); (G.H.)
| | - Guillaume Herlem
- Unité de Recherche SINERGIES, UFR Sciences et Techniques, Centre Hospitalier, 16 Route de Gray, 25030 Besançon, France (N.A.); (G.H.)
| | - John Palmeri
- Laboratoire Charles Coulomb (L2C, UMR CNRS 5221), Université Montpellier, Place Eugène Bataillon, 34090 Montpellier, France; (J.P.); (F.H.)
| | - Manoel Manghi
- Laboratoire de Physique Théorique (LPT, UMR CNRS 5152), Université Toulouse III—Paul Sabatier, 31062 Toulouse, France;
| | - François Henn
- Laboratoire Charles Coulomb (L2C, UMR CNRS 5221), Université Montpellier, Place Eugène Bataillon, 34090 Montpellier, France; (J.P.); (F.H.)
| | - Fabien Picaud
- Unité de Recherche SINERGIES, UFR Sciences et Techniques, Centre Hospitalier, 16 Route de Gray, 25030 Besançon, France (N.A.); (G.H.)
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27
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Feng Z, Lei Z, Yao Y, Liu J, Wu B, Ouyang W. Anisotropic Interfacial Force Field for Interfaces of Water with Hexagonal Boron Nitride. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:18198-18207. [PMID: 38063463 DOI: 10.1021/acs.langmuir.3c01612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
This study introduces an anisotropic interfacial potential that provides an accurate description of the van der Waals (vdW) interactions between water and hexagonal boron nitride (h-BN) at their interface. Benchmarked against the strongly constrained and appropriately normed functional, the developed force field demonstrates remarkable consistency with reference data sets, including binding energy curves and sliding potential energy surfaces for various configurations involving a water molecule adsorbed atop the h-BN surface. These findings highlight the significant improvement achieved by the developed force field in empirically describing the anisotropic vdW interactions of the water/h-BN heterointerfaces. Utilizing this anisotropic force field, molecular dynamics simulations demonstrate that atomically flat, pristine h-BN exhibits inherent hydrophobicity. However, when atomic-step surface roughness is introduced, the wettability of h-BN undergoes a significant change, leading to a hydrophilic nature. The calculated water contact angle (WCA) for the roughened h-BN surface is approximately 64°, which closely aligns with experimental WCA values ranging from 52° to 67°. These findings indicate the high probability of the presence of atomic steps on the surfaces of the experimental h-BN samples, emphasizing the need for further experimental verification. The development of the anisotropic interfacial force field for accurately describing interactions at the water/h-BN heterointerfaces is a significant advancement in accurately simulating the wettability of two-dimensional (2D) materials, offering a reliable tool for studying the dynamic and transport properties of water at these interfaces, with implications for materials science and nanotechnology.
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Affiliation(s)
- Zhicheng Feng
- Department of Engineering Mechanics, School of Civil Engineering, Wuhan University, Wuhan, Hubei 430072, China
| | - Zhangke Lei
- Department of Engineering Mechanics, School of Civil Engineering, Wuhan University, Wuhan, Hubei 430072, China
| | - Yuanpeng Yao
- Department of Engineering Mechanics, School of Civil Engineering, Wuhan University, Wuhan, Hubei 430072, China
| | - Jianxin Liu
- Department of Engineering Mechanics, School of Civil Engineering, Wuhan University, Wuhan, Hubei 430072, China
| | - Bozhao Wu
- Department of Engineering Mechanics, School of Civil Engineering, Wuhan University, Wuhan, Hubei 430072, China
| | - Wengen Ouyang
- Department of Engineering Mechanics, School of Civil Engineering, Wuhan University, Wuhan, Hubei 430072, China
- State Key Laboratory of Water Resources & Hydropower Engineering Science, Wuhan University, Wuhan, Hubei 430072, China
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28
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Seltzer AM, Shackleton SA, Bourg IC. Solubility Equilibrium Isotope Effects of Noble Gases in Water: Theory and Observations. J Phys Chem B 2023; 127:9802-9812. [PMID: 37937341 DOI: 10.1021/acs.jpcb.3c05651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
The abundance and isotopic composition of noble gases dissolved in water have many applications in the geosciences. In recent years, new analytical techniques have opened the door to the use of high-precision measurements of noble gas isotopes as tracers for groundwater hydrology, oceanography, mantle geochemistry, and paleoclimatology. These analytical advances have brought about new measurements of solubility equilibrium isotope effects (SEIEs) in water (i.e., the relative solubilities of noble gas isotopes) and their sensitivities to the temperature and salinity. Here, we carry out a suite of classical molecular dynamics (MD) simulations and employ the theoretical method of quantum correction to estimate SEIEs for comparison with experimental observations. We find that classical MD simulations can accurately predict SEIEs for the isotopes of Ar, Kr, and Xe to order 0.01‰, on the scale of analytical uncertainty. However, MD simulations consistently overpredict the SEIEs of Ne and He by up to 40% of observed values. We carry out sensitivity tests at different temperatures, salinities, and pressures and employ different sets of interatomic potential parameters and water models. For all noble gas isotopes, the TIP4P water model is found to reproduce observed SEIEs more accurately than the SPC/E and TIP4P/ice models. Classical MD simulations also accurately capture the sign and approximate magnitude of temperature and salinity sensitivities of SEIEs for heavy noble gases. We find that experimental and modeled SEIEs generally follow an inverse-square mass dependence, which implies that the mean-square force experienced by a noble gas atom within a solvation shell is similar for all noble gases. This inverse-square mass proportionality is nearly exact for Ar, Kr, and Xe isotopes, but He and Ne exhibit a slightly weaker mass dependence. We hypothesize that the apparent dichotomy between He-Ne and Ar-Kr-Xe SEIEs may result from atomic size differences, whereby the smaller noble gases are more likely to spontaneously fit within cavities of water without breaking water-water H-bonds, thereby experiencing softer collisions during translation within a solvation shell. We further speculate that the overprediction of simulated He and Ne SEIEs may result from the neglection of higher-order quantum corrections or the overly stiff representation of van der Waals repulsion by the widely used Lennard-Jones 6-12 potential model. We suggest that new measurements of SEIEs of heavy and light noble gases may represent a novel set of constraints with which to refine hydrophobic solvation theories and optimize the set of interatomic potential models used in MD simulations of water and noble gases.
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Affiliation(s)
- Alan M Seltzer
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543-1050,United States
| | - Sarah A Shackleton
- Department of Geosciences, Princeton University, Princeton, New Jersey 08544,United States
| | - Ian C Bourg
- Department of Civil and Environmental Engineering (CEE) and High Meadows Environmental Institute (HMEI), Princeton University, Princeton, New Jersey 08544,United States
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29
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Ibrahim M, Wenzel C, Lallemang M, Balzer BN, Schwierz N. Adsorbing DNA to Mica by Cations: Influence of Valency and Ion Type. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:15553-15562. [PMID: 37877163 DOI: 10.1021/acs.langmuir.3c01835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Ion-mediated attraction between DNA and mica plays a crucial role in biotechnological applications and molecular imaging. Here, we combine molecular dynamics simulations and single-molecule atomic force microscopy experiments to characterize the detachment forces of single-stranded DNA at mica surfaces mediated by the metal cations Li+, Na+, K+, Cs+, Mg2+, and Ca2+. Ion-specific adsorption at the mica/water interface compensates (Li+ and Na+) or overcompensates (K+, Cs+, Mg2+, and Ca2+) the bare negative surface charge of mica. In addition, direct and water-mediated contacts are formed between the ions, the phosphate oxygens of DNA, and mica. The different contact types give rise to low- and high-force pathways and a broad distribution of detachment forces. Weakly hydrated ions, such as Cs+ and water-mediated contacts, lead to low detachment forces and high mobility of the DNA on the surface. Direct ion-DNA or ion-surface contacts lead to significantly higher forces. The comprehensive view gained from our combined approach allows us to highlight the most promising cations for imaging in physiological conditions: K+, which overcompensates the negative mica charge and induces long-ranged attractions. Mg2+ and Ca2+, which form a few specific and long-lived contacts to bind DNA with high affinity.
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Affiliation(s)
- Mohd Ibrahim
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Christiane Wenzel
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Max Lallemang
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Bizan N Balzer
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Str. 21, 79104 Freiburg, Germany
| | - Nadine Schwierz
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
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30
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Yamaguchi S, Takayama T, Otosu T. Appraisal of TIP4P-type models at water surface. J Chem Phys 2023; 159:171101. [PMID: 37909448 DOI: 10.1063/5.0171999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/03/2023] [Indexed: 11/03/2023] Open
Abstract
In view of the current situation in which non-polarizable rigid water models have been scarcely examined against surface-specific properties, we appraise TIP4P-type models at the liquid water surface on the basis of heterodyne-detected sum frequency generation (HD-SFG) spectroscopy. We find in the HD-SFG spectrum of the water surface that the peak frequency of the hydrogen-bonded OH band, the half width at half maximum of the hydrogen-bonded OH band, and the full width at half maximum of the free OH band are best reproduced by TIP4P, TIP4P/Ew, and TIP4P/Ice, respectively, whereas it is already well known that TIP4P/2005 best reproduces the surface tension. These TIP4P-type models perform better at the water surface in terms of the present appraisal items than some polarizable models in the literature.
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Affiliation(s)
- Shoichi Yamaguchi
- Department of Applied Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura, Saitama 338-8570, Japan
| | - Tetsuyuki Takayama
- Department of Applied Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura, Saitama 338-8570, Japan
| | - Takuhiro Otosu
- Department of Applied Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura, Saitama 338-8570, Japan
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31
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Mussa A, Berthelard R, Caupin F, Issenmann B. Viscosity and Stokes-Einstein relation in deeply supercooled water under pressure. J Chem Phys 2023; 159:151103. [PMID: 37846950 DOI: 10.1063/5.0169743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/21/2023] [Indexed: 10/18/2023] Open
Abstract
We report measurements of the shear viscosity η in water up to 150 MPa and down to 229.5 K. This corresponds to more than 30 K supercooling below the melting line. The temperature dependence is non-Arrhenius at all pressures, but its functional form at 0.1 MPa is qualitatively different from that at all pressures above 20 MPa. The pressure dependence is non-monotonic, with a pressure-induced decrease of viscosity by more than 50% at low temperature. Combining our data with literature data on the self-diffusion coefficient Ds of water, we check the Stokes-Einstein relation which, based on hydrodynamics, predicts constancy of Dsη/T, where T is the temperature. The observed temperature and pressure dependence of Dsη/T is analogous to that obtained in simulations of a realistic water model. This analogy suggests that our data are compatible with the existence of a liquid-liquid critical point at positive pressure in water.
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Affiliation(s)
- Alexandre Mussa
- Institut Lumière Matière, Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Universitaire de France, F-69622 Villeurbanne, France
| | - Romain Berthelard
- Institut Lumière Matière, Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Universitaire de France, F-69622 Villeurbanne, France
| | - Frédéric Caupin
- Institut Lumière Matière, Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Universitaire de France, F-69622 Villeurbanne, France
| | - Bruno Issenmann
- Institut Lumière Matière, Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Universitaire de France, F-69622 Villeurbanne, France
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32
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Eslami Moghadam M, Rezaeisadat M, Shahryari E, Mansouri-Torshizi H, Heydari M. Biological interaction of Pt complex with imidazole derivative as an anticancer compound with DNA: Experimental and theoretical studies. Int J Biol Macromol 2023; 249:126097. [PMID: 37543270 DOI: 10.1016/j.ijbiomac.2023.126097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 07/18/2023] [Accepted: 07/25/2023] [Indexed: 08/07/2023]
Abstract
This investigation is applied to find out interesting information on DNA binding mode with Pt(II) derivative of two N, N bidentate ligands in treating cancer. Thus, one new water-soluble platinum complex with FIP and phen with a new formula of [Pt(phen)(FIP)](NO3)2 was prepared and specified. DFT data can be used to evaluate geometry parameters. Based on the ADMET prediction, this complex can be considered a drug-like agent. Cytotoxicity property was evaluated against some human cancerous MCF7, A549, and HCT116 cell lines. Accumulation of Pt complex, cisplatin, and oxaliplatin in each cancerous cell was determined, which is probably related to their lipophilicity and solubility properties. The binding mode of the complex to ct-DNA was investigated by fluorescence spectroscopy, circular dichroism, and molecular docking simulation. The viscosity of DNA by different concentrations of EB and Pt complex titration shows Pt complex interacts with DNA via groove binding like the spectroscopic binding result. In the MD study, DNA helix, RMSD, and RMSF analysis showed that DNA stability decreased and that the majority of residues left the initial state. DNA increased residual deviations and flexibility are linked to an increase in its gyratory radius, which is consistent with the findings of the experiments.
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Affiliation(s)
| | | | - Elaheh Shahryari
- Department of Physical Sciences, Emporia State University, Campus Box, 4030, KS, USA
| | | | - Maryam Heydari
- Chemistry & Chemical Engineering Research Center of Iran, Tehran, Iran
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33
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La Francesca P, Gallo P. Supercooled solutions of sodium perchlorate in TIP4P/2005 water: The effect of martian solutes on thermodynamics and structure. J Chem Phys 2023; 159:124501. [PMID: 38127381 DOI: 10.1063/5.0168587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/04/2023] [Indexed: 12/23/2023] Open
Abstract
We study the thermodynamic behavior of sodium perchlorate solutions in supercooled water through molecular dynamics numerical simulations. These solutions are of special interest because of the recent experimental results that led to hypothesize the presence of liquid water in perchlorate solutions beneath the Martian soil. We model water using the TIP4P/2005 potential. The results we obtain for solutions with concentrations 1.63 and 15.4 wt% are in agreement with those of a system undergoing a liquid-liquid phase transition where the liquid-liquid critical point shifts to slightly higher temperatures and lower pressures. The structure of the system is also analyzed, and we come to the conclusion that, even at the highest concentration considered, water retains its anomalous behavior.
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Affiliation(s)
- P La Francesca
- Dipartimento di Matematica e Fisica, Università Degli Studi Roma Tre, via della Vasca Navale 84, 00146 Rome, Italy
| | - P Gallo
- Dipartimento di Matematica e Fisica, Università Degli Studi Roma Tre, via della Vasca Navale 84, 00146 Rome, Italy
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34
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Busch J, Paschek D. OrthoBoXY: A Simple Way to Compute True Self-Diffusion Coefficients from MD Simulations with Periodic Boundary Conditions without Prior Knowledge of the Viscosity. J Phys Chem B 2023; 127:7983-7987. [PMID: 37683293 DOI: 10.1021/acs.jpcb.3c04492] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2023]
Abstract
Recently, an analytical expression for the system size dependence and direction-dependence of self-diffusion coefficients for neat liquids due to hydrodynamic interactions has been derived for molecular dynamics (MD) simulations using orthorhombic unit cells. Based on this description, we show that for systems with a "magic" box length ratio of Lz/Lx = Lz/Ly = 2.7933596497 the computed self-diffusion coefficients Dx and Dy in the x- and y-direction become system-size independent and represent the true self-diffusion coefficient D0 = (Dx + Dy)/2. Moreover, by using this particular box geometry, the viscosity can be determined with a reasonable degree of accuracy from the difference of components of the diffusion coefficients in x-, y-, and z-directions using the simple expression η = kBT × 8.1711245653/[3πLz(Dx + Dy - 2Dz)], where kB denotes Boltzmann's constant and T represents the temperature. MD simulations of TIP4P/2005 water for various system sizes using both orthorhombic and cubic box geometries are used to test the approach.
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Affiliation(s)
- Johanna Busch
- Institut für Chemie, Abteilung Physikalische und Theoretische Chemie, Universität Rostock, Albert-Einstein-Str. 27, D-18059 Rostock, Germany
| | - Dietmar Paschek
- Institut für Chemie, Abteilung Physikalische und Theoretische Chemie, Universität Rostock, Albert-Einstein-Str. 27, D-18059 Rostock, Germany
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35
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Cinq N, Simon A, Louisnard F, Cuny J. Accurate SCC-DFTB Parametrization of Liquid Water with Improved Atomic Charges and Iterative Boltzmann Inversion. J Phys Chem B 2023; 127:7590-7601. [PMID: 37603798 DOI: 10.1021/acs.jpcb.3c03479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
This work presents improvements of the description of liquid water within the self-consistent-charge density-functional based tight-binding scheme combining the use of Weighted Mulliken (WMull) charges and optimized O-H repulsive potential through the iterative Boltzmann inversion (IBI) process. The quality of the newly developed models is validated considering pair radial distribution functions (RDFs), as well as other structural, energetic, thermodynamic, and dynamic properties. The use of WMull charges certainly improves the agreement with experimental data, however leading to over-structured RDFs at short distance, that can be further improved by considering an optimized O-H repulsive potential obtained by the IBI process. Three different schemes were used to optimize this potential: (i) optimization including short O-H distances. This led to accurate RDFs as well as improved self-diffusion coefficient and heat of vaporization, while the proton transfer energy barrier is severely deteriorated; (ii) optimization starting at long distance. The proton transfer energy barrier is recovered while the heat of vaporization is deteriorated and the O-H RDF is less accurate at short distance; (iii) optimization within the path-integral molecular dynamics scheme which allows us to exclude nuclear quantum effects from the repulsive potential. The latter potential, in conjunction with the WMull improved atomic charges, provides similar results as (i) for structural, dynamic, and thermodynamic properties while recovering a large part of the proton transfer energy barrier. It therefore offers a good compromise to study both dynamic properties and chemistry within liquid water at a quantum chemical level.
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Affiliation(s)
- Nicolas Cinq
- Laboratoire de Chimie et Physique Quantiques (LCPQ), FeRMI Institute, Université de Toulouse [UT3] and CNRS, Toulouse F-31062, France
| | - Aude Simon
- Laboratoire de Chimie et Physique Quantiques (LCPQ), FeRMI Institute, Université de Toulouse [UT3] and CNRS, Toulouse F-31062, France
| | - Fernand Louisnard
- Laboratoire de Chimie et Physique Quantiques (LCPQ), FeRMI Institute, Université de Toulouse [UT3] and CNRS, Toulouse F-31062, France
| | - Jérôme Cuny
- Laboratoire de Chimie et Physique Quantiques (LCPQ), FeRMI Institute, Université de Toulouse [UT3] and CNRS, Toulouse F-31062, France
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36
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Blazquez S, Abascal JLF, Lagerweij J, Habibi P, Dey P, Vlugt TJH, Moultos OA, Vega C. Computation of Electrical Conductivities of Aqueous Electrolyte Solutions: Two Surfaces, One Property. J Chem Theory Comput 2023; 19:5380-5393. [PMID: 37506381 PMCID: PMC10448725 DOI: 10.1021/acs.jctc.3c00562] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Indexed: 07/30/2023]
Abstract
In this work, we computed electrical conductivities under ambient conditions of aqueous NaCl and KCl solutions by using the Einstein-Helfand equation. Common force fields (charge q = ±1 e) do not reproduce the experimental values of electrical conductivities, viscosities, and diffusion coefficients. Recently, we proposed the idea of using different charges to describe the potential energy surface (PES) and the dipole moment surface (DMS). In this work, we implement this concept. The equilibrium trajectories required to evaluate electrical conductivities (within linear response theory) were obtained by using scaled charges (with the value q = ±0.75 e) to describe the PES. The potential parameters were those of the Madrid-Transport force field, which accurately describe viscosities and diffusion coefficients of these ionic solutions. However, integer charges were used to compute the conductivities (thus describing the DMS). The basic idea is that although the scaled charge describes the ion-water interaction better, the integer charge reflects the value of the charge that is transported due to the electric field. The agreement obtained with experiments is excellent, as for the first time electrical conductivities (and the other transport properties) of NaCl and KCl electrolyte solutions are described with high accuracy for the whole concentration range up to their solubility limit. Finally, we propose an easy way to obtain a rough estimate of the actual electrical conductivity of the potential model under consideration using the approximate Nernst-Einstein equation, which neglects correlations between different ions.
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Affiliation(s)
- Samuel Blazquez
- Dpto.
Química Física I, Fac. Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Jose L. F. Abascal
- Dpto.
Química Física I, Fac. Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Jelle Lagerweij
- Engineering
Thermodynamics, Process and Energy Department, Faculty of Mechanical,
Maritime and Materials Engineering, Delft
University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
| | - Parsa Habibi
- Engineering
Thermodynamics, Process and Energy Department, Faculty of Mechanical,
Maritime and Materials Engineering, Delft
University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
- Department
of Materials Science and Engineering, Faculty of Mechanical, Maritime
and Materials Engineering, Delft University
of Technology, Mekelweg
2, 2628CD Delft, The Netherlands
| | - Poulumi Dey
- Department
of Materials Science and Engineering, Faculty of Mechanical, Maritime
and Materials Engineering, Delft University
of Technology, Mekelweg
2, 2628CD Delft, The Netherlands
| | - Thijs J. H. Vlugt
- Engineering
Thermodynamics, Process and Energy Department, Faculty of Mechanical,
Maritime and Materials Engineering, Delft
University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
| | - Othonas A. Moultos
- Engineering
Thermodynamics, Process and Energy Department, Faculty of Mechanical,
Maritime and Materials Engineering, Delft
University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
| | - Carlos Vega
- Dpto.
Química Física I, Fac. Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
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37
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Li M, Lv L, Fang T, Hao L, Li S, Dong S, Wu Y, Dong X, Liu H. Self-Consistent Implementation of a Solvation Free Energy Framework to Predict the Salt Solubilities of Six Alkali Halides. J Chem Theory Comput 2023; 19:5586-5601. [PMID: 37471389 DOI: 10.1021/acs.jctc.3c00083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
To assess the salt solubilities of six alkali halides in aqueous systems, we proposed a thermodynamic cycle and an efficient molecular modeling methodology. The Gibbs free energy changes for vaporization, dissociation, and dissolution were calculated using the experimental data of ionic thermodynamic properties obtained from the NBS tables. Additionally, the Marcus' and Tissandier's solvation free energy data for Li+, Na+, K+, Cl-, and Br- ions were compared with the conventional solvation free energies by substituting into our self-consistent thermodynamic cycle. Furthermore, Tissandier's absolute solvation free energy data were used as the training set to refit the Lennard-Jones parameters of OPLS-AA force field for ions. To predict salt solubilities, an assumption of a pseudo-solvent was proposed to characterize the coupling work of a solute with its environment from infinitely diluted to saturated solutions, indicating that the Gibbs energy change of solvation process is a function of ionic strength. Following the self-consistency of the cycle, the newly derived formulas were used to determine the salt solubilities by interpolating the intersection of Gibbs free energy of dissolution and the zero free energy line. The refined ion parameters can also predict the structure and thermodynamic properties of aqueous electrolyte solutions, such as densities, pair correlation functions, hydration numbers, mean activity coefficients, vapor pressures, and the radial dependences of the net charge at 298.15 K and 1 bar. Our method can be used to characterize the solid-liquid equilibria of ions or charged particles in aqueous systems. Furthermore, for highly concentrated strong electrolyte systems, it is essential to introduce accurate water models and polarizable force fields.
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Affiliation(s)
- Miyi Li
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 10081, China
| | - Liqiang Lv
- College of Chemical Engineering, Shijiazhuang University, Hebei, Shijiazhuang 050035, China
| | - Tao Fang
- Beijing Institute of Aerospace Testing Technology, Beijing 100074, China
| | - Long Hao
- Beijing Institute of Aerospace Testing Technology, Beijing 100074, China
| | - Shenhui Li
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 10081, China
| | - Shoulong Dong
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 10081, China
| | - Yufeng Wu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 10081, China
| | - Xiao Dong
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 10081, China
| | - Helei Liu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 10081, China
- Key Laboratory of Low-Carbon Conversion Science & Engineering, Shanghai Advanced Research Institute, Chinese Academy of Sciences (Shanghai Advanced Research Institute, Chinese Academy of Sciences), Shanghai 201210, China
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38
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Zeng J, Zhang D, Lu D, Mo P, Li Z, Chen Y, Rynik M, Huang L, Li Z, Shi S, Wang Y, Ye H, Tuo P, Yang J, Ding Y, Li Y, Tisi D, Zeng Q, Bao H, Xia Y, Huang J, Muraoka K, Wang Y, Chang J, Yuan F, Bore SL, Cai C, Lin Y, Wang B, Xu J, Zhu JX, Luo C, Zhang Y, Goodall REA, Liang W, Singh AK, Yao S, Zhang J, Wentzcovitch R, Han J, Liu J, Jia W, York DM, E W, Car R, Zhang L, Wang H. DeePMD-kit v2: A software package for deep potential models. J Chem Phys 2023; 159:054801. [PMID: 37526163 PMCID: PMC10445636 DOI: 10.1063/5.0155600] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/03/2023] [Indexed: 08/02/2023] Open
Abstract
DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features, such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, DP-range correction, DP long range, graphics processing unit support for customized operators, model compression, non-von Neumann molecular dynamics, and improved usability, including documentation, compiled binary packages, graphical user interfaces, and application programming interfaces. This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, this article presents a comprehensive procedure for conducting molecular dynamics as a representative application, benchmarks the accuracy and efficiency of different models, and discusses ongoing developments.
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Affiliation(s)
- Jinzhe Zeng
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | | | - Denghui Lu
- HEDPS, CAPT, College of Engineering, Peking University, Beijing 100871, People’s Republic of China
| | - Pinghui Mo
- College of Electrical and Information Engineering, Hunan University, Changsha, People’s Republic of China
| | - Zeyu Li
- Yuanpei College, Peking University, Beijing 100871, People’s Republic of China
| | - Yixiao Chen
- Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08540, USA
| | - Marián Rynik
- Department of Experimental Physics, Comenius University, Mlynská Dolina F2, 842 48 Bratislava, Slovakia
| | - Li’ang Huang
- Center for Quantum Information, Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing 100084, People’s Republic of China
| | | | - Shaochen Shi
- ByteDance Research, Zhonghang Plaza, No. 43, North 3rd Ring West Road, Haidian District, Beijing, People’s Republic of China
| | | | - Haotian Ye
- Yuanpei College, Peking University, Beijing 100871, People’s Republic of China
| | - Ping Tuo
- AI for Science Institute, Beijing 100080, People’s Republic of China
| | - Jiabin Yang
- Baidu, Inc., Beijing, People’s Republic of China
| | | | - Yifan Li
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | | | - Qiyu Zeng
- Department of Physics, National University of Defense Technology, Changsha, Hunan 410073, People’s Republic of China
| | | | - Yu Xia
- ByteDance Research, Zhonghang Plaza, No. 43, North 3rd Ring West Road, Haidian District, Beijing, People’s Republic of China
| | | | - Koki Muraoka
- Department of Chemical System Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yibo Wang
- DP Technology, Beijing 100080, People’s Republic of China
| | | | - Fengbo Yuan
- DP Technology, Beijing 100080, People’s Republic of China
| | - Sigbjørn Løland Bore
- Hylleraas Centre for Quantum Molecular Sciences and Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, 0315 Oslo, Norway
| | | | - Yinnian Lin
- Wangxuan Institute of Computer Technology, Peking University, Beijing 100871, People’s Republic of China
| | - Bo Wang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, People’s Republic of China
| | - Jiayan Xu
- School of Chemistry and Chemical Engineering, Queen’s University Belfast, Belfast BT9 5AG, United Kingdom
| | - Jia-Xin Zhu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Chenxing Luo
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, USA
| | - Yuzhi Zhang
- DP Technology, Beijing 100080, People’s Republic of China
| | | | - Wenshuo Liang
- DP Technology, Beijing 100080, People’s Republic of China
| | - Anurag Kumar Singh
- Department of Data Science, Indian Institute of Technology, Palakkad, Kerala, India
| | - Sikai Yao
- DP Technology, Beijing 100080, People’s Republic of China
| | - Jingchao Zhang
- NVIDIA AI Technology Center (NVAITC), Santa Clara, California 95051, USA
| | | | - Jiequn Han
- Center for Computational Mathematics, Flatiron Institute, New York, New York 10010, USA
| | - Jie Liu
- College of Electrical and Information Engineering, Hunan University, Changsha, People’s Republic of China
| | | | - Darrin M. York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | | | - Roberto Car
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | | | - Han Wang
- Author to whom correspondence should be addressed:
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39
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Kanagalingam G, Schmitt S, Fleckenstein F, Stephan S. Data scheme and data format for transferable force fields for molecular simulation. Sci Data 2023; 10:495. [PMID: 37500652 PMCID: PMC10374650 DOI: 10.1038/s41597-023-02369-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 07/07/2023] [Indexed: 07/29/2023] Open
Abstract
A generalized data scheme for transferable classical force fields used in molecular simulations, i.e. molecular dynamics and Monte Carlo simulation, is presented. The data scheme is implemented in an SQL-based data format. The data scheme and data format is machine readable, re-usable, and interoperable. A transferable force field is a chemical construction plan specifying intermolecular and intramolecular interactions between different types of atoms or different chemical groups and can be used for building a model for a given component. The data scheme proposed in this work (named TUK-FFDat) formalizes digitally these chemical construction plans, i.e. transferable force fields. It can be applied to all-atom as well as united-atom transferable force fields. The general applicability of the data scheme is demonstrated for different types of force fields (TraPPE, OPLS-AA, and Potoff). Furthermore, conversion tools for translating the data scheme between .xls spread sheet format and the SQL-based data format are provided. The data format can readily be integrated in existing workflows, simulation engines, and force field databases as well as for linking such.
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Affiliation(s)
- Gajanan Kanagalingam
- Laboratory of Engineering Thermodynamics (LTD), RPTU Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Sebastian Schmitt
- Laboratory of Engineering Thermodynamics (LTD), RPTU Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Florian Fleckenstein
- Laboratory of Engineering Thermodynamics (LTD), RPTU Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Simon Stephan
- Laboratory of Engineering Thermodynamics (LTD), RPTU Kaiserslautern, Kaiserslautern, 67663, Germany.
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40
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Saurabh S, Li Z, Hollowell P, Waigh T, Li P, Webster J, Seddon JM, Kalonia C, Lu JR, Bresme F. Structure and interaction of therapeutic proteins in solution: a combined simulation and experimental study. Mol Phys 2023; 121:e2236248. [PMID: 38107421 PMCID: PMC10721229 DOI: 10.1080/00268976.2023.2236248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/30/2023] [Indexed: 12/19/2023]
Abstract
The aggregation of therapeutic proteins in solution has attracted significant interest, driving efforts to understand the relationship between microscopic structural changes and protein-protein interactions determining aggregation processes in solution. Additionally, there is substantial interest in being able to predict aggregation based on protein structure as part of molecular developability assessments. Molecular Dynamics provides theoretical tools to complement experimental studies and to interrogate and identify the microscopic mechanisms determining aggregation. Here we perform all-atom MD simulations to study the structure and inter-protein interaction of the Fab and Fc fragments of the monoclonal antibody (mAb) COE3. We unravel the role of ion-protein interactions in building the ionic double layer and determining effective inter-protein interaction. Further, we demonstrate, using various state-of-the-art force fields (charmm, gromos, amber, opls/aa), that the protein solvation, ionic structure and protein-protein interaction depend significantly on the force field parameters. We perform SANS and Static Light Scattering experiments to assess the accuracy of the different forcefields. Comparison of the simulated and experimental results reveal significant differences in the forcefields' performance, particularly in their ability to predict the protein size in solution and inter-protein interactions quantified through the second virial coefficients. In addition, the performance of the forcefields is correlated with the protein hydration structure.
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Affiliation(s)
- Suman Saurabh
- Department of Chemistry, Molecular Sciences Research Hub Imperial College, London, United Kingdom
| | - Zongyi Li
- Biological Physics Group, School of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Manchester, UK
| | - Peter Hollowell
- Biological Physics Group, School of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Manchester, UK
| | - Thomas Waigh
- Biological Physics Group, School of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Manchester, UK
- Photon Science Institute, The University of Manchester, Manchester, UK
| | - Peixun Li
- STFC ISIS Facility, Rutherford Appleton Laboratory, Didcot, UK
| | - John Webster
- STFC ISIS Facility, Rutherford Appleton Laboratory, Didcot, UK
| | - John M. Seddon
- Department of Chemistry, Molecular Sciences Research Hub Imperial College, London, United Kingdom
| | - Cavan Kalonia
- Dosage Form Design and Development, BioPharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Jian R. Lu
- Biological Physics Group, School of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Manchester, UK
| | - Fernando Bresme
- Department of Chemistry, Molecular Sciences Research Hub Imperial College, London, United Kingdom
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41
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Peralta A, Odriozola G. A Neural-Network-Optimized Hydrogen Peroxide Pairwise Additive Model for Classical Simulations. J Chem Theory Comput 2023; 19:4172-4181. [PMID: 37306692 PMCID: PMC10921400 DOI: 10.1021/acs.jctc.3c00287] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Indexed: 06/13/2023]
Abstract
We have developed an all-atom pairwise additive model for hydrogen peroxide using an optimization procedure based on artificial neural networks (ANNs). The model is based on experimental molecular geometry and includes a dihedral potential that hinders the cis-type configuration and allows for crossing the trans one, defined between the planes that have the two oxygen atoms and each hydrogen. The model's parametrization is achieved by training simple ANNs to minimize a target function that measures the differences between various thermodynamic and transport properties and the corresponding experimental values. Finally, we evaluated a range of properties for the optimized model and its mixtures with SPC/E water, including bulk-liquid properties (density, thermal expansion coefficient, adiabatic compressibility, etc.) and properties of systems at equilibrium (vapor and liquid density, vapor pressure and composition, surface tension, etc.). Overall, we obtained good agreement with experimental data.
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Affiliation(s)
- Alvaro
Ramos Peralta
- Área de Física de Procesos
Irreversibles, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Azcapotzalco, Av. San Pablo 180, 02200 Ciudad de México, Mexico
| | - Gerardo Odriozola
- Área de Física de Procesos
Irreversibles, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Azcapotzalco, Av. San Pablo 180, 02200 Ciudad de México, Mexico
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42
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Chaudhury A, Moorjani B, Chatterjee S, Adhikari J, Hait S. Molecular insights into the dissociation of carbon dioxide hydrates in the presence of an ionic liquid, [BMIM][PF6]. Chem Phys 2023; 571:111943. [DOI: 10.1016/j.chemphys.2023.111943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
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43
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Ibrahim M, Gilbert J, Heinz M, Nylander T, Schwierz N. Structural insights on ionizable Dlin-MC3-DMA lipids in DOPC layers by combining accurate atomistic force fields, molecular dynamics simulations and neutron reflectivity. NANOSCALE 2023. [PMID: 37377412 DOI: 10.1039/d3nr00987d] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Ionizable lipids such as the promising Dlin-MC3-DMA (MC3) are essential for the successful design of lipid nanoparticles (LNPs) as drug delivery agents. Combining molecular dynamics simulations with experimental data, such as neutron reflectivity experiments and other scattering techniques, is essential to provide insights into the internal structure of LNPs, which is not fully understood to date. However, the accuracy of the simulations relies on the choice of force field parameters and high-quality experimental data is indispensable to verify the parametrization. For MC3, different parameterizations in combination with the CHARMM and the Slipids force fields have recently emerged. Here, we complement the existing efforts by providing parameters for cationic and neutral MC3 compatible with the AMBER Lipid17 force field. Subsequently, we carefully assess the accuracy of the different force fields by providing a direct comparison to neutron reflectivity experiments of mixed lipid bilayers consisting of MC3 and DOPC at different pHs. At low pH (cationic MC3) and at high pH (neutral MC3) the newly developed MC3 parameters in combination with AMBER Lipid17 for DOPC give good agreement with the experiments. Overall, the agreement is similar compared to the Park-Im parameters for MC3 in combination with the CHARMM36 force field for DOPC. The Ermilova-Swenson MC3 parameters in combination with the Slipids force field underestimate the bilayer thickness. While the distribution of cationic MC3 is very similar, the different force fields for neutral MC3 reveal distinct differences ranging from strong accumulation in the membrane center (current MC3/AMBER Lipid17 DOPC), over mild accumulation (Park-Im MC3/CHARMM36 DOPC) to surface accumulation (Ermilova-Swenson MC3/Slipids DOPC). These pronounced differences highlight the importance of accurate force field parameters and their experimental validation.
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Affiliation(s)
- Mohd Ibrahim
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Jennifer Gilbert
- Physical Chemistry, Department of Chemistry Lund University, P.O Box 124, SE-22100 Lund, Sweden.
- NanoLund, Lund University, Professorsgatan 1, 223 63 Lund, Sweden
| | - Marcel Heinz
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Tommy Nylander
- Physical Chemistry, Department of Chemistry Lund University, P.O Box 124, SE-22100 Lund, Sweden.
- NanoLund, Lund University, Professorsgatan 1, 223 63 Lund, Sweden
- LINXS Institute of Advanced Neutron and X-Ray Science, Scheelevägen 19, 223 70, Lund, Sweden
- School of Chemical Engineering and Translational Nanobioscience Research Center, Sungkyunkwan University, Suwon, Republic of Korea
| | - Nadine Schwierz
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
- Institute of Physics, University of Augsburg, 86159 Augsburg, Germany.
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44
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Dommer A, Wauer NA, Angle KJ, Davasam A, Rubio P, Luo M, Morris CK, Prather KA, Grassian VH, Amaro RE. Revealing the Impacts of Chemical Complexity on Submicrometer Sea Spray Aerosol Morphology. ACS CENTRAL SCIENCE 2023; 9:1088-1103. [PMID: 37396863 PMCID: PMC10311664 DOI: 10.1021/acscentsci.3c00184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Indexed: 07/04/2023]
Abstract
Sea spray aerosol (SSA) ejected through bursting bubbles at the ocean surface is a complex mixture of salts and organic species. Submicrometer SSA particles have long atmospheric lifetimes and play a critical role in the climate system. Composition impacts their ability to form marine clouds, yet their cloud-forming potential is difficult to study due to their small size. Here, we use large-scale molecular dynamics (MD) simulations as a "computational microscope" to provide never-before-seen views of 40 nm model aerosol particles and their molecular morphologies. We investigate how increasing chemical complexity impacts the distribution of organic material throughout individual particles for a range of organic constituents with varying chemical properties. Our simulations show that common organic marine surfactants readily partition between both the surface and interior of the aerosol, indicating that nascent SSA may be more heterogeneous than traditional morphological models suggest. We support our computational observations of SSA surface heterogeneity with Brewster angle microscopy on model interfaces. These observations indicate that increased chemical complexity in submicrometer SSA leads to a reduced surface coverage by marine organics, which may facilitate water uptake in the atmosphere. Our work thus establishes large-scale MD simulations as a novel technique for interrogating aerosols at the single-particle level.
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45
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Eslami Moghadam M, Rezaeisadat M, Mansouri-Torshizi H, Hosseinzadeh S, Daneshyar H. New anticancer potential Pt complex with tertamyl dithiocarbamate ligand: Synthesis, DNA targeting behavior, molecular dynamic, and biological activity. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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46
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R Leivas F, Barbosa MC. Functionalized carbon nanocones performance in water harvesting. J Chem Phys 2023; 158:2890471. [PMID: 37184010 DOI: 10.1063/5.0142718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/30/2023] [Indexed: 05/16/2023] Open
Abstract
In this work, we investigate the water capture process for functionalized carbon nanocones (CNCs) through molecular dynamic simulations in the following three scenarios: a single CNC in contact with a reservoir containing liquid water, a single CNC in contact with a water vapor reservoir, and a combination of more than one CNC in contact with vapor. We found that water flows through the nanocones when in contact with the liquid reservoir if the nanocone tip presents hydrophilic functionalization. In contact with steam, we observed the formation of droplets at the base of the nanocone only when hydrophilic functionalization is present. Then, water flows through in a linear manner, a process that is more efficient than that in the liquid reservoir regime. The scalability of the process is tested by analyzing the water flow through more than one nanocone. The results suggest that the distance between the nanocones is a fundamental ingredient for the efficiency of water harvesting.
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Affiliation(s)
- Fernanda R Leivas
- Instituto de Física, Universidade Federal do Rio Grande do Sul, CP 15051, 91501-970 Porto Alegre, RS, Brazil
| | - Marcia C Barbosa
- Instituto de Física, Universidade Federal do Rio Grande do Sul, CP 15051, 91501-970 Porto Alegre, RS, Brazil
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47
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Perin L, Gallo P. Phase Diagram of Aqueous Solutions of LiCl: a Study of Concentration Effects on the Anomalies of Water. J Phys Chem B 2023; 127:4613-4622. [PMID: 37167579 DOI: 10.1021/acs.jpcb.3c00703] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
We perform molecular dynamics simulations in order to study thermodynamics and the structure of supercooled aqueous solutions of lithium chloride (LiCl) at concentrations c = 0.678 and 2.034 mol/kg. We model the solvent using the TIP4P/2005 potential and the ions using the Madrid-2019 force field, a force field particularly suited for studying this solution. We find that, for c = 0.678 mol/kg, the behavior of the equation of state, studied in the P-T plane, indicates the presence of a liquid-liquid phase transition, similar to what was previously found for bulk water. We estimate the position of the liquid-liquid critical point to be at Tc ≈ 174 K, Pc ≈ 1775 bar, and ρc ≈ 1.065 g/cm3. When the concentration is tripled to c = 2.034 mol/kg, no critical point is observed, indicating its possible disappearance at this concentration. We also study the water-water and water-ions structure in the two solutions, and we find that at the concentrations examined the effect of ions on the water-water structure is not strong, and all the features found in bulk water are preserved. We also calculate the hydration number of the Li and Cl ions, and in line with experiments, we find the value of 4 for Li+ and between 5.5 and 6 for Cl-, confirming the good performances of the Madrid-2019 force field.
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Affiliation(s)
- Leonardo Perin
- Dipartimento di Fisica, Università Roma Tre, Via della Vasca Navale 84, I-00146 Roma, Italy
| | - Paola Gallo
- Dipartimento di Fisica, Università Roma Tre, Via della Vasca Navale 84, I-00146 Roma, Italy
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48
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Tillotson MJ, Diamantonis NI, Buda C, Bolton LW, Müller EA. Molecular modelling of the thermophysical properties of fluids: expectations, limitations, gaps and opportunities. Phys Chem Chem Phys 2023; 25:12607-12628. [PMID: 37114325 DOI: 10.1039/d2cp05423j] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
This manuscript provides an overview of the current state of the art in terms of the molecular modelling of the thermophysical properties of fluids. It is intended to manage the expectations and serve as guidance to practising physical chemists, chemical physicists and engineers in terms of the scope and accuracy of the more commonly available intermolecular potentials along with the peculiarities of the software and methods employed in molecular simulations while providing insights on the gaps and opportunities available in this field. The discussion is focused around case studies which showcase both the precision and the limitations of frequently used workflows.
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Affiliation(s)
- Marcus J Tillotson
- Department of Chemical Engineering, Imperial College London, London, UK.
| | | | | | | | - Erich A Müller
- Department of Chemical Engineering, Imperial College London, London, UK.
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49
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Han B, Isborn CM, Shi L. Incorporating Polarization and Charge Transfer into a Point-Charge Model for Water Using Machine Learning. J Phys Chem Lett 2023; 14:3869-3877. [PMID: 37067482 DOI: 10.1021/acs.jpclett.3c00036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Rigid nonpolarizable water models with fixed point charges have been widely employed in molecular dynamics simulations due to their efficiency and reasonable accuracy for the potential energy surface. However, the dipole moment surface of water is not necessarily well-described by the same fixed charges, leading to failure in reproducing dipole-related properties. Here, we developed a machine-learning model trained against electronic structure data to assign point charges for water, and the resulting dipole moment surface significantly improved the predictions of the dielectric constant and the low-frequency IR spectrum of liquid water. Our analysis reveals that within our atom-centered point-charge description of the dipole moment surface, the intermolecular charge transfer is the major source of the peak intensity at 200 cm-1, whereas the intramolecular polarization controls the enhancement of the dielectric constant. The effects of exact Hartree-Fock exchange in the hybrid density functional on these properties are also discussed.
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Affiliation(s)
- Bowen Han
- Chemistry and Biochemistry, University of California, Merced, California 95343, United States
| | - Christine M Isborn
- Chemistry and Biochemistry, University of California, Merced, California 95343, United States
| | - Liang Shi
- Chemistry and Biochemistry, University of California, Merced, California 95343, United States
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Ho CH, Valentine ML, Chen Z, Xie H, Farha O, Xiong W, Paesani F. Structure and thermodynamics of water adsorption in NU-1500-Cr. Commun Chem 2023; 6:70. [PMID: 37061604 PMCID: PMC10105746 DOI: 10.1038/s42004-023-00870-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/28/2023] [Indexed: 04/17/2023] Open
Abstract
Metal-organic frameworks (MOFs) are a class of materials with diverse chemical and structural properties, and have been shown to effectively adsorb various types of guest molecules. The mechanism of water adsorption in NU-1500-Cr, a high-performance atmospheric water harvesting MOF, is investigated using a combination of molecular dynamics simulations and infrared spectroscopy. Calculations of thermodynamic and dynamical properties of water as a function of relative humidity allow for following the adsorption process from the initial hydration stage to complete filling of the MOF pores. Initial hydration begins at the water molecules that saturate the open Cr3+ sites of the framework, which is then followed by the formation of water chains that extend along the channels connecting the hexagonal pores of the framework. Water present in these channels gradually coalesces and fills the hexagonal pores sequentially after the channels are completely hydrated. The development of hydrogen-bond networks inside the MOF pores as a function of relative humidity is characterized at the molecular level using experimental and computational infrared spectroscopy. A detailed analysis of the OH-stretch vibrational band indicates that the low-frequency tail stems from strongly polarized hydrogen-bonded water molecules, suggesting the presence of some structural disorder in the experimental samples. Strategies for designing efficient water harvesting MOFs are also proposed based on the mechanism of water adsorption in NU-1500-Cr.
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Affiliation(s)
- Ching-Hwa Ho
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Mason L Valentine
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Zhijie Chen
- Department of Chemistry and International Institute of Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Haomiao Xie
- Department of Chemistry and International Institute of Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Omar Farha
- Department of Chemistry and International Institute of Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Wei Xiong
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA.
- Materials Science and Engineering, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA.
- Materials Science and Engineering, University of California San Diego, La Jolla, CA, 92093, USA.
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, 92093, USA.
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