1
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Han H, Park Y, Kim Y, Ding F, Shin HJ. Controlled dissolution of a single ion from a salt interface. Nat Commun 2024; 15:2401. [PMID: 38493203 PMCID: PMC10944500 DOI: 10.1038/s41467-024-46704-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 03/07/2024] [Indexed: 03/18/2024] Open
Abstract
Interactions between monatomic ions and water molecules are fundamental to understanding the hydration of complex polyatomic ions and ionic process. Among the simplest and well-established ion-related reactions is dissolution of salt in water, which is an endothermic process requiring an increase in entropy. Extensive efforts have been made to date; however, most studies at single-ion level have been limited to theoretical approaches. Here, we demonstrate the salt dissolution process by manipulating a single water molecule at an under-coordinated site of a sodium chloride film. Manipulation of molecule in a controlled manner enables us to understand ion-water interaction as well as dynamics of water molecules at NaCl interfaces, which are responsible for the selective dissolution of anions. The water dipole polarizes the anion in the NaCl ionic crystal, resulting in strong anion-water interaction and weakening of the ionic bonds. Our results provide insights into a simple but important elementary step of the single-ion chemistry, which may be useful in ion-related sciences and technologies.
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Affiliation(s)
- Huijun Han
- Department of Materials Science and Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Yunjae Park
- Center for Multidimensional Carbon Materials, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
| | - Yohan Kim
- Department of Materials Science and Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Feng Ding
- Department of Materials Science and Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
- Shenzhen Institute of Advanced Technology, Chinese Academy of Science, Shenzhen, 518055, China.
| | - Hyung-Joon Shin
- Department of Materials Science and Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
- Center for Multidimensional Carbon Materials, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea.
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2
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Sanz Matias A, Roncoroni F, Sundararaman S, Prendergast D. Ca-dimers, solvent layering, and dominant electrochemically active species in Ca(BH 4) 2 in THF. Nat Commun 2024; 15:1397. [PMID: 38360965 DOI: 10.1038/s41467-024-45672-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 02/01/2024] [Indexed: 02/17/2024] Open
Abstract
Divalent ions (Mg, Ca, and Zn) are being considered as competitive, safe, and earth-abundant alternatives to Li-ion electrochemistry, but present challenges for stable cycling due to undesirable interfacial phenomena. We explore the formation of electroactive species in the electrolyte Ca(BH4)2∣THF using molecular dynamics coupled with a continuum model of bulk and interfacial speciation. Free-energy analysis and unsupervised learning indicate a majority population of neutral Ca dimers and monomers with diverse molecular conformations and an order of magnitude lower concentration of the primary electroactive charged species - the monocation, CaBH[Formula: see text] - produced via disproportionation of neutral complexes. Dense layering of THF molecules within ~1 nm of the electrode surface strongly modulates local electrolyte species populations. A dramatic increase in monocation population in this interfacial zone is induced at negative bias. We see no evidence for electrochemical activity of fully-solvated Ca2+. The consequences for performance are discussed in light of this molecular-scale insight.
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Affiliation(s)
- Ana Sanz Matias
- Joint Center for Energy Storage Research, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Fabrice Roncoroni
- Joint Center for Energy Storage Research, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Siddharth Sundararaman
- Joint Center for Energy Storage Research, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - David Prendergast
- Joint Center for Energy Storage Research, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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3
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Chakrabarti R, Verma L, Hadjiev VG, Palmer JC, Vekilov PG. The elementary reactions for incorporation into crystals. Proc Natl Acad Sci U S A 2024; 121:e2320201121. [PMID: 38315836 PMCID: PMC10873555 DOI: 10.1073/pnas.2320201121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 12/26/2023] [Indexed: 02/07/2024] Open
Abstract
The growth rates of crystals are largely dictated by the chemical reaction between solute and kinks, in which a solute molecule severs its bonds with the solvent and establishes new bonds with the kink. Details on this sequence of bond breaking and rebuilding remain poorly understood. To elucidate the reaction at the kinks we employ four solvents with distinct functionalities as reporters on the microscopic structures and their dynamics along the pathway into a kink. We combine time-resolved in situ atomic force microscopy and x-ray and optical methods with molecular dynamics simulations. We demonstrate that in all four solvents the solute, etioporphyrin I, molecules reach the steps directly from the solution; this finding identifies the measured rate constant for step growth as the rate constant of the reaction between a solute molecule and a kink. We show that the binding of a solute molecule to a kink divides into two elementary reactions. First, the incoming solute molecule sheds a fraction of its solvent shell and attaches to molecules from the kink by bonds distinct from those in its fully incorporated state. In the second step, the solute breaks these initial bonds and relocates to the kink. The strength of the preliminary bonds with the kink determines the free energy barrier for incorporation into a kink. The presence of an intermediate state, whose stability is controlled by solvents and additives, may illuminate how minor solution components guide the construction of elaborate crystal architectures in nature and the search for solution compositions that suppress undesirable or accelerate favored crystallization in industry.
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Affiliation(s)
- Rajshree Chakrabarti
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX77204-4004
| | - Lakshmanji Verma
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX77204-4004
| | - Viktor G. Hadjiev
- Texas Center for Superconductivity, University of Houston, Houston, TX77004-50024
| | - Jeremy C. Palmer
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX77204-4004
| | - Peter G. Vekilov
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX77204-4004
- Department of Chemistry, University of Houston, Houston, TX77204-5003
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4
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Seepma SYMH, Kuipers BWM, Wolthers M. Impact of Solution {Ba 2+}:{SO 42-} on Charge Evolution of Forming and Growing Barite (BaSO 4) Crystals: A ζ-Potential Measurement Investigation. ACS OMEGA 2023; 8:43521-43537. [PMID: 38027339 PMCID: PMC10666142 DOI: 10.1021/acsomega.3c03727] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 10/06/2023] [Accepted: 10/12/2023] [Indexed: 12/01/2023]
Abstract
The impact of solution stoichiometry on formation of BaSO4 (barite) crystals and the development of surface charge was investigated at various predefined stoichiometries (raq = 0.01, 0.1, 1, 10, and 100, where raq = {Ba2+}:{SO42-}). Synthesis experiments and zeta potential (ζ-potential) measurements were conducted at a fixed initial degree of supersaturation (Ωbarite = 1000, where Ωbarite = {Ba2+}{SO42-}/Ksp), at circumneutral pH of ∼6, 0.02 M NaCl, and ambient temperature and pressure. Mixed-mode measurement-phase analysis light scattering (M3-PALS) showed that the particles stayed negative for raq < 1 during barite crystal formation and positive for raq > 1. At raq = 1, two populations with a positive or negative ζ-potential prevailed for ∼2.5 h before a population with a circumneutral ζ-potential (-10 to +10 mV) remained. We relate the observations of particle charge evolution to particle size and morphology evolution under the experimental conditions. Furthermore, we showed that the ζ-potential became more negative when the pH was increased for every raq. In addition, our results demonstrated that the type of monovalent background electrolyte did not influence the ζ-potential of barite crystals significantly, although NaCl showed slightly different behavior compared to KCl and NaNO3. Our results show the important role of surface charge (evolution) during ionic crystal formation under nonstoichiometric conditions. Moreover, our combined scanning electron microscopy and ζ-potential results imply that the surface charge during particle formation can be influenced by solution stoichiometry, besides the pH and ionic strength, and may aid in predicting the fate of barite in environmental settings and in understanding and improving industrial barite (surface chemistry) processes.
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Affiliation(s)
- Sergěj Y. M. H. Seepma
- Department
of Earth Sciences, Utrecht University, Princetonlaan 8A, Utrecht 3584 CB, The Netherlands
| | - Bonny W. M. Kuipers
- Van
‘t Hoff Laboratory for Physical and Colloid Chemistry, Debye
Institute for Nanomaterials Science, Utrecht
University, Padualaan
8, Utrecht 3584 CH, The Netherlands
| | - Mariëtte Wolthers
- Department
of Earth Sciences, Utrecht University, Princetonlaan 8A, Utrecht 3584 CB, The Netherlands
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5
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Naleem N, Abreu CRA, Warmuz K, Tong M, Kirmizialtin S, Tuckerman ME. An exploration of machine learning models for the determination of reaction coordinates associated with conformational transitions. J Chem Phys 2023; 159:034102. [PMID: 37458344 DOI: 10.1063/5.0147597] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 06/23/2023] [Indexed: 07/20/2023] Open
Abstract
Determining collective variables (CVs) for conformational transitions is crucial to understanding their dynamics and targeting them in enhanced sampling simulations. Often, CVs are proposed based on intuition or prior knowledge of a system. However, the problem of systematically determining a proper reaction coordinate (RC) for a specific process in terms of a set of putative CVs can be achieved using committor analysis (CA). Identifying essential degrees of freedom that govern such transitions using CA remains elusive because of the high dimensionality of the conformational space. Various schemes exist to leverage the power of machine learning (ML) to extract an RC from CA. Here, we extend these studies and compare the ability of 17 different ML schemes to identify accurate RCs associated with conformational transitions. We tested these methods on an alanine dipeptide in vacuum and on a sarcosine dipeptoid in an implicit solvent. Our comparison revealed that the light gradient boosting machine method outperforms other methods. In order to extract key features from the models, we employed Shapley Additive exPlanations analysis and compared its interpretation with the "feature importance" approach. For the alanine dipeptide, our methodology identifies ϕ and θ dihedrals as essential degrees of freedom in the C7ax to C7eq transition. For the sarcosine dipeptoid system, the dihedrals ψ and ω are the most important for the cisαD to transαD transition. We further argue that analysis of the full dynamical pathway, and not just endpoint states, is essential for identifying key degrees of freedom governing transitions.
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Affiliation(s)
- Nawavi Naleem
- Chemistry Program, Science Division, New York University, Abu Dhabi, UAE
| | - Charlles R A Abreu
- Chemical Engineering Department, Escola de Química, Universidade Federal do Rio de Janeiro, 21941-909 Rio de Janeiro, RJ, Brazil
| | - Krzysztof Warmuz
- Computer Science Program, Science Division, New York University, Abu Dhabi, UAE
| | - Muchen Tong
- Department of Chemistry, New York University (NYU), New York, New York 10003, USA
| | - Serdal Kirmizialtin
- Chemistry Program, Science Division, New York University, Abu Dhabi, UAE
- Department of Chemistry, New York University (NYU), New York, New York 10003, USA
- Center for Smart Engineering Materials, New York University, Abu Dhabi, UAE
| | - Mark E Tuckerman
- Department of Chemistry, New York University (NYU), New York, New York 10003, USA
- Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, USA
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Rd. North, Shanghai 200062, China
- Simons Center for Computational Physical Chemistry at New York University, New York, New York 10003, USA
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6
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Burgin T, Ellis S, Mayes HB. ATESA: An Automated Aimless Shooting Workflow. J Chem Theory Comput 2023; 19:235-244. [PMID: 36520006 DOI: 10.1021/acs.jctc.2c00543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Transition path sampling methods are powerful tools for studying the dynamics of rare events in molecular simulations. However, these methods are generally restricted to experts with the knowledge and resources to properly set up and analyze the often hundreds of thousands of simulations that constitute a complete study. Aimless Transition Ensemble Sampling and Analysis (ATESA) is a new open-source software program written in Python that automates a full transition path sampling workflow based on the aimless shooting algorithm, streamlining the process and reducing the barrier to use for researchers new to this approach. This introduction to ATESA includes a demonstration of a complete transition path sampling process flow for an example reaction, including finding an initial transition state, sampling with aimless shooting, building a reaction coordinate with inertial likelihood maximization, verifying that coordinate with committor analysis, and measuring the reaction energy profile with umbrella sampling. We also describe our implementation of a termination criterion for aimless shooting based on the Godambe information calculated during model building with likelihood maximization as well as a novel approach to constraining simulations to the desired rare event pathway during umbrella sampling.
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Affiliation(s)
- Tucker Burgin
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Samuel Ellis
- The Molecular Sciences Software Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24060, United States.,Department of Chemistry, Virginia Tech University, Blacksburg, Virginia 24061, United States
| | - Heather B Mayes
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
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7
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Broad A, Darkins R, Duffy DM, Ford IJ. Calcite Kinks Grow via a Multistep Mechanism. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2022; 126:15980-15985. [PMID: 36185702 PMCID: PMC9514807 DOI: 10.1021/acs.jpcc.2c04116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/18/2022] [Indexed: 06/16/2023]
Abstract
The classical model of crystal growth assumes that kinks grow via a sequence of independent adsorption events where each solute transitions from the solution directly to the crystal lattice site. Here, we challenge this view by showing that some calcite kinks grow via a multistep mechanism where the solute adsorbs to an intermediate site and only transitions to the lattice site upon the adsorption of a second solute. We compute the free energy curves for Ca and CO3 ions adsorbing to a large selection of kink types, and we identify kinks terminated both by Ca ions and by CO3 ions that grow in this multistep way.
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8
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Silvestri A, Raiteri P, Gale JD. Obtaining Consistent Free Energies for Ion Binding at Surfaces from Solution: Pathways versus Alchemy for Determining Kink Site Stability. J Chem Theory Comput 2022; 18:5901-5919. [PMID: 36073829 DOI: 10.1021/acs.jctc.2c00787] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ion incorporation or removal from a solid at the interface with solution is a fundamental part of crystal growth. Despite this, there have been few quantitative determinations of the thermodynamics for such processes from atomistic molecular dynamics due to the associated technical challenges. In this study, we compute the free energies for ion removal from kink sites at the interface between NaCl and water as an illustrative example. To examine the influence of the free energy technique used, we compare methods that follow an explicit pathway for dissolution with those that focus on the thermodynamics of the initial and final states using metadynamics and free energy perturbation, respectively. While the initial results of the two approaches are found to be completely different, it is demonstrated that the thermodynamics can be reconciled with appropriate corrections for the standard states, thus illustrating the need for caution in interpreting raw free energy curves for ion binding as widely found in the literature. In addition, a new efficient approach is introduced to correct for the system size dependence of kink site energies both due to the periodic interaction of charges in an inhomogeneous dielectric system and due to the dipolar interactions between pairs of kinks along a row. Ultimately, it is shown that with suitable care, both classes of free energy techniques are capable of producing kink site stabilities that are consistent with the solubility of the underlying bulk solid. However, the precise values for individual kink sites exhibit a small systematic offset, which can be ascribed to the contribution of the interfacial potential to the pathway-based results. For the case of NaCl, the free energies of the kink sites relative to a 1 M aqueous solution for Na+ and Cl- are found to be surprisingly different and of opposite sign, despite the ions having very similar hydration free energies.
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Affiliation(s)
- Alessandro Silvestri
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University, P.O. Box U1987, Perth, Western Australia 6845, Australia
| | - Paolo Raiteri
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University, P.O. Box U1987, Perth, Western Australia 6845, Australia
| | - Julian D Gale
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University, P.O. Box U1987, Perth, Western Australia 6845, Australia
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9
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Yaprintsev M, Vasil'ev A, Ivanov O, Popkov D. Interconnected effects of Sm-doping on grain structure and transport properties of the textured Bi2-Sm Te2.7Se0.3 compounds. J SOLID STATE CHEM 2022. [DOI: 10.1016/j.jssc.2022.123176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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10
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Bjelobrk Z, Rajagopalan AK, Mendels D, Karmakar T, Parrinello M, Mazzotti M. Solubility of Organic Salts in Solvent-Antisolvent Mixtures: A Combined Experimental and Molecular Dynamics Simulations Approach. J Chem Theory Comput 2022; 18:4952-4959. [PMID: 35833664 PMCID: PMC9367008 DOI: 10.1021/acs.jctc.2c00304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We combine molecular dynamics simulations with experiments to estimate solubilities of an organic salt in complex growth environments. We predict the solubility by simulations of the growth and dissolution of ions at the crystal surface kink sites at different solution concentrations. Thereby, the solubility is identified as the solution's salt concentration, where the energy of the ion pair dissolved in solution equals the energy of the ion pair crystallized at the kink sites. The simulation methodology is demonstrated for the case of anhydrous sodium acetate crystallized from various solvent-antisolvent mixtures. To validate the predicted solubilities, we have measured the solubilities of sodium acetate in-house, using an experimental setup and measurement protocol that guarantees moisture-free conditions, which is key for a hygroscopic compound like sodium acetate. We observe excellent agreement between the experimental and the computationally evaluated solubilities for sodium acetate in different solvent-antisolvent mixtures. Given the agreement and the rich data the simulations produce, we can use them to complement experimental tasks, which in turn will reduce time and capital in the design of complicated industrial crystallization processes of organic salts.
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Affiliation(s)
- Zoran Bjelobrk
- Institute of Energy and Process Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Ashwin Kumar Rajagopalan
- Department of Chemical Engineering, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Dan Mendels
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Tarak Karmakar
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi 110016, India
| | - Michele Parrinello
- Istituto Italiano di Tecnologia (IIT), Via Morego, 30, Genova 16163, Italy
| | - Marco Mazzotti
- Institute of Energy and Process Engineering, ETH Zürich, Zürich CH-8092, Switzerland
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11
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Gebauer D, Gale JD, Cölfen H. Crystal Nucleation and Growth of Inorganic Ionic Materials from Aqueous Solution: Selected Recent Developments, and Implications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107735. [PMID: 35678091 DOI: 10.1002/smll.202107735] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/07/2022] [Indexed: 05/27/2023]
Abstract
In this review article, selected, latest theoretical, and experimental developments in the field of nucleation and crystal growth of inorganic materials from aqueous solution are highlighted, with a focus on literature after 2015 and on non-classical pathways. A key point is to emphasize the so far underappreciated role of water and solvent entropy in crystallization at all stages from solution speciation through to the final crystal. While drawing on examples from current inorganic materials where non-classical behavior has been proposed, the potential of these approaches to be adapted to a wide-range of systems is also discussed, while considering the broader implications of the current re-assessment of pathways for crystallization. Various techniques that are suitable for the exploration of crystallization pathways in aqueous solution, from nucleation to crystal growth are summarized, and a flow chart for the assignment of specific theories based on experimental observations is proposed.
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Affiliation(s)
- Denis Gebauer
- Leibniz University Hannover, Institute of Inorganic Chemistry, Callinstr. 9, 30167, Hannover, Germany
| | - Julian D Gale
- Curtin Institute for Computation/The Institute for Geoscience Research (TiGER), School of Molecular and Life Sciences, Curtin University, PO Box U1987, Perth, Western Australia, 6845, Australia
| | - Helmut Cölfen
- University of Konstanz, Physical Chemistry, Universitätsstr. 10, 78465, Konstanz, Germany
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12
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Zhao X, Liu Y, Lin D, Zhu W, Ma N, Xu WW, Zhao W, Sun Y, Zeng XC. Anomalous Phase Behaviors of Monolayer NaCl Aqueous Solutions Induced by Effective Coulombic Interactions within Angstrom-Scale Slits. J Phys Chem Lett 2022; 13:2704-2710. [PMID: 35302778 DOI: 10.1021/acs.jpclett.2c00501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Interests in subnanofluidic devices have called for molecular dynamics (MD) simulation studies of the thermodynamic behavior of monolayer salt solution within angstrom-scale slits. However, it still remains a grand challenge to accurately describe the Coulombic interactions by incorporating the effects of charge transfer and electronic dielectric screening. Herein, by using the electronic continuum model, where the effective ion charges are fine-tuned with a scaling factor of λ, we present simulation evidence that the effective Coulombic interactions among Na+/Cl- ions can strongly affect the behavior of monolayer ionic aqueous solution. Our microsecond-scale MD simulations show that only the counterions with moderate effective charges (0.3 ≤ λ ≤ 0.8) can dissolve in monolayer water, whereas the high effective charges (λ ≥ 0.85) induce ions to assemble into monolayer nanocrystals, and ions with the low effective charges (λ ≤ 0.2) exhibit gas-like nanobubble. These findings could provide deeper insights into the physical chemistry behind subnanofluidic iontronic devices.
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Affiliation(s)
- Xiaorong Zhao
- Department of Physics, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Yuying Liu
- Department of Physics, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Dongdong Lin
- Department of Physics, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Weiduo Zhu
- Department of Physics, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Nan Ma
- Department of Physics, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Wen Wu Xu
- Department of Physics, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Wenhui Zhao
- Department of Physics, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Yunxiang Sun
- Department of Physics, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Xiao Cheng Zeng
- Department of Chemistry, University of Nebraska─Lincoln, Lincoln, Nebraska 68588, United States
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13
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Kikutsuji T, Mori Y, Okazaki KI, Mori T, Kim K, Matubayasi N. Explaining reaction coordinates of alanine dipeptide isomerization obtained from deep neural networks using Explainable Artificial Intelligence (XAI). J Chem Phys 2022; 156:154108. [DOI: 10.1063/5.0087310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A method for obtaining appropriate reaction coordinates is required to identify transition states distinguishing product and reactant in complex molecular systems. Recently, abundant research has been devoted to obtaining reaction coordinates using artificial neural networks from deep learning literature, where many collective variables are typically utilized in the input layer. However, it is difficult to explain the details of which collective variables contribute to the predicted reaction coordinates owing to the complexity of the nonlinear functions in deep neural networks. To overcome this limitation, we used Explainable Artificial Intelligence (XAI) methods of the Local Interpretable Model-agnostic Explanation (LIME) and the game theory-based framework known as Shapley Additive exPlanations (SHAP). We demonstrated that XAI enables us to obtain the degree of contribution of each collective variable to reaction coordinates that is determined by nonlinear regressions with deep learning for the committor of the alanine dipeptide isomerization in vacuum. In particular, both LIME and SHAP provide important features to the predicted reaction coordinates, which are characterized by appropriate dihedral angles consistent with those previously reported from the committor test analysis. The present study offers an AI-aided framework to explain the appropriate reaction coordinates, which acquires considerable significance when the number of degrees of freedom increases.
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Affiliation(s)
| | | | - Kei-ichi Okazaki
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Japan
| | - Toshifumi Mori
- Kyushu University Institute for Materials Chemistry and Engineering, Japan
| | - Kang Kim
- Graduate School of Engineering Science, Osaka University - Toyonaka Campus, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Japan
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14
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Dighe AV, Coliaie P, Podupu PKR, Singh MR. Selective desolvation in two-step nucleation mechanism steers crystal structure formation. NANOSCALE 2022; 14:1723-1732. [PMID: 35018395 DOI: 10.1039/d1nr06346d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The two-step nucleation (TSN) theory and crystal structure prediction (CSP) techniques are two disjointed yet popular methods to predict nucleation rate and crystal structure, respectively. The TSN theory is a well-established mechanism to describe the nucleation of a wide range of crystalline materials in different solvents. However, it has never been expanded to predict the crystal structure or polymorphism. On the contrary, the existing CSP techniques only empirically account for the solvent effects. As a result, the TSN theory and CSP techniques continue to evolve as separate methods to predict two essential attributes of nucleation - rate and structure. Here we bridge this gap and show for the first time how a crystal structure is formed within the framework of TSN theory. A sequential desolvation mechanism is proposed in TSN, where the first step involves partial desolvation to form dense clusters followed by selective desolvation of functional groups directing the formation of crystal structure. We investigate the effect of the specific interaction on the degree of solvation around different functional groups of glutamic acid molecules using molecular simulations. The simulated energy landscape and activation barriers at increasing supersaturations suggest sequential and selective desolvation. We validate computationally and experimentally that the crystal structure formation and polymorph selection are due to a previously unrecognized consequence of supersaturation-driven asymmetric desolvation of molecules.
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Affiliation(s)
- Anish V Dighe
- Department of Chemical Engineering, University of Illinois Chicago, Chicago, IL 60607, USA.
| | - Paria Coliaie
- Department of Chemical Engineering, University of Illinois Chicago, Chicago, IL 60607, USA.
| | - Prem K R Podupu
- Department of Chemical Engineering, University of Illinois Chicago, Chicago, IL 60607, USA.
| | - Meenesh R Singh
- Department of Chemical Engineering, University of Illinois Chicago, Chicago, IL 60607, USA.
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15
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Finney AR, Salvalaglio M. Bridging the gap between mesoscopic and molecular models of solid/liquid interfaces out-of-equilibrium. Chem Eng Res Des 2022. [DOI: 10.1016/j.cherd.2022.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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16
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Zou Z, Tsai ST, Tiwary P. Toward Automated Sampling of Polymorph Nucleation and Free Energies with the SGOOP and Metadynamics. J Phys Chem B 2021; 125:13049-13056. [PMID: 34788047 DOI: 10.1021/acs.jpcb.1c07595] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding the driving forces behind the nucleation of different polymorphs is of great importance for material sciences and the pharmaceutical industry. This includes understanding the reaction coordinate that governs the nucleation process and correctly calculating the relative free energies of different polymorphs. Here, we demonstrate, for the prototypical case of urea nucleation from the melt, how one can learn such a one-dimensional reaction coordinate as a function of prespecified order parameters and use it to perform efficient biased all-atom molecular dynamics simulations. The reaction coordinate is learnt as a function of the generic thermodynamic and structural order parameters using the "spectral gap optimization of order parameters (SGOOP)" approach [Tiwary, P. and Berne, B. J. Proc. Natl. Acad. Sci. U.S.A. (2016)] and is biased using well-tempered metadynamics simulations. The reaction coordinate gives insights into the role played by different structural and thermodynamics order parameters, and the biased simulations obtain accurate relative free energies for different polymorphs. This includes an accurate prediction of the approximate pressure at which urea undergoes a phase transition and one of the metastable polymorphs becomes the most stable conformation. We believe the ideas demonstrated in this work will facilitate efficient sampling of nucleation in complex, generic systems.
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Affiliation(s)
- Ziyue Zou
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Sun-Ting Tsai
- Department of Physics, University of Maryland, College Park, Maryland 20742, United States.,Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
| | - Pratyush Tiwary
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States.,Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
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17
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Zhao W, Sun Y, Zhu W, Jiang J, Zhao X, Lin D, Xu W, Duan X, Francisco JS, Zeng XC. Two-dimensional monolayer salt nanostructures can spontaneously aggregate rather than dissolve in dilute aqueous solutions. Nat Commun 2021; 12:5602. [PMID: 34556665 PMCID: PMC8460741 DOI: 10.1038/s41467-021-25938-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/02/2021] [Indexed: 11/29/2022] Open
Abstract
It is well known that NaCl salt crystals can easily dissolve in dilute aqueous solutions at room temperature. Herein, we reported the first computational evidence of a novel salt nucleation behavior at room temperature, i.e., the spontaneous formation of two-dimensional (2D) alkali chloride crystalline/non-crystalline nanostructures in dilute aqueous solution under nanoscale confinement. Microsecond-scale classical molecular dynamics (MD) simulations showed that NaCl or LiCl, initially fully dissolved in confined water, can spontaneously nucleate into 2D monolayer nanostructures with either ordered or disordered morphologies. Notably, the NaCl nanostructures exhibited a 2D crystalline square-unit pattern, whereas the LiCl nanostructures adopted non-crystalline 2D hexagonal ring and/or zigzag chain patterns. These structural patterns appeared to be quite generic, regardless of the water and ion models used in the MD simulations. The generic patterns formed by 2D monolayer NaCl and LiCl nanostructures were also confirmed by ab initio MD simulations. The formation of 2D salt structures in dilute aqueous solution at room temperature is counterintuitive. Free energy calculations indicated that the unexpected spontaneous salt nucleation behavior can be attributed to the nanoscale confinement and strongly compressed hydration shells of ions. Aqueous solutions under nanoscale confinement exhibit interesting physicochemical properties. This work reports evidence on the spontaneous formation of two-dimensional alkali chloride crystalline/non-crystalline nanostructures in dilute aqueous solution under nanoscale confinement by computer simulations.
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Affiliation(s)
- Wenhui Zhao
- Department of Physics, Ningbo University, Ningbo, 315211, China
| | - Yunxiang Sun
- Department of Physics, Ningbo University, Ningbo, 315211, China
| | - Weiduo Zhu
- Department of Materials Science and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Jian Jiang
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Xiaorong Zhao
- Department of Physics, Ningbo University, Ningbo, 315211, China
| | - Dongdong Lin
- Department of Physics, Ningbo University, Ningbo, 315211, China
| | - Wenwu Xu
- Department of Physics, Ningbo University, Ningbo, 315211, China
| | - Xiangmei Duan
- Department of Physics, Ningbo University, Ningbo, 315211, China
| | - Joseph S Francisco
- Department of Earth and Environmental Science, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Xiao Cheng Zeng
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA. .,Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
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18
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A survey on fractionation: the optimal control of distilling in batch and semibatch configurations. REV CHEM ENG 2021. [DOI: 10.1515/revce-2021-0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Since the middle of the last century, discussion about the operation of discontinuous fractionation to meet multifarious goals, such as product purity and recovery rate, by monitoring process variables including reflux or/and heat duty, is been on. The engineering practice showed intolerable events to occur; hereof the operation must be supervised, which makes it difficult to be in agreement with the batch distillation objectives. Hence, to uphold the effectuation of new operating policies into the industrial “know-how” techniques, different optimal control strategies can be conceived. The objective of this work is to offer a literature survey on the investigations of optimal control functioning for selected simple distillation column configurations employed in batch/semibatch distillation of homogeneous/reactive mixtures, as well as the approaches used in this regard. Available optimal control schemes have been reviewed in detail, emphasizing its major assets.
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19
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Liu F, Zhao D, Sun D. Stability of Two-Dimensional Ionic Clusters at Solid-Liquid Interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:6373-6379. [PMID: 34000803 DOI: 10.1021/acs.langmuir.0c03461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The stability of two-dimensional clusters (2DCs) at the interface between ionic crystals and their solutions was investigated by molecular dynamics simulations. We found that 2DCs show a remarkable feature of odd-even alternation in stability. In NaCl and NaBr systems, the clusters containing an odd number of ions are more stable than those with an even number of ions, while in KCl systems, it is the other way round. Accordingly, the stability of water molecules in the first hydration shell of 2DCs also shows an odd-even alternation, which is consistent with the associated 2DCs. The odd-even alternation is discussed based on a competition mechanism between two factors: the Coulomb repulsion in charged 2DCs and the interaction between charges and water dipoles. Our discussion indicates that this odd-even alternation should be a universal feature in similar systems and would be important for understanding the nucleation and crystallization of solutions on ionic crystal surfaces.
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Affiliation(s)
- Feng Liu
- Engineering Research Center for Nanophotonics & Advanced Instrument (MOE), School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
| | - Di Zhao
- Engineering Research Center for Nanophotonics & Advanced Instrument (MOE), School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
| | - Deyan Sun
- Engineering Research Center for Nanophotonics & Advanced Instrument (MOE), School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
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20
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Baskin A, Lawson JW, Prendergast D. Anion-Assisted Delivery of Multivalent Cations to Inert Electrodes. J Phys Chem Lett 2021; 12:4347-4356. [PMID: 33929859 DOI: 10.1021/acs.jpclett.1c00943] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
To understand and control key electrochemical processes-metal plating, corrosion, intercalation, etc.-requires molecular-scale details of the active species at electrochemical interfaces and their mechanisms for desolvation from the electrolyte. Using free energy sampling techniques we reveal the interfacial speciation of divalent cations in ether-based electrolytes and mechanisms for their delivery to an inert graphene electrode interface. Surprisingly, we find that anion solvophobicity drives a high population of anion-containing species to the interface that facilitate the delivery of divalent cations, even to negatively charged electrodes. Our simulations indicate that cation desolvation is greatly facilitated by cation-anion coupling. We propose anion solvophobicity as a molecular-level descriptor for rational design of electrolytes with increased efficiency for electrochemical processes limited by multivalent cation desolvation.
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Affiliation(s)
- Artem Baskin
- NASA Ames Research Center, Moffett Field, California 94035, United States
| | - John W Lawson
- NASA Ames Research Center, Moffett Field, California 94035, United States
| | - David Prendergast
- Joint Center for Energy Storage Research, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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21
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Yaprintsev M, Ivanov O, Vasil’ev A, Zhezhu M, Yaprintseva E. Effect of Sm-doping on microstructure and thermoelectric properties of textured n-type Bi2Te2.7Se0.3 compound due to change in ionic bonding fraction. J SOLID STATE CHEM 2021. [DOI: 10.1016/j.jssc.2021.122047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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22
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Bolhuis PG, Swenson DWH. Transition Path Sampling as Markov Chain Monte Carlo of Trajectories: Recent Algorithms, Software, Applications, and Future Outlook. ADVANCED THEORY AND SIMULATIONS 2021. [DOI: 10.1002/adts.202000237] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Peter G. Bolhuis
- Amsterdam Center for Multiscale Modeling van 't Hoff Institute for Molecular Sciences University of Amsterdam PO Box 94157 1090 GD Amsterdam The Netherlands
| | - David W. H. Swenson
- Centre Blaise Pascal Ecole Normale Superieure 46, allée d'Italie 69364 Lyon Cedex 07 France
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23
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Khanna V, Doherty MF, Peters B. Absolute chemical potentials for complex molecules in fluid phases: A centroid reference for predicting phase equilibria. J Chem Phys 2020; 153:214504. [PMID: 33291889 DOI: 10.1063/5.0025844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Solid-fluid phase equilibria are difficult to predict in simulations because bound degrees of freedom in the crystal phase must be converted to free translations and rotations in the fluid phase. Here, we avoid the solid-to-fluid transformation step by starting with chemical potentials for two reference systems, one for the fluid phase and one for the solid phase. For the solid, we start from the Einstein crystal and transform to the fully interacting molecular crystal. For the fluid phase, we introduce a new reference system, the "centroid," and then transform to gas phase molecules. We illustrate the new calculations by predicting the sublimation vapor pressure of succinic acid in the temperature range of 300 K-350 K.
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Affiliation(s)
- Vikram Khanna
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Michael F Doherty
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Baron Peters
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
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24
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Hill AR, Cubillas P, Gebbie-Rayet JT, Trueman M, de Bruyn N, Harthi ZA, Pooley RJS, Attfield MP, Blatov VA, Proserpio DM, Gale JD, Akporiaye D, Arstad B, Anderson MW. CrystalGrower: a generic computer program for Monte Carlo modelling of crystal growth. Chem Sci 2020; 12:1126-1146. [PMID: 34163880 PMCID: PMC8179067 DOI: 10.1039/d0sc05017b] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
A Monte Carlo crystal growth simulation tool, CrystalGrower, is described which is able to simultaneously model both the crystal habit and nanoscopic surface topography of any crystal structure under conditions of variable supersaturation or at equilibrium. This tool has been developed in order to permit the rapid simulation of crystal surface maps generated by scanning probe microscopies in combination with overall crystal habit. As the simulation is based upon a coarse graining at the nanoscopic level features such as crystal rounding at low supersaturation or undersaturation conditions are also faithfully reproduced. CrystalGrower permits the incorporation of screw dislocations with arbitrary Burgers vectors and also the investigation of internal point defects in crystals. The effect of growth modifiers can be addressed by selective poisoning of specific growth sites. The tool is designed for those interested in understanding and controlling the outcome of crystal growth through a deeper comprehension of the key controlling experimental parameters. Generic in silico methodology – CrystalGrower – for simulating crystal habit and nanoscopic surface topology to determine crystallisation free energies.![]()
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Affiliation(s)
- Adam R Hill
- Centre for Nanoporous Materials, School of Chemistry, The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Pablo Cubillas
- Centre for Nanoporous Materials, School of Chemistry, The University of Manchester Oxford Road Manchester M13 9PL UK
| | - James T Gebbie-Rayet
- Centre for Nanoporous Materials, School of Chemistry, The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Mollie Trueman
- Centre for Nanoporous Materials, School of Chemistry, The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Nathan de Bruyn
- Centre for Nanoporous Materials, School of Chemistry, The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Zulaikha Al Harthi
- Centre for Nanoporous Materials, School of Chemistry, The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Rachel J S Pooley
- Centre for Nanoporous Materials, School of Chemistry, The University of Manchester Oxford Road Manchester M13 9PL UK .,ASTAR, Institute of Materials Research and Engineering Fusionopolis 2 Singapore
| | - Martin P Attfield
- Centre for Nanoporous Materials, School of Chemistry, The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Vladislav A Blatov
- Samara Center for Theoretical Materials Science (SCTMS), Samara State Technical University Molodogvardeyskaya Street 244 Samara 443100 Russia.,Samara Center for Theoretical Materials Science (SCTMS), Samara University Academician Pavlov Street 1 Samara 443011 Russia
| | - Davide M Proserpio
- Samara Center for Theoretical Materials Science (SCTMS), Samara State Technical University Molodogvardeyskaya Street 244 Samara 443100 Russia.,Università degli Studi di Milano, Dipartimento di Chimica Via Camillo Golgi 19 20133 Milano Italy
| | - Julian D Gale
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University GPO Box U1987 Perth Western Australia 6845 Australia
| | | | | | - Michael W Anderson
- Centre for Nanoporous Materials, School of Chemistry, The University of Manchester Oxford Road Manchester M13 9PL UK .,Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University GPO Box U1987 Perth Western Australia 6845 Australia
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25
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Warzecha M, Verma L, Johnston BF, Palmer JC, Florence AJ, Vekilov PG. Olanzapine crystal symmetry originates in preformed centrosymmetric solute dimers. Nat Chem 2020; 12:914-920. [PMID: 32968232 DOI: 10.1038/s41557-020-0542-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 08/04/2020] [Indexed: 12/14/2022]
Abstract
The symmetries of a crystal are notoriously uncorrelated to those of its constituent molecules. This symmetry breaking is typically thought to occur during crystallization. Here we demonstrate that one of the two symmetry elements of olanzapine crystals, an inversion centre, emerges in solute dimers extant in solution prior to crystallization. We combine time-resolved in situ scanning probe microscopy to monitor the crystal growth processes with all-atom molecular dynamics simulations. We show that crystals grow non-classically, predominantly by incorporation of centrosymmetric dimers. The growth rate of crystal layers exhibits a quadratic dependence on the solute concentration, characteristic of the second-order kinetics of the incorporation of dimers, which exist in equilibrium with a majority of monomers. We show that growth by dimers is preferred due to overwhelming accumulation of adsorbed dimers on the crystal surface, where it is complemented by dimerization and expedites dimer incorporation into growth sites.
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Affiliation(s)
- Monika Warzecha
- EPSRC CMAC Future Manufacturing Research Hub, c/o Strathclyde Institute of Pharmacy and Biomedical Sciences, Technology and Innovation Centre, Glasgow, UK
| | - Lakshmanji Verma
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Blair F Johnston
- EPSRC CMAC Future Manufacturing Research Hub, c/o Strathclyde Institute of Pharmacy and Biomedical Sciences, Technology and Innovation Centre, Glasgow, UK.,National Physical Laboratory, Teddington, UK
| | - Jeremy C Palmer
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA.
| | - Alastair J Florence
- EPSRC CMAC Future Manufacturing Research Hub, c/o Strathclyde Institute of Pharmacy and Biomedical Sciences, Technology and Innovation Centre, Glasgow, UK.
| | - Peter G Vekilov
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA. .,Department of Chemistry, University of Houston, Houston, TX, USA.
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26
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Mori Y, Okazaki KI, Mori T, Kim K, Matubayasi N. Learning reaction coordinates via cross-entropy minimization: Application to alanine dipeptide. J Chem Phys 2020; 153:054115. [DOI: 10.1063/5.0009066] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Yusuke Mori
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | | | - Toshifumi Mori
- Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan
- The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
| | - Kang Kim
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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27
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Wang X, Toroz D, Kim S, Clegg SL, Park GS, Di Tommaso D. Density functional theory based molecular dynamics study of solution composition effects on the solvation shell of metal ions. Phys Chem Chem Phys 2020; 22:16301-16313. [PMID: 32647838 DOI: 10.1039/d0cp01957g] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present an ab initio molecular dynamics study of the alkali metal ions Li+, Na+, K+ and Cs+, and of the alkaline earth metal ions Mg2+ and Ca2+ in both pure water and electrolyte solutions containing the counterions Cl- and SO42-. Simulations were conducted using different density functional theory methods (PBE, BLYP and revPBE), with and without the inclusion of dispersion interactions (-D3). Analysis of the ion-water structure and interaction strength, water exchange between the first and second hydration shell, and hydrogen bond network and low-frequency reorientation dynamics around the metal ions have been used to characterise the influence of solution composition on the ionic solvation shell. Counterions affect the properties of the hydration shell not only when they are directly coordinated to the metal ion, but also when they are at the second coordination shell. Chloride ions reduce the sodium hydration shell and expand the calcium hydration shell by stabilizing under-coordinated hydrated Na(H2O)5+ complexes and over-coordinated Ca(H2O)72+. The same behaviour is observed in CaSO4(aq), where Ca2+ and SO42- form almost exclusively solvent-shared ion pairs. Water exchange between the first and second hydration shell around Ca2+ in CaSO4(aq) is drastically decelerated compared with the simulations of the hydrated metal ion (single Ca2+, no counterions). Velocity autocorrelation function analysis, used to probe the strength of the local ion-water interaction, shows a smoother decay of Mg2+ in MgCl2(aq), which is a clear indication of a looser inter-hexahedral vibration in the presence of chloride ions located in the second coordination shell of Mg2+. The hydrogen bond statistics and orientational dynamics in the ionic solvation shell show that the influence on the water-water network cannot only be ascribed to the specific cation-water interaction, but also to the subtle interplay between the level of hydration of the ions, and the interactions between ions, especially those of opposite charge. As many reactive processes involving solvated metal ions occur in environments that are far from pure water but rich in ions, this computational study shows how the solution composition can result in significant differences in behaviour and function of the ionic solvation shell.
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Affiliation(s)
- Xiangwen Wang
- School of Biological and Chemical Sciences, Materials Research Institute, Thomas Young Centre, Queen Mary University of London, Mile End Road, E1 4NS, London, UK.
| | - Dimitrios Toroz
- School of Biological and Chemical Sciences, Materials Research Institute, Thomas Young Centre, Queen Mary University of London, Mile End Road, E1 4NS, London, UK.
| | - Seonmyeong Kim
- Center for THz-driven Biological Systems, Department of Physics and Astronomy, Seoul National University, Seoul, 08826, Republic of Korea and Advanced Institutes of Convergence Technology, Seoul National University, Suwon-Si, Gyeonggi-do 16229, Republic of Korea
| | - Simon L Clegg
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Gun-Sik Park
- Center for THz-driven Biological Systems, Department of Physics and Astronomy, Seoul National University, Seoul, 08826, Republic of Korea and Advanced Institutes of Convergence Technology, Seoul National University, Suwon-Si, Gyeonggi-do 16229, Republic of Korea
| | - Devis Di Tommaso
- School of Biological and Chemical Sciences, Materials Research Institute, Thomas Young Centre, Queen Mary University of London, Mile End Road, E1 4NS, London, UK.
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28
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Leitold C, Mundy CJ, Baer MD, Schenter GK, Peters B. Solvent reaction coordinate for an SN2 reaction. J Chem Phys 2020; 153:024103. [DOI: 10.1063/5.0002766] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Christian Leitold
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Christopher J. Mundy
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Marcel D. Baer
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Gregory K. Schenter
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Baron Peters
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Chemistry and Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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29
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Panagiotopoulos AZ. Simulations of activities, solubilities, transport properties, and nucleation rates for aqueous electrolyte solutions. J Chem Phys 2020; 153:010903. [DOI: 10.1063/5.0012102] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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30
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Liu F, Sun D. Ion Distribution and Hydration Structure at Solid-Liquid Interface between NaCl Crystal and Its Solution. ACS OMEGA 2019; 4:18692-18698. [PMID: 31737830 PMCID: PMC6854578 DOI: 10.1021/acsomega.9b02620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 10/21/2019] [Indexed: 06/10/2023]
Abstract
The interface structure between NaCl crystal and its solution has been investigated at the saturated concentration of 298 K by molecular dynamics simulations. We have found that there are many fine structures at this complex interface. Near the surface of crystal, most of Na+ only coordinate with water molecules, while almost all Cl- coordinate with Na+ in addition to water molecules. An ion coordinating with more water molecules is farther away from the epitaxial position of lattice. As approaching to the interface, the first hydration shell of ions has the tendency of being ordered, while the orientation of dipole of water molecules in the first hydration shell becomes more disordered than that in the solution. Generally, the first hydration shell of Na+ is less affected by nearest Cl-, whereas the first hydration shell of Cl- is significantly affected by nearest Na+.
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31
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Solvent fluctuations in the solvation shell determine the activation barrier for crystal growth rates. Proc Natl Acad Sci U S A 2019; 116:23954-23959. [PMID: 31712439 DOI: 10.1073/pnas.1910691116] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Solution crystallization is a common technique to grow advanced, functional crystalline materials. Supersaturation, temperature, and solvent composition are known to influence the growth rates and thereby properties of crystalline materials; however, a satisfactory explanation of how these factors affect the activation barrier for growth rates has not been developed. We report here that these effects can be attributed to a previously unrecognized consequence of solvent fluctuations in the solvation shell of solute molecules attaching to the crystal surface. With increasing supersaturation, the average hydration number of the glutamic acid molecule decreases and can reach an asymptotic limit corresponding to the number of adsorption sites on the molecule. The hydration number of the glutamic acid molecule also fluctuates due to the rapid exchange of solvent in the solvation shell and local variation in the supersaturation. These rapid fluctuations allow quasi-equilibrium between fully solvated and partially desolvated states of molecules, which can be used to construct a double-well potential and thereby to identify the transition state and the required activation barrier. The partially desolvated molecules are not stable and can attach spontaneously to the crystal surface. The activation barrier versus hydration number follows the Evans-Polanyi relation. The predicted absolute growth rates of the α-glutamic acid crystal at lower supersaturations are in reasonable agreement with the experimental observations.
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32
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Koskamp J, Ruiz-Hernandez SE, Di Tommaso D, Elena AM, De Leeuw NH, Wolthers M. Reconsidering Calcium Dehydration as the Rate-Determining Step in Calcium Mineral Growth. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2019; 123:26895-26903. [PMID: 31737161 PMCID: PMC6849658 DOI: 10.1021/acs.jpcc.9b06403] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/15/2019] [Indexed: 06/10/2023]
Abstract
The dehydration of cations is generally accepted as the rate-limiting step in many processes. Molecular dynamics (MD) can be used to investigate the dynamics of water molecules around cations, and two different methods exist to obtain trajectory-based water dehydration frequencies. Here, these two different post-processing methods (direct method versus survival function) have been implemented to obtain calcium dehydration frequencies from a series of trajectories obtained using a range of accepted force fields. None of the method combinations reproduced the commonly accepted experimental water exchange frequency of 10-8.2 s-1. Instead, our results suggest much faster water dynamics, comparable with more accurate ab initio MD simulations and with experimental values obtained using neutron scattering techniques. We obtained the best agreement using the survival function method to characterize the water dynamics, and we show that different method combinations significantly affect the outcome. Our work strongly suggests that the fast water exchange kinetics around the calcium ions is not rate-limiting for reactions involving dissolved/solvated calcium. Our results further suggest that, for alkali and most of the earth alkali metals, mechanistic rate laws for growth, dissolution, and adsorption, which are based on the principle of rate-limiting cation dehydration, need careful reconsideration.
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Affiliation(s)
- Janou
A. Koskamp
- Department
of Earth Sciences-Geochemistry, Utrecht
University, 3584 CB Utrecht, The Netherlands
| | | | - Devis Di Tommaso
- Materials
Research Institute and School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, E1 4NS London, United Kingdom
| | | | - Nora H. De Leeuw
- Department
of Earth Sciences-Geochemistry, Utrecht
University, 3584 CB Utrecht, The Netherlands
- School
of Chemistry, Cardiff University, Main Building Park Place, Cardiff CF10 3AT, United Kingdom
| | - Mariette Wolthers
- Department
of Earth Sciences-Geochemistry, Utrecht
University, 3584 CB Utrecht, The Netherlands
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Brotzakis ZF, Bolhuis PG. Approximating free energy and committor landscapes in standard transition path sampling using virtual interface exchange. J Chem Phys 2019; 151:174111. [DOI: 10.1063/1.5119252] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Z. Faidon Brotzakis
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Peter G. Bolhuis
- Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
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34
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Karmakar T, Piaggi PM, Parrinello M. Molecular Dynamics Simulations of Crystal Nucleation from Solution at Constant Chemical Potential. J Chem Theory Comput 2019; 15:6923-6930. [DOI: 10.1021/acs.jctc.9b00795] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Tarak Karmakar
- Department of Chemistry and Applied Biosciences, ETH Zürich, c/o USI Campus, Via Giuseppe Buffi 13, CH-6900, Lugano, Ticino, Switzerland
- Facoltà di Informatica, Istituto di Scienze Computationali, Università della Svizzera Italiana, Via Giuseppe Buffi 13, CH-6900, Lugano, Ticino, Switzerland
| | - Pablo M. Piaggi
- Department of Chemistry and Applied Biosciences, ETH Zürich, c/o USI Campus, Via Giuseppe Buffi 13, CH-6900, Lugano, Ticino, Switzerland
- Facoltà di Informatica, Istituto di Scienze Computationali, Università della Svizzera Italiana, Via Giuseppe Buffi 13, CH-6900, Lugano, Ticino, Switzerland
| | - Michele Parrinello
- Department of Chemistry and Applied Biosciences, ETH Zürich, c/o USI Campus, Via Giuseppe Buffi 13, CH-6900, Lugano, Ticino, Switzerland
- Facoltà di Informatica, Istituto di Scienze Computationali, Università della Svizzera Italiana, Via Giuseppe Buffi 13, CH-6900, Lugano, Ticino, Switzerland
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35
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Paul S, Nair NN, Vashisth H. Phase space and collective variable based simulation methods for studies of rare events. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1634268] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Sanjib Paul
- Department of Chemical Engineering, University of New Hampshire, Durham, NH, USA
| | - Nisanth N. Nair
- Department of Chemistry, Indian Institute of Technology, Kanpur, India
| | - Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, Durham, NH, USA
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36
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Zhai H, Wang L, Putnis CV. Inhibition of Spiral Growth and Dissolution at the Brushite (010) Interface by Chondroitin 4-Sulfate. J Phys Chem B 2019; 123:845-851. [PMID: 30615454 DOI: 10.1021/acs.jpcb.8b11531] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Modulation of mineralization and demineralization of calcium phosphates (Ca-Ps) with organic macromolecules is a critical process which prevents human kidney stone disease. As a long unbranched polysaccharide of urinary glycosaminoglycans, chondroitin 4-sulfate (Ch4S) has been shown to play an essential role in inhibiting the formation of kidney stones. However, the mechanism of the role of Ch4S remains poorly understood. Here, we used in situ atomic force microscopy to observe the growth and dissolution of spirals on brushite (CaHPO4·2H2O) (010) surfaces. The results show that Ch4S preferentially inhibits the [101]Cc step growth/dissolution by step pinning. This step-specific effect appears to be related to specific binding of Ch4S to Ca sites, as the observed inhibition is not seen in other crystallographic directions where there are fewer Ca terminations. Moreover, Ch4S promotes an increase in the terrace width of [101̅]Cc by the modification of the interfacial energies of the step edge. These in vitro direct observations of Ch4S modulating brushite mineralization and demineralization reveal a dual control of both step kinetics and interfacial energy.
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Affiliation(s)
- Hang Zhai
- College of Resources and Environment , Huazhong Agricultural University , Wuhan 430070 , China
| | - Lijun Wang
- College of Resources and Environment , Huazhong Agricultural University , Wuhan 430070 , China
| | - Christine V Putnis
- Institut für Mineralogie , University of Münster , 48149 Münster , Germany.,Department of Chemistry , Curtin University , Perth 6845 , Australia
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37
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Roy S, Bryantsev VS. Finding Order in the Disordered Hydration Shell of Rapidly Exchanging Water Molecules around the Heaviest Alkali Cs+ and Fr+. J Phys Chem B 2018; 122:12067-12076. [DOI: 10.1021/acs.jpcb.8b08414] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Santanu Roy
- Chemical Science Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Vyacheslav S. Bryantsev
- Chemical Science Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
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38
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Shen Z, Kerisit SN, Stack AG, Rosso KM. Free-Energy Landscape of the Dissolution of Gibbsite at High pH. J Phys Chem Lett 2018; 9:1809-1814. [PMID: 29575896 DOI: 10.1021/acs.jpclett.8b00484] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The individual elementary reactions involved in the dissolution of a solid into solution remain mostly speculative due to a lack of direct experimental probes. In this regard, we have applied atomistic simulations to map the free-energy landscape of the dissolution of gibbsite from a step edge as a model of metal hydroxide dissolution. The overall reaction combines kink formation and kink propagation. Two individual reactions were found to be rate-limiting for kink formation, that is, the displacement of Al from a step site to a ledge adatom site and its detachment from ledge/terrace adatom sites into the solution. As a result, a pool of mobile and labile adsorbed species, or adatoms, exists before the release of Al into solution. Because of the quasi-hexagonal symmetry of gibbsite, kink site propagation can occur in multiple directions. Overall, our results will enable the development of microscopic mechanistic models of metal oxide dissolution.
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Affiliation(s)
- Zhizhang Shen
- Physical Sciences Division, Physical & Computational Sciences Directorate , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Sebastien N Kerisit
- Physical Sciences Division, Physical & Computational Sciences Directorate , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Andrew G Stack
- Chemical Science Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
| | - Kevin M Rosso
- Physical Sciences Division, Physical & Computational Sciences Directorate , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
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