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Guidarelli Mattioli F, Sciortino F, Russo J. Are Neural Network Potentials Trained on Liquid States Transferable to Crystal Nucleation? A Test on Ice Nucleation in the mW Water Model. J Phys Chem B 2023; 127:3894-3901. [PMID: 37075256 PMCID: PMC10165654 DOI: 10.1021/acs.jpcb.3c00693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/06/2023] [Indexed: 04/21/2023]
Abstract
Neural network potentials (NNPs) are increasingly being used to study processes that happen on long time scales. A typical example is crystal nucleation, which rate is controlled by the occurrence of a rare fluctuation, i.e., the appearance of the critical nucleus. Because the properties of this nucleus are far from those of the bulk crystal, it is yet unclear whether NN potentials trained on equilibrium liquid states can accurately describe nucleation processes. So far, nucleation studies on NNPs have been limited to ab initio models whose nucleation properties are unknown, preventing an accurate comparison. Here we train a NN potential on the mW model of water─a classical three-body potential whose nucleation time scale is accessible in standard simulations. We show that a NNP trained only on a small number of liquid state points can reproduce with great accuracy the nucleation rates and free energy barriers of the original model, computed from both spontaneous and biased trajectories, strongly supporting the use of NNPs to study nucleation events.
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Affiliation(s)
| | | | - John Russo
- Sapienza University of Rome, Piazzale Aldo Moro 2, 00185 Rome, Italy
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2
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Borah RR, Deka RP. Stabilization of Zn group dimers: A theoretical study. J Comput Chem 2022. [DOI: 10.1002/jcc.26972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Ritam R. Borah
- Advanced Computational Chemistry Centre Cotton University Guwahati India
| | - Rinu P. Deka
- Advanced Computational Chemistry Centre Cotton University Guwahati India
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3
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Russo J, Leoni F, Martelli F, Sciortino F. The physics of empty liquids: from patchy particles to water. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2022; 85:016601. [PMID: 34905739 DOI: 10.1088/1361-6633/ac42d9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Empty liquids represent a wide class of materials whose constituents arrange in a random network through reversible bonds. Many key insights on the physical properties of empty liquids have originated almost independently from the study of colloidal patchy particles on one side, and a large body of theoretical and experimental research on water on the other side. Patchy particles represent a family of coarse-grained potentials that allows for a precise control of both the geometric and the energetic aspects of bonding, while water has arguably the most complex phase diagram of any pure substance, and a puzzling amorphous phase behavior. It was only recently that the exchange of ideas from both fields has made it possible to solve long-standing problems and shed new light on the behavior of empty liquids. Here we highlight the connections between patchy particles and water, focusing on the modelling principles that make an empty liquid behave like water, including the factors that control the appearance of thermodynamic and dynamic anomalies, the possibility of liquid-liquid phase transitions, and the crystallization of open crystalline structures.
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Affiliation(s)
- John Russo
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Fabio Leoni
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Fausto Martelli
- IBM Research Europe, Hartree Centre, Daresbury WA4 4AD, United Kingdom
| | - Francesco Sciortino
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
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5
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P Lamas C, R Espinosa J, M Conde M, Ramírez J, Montero de Hijes P, G Noya E, Vega C, Sanz E. Homogeneous nucleation of NaCl in supersaturated solutions. Phys Chem Chem Phys 2021; 23:26843-26852. [PMID: 34817484 DOI: 10.1039/d1cp02093e] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The seeding method is an approximate approach to investigate nucleation that combines molecular dynamics simulations with classical nucleation theory. Recently, this technique has been successfully implemented in a broad range of nucleation studies. However, its accuracy is subject to the arbitrary choice of the order parameter threshold used to distinguish liquid-like from solid-like molecules. We revisit here the crystallization of NaCl from a supersaturated brine solution and show that consistency between seeding and rigorous methods, like Forward Flux Sampling (from previous work) or spontaneous crystallization (from this work), is achieved by following a mislabelling criterion to select such threshold (i.e. equaling the fraction of the mislabelled particles in the bulk parent and nucleating phases). This work supports the use of seeding to obtain fast and reasonably accurate nucleation rate estimates and the mislabelling criterion as one giving the relevant cluster size for classical nucleation theory in crystallization studies.
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Affiliation(s)
- C P Lamas
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain. .,Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, CSIC, Calle Serrano 119, 28006 Madrid, Spain
| | - J R Espinosa
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0H3, UK
| | - M M Conde
- Departamento de Ingeniería Química Industrial y Medio Ambiente, Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid, 28006, Madrid, Spain
| | - J Ramírez
- Departamento de Ingeniería Química Industrial y Medio Ambiente, Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid, 28006, Madrid, Spain
| | - P Montero de Hijes
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain.
| | - E G Noya
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, CSIC, Calle Serrano 119, 28006 Madrid, Spain
| | - C Vega
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain.
| | - E Sanz
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain.
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6
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Gallo P, Bachler J, Bove LE, Böhmer R, Camisasca G, Coronas LE, Corti HR, de Almeida Ribeiro I, de Koning M, Franzese G, Fuentes-Landete V, Gainaru C, Loerting T, de Oca JMM, Poole PH, Rovere M, Sciortino F, Tonauer CM, Appignanesi GA. Advances in the study of supercooled water. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2021; 44:143. [PMID: 34825973 DOI: 10.1140/epje/s10189-021-00139-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/17/2021] [Indexed: 06/13/2023]
Abstract
In this review, we report recent progress in the field of supercooled water. Due to its uniqueness, water presents numerous anomalies with respect to most simple liquids, showing polyamorphism both in the liquid and in the glassy state. We first describe the thermodynamic scenarios hypothesized for the supercooled region and in particular among them the liquid-liquid critical point scenario that has so far received more experimental evidence. We then review the most recent structural indicators, the two-state model picture of water, and the importance of cooperative effects related to the fact that water is a hydrogen-bonded network liquid. We show throughout the review that water's peculiar properties come into play also when water is in solution, confined, and close to biological molecules. Concerning dynamics, upon mild supercooling water behaves as a fragile glass former following the mode coupling theory, and it turns into a strong glass former upon further cooling. Connections between the slow dynamics and the thermodynamics are discussed. The translational relaxation times of density fluctuations show in fact the fragile-to-strong crossover connected to the thermodynamics arising from the existence of two liquids. When considering also rotations, additional crossovers come to play. Mobility-viscosity decoupling is also discussed in supercooled water and aqueous solutions. Finally, the polyamorphism of glassy water is considered through experimental and simulation results both in bulk and in salty aqueous solutions. Grains and grain boundaries are also discussed.
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Affiliation(s)
- Paola Gallo
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, Via della Vasca Navale 84, 00146, Roma, Italy.
| | - Johannes Bachler
- Institute of Physical Chemistry, University of Innsbruck, Innrain 52c, A-6020, Innsbruck, Austria
| | - Livia E Bove
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185, Roma, Italy
- Sorbonne Université, CNRS UMR 7590, IMPMC, 75005, Paris, France
| | - Roland Böhmer
- Fakultät Physik, Technische Universität Dortmund, 44221, Dortmund, Germany
| | - Gaia Camisasca
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, Via della Vasca Navale 84, 00146, Roma, Italy
| | - Luis E Coronas
- Secció de Física Estadística i Interdisciplinària-Departament de Física de la Matèria Condensada, Universitat de Barcelona, & Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, C. Martí i Franquès 1, 08028, Barcelona, Spain
| | - Horacio R Corti
- Departamento de Física de la Materia Condensada, Centro Atómico Constituyentes, Comisión Nacional de Energía Atómica, B1650LWP, Buenos Aires, Argentina
| | - Ingrid de Almeida Ribeiro
- Instituto de Física "Gleb Wataghin", Universidade Estadual de Campinas, UNICAMP, 13083-859, Campinas, São Paulo, Brazil
| | - Maurice de Koning
- Instituto de Física "Gleb Wataghin", Universidade Estadual de Campinas, UNICAMP, 13083-859, Campinas, São Paulo, Brazil
- Center for Computing in Engineering & Sciences, Universidade Estadual de Campinas, UNICAMP, 13083-861, Campinas, São Paulo, Brazil
| | - Giancarlo Franzese
- Secció de Física Estadística i Interdisciplinària-Departament de Física de la Matèria Condensada, Universitat de Barcelona, & Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, C. Martí i Franquès 1, 08028, Barcelona, Spain
| | - Violeta Fuentes-Landete
- Institute of Physical Chemistry, University of Innsbruck, Innrain 52c, A-6020, Innsbruck, Austria
| | - Catalin Gainaru
- Fakultät Physik, Technische Universität Dortmund, 44221, Dortmund, Germany
| | - Thomas Loerting
- Institute of Physical Chemistry, University of Innsbruck, Innrain 52c, A-6020, Innsbruck, Austria
| | | | - Peter H Poole
- Department of Physics, St. Francis Xavier University, Antigonish, NS, B2G 2W5, Canada
| | - Mauro Rovere
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, Via della Vasca Navale 84, 00146, Roma, Italy
| | - Francesco Sciortino
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185, Roma, Italy
| | - Christina M Tonauer
- Institute of Physical Chemistry, University of Innsbruck, Innrain 52c, A-6020, Innsbruck, Austria
| | - Gustavo A Appignanesi
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000, Bahía Blanca, Argentina
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7
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Mukherjee S, Bagchi B. Theoretical analyses of pressure induced glass transition in water: Signatures of surprising diffusion-entropy scaling across the transition. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1930222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Saumyak Mukherjee
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, India
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9
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Abstract
Water determines the properties of biological systems. Therefore, understanding the nature of the mutual interaction between water and biosystems is of primary importance for a proper assessment of any biological activity, e.g., the efficacy of new drugs or vaccines. A convenient way to characterize the interactions between biosystems and water is to analyze their impact on water density and dynamics in the proximity of the interfaces. It is commonly accepted that water bulk density and dynamical properties are recovered at distances of the order of 1 nm away from the surface of biological systems. This notion leads to the definition of hydration or biological water as the nanoscopic layer of water covering the surface of biosystems and to the expectation that all the effects of the water-interface interaction are limited to this thin region. Here, we review some of our latest contributions, showing that phospholipid membranes affect the water dynamics, structural properties, and hydrogen bond network at a distance that is more than twice as large as the commonly evoked ∼1nm thick layer and of the order of 2.4 nm. Furthermore, we unveil that at a shorter distance ∼0.5nm from the membrane, instead, there is an additional interface between lipid-bound and unbound water. Bound water has a structural role in the stability of the membrane. Our results imply that the concept of hydration water should be revised or extended and pave the way to a deeper understanding of the mutual interactions between water and biological systems.
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Bianco V, de Hijes PM, Lamas CP, Sanz E, Vega C. Anomalous Behavior in the Nucleation of Ice at Negative Pressures. PHYSICAL REVIEW LETTERS 2021; 126:015704. [PMID: 33480790 DOI: 10.1103/physrevlett.126.015704] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/14/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
Ice nucleation is a phenomenon that, despite the relevant implications for life, atmospheric sciences, and technological applications, is far from being completely understood, especially under extreme thermodynamic conditions. In this work we present a computational investigation of the homogeneous ice nucleation at negative pressures. By means of the seeding technique we estimate the size of the ice critical nucleus N_{c} for the TIP4P/Ice water model. This is done along the isotherms 230, 240, and 250 K, from positive to negative pressures until reaching the liquid-gas kinetic stability limit (where cavitation cannot be avoided). We find that N_{c} is nonmonotonic upon depressurization, reaching a minimum at negative pressures in the doubly metastable region of water. According to classical nucleation theory we establish the nucleation rate J and the surface tension γ, revealing a retracing behavior of both when the liquid-gas kinetic stability limit is approached. We also predict a reentrant behavior of the homogeneous nucleation line. The reentrance of these properties is related to the reentrance of the coexistence line at negative pressure, revealing new anomalies of water. The results of this work suggest the possibility of having metastable samples of liquid water for long times at negative pressure provided that heterogeneous nucleation is suppressed.
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Affiliation(s)
- Valentino Bianco
- Departamento de Quimica Fisica, Facultad de Quimica, Universidad Complutense de Madrid, Ciudad Universitaria, Madrid 28040, Spain
| | - P Montero de Hijes
- Departamento de Quimica Fisica, Facultad de Quimica, Universidad Complutense de Madrid, Ciudad Universitaria, Madrid 28040, Spain
| | - Cintia P Lamas
- Departamento de Quimica Fisica, Facultad de Quimica, Universidad Complutense de Madrid, Ciudad Universitaria, Madrid 28040, Spain
| | - Eduardo Sanz
- Departamento de Quimica Fisica, Facultad de Quimica, Universidad Complutense de Madrid, Ciudad Universitaria, Madrid 28040, Spain
| | - Carlos Vega
- Departamento de Quimica Fisica, Facultad de Quimica, Universidad Complutense de Madrid, Ciudad Universitaria, Madrid 28040, Spain
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11
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Li G, Meng L, Zhang H, Li X, Zeng Y. Electronic structure of triangular M 3 (M = B, Al, Ga): nonclassical three-center two electron π bond and σ delocalization. Phys Chem Chem Phys 2020; 22:18071-18077. [PMID: 32760940 DOI: 10.1039/d0cp02594a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The small molecule clusters have received more and more attention due to their widespread applications in chemical insulators, explosives, semiconductors and the high energy density materials industry. The electron deficiency of group IIIA elements endows their clusters with interesting properties. In this work, the electronic structures of M3 (M = B, Al, Ga) have been investigated by means of a complete active space self-consistent field (CASSCF) method. The nature of the chemical bond has been analyzed using the quantum theory of atoms in molecules (QTAIM) and electron localization function (ELF) analyses. The following conclusions can be drawn: in M3 (M = B, Al, Ga) clusters, two π electrons are shared by three atoms forming a 3c-2e delocalization π bond. Going from B3 to Al3 to Ga3, more and more electrons move from the bond pair to the outside of the M atom, which leads to a gradual enhancement of the delocalization of σ electrons. Aromaticity and the adaptive natural density partitioning (AdNDP) analyses reveal the existence of the 3c-2e π bond and delocalization of σ electrons in the studied systems.
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Affiliation(s)
- Guangxia Li
- Institute of Computational Quantum Chemistry, College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang 050024, P. R. China.
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12
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Gallo P, Loerting T, Sciortino F. Supercooled water: A polymorphic liquid with a cornucopia of behaviors. J Chem Phys 2019; 151:210401. [DOI: 10.1063/1.5135706] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Paola Gallo
- Department of Mathematics and Physics, University Roma Tre Via della Vasca Navale 84, I-00146 Rome, Italy
| | - Thomas Loerting
- Institute of Physical Chemistry, University of Innsbruck Innrain 52c, A-6020 Innsbruck, Austria
| | - Francesco Sciortino
- Department of Physics, Sapienza Universitá di Roma, Piazzale Aldo Moro 2, I-00185 Roma, Italy
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