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Iorio A, Perin L, Gallo P. Structure and slow dynamics of protein hydration water with cryopreserving DMSO and trehalose upon cooling. J Chem Phys 2024; 160:244502. [PMID: 38912631 DOI: 10.1063/5.0205569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/05/2024] [Indexed: 06/25/2024] Open
Abstract
We study, through molecular dynamics simulations, three aqueous solutions with one lysozyme protein and three different concentrations of trehalose and dimethyl sulfoxide (DMSO). We analyze the structural and dynamical properties of the protein hydration water upon cooling. We find that trehalose plays a major role in modifying the structure of the network of HBs between water molecules in the hydration layer of the protein. The dynamics of hydration water presents, in addition to the α-relaxation, typical of glass formers, a slower long-time relaxation process, which greatly slows down the dynamics of water, particularly in the systems with trehalose, where it becomes dominant at low temperatures. In all the solutions, we observe, from the behavior of the α-relaxation times, a shift of the Mode Coupling Theory crossover temperature and the fragile-to-strong crossover temperature toward higher values with respect to bulk water. We also observe a strong-to-strong crossover from the temperature behavior of the long-relaxation times. In the aqueous solution with only DMSO, the transition shifts to a lower temperature than in the case with only lysozyme reported in the literature. We observe that the addition of trehalose to the mixture has the opposite effect of restoring the original location of the strong-to-strong crossover. In all the solutions analyzed in this work, the observed temperature of the protein dynamical transition is slightly shifted at lower temperatures than that of the strong-to-strong crossover, but their relative order is the same, showing a correlation between the motion of the protein and that of the hydration water.
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Affiliation(s)
- Antonio Iorio
- Dipartimento di Fisica, Università Roma Tre, Via della Vasca Navale 84, I-00146 Roma, Italy
| | - Leonardo Perin
- Dipartimento di Fisica, Università Roma Tre, Via della Vasca Navale 84, I-00146 Roma, Italy
| | - Paola Gallo
- Dipartimento di Fisica, Università Roma Tre, Via della Vasca Navale 84, I-00146 Roma, Italy
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2
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Lupi L, Gallo P. Glassy dynamics of water in TIP4P/Ice aqueous solutions of trehalose in comparison with the bulk phase. J Chem Phys 2023; 159:154504. [PMID: 37850697 DOI: 10.1063/5.0168933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/25/2023] [Indexed: 10/19/2023] Open
Abstract
We perform molecular dynamics simulations of TIP4P/Ice water in solution with trehalose for 3.65 and 18.57 wt. % concentrations and of bulk TIP4P/Ice water at ambient pressure, to characterize the structure and dynamics of water in a sugar aqueous solution in the supercooled region. We find here that TIP4P/Ice water in solution with trehalose molecules follows the Mode Coupling Theory and undergoes a fragile to strong transition up to the highest concentration investigated, similar to the bulk. Moreover, we perform a Mode Coupling Theory test, showing that the Time Temperature Superposition principle holds for both bulk TIP4P/Ice water and for TIP4P/Ice water in the solutions and we calculate the exponents of the theory. The direct comparison of the dynamical results for bulk water and water in the solutions shows upon cooling along the isobar a fastening of water dynamics for lower temperatures, T < 240 K. We found that the counter-intuitive behavior for the low temperature solutions can be explained with the diffusion anomaly of water leading us to the conclusion that the fastening observed below T = 240 K in water dynamics is only fictitious, due to the fact that the density of water molecules in the solutions is higher than the density of the bulk at the same temperature and pressure. This result should be taken into account in experimental investigations which are often carried out at constant pressure.
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Affiliation(s)
- Laura Lupi
- Dipartimento di Matematica e Fisica, Università Roma Tre, Via della Vasca Navale 84, 00146 Rome, Italy
| | - Paola Gallo
- Dipartimento di Matematica e Fisica, Università Roma Tre, Via della Vasca Navale 84, 00146 Rome, Italy
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3
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Woods KN. Modeling of protein hydration dynamics is supported by THz spectroscopy of highly diluted solutions. Front Chem 2023; 11:1131935. [PMID: 37361018 PMCID: PMC10290188 DOI: 10.3389/fchem.2023.1131935] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 05/30/2023] [Indexed: 06/28/2023] Open
Abstract
In this investigation, we report the effect on the microscopic dynamics and interactions of the cytokine interferon gamma (IFN-γ) and antibodies to IFN-γ (anti-IFN-γ) and to the interferon gamma receptor 1 (anti-IFNGR1) prepared in highly dilute (HD) solutions of initial proteins. THz spectroscopy measurements have been conducted as a means to analyze and characterize the collective dynamics of the HD samples. MD simulations have also been performed that have successfully reproduced the observed signatures from experimental measurement. Using this joint experimental-computational approach we determine that the HD process associated with the preparation of the highly diluted samples used in this investigation induces a dynamical transition that results in collective changes in the hydrogen-bond network of the solvent. The dynamical transition in the solvent is triggered by changes in the mobility and hydrogen-bonding interactions of the surface molecules in the HD samples and is characterized by dynamical heterogeneity. We have uncovered that the reorganization of the sample surface residue dynamics at the solvent-protein interface leads to both structural and kinetic heterogeneous dynamics that ultimately create interactions that enhance the binding probability of the antigen binding site. Our results indicate that the modified interfacial dynamics of anti-IFN-γ and anti-IFGNR1 that we probe experimentally are directly associated with alterations in the complementarity regions of the distinct antibodies that designate both antigen-antibody affinity and recognition.
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Roy P, Menon S, Sengupta N. Dynamical Manifestations of Supercooling in Amyloid Hydration. J Phys Chem B 2021; 126:44-53. [PMID: 34941279 DOI: 10.1021/acs.jpcb.1c07724] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The effect of extreme temperature on amyloidogenic species remains sparsely explored. In a recent study (J. Phys. Chem. Lett., 2019, 10, (10)), we employed exhaustive molecular dynamics simulations to explore the cold thermal response of a putative small amyloid oligomer and to elicit the role of solvent modulation. Herein, we investigate the dynamical response of the hydration waters of the oligomer within the supercooled states. Using NMR-based formalism, we delineate the entropic response in terms of the side-chain conformational entropy that corroborates the weakening of the hydrophobic core with lowering of temperature. The translational dynamics of the protein and hydration waters reveal the coupling of protein dynamical fluctuations with solvent dynamics under supercooled conditions. Probing the translational motion as a space-time correlation indicates glassy dynamics exhibited by hydration waters in the supercooled regime. Caging of the water molecules with lowering of temperature and the resultant hopping dynamics are reflected in the longer β-relaxation timescales of translational motion. Furthermore, we utilized mode-coupling theory (MCT) and derived the ideal glass transition temperature from translational and rotational dynamics, around ∼196 and 209 K, respectively. Interestingly, rotational motion in the supercooled regime deviates from the MCT law, exhibits Arrhenius motion, and marks a fragile-to-strong crossover at 227 K. The low-frequency vibrational modes also coincide with the dynamical transition. This exposition lends dynamical insights into the hydration coupling of an amyloid aggregate under cryogenic conditions.
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Affiliation(s)
- Priti Roy
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India 741246
| | - Sneha Menon
- Tata Institute of Fundamental Research Hyderabad, Telangana 500046, India
| | - Neelanjana Sengupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India 741246
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5
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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: 34] [Impact Index Per Article: 11.3] [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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Corti HR, Appignanesi GA, Barbosa MC, Bordin JR, Calero C, Camisasca G, Elola MD, Franzese G, Gallo P, Hassanali A, Huang K, Laria D, Menéndez CA, de Oca JMM, Longinotti MP, Rodriguez J, Rovere M, Scherlis D, Szleifer I. Structure and dynamics of nanoconfined water and aqueous solutions. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2021; 44:136. [PMID: 34779954 DOI: 10.1140/epje/s10189-021-00136-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
This review is devoted to discussing recent progress on the structure, thermodynamic, reactivity, and dynamics of water and aqueous systems confined within different types of nanopores, synthetic and biological. Currently, this is a branch of water science that has attracted enormous attention of researchers from different fields interested to extend the understanding of the anomalous properties of bulk water to the nanoscopic domain. From a fundamental perspective, the interactions of water and solutes with a confining surface dramatically modify the liquid's structure and, consequently, both its thermodynamical and dynamical behaviors, breaking the validity of the classical thermodynamic and phenomenological description of the transport properties of aqueous systems. Additionally, man-made nanopores and porous materials have emerged as promising solutions to challenging problems such as water purification, biosensing, nanofluidic logic and gating, and energy storage and conversion, while aquaporin, ion channels, and nuclear pore complex nanopores regulate many biological functions such as the conduction of water, the generation of action potentials, and the storage of genetic material. In this work, the more recent experimental and molecular simulations advances in this exciting and rapidly evolving field will be reported and critically discussed.
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Affiliation(s)
- Horacio R Corti
- Departmento de Física de la Materia Condensada & Instituto de Nanociencia y Nanotecnología (CNEA-CONICET), Comisión Nacional de Energía Atómica, B1650LWP, Buenos Aires, Argentina.
| | - Gustavo A Appignanesi
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, 8000, Bahía Blanca, Argentina
| | - Marcia C Barbosa
- Institute of Physics, Federal University of Rio Grande do Sul, 91501-970, Porto Alegre, Brazil
| | - J Rafael Bordin
- Department of Physics, Institute of Physics and Mathematics, 96050-500, Pelotas, RS, Brazil
| | - Carles Calero
- 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, 08028, Barcelona, Spain
| | - Gaia Camisasca
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, 00146, Roma, Italy
| | - M Dolores Elola
- Departmento de Física de la Materia Condensada & Instituto de Nanociencia y Nanotecnología (CNEA-CONICET), Comisión Nacional de Energía Atómica, B1650LWP, Buenos Aires, Argentina
| | - 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, 08028, Barcelona, Spain
| | - Paola Gallo
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, 00146, Roma, Italy
| | - Ali Hassanali
- Condensed Matter and Statistical Physics Section (CMSP), The International Center for Theoretical Physics (ICTP), Trieste, Italy
| | - Kai Huang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Daniel Laria
- Departmento de Física de la Materia Condensada & Instituto de Nanociencia y Nanotecnología (CNEA-CONICET), Comisión Nacional de Energía Atómica, B1650LWP, Buenos Aires, Argentina
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Cintia A Menéndez
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, 8000, Bahía Blanca, Argentina
| | - Joan M Montes de Oca
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, 8000, Bahía Blanca, Argentina
| | - M Paula Longinotti
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Javier Rodriguez
- Departmento de Física de la Materia Condensada & Instituto de Nanociencia y Nanotecnología (CNEA-CONICET), Comisión Nacional de Energía Atómica, B1650LWP, Buenos Aires, Argentina
- Escuela de Ciencia y Tecnología, Universidad Nacional de General San Martín, San Martín, Buenos Aires, Argentina
| | - Mauro Rovere
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, 00146, Roma, Italy
| | - Damián Scherlis
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Igal Szleifer
- Biomedical Engineering Department, Northwestern University, Evanston, USA
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Dubey V, Dueby S, Daschakraborty S. Breakdown of the Stokes-Einstein relation in supercooled water: the jump-diffusion perspective. Phys Chem Chem Phys 2021; 23:19964-19986. [PMID: 34515269 DOI: 10.1039/d1cp02202d] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Although water is the most ubiquitous liquid it shows many thermodynamic and dynamic anomalies. Some of the anomalies further intensify in the supercooled regime. While many experimental and theoretical studies have focused on the thermodynamic anomalies of supercooled water, fewer studies explored the dynamical anomalies very extensively. This is due to the intricacy of the experimental measurement of the dynamical properties of supercooled water. Violation of the Stokes-Einstein relation (SER), an important relation connecting the diffusion of particles with the viscosity of the medium, is one of the major dynamical anomalies. In absence of experimentally measured viscosity, researchers used to check the validity of SER indirectly using average translational relaxation time or α-relaxation time. Very recently, the viscosity of supercooled water was accurately measured at a wide range of temperatures and pressures. This allowed direct verification of the SER at different temperature-pressure thermodynamic state points. An increasing breakdown of the SER was observed with decreasing temperature. Increasing pressure reduces the extent of breakdown. Although some well-known theories explained the above breakdown, a detailed molecular mechanism was still elusive. Recently, a translational jump-diffusion (TJD) approach has been able to quantitatively explain the breakdown of the SER in pure supercooled water and an aqueous solution of methanol. The objective of this article is to present a detailed and state-of-the-art analysis of the past and present works on the breakdown of SER in supercooled water with a specific focus on the new TJD approach for explaining the breakdown of the SER.
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Affiliation(s)
- Vikas Dubey
- Department of Chemistry, Indian Institute of Technology Patna, Bihar 801106, India.
| | - Shivam Dueby
- Department of Chemistry, Indian Institute of Technology Patna, Bihar 801106, India.
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Pastore R, Kikutsuji T, Rusciano F, Matubayasi N, Kim K, Greco F. Breakdown of the Stokes-Einstein relation in supercooled liquids: A cage-jump perspective. J Chem Phys 2021; 155:114503. [PMID: 34551555 DOI: 10.1063/5.0059622] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The breakdown of the Stokes-Einstein relation in supercooled liquids, which is the increase in the ratio τατD between the two macroscopic times for structural relaxation and diffusion on decreasing the temperature, is commonly ascribed to dynamic heterogeneities, but a clear-cut microscopic interpretation is still lacking. Here, we tackle this issue exploiting the single-particle cage-jump framework to analyze molecular dynamics simulations of soft disk assemblies and supercooled water. We find that τατD∝⟨tp⟩⟨tc⟩, where ⟨tp⟩ and ⟨tc⟩ are the cage-jump times characterizing slow and fast particles, respectively. We further clarify that this scaling does not arise from a simple term-by-term proportionality; rather, the relations τα∝⟨tp⟩⟨ΔrJ 2⟩ and τD∝⟨tc⟩⟨ΔrJ 2⟩ effectively connect the macroscopic and microscopic timescales, with the mean square jump length ⟨ΔrJ 2⟩ shrinking on cooling. Our work provides a microscopic perspective on the Stokes-Einstein breakdown and generalizes previous results on lattice models to the case of more realistic glass-formers.
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Affiliation(s)
- Raffaele Pastore
- Department of Chemical, Materials and Production Engineering, University of Naples Federico II, P.le Tecchio 80, Napoli 80125, Italy
| | - Takuma Kikutsuji
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Francesco Rusciano
- Department of Chemical, Materials and Production Engineering, University of Naples Federico II, P.le Tecchio 80, Napoli 80125, Italy
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Kang Kim
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Francesco Greco
- Department of Chemical, Materials and Production Engineering, University of Naples Federico II, P.le Tecchio 80, Napoli 80125, Italy
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9
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Lupi L, Vázquez Ramírez B, Gallo P. Dynamical crossover and its connection to the Widom line in supercooled TIP4P/Ice water. J Chem Phys 2021; 155:054502. [PMID: 34364341 DOI: 10.1063/5.0059190] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We perform molecular dynamics simulations with the TIP4P/Ice water model to characterize the relationship between dynamics and thermodynamics of liquid water in the supercooled region. We calculate the relevant properties of the phase diagram, and we find that TIP4P/Ice presents a retracing line of density maxima, similar to what was previously found for atomistic water models and models of other tetrahedral liquids. For this model, a liquid-liquid critical point between a high-density liquid and a low-density liquid was recently found. We compute the lines of the maxima of isothermal compressibility and the minima of the coefficient of thermal expansion in the one phase region, and we show that these lines point to the liquid-liquid critical point while collapsing on the Widom line. This line is the line of the maxima of correlation length that emanates from a second order critical point in the one phase region. Supercooled water was found to follow mode coupling theory and to undergo a transition from a fragile to a strong behavior right at the crossing of the Widom line. We find here that this phenomenology also happens for TIP4P/Ice. Our results appear, therefore, to be a general characteristic of supercooled water, which does not depend on the interaction potential used, and they reinforce the idea that the dynamical crossover from a region where the relaxation mechanism is dominated by cage relaxation to a region where cages are frozen and hopping dominates is correlated in water to a phase transition between a high-density liquid and a low-density liquid.
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Affiliation(s)
- Laura Lupi
- Dipartimento di Matematica e Fisica, Università Roma Tre, Via della Vasca Navale 84, 00146 Rome, Italy
| | - Benjamín Vázquez Ramírez
- Dipartimento di Matematica e Fisica, Università Roma Tre, Via della Vasca Navale 84, 00146 Rome, Italy
| | - Paola Gallo
- Dipartimento di Matematica e Fisica, Università Roma Tre, Via della Vasca Navale 84, 00146 Rome, Italy
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10
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Woods KN. New insights into the microscopic interactions associated with the physical mechanism of action of highly diluted biologics. Sci Rep 2021; 11:13774. [PMID: 34215838 PMCID: PMC8253741 DOI: 10.1038/s41598-021-93326-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/21/2021] [Indexed: 11/08/2022] Open
Abstract
In this investigation, we report the effect on the microscopic dynamics and interactions of the cytokine interferon gamma (IFN-γ) and antibodies to IFN-γ (anti-IFN-γ) and to the interferon gamma receptor 1 (anti-IFNGR1) prepared in exceptionally dilute solutions of initial proteins. Using both THz spectroscopy and molecular dynamics simulations we have uncovered that the high dilution method of sample preparation results in the reorganization of the sample surface residue dynamics at the solvent-protein interface that leads to both structural and kinetic heterogeneous dynamics that ultimately create interactions that enhance the binding probability of the antigen binding site. Our results indicate that the modified interfacial dynamics of anti-IFN-γ and anti-IFGNR1 that we probe experimentally are directly associated with alterations in the complementarity regions of the distinct antibodies that designate both antigen-antibody affinity and recognition.
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Affiliation(s)
- Kristina N Woods
- Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians-Universität, 80538, Munich, Germany.
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11
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Camisasca G, De Marzio M, Gallo P. Effect of trehalose on protein cryoprotection: Insights into the mechanism of slowing down of hydration water. J Chem Phys 2021; 153:224503. [PMID: 33317300 DOI: 10.1063/5.0033526] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study, with molecular dynamics simulations, a lysozyme protein immersed in a water-trehalose solution upon cooling. The aim is to understand the cryoprotectant role played by this disaccharide through the modifications that it induces on the slow dynamics of protein hydration water with its presence. The α-relaxation shows a fragile to strong crossover about 20° higher than that in the bulk water phase and 15° higher than that in lysozyme hydration water without trehalose. The protein hydration water without trehalose was found to show a second slower relaxation exhibiting a strong to strong crossover coupled with the protein dynamical transition. This slower relaxation time importantly appears enormously slowed down in our cryoprotectant solution. On the other hand, this long-relaxation in the presence of trehalose is also connected with a stronger damping of the protein structural fluctuations than that found when the protein is in contact with the pure hydration water. Therefore, this appears to be the mechanism through which trehalose manifests its cryoprotecting function.
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Affiliation(s)
- Gaia Camisasca
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, Via della Vasca Navale 84, 00146 Roma, Italy
| | - Margherita De Marzio
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, Via della Vasca Navale 84, 00146 Roma, Italy
| | - Paola Gallo
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, Via della Vasca Navale 84, 00146 Roma, Italy
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12
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Horstmann R, Vogel M. Relations between thermodynamics, structures, and dynamics for modified water models in their supercooled regimes. J Chem Phys 2021; 154:054502. [DOI: 10.1063/5.0037080] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- R. Horstmann
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
| | - M. Vogel
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
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13
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Tenuzzo L, Camisasca G, Gallo P. Protein-Water and Water-Water Long-Time Relaxations in Protein Hydration Water upon Cooling-A Close Look through Density Correlation Functions. Molecules 2020; 25:molecules25194570. [PMID: 33036320 PMCID: PMC7583983 DOI: 10.3390/molecules25194570] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 11/16/2022] Open
Abstract
We report results on the translational dynamics of the hydration water of the lysozyme protein upon cooling obtained by means of molecular dynamics simulations. The self van Hove functions and the mean square displacements of hydration water show two different temperature activated relaxation mechanisms, determining two dynamic regimes where transient trapping of the molecules is followed by hopping phenomena to allow to the structural relaxations. The two caging and hopping regimes are different in their nature. The low-temperature hopping regime has a time scale of tenths of nanoseconds and a length scale on the order of 2–3 water shells. This is connected to the nearest-neighbours cage effect and restricted to the supercooling, it is absent at high temperature and it is the mechanism to escape from the cage also present in bulk water. The second hopping regime is active at high temperatures, on the nanoseconds time scale and over distances of nanometers. This regime is connected to water displacements driven by the protein motion and it is observed very clearly at high temperatures and for temperatures higher than the protein dynamical transition. Below this temperature, the suppression of protein fluctuations largely increases the time-scale of the protein-related hopping phenomena at least over 100 ns. These protein-related hopping phenomena permit the detection of translational motions of hydration water molecules longly persistent in the hydration shell of the protein.
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14
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Voloshin V, Smolin N, Geiger A, Winter R, Medvedev NN. Dynamics of TMAO and urea in the hydration shell of the protein SNase. Phys Chem Chem Phys 2019; 21:19469-19479. [PMID: 31461098 DOI: 10.1039/c9cp03184g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Using all-atom molecular dynamics simulations of aqueous solutions of the globular protein SNase, the dynamic behavior of water molecules and cosolvents (trimethylamine-N-oxide (TMAO) and urea) in the hydration shell of the protein was studied for different solvent compositions. TMAO is a potent protein-stabilizing osmolyte, whereas urea is known to destabilize proteins. For molecules that are initially located in successive narrow layers at a given distance from the protein, the mean displacements and the distribution of displacements for short time intervals are calculated. For molecules that are initially located in solvation shells of a given thickness around the protein, the characteristic residence times in these shells are determined to characterize the dynamic behavior of the solvent molecules as a function of the distance to the protein. A combined consideration of these characteristics allows to reveal additional features of the dynamics of the cosolvents. It is shown that TMAO molecules leave the nearest vicinity of the protein faster than urea molecules, despite the fact that the mobility of TMAO molecules, measured by their mean displacements, is lower than that of urea. Moreover, we show that the rate of release of TMAO molecules from the hydration shell is lower in ternary (TMAO + urea + H2O) solvent mixtures than in the binary ones. This is consistent with a recent observation that the fraction of TMAO near the protein decreases in the presence of urea. From the analysis of the decay of the number of particles initially located in the region of the first peak of the distribution function of solvent molecules around the protein, we estimated that about 20 water molecules and 6-7 urea molecules stay near the protein for more than 1000 ps.
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Affiliation(s)
- Vladimir Voloshin
- Institute of Chemical Kinetics and Combustion, SB RAS, 630090 Novosibirsk, Russia.
| | - Nikolai Smolin
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, Illinois 60153, USA
| | - Alfons Geiger
- Physikalische Chemie, Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44221 Dortmund, Germany.
| | - Roland Winter
- Physikalische Chemie, Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44221 Dortmund, Germany.
| | - Nikolai N Medvedev
- Institute of Chemical Kinetics and Combustion, SB RAS, 630090 Novosibirsk, Russia. and Novosibirsk State University, 630090 Novosibirsk, Russia
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15
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Iorio A, Camisasca G, Rovere M, Gallo P. Characterization of hydration water in supercooled water-trehalose solutions: The role of the hydrogen bonds network. J Chem Phys 2019; 151:044507. [PMID: 31370561 DOI: 10.1063/1.5108579] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The structural and dynamical properties of hydration water in aqueous solutions of trehalose are studied with molecular dynamics simulation. We simulate the systems in the supercooled region to investigate how the interaction with the trehalose molecules modifies the hydrogen bond network, the structural relaxation, and the diffusion properties of hydration water. The analysis is performed by considering the radial distribution functions, the residence time of water molecules in the hydration shell, the two body excess entropy, and the hydrogen bond water-water and water-trehalose correlations of the hydration water. The study of the two body excess entropy shows the presence of a fragile to strong crossover in supercooled hydration water also found in the relaxation time of the water-water hydrogen bond correlation function, and this is in agreement with predictions of the mode coupling theory and of previous studies of the oxygen-oxygen density correlators [A. Iorio et al., J. Mol. Liq. 282, 617 (2019); Sci. China: Phys., Mech. Astron. 62, 107011 (2019)]. The water-trehalose hydrogen bond correlation function instead evidences a strong to strong crossover in the relaxation time, and this crossover is related to a trehalose dynamical transition. This signals the role that the strong interplay between the soluted molecules and the surrounding solvent has in determining the dynamical transition common to both components of the system that happens upon cooling and that is similar to the well known protein dynamical transition. We connect our results with the cryoprotecting role of trehalose molecules.
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Affiliation(s)
- A Iorio
- Dipartimento di Matematica e Fisica, Università Roma Tre, Via della Vasca Navale 84, 00146 Rome, Italy
| | - G Camisasca
- Department of Physics, AlbaNova University Center, Stockholm University, S-106 91 Stockholm, Sweden
| | - M Rovere
- Dipartimento di Matematica e Fisica, Università Roma Tre, Via della Vasca Navale 84, 00146 Rome, Italy
| | - P Gallo
- Dipartimento di Matematica e Fisica, Università Roma Tre, Via della Vasca Navale 84, 00146 Rome, Italy
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16
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Voloshin VP, Medvedev NN. Mobility of Water, Urea and Trimethylamine-N-Oxide Molecules in the Vicinity of Globular Protein. J STRUCT CHEM+ 2019. [DOI: 10.1134/s0022476619060088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Camisasca G, Galamba N, Wikfeldt KT, Pettersson LGM. Translational and rotational dynamics of high and low density TIP4P/2005 water. J Chem Phys 2019; 150:224507. [PMID: 31202216 DOI: 10.1063/1.5079956] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We use molecular dynamics simulations using TIP4P/2005 to investigate the self- and distinct-van Hove functions for different local environments of water, classified using the local structure index as an order parameter. The orientational dynamics were studied through the calculation of the time-correlation functions of different-order Legendre polynomials in the OH-bond unit vector. We found that the translational and orientational dynamics are slower for molecules in a low-density local environment and correspondingly the mobility is enhanced upon increasing the local density, consistent with some previous works, but opposite to a recent study on the van Hove function. From the analysis of the distinct dynamics, we find that the second and fourth peaks of the radial distribution function, previously identified as low density-like arrangements, show long persistence in time. The analysis of the time-dependent interparticle distance between the central molecule and the first coordination shell shows that particle identity persists longer than distinct van Hove correlations. The motion of two first-nearest-neighbor molecules thus remains coupled even when this correlation function has been completely decayed. With respect to the orientational dynamics, we show that correlation functions of molecules in a low-density environment decay exponentially, while molecules in a local high-density environment exhibit bi-exponential decay, indicating that dynamic heterogeneity of water is associated with the heterogeneity among high-density and between high-density and low-density species. This bi-exponential behavior is associated with the existence of interstitial waters and the collapse of the second coordination sphere in high-density arrangements, but not with H-bond strength.
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Affiliation(s)
- Gaia Camisasca
- Department of Physics, Stockholm University, 106 91 Stockholm, Sweden
| | - Nuno Galamba
- Centre of Chemistry and Biochemistry and Biosystems and Integrative Sciences Institute, Faculty of Sciences of the University of Lisbon, C8, Campo Grande, 1749-016 Lisbon, Portugal
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18
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Kikutsuji T, Kim K, Matubayasi N. Diffusion dynamics of supercooled water modeled with the cage-jump motion and hydrogen-bond rearrangement. J Chem Phys 2019; 150:204502. [DOI: 10.1063/1.5095978] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Takuma Kikutsuji
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Kang Kim
- Division of Chemical Engineering, 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, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
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19
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Iorio A, Camisasca G, Gallo P. Slow dynamics of hydration water and the trehalose dynamical transition. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.02.088] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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20
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Qiao Z, Xie WJ, Cai X, Gao YQ. Interlayer hopping dynamics of bilayer water confined between graphene sheets. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.02.046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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21
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Martelli F. Unravelling the contribution of local structures to the anomalies of water: The synergistic action of several factors. J Chem Phys 2019; 150:094506. [PMID: 30849899 DOI: 10.1063/1.5087471] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigate the microscopic origin of water's anomalies by inspecting the hydrogen bond network (HBN) and the spatial organization of low-density-liquid (LDL) like and high-density-liquid (HDL) like environments. Specifically, we simulate-via classical molecular dynamics simulations-the isobaric cooling of a sample composed of 512 water molecules from ambient to deeply undercooled conditions at three pressures, namely, 1 bar, 400 bars, and 1000 bars. In correspondence with the Widom line (WL), (i) the HDL-like dominating cluster undergoes fragmentation caused by the percolation of LDL-like aggregates following a spinodal-like kinetics; (ii) such fragmentation always occurs at a "critical" concentration of ∼20%-30% in LDL; (iii) the HBN within LDL-like environments is characterized by an equal number of pentagonal and hexagonal rings that create a state of maximal frustration between a configuration that promotes crystallization (hexagonal ring) and a configuration that hinders it (pentagonal ring); (iv) the spatial organization of HDL-like environments shows a marked variation. Moreover, the inspection of the global symmetry shows that the intermediate-range order decreases in correspondence with the WL and such a decrease becomes more pronounced upon increasing the pressure, hence supporting the hypothesis of a liquid-liquid critical point. Our results reveal and rationalize the complex microscopic origin of water's anomalies as the cooperative effect of several factors acting synergistically. Beyond implications for water, our findings may be extended to other materials displaying anomalous behaviours.
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Affiliation(s)
- Fausto Martelli
- IBM Research, Hartree Centre, Daresbury WA4 4AD, United Kingdom
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22
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Shi R, Russo J, Tanaka H. Common microscopic structural origin for water's thermodynamic and dynamic anomalies. J Chem Phys 2018; 149:224502. [PMID: 30553247 DOI: 10.1063/1.5055908] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Water displays a vast array of unique properties, known as water's anomalies, whose origin remains subject to hot debate. Our aim in this article is to provide a unified microscopic physical picture of water's anomalies in terms of locally favored structures, encompassing both thermodynamic and dynamic anomalies, which are often attributed to different origins. We first identify locally favored structures via a microscopic structural descriptor that measures local translational order and provide direct evidence that they have a hierarchical impact on the anomalies. At each state point, the strength of thermodynamic anomalies is directly proportional to the amount of locally favored structures, while the dynamic properties of each molecule depend on the local structure surrounding both itself and its nearest neighbors. To incorporate this, we develop a novel hierarchical two-state model. We show by extensive simulations of two popular water models that both thermodynamic and kinetic anomalies can be almost perfectly explained by the temperature and pressure dependence of these local and non-local versions of the same structural descriptor, respectively. Moreover, our scenario makes three unique predictions in supercooled water, setting it apart from other scenarios: (1) Presence of an "Arrhenius-to-Arrhenius" crossover upon cooling, as the origin of the apparent "fragile-to-strong" transition; (2) maximum of dynamic heterogeneity around 20 K below the Widom line and far above the glass transition; (3) violation of the Stokes-Einstein-Debye relation at ∼2T g, rather than 1.2T g typical of normal glass-formers. These predictions are verified by recent measurement of water's diffusion at very low temperatures (point 1) and discoveries from our extensive simulations (points 2-3). We suggest that the same scenario may generally apply to water-like anomalies in liquids tending to form locally favored structures, including not only other important tetrahedral liquids such as silicon, germanium, and silica, but also metallic and chalcogenide liquids.
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Affiliation(s)
- Rui Shi
- Department of Fundamental Engineering, Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - John Russo
- Department of Fundamental Engineering, Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Hajime Tanaka
- Department of Fundamental Engineering, Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
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23
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Hestand NJ, Skinner JL. Perspective: Crossing the Widom line in no man’s land: Experiments, simulations, and the location of the liquid-liquid critical point in supercooled water. J Chem Phys 2018; 149:140901. [DOI: 10.1063/1.5046687] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Nicholas J. Hestand
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - J. L. Skinner
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
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24
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25
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Origin of the emergent fragile-to-strong transition in supercooled water. Proc Natl Acad Sci U S A 2018; 115:9444-9449. [PMID: 30181283 DOI: 10.1073/pnas.1807821115] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Liquids can be broadly classified into two categories, fragile and strong ones, depending on how their dynamical properties change with temperature. The dynamics of a strong liquid obey the Arrhenius law, whereas the fragile one displays a super-Arrhenius law, with a much steeper slowing down upon cooling. Recently, however, it was discovered that many materials such as water, oxides, and metals do not obey this simple classification, apparently exhibiting a fragile-to-strong transition far above [Formula: see text] Such a transition is particularly well known for water, and it is now regarded as one of water's most important anomalies. This phenomenon has been attributed to either an unusual glass transition behavior or the crossing of a Widom line emanating from a liquid-liquid critical point. Here by computer simulations of two popular water models and through analyses of experimental data, we show that the emergent fragile-to-strong transition is actually a crossover between two Arrhenius regimes with different activation energies, which can be naturally explained by a two-state description of the dynamics. Our finding provides insight into the fragile-to-strong transition observed in a wide class of materials.
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26
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Camisasca G, De Marzio M, Rovere M, Gallo P. High density liquid structure enhancement in glass forming aqueous solution of LiCl. J Chem Phys 2018; 148:222829. [DOI: 10.1063/1.5024375] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- G. Camisasca
- Dipartimento di Matematica e Fisica, Università “Roma Tre,” Via della Vasca Navale 84, 00146 Roma, Italy
| | - M. De Marzio
- Dipartimento di Matematica e Fisica, Università “Roma Tre,” Via della Vasca Navale 84, 00146 Roma, Italy
| | - M. Rovere
- Dipartimento di Matematica e Fisica, Università “Roma Tre,” Via della Vasca Navale 84, 00146 Roma, Italy
| | - P. Gallo
- Dipartimento di Matematica e Fisica, Università “Roma Tre,” Via della Vasca Navale 84, 00146 Roma, Italy
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27
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Pafong Sanjon E, Drossel B, Vogel M. Effects of the bond polarity on the structural and dynamical properties of silica-like liquids. J Chem Phys 2018; 148:104506. [PMID: 29544292 DOI: 10.1063/1.5017681] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Silica is a network-forming liquid that shares many properties with water due to its tetrahedral structure. It undergoes a transition from a fragile to a strong liquid as the temperature is decreased, which is accompanied by a structural change to lower density and higher tetrahedral order. In order to disentangle the effects of Coulomb and van der Waals interactions on the structure and dynamics of liquid silica, we modify the bond polarity by changing the partial charges assigned to each atom. Using molecular dynamics simulations, we show that density, tetrahedral order, and structural relaxation times decrease when reducing bond polarity. Moreover, we find that the density maximum and the fragile-to-strong transition move to lower temperatures until they eventually vanish when the partial charges are decreased below approximately 75% of their regular value. Irrespective of whether strong or fragile behavior exists, structural relaxation is governed by hopping motion at sufficiently low temperatures. As long as there is a strong regime, the energy barrier associated with strong dynamics decreases with decreasing partial charges, but the dependence on the bond polarity differs from that of the activation energy in the Arrhenius regime at high temperatures. We show that the fragile-to-strong transition is associated with structural changes occurring between the first and second coordination shells that lead to a decrease in density and an increase in tetrahedral order. In particular, independent of the value of the partial charges, the distribution of the local structures is the same at this dynamic crossover, but we find no evidence that the effect occurs upon crossing the Widom line. In the fragile regime at intermediate temperatures, the relaxation times are well described by a previously proposed model which decomposes the apparent activation energy into a constant single-particle contribution and a temperature-dependent collective contribution. However, our results for silica-like melts do not obey several common relations of the model parameters reported for molecular glass formers.
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Affiliation(s)
- E Pafong Sanjon
- Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
| | - B Drossel
- Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
| | - M Vogel
- Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
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28
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Swenson J. Possible relations between supercooled and glassy confined water and amorphous bulk ice. Phys Chem Chem Phys 2018; 20:30095-30103. [DOI: 10.1039/c8cp05688a] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A proposed relaxation scenario of bulk water based on studies of confined water and low density amorphous ice.
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Affiliation(s)
- Jan Swenson
- Department of Physics, Chalmers University of Technology
- SE-412 96 Göteborg
- Sweden
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29
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30
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De Marzio M, Camisasca G, Conde MM, Rovere M, Gallo P. Structural properties and fragile to strong transition in confined
water. J Chem Phys 2017; 146:084505. [DOI: 10.1063/1.4975624] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- M. De Marzio
- Dipartimento di Matematica e Fisica, Università “Roma Tre,”
Via della Vasca Navale 84, 00146 Roma, Italy
| | - G. Camisasca
- Dipartimento di Matematica e Fisica, Università “Roma Tre,”
Via della Vasca Navale 84, 00146 Roma, Italy
| | - M. M. Conde
- Dipartimento di Matematica e Fisica, Università “Roma Tre,”
Via della Vasca Navale 84, 00146 Roma, Italy
| | - M. Rovere
- Dipartimento di Matematica e Fisica, Università “Roma Tre,”
Via della Vasca Navale 84, 00146 Roma, Italy
| | - P. Gallo
- Dipartimento di Matematica e Fisica, Università “Roma Tre,”
Via della Vasca Navale 84, 00146 Roma, Italy
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