1
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Förster M, Ukoji N, Sahle CJ, Niskanen J, Sakrowski R, Surmeier G, Weis C, Irifune T, Imoto S, Yavas H, Huotari S, Marx D, Sternemann C, Tse JS. Generating interstitial water within the persisting tetrahedral H-bond network explains density increase upon compressing liquid water. Proc Natl Acad Sci U S A 2024; 121:e2403662121. [PMID: 39284048 DOI: 10.1073/pnas.2403662121] [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: 02/23/2024] [Accepted: 07/16/2024] [Indexed: 10/02/2024] Open
Abstract
Despite its ubiquitous nature, the atomic structure of water in its liquid state is still controversially debated. We use a combination of X-ray Raman scattering spectroscopy in conjunction with ab initio and path integral molecular dynamics simulations to study the local atomic and electronic structure of water under high pressure conditions. Systematically increasing fingerprints of non-hydrogen-bonded H[Formula: see text]O molecules in the first hydration shell are identified in the experimental and computational oxygen K-edge excitation spectra. This provides evidence for a compaction mechanism in terms of a continuous collapse of the second hydration shell with increasing pressure via generation of interstitial water within locally tetrahedral hydrogen-bonding environments.
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Affiliation(s)
- Mirko Förster
- Fakultät Physik/DELTA, Technische Universität Dortmund, Dortmund 44227, Germany
| | - Nnanna Ukoji
- Department of Physics and Engineering Physics, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada
| | | | - Johannes Niskanen
- Department of Physics and Astronomy, University of Turku, Turun yliopisto FI-20014, Finland
| | - Robin Sakrowski
- Fakultät Physik/DELTA, Technische Universität Dortmund, Dortmund 44227, Germany
| | - Göran Surmeier
- Fakultät Physik/DELTA, Technische Universität Dortmund, Dortmund 44227, Germany
| | - Christopher Weis
- Fakultät Physik/DELTA, Technische Universität Dortmund, Dortmund 44227, Germany
| | - Tetsuo Irifune
- Geodynamics Research Center, Ehime University, Matsuyama 790, Japan
| | - Sho Imoto
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, Bochum 44780, Germany
| | - Hasan Yavas
- Deutsches Elektronen-Synchrotron, Hamburg 22607, Germany
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Simo Huotari
- Department of Physics, University of Helsinki, Helsinki FI-00014, Finland
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, Bochum 44780, Germany
| | | | - John S Tse
- Department of Physics and Engineering Physics, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada
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2
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Mokshin AV, Vlasov RV. Liquid-Liquid Crossover in Water Model: Local Structure vs Kinetics of Hydrogen Bonds. J Phys Chem B 2024. [PMID: 38411102 DOI: 10.1021/acs.jpcb.3c07650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
In equilibrium and supercooled liquids, polymorphism is manifested by thermodynamic regions defined in the phase diagram, which are predominantly of different short- and medium-range order (local structure). It is found that on the phase diagram of the water model, the thermodynamic region corresponding to the equilibrium liquid phase is divided by a line of the smooth liquid-liquid crossover. In the case of the water model TIP4P/2005, this crossover is revealed by various local order parameters and corresponds to pressures on the order of 3150 ± 350 atm at ambient temperature. In the vicinity of the crossover, the dynamics of water molecules change significantly, which is reflected, in particular, in the fact that the self-diffusion coefficient reaches its maximum values. In addition, changes in the structure also manifest themselves in changes in the kinetics of hydrogen bonding, which are captured by values of such quantities as the average lifetime of hydrogen bonding, the average lifetimes of different local coordination numbers, and the frequencies of changes in different local coordination numbers. An interpretation of the hydrogen bond kinetics in terms of the free energy landscape concept in the space of possible coordination numbers is proposed.
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Affiliation(s)
- Anatolii V Mokshin
- Department of Computational Physics, Kazan (Volga Region) Federal University, Kazan 420008, Russia
| | - Roman V Vlasov
- Department of Computational Physics, Kazan (Volga Region) Federal University, Kazan 420008, Russia
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3
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Daidone I, Foffi R, Amadei A, Zanetti-Polzi L. A statistical mechanical model of supercooled water based on minimal clusters of correlated molecules. J Chem Phys 2023; 159:094502. [PMID: 37655770 DOI: 10.1063/5.0157505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/14/2023] [Indexed: 09/02/2023] Open
Abstract
In this paper, we apply a theoretical model for fluid state thermodynamics to investigate simulated water in supercooled conditions. This model, which we recently proposed and applied to sub- and super-critical fluid water [Zanetti-Polzi et al., J. Chem. Phys. 156(4), 44506 (2022)], is based on a combination of the moment-generating functions of the enthalpy and volume fluctuations as provided by two gamma distributions and provides the free energy of the system as well as other relevant thermodynamic quantities. The application we make here provides a thermodynamic description of supercooled water fully consistent with that expected by crossing the liquid-liquid Widom line, indicating the presence of two distinct liquid states. In particular, the present model accurately reproduces the Widom line temperatures estimated with other two-state models and well describes the heat capacity anomalies. Differently from previous models, according to our description, a cluster of molecules that extends beyond the first hydration shell is necessary to discriminate between the statistical fluctuation regimes typical of the two liquid states.
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Affiliation(s)
- Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, via Vetoio (Coppito 1), L'Aquila 67010, Italy
| | - Riccardo Foffi
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zürich, Laura-Hezner-Weg 7, 8093 Zürich, Switzerland
| | - Andrea Amadei
- Department of Chemical and Technological Sciences, University of Rome "Tor Vergata," Via della Ricerca Scientifica, I-00185 Rome, Italy
| | - Laura Zanetti-Polzi
- Center S3, CNR-Institute of Nanoscience, Via Campi 213/A, 41125 Modena, Italy
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4
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Liu R, Chen M. Characterization of the Hydrogen-Bond Network in High-Pressure Water by Deep Potential Molecular Dynamics. J Chem Theory Comput 2023; 19:5602-5608. [PMID: 37535904 DOI: 10.1021/acs.jctc.3c00445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
The hydrogen-bond (H-bond) network of high-pressure water is investigated by neural-network-based molecular dynamics (MD) simulations with first-principles accuracy. The static structure factors (SSFs) of water at three densities, i.e., 1, 1.115, and 1.24 g/cm3, are directly evaluated from 512 water MD trajectories, which are in quantitative agreement with the experiments. We propose a new method to decompose the computed SSF and identify the changes in the SSF with respect to the changes in H-bond structures. We find that a larger water density results in a higher probability for one or two non-H-bonded water molecules to be inserted into the inner shell, explaining the changes in the tetrahedrality of water under pressure. We predict that the structure of the accepting end of water molecules is more easily influenced by the pressure than by the donating end. Our work sheds new light on explaining the SSF and H-bond properties in related fields.
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Affiliation(s)
- Renxi Liu
- HEDPS, CAPT, College of Engineering, Peking University, Beijing 100871, P. R. China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 90871, P. R. China
| | - Mohan Chen
- HEDPS, CAPT, College of Engineering, Peking University, Beijing 100871, P. R. China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 90871, P. R. China
- AI for Science Institute, Beijing 100080, P. R. China
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5
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Capelli R, Muniz-Miranda F, Pavan GM. Ephemeral ice-like local environments in classical rigid models of liquid water. J Chem Phys 2022; 156:214503. [DOI: 10.1063/5.0088599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Despite great efforts over the past 50 years, the simulation of water still presents significant challenges and open questions. At room temperature and pressure, the collective molecular interactions and dynamics of water molecules may form local structural arrangements that are non-trivial to classify. Here, we employ a data-driven approach built on Smooth Overlap of Atomic Position (SOAP) that allows us to compare and classify how widely used classical models represent liquid water. Macroscopically, the obtained results are rationalized based on water thermodynamic observables. Microscopically, we directly observe how transient ice-like ordered environments may dynamically/statistically form in liquid water, even above freezing temperature, by comparing the SOAP spectra for different ice structures with those of the simulated liquid systems. This confirms recent ab initio-based calculations but also reveals how the emergence of ephemeral local ice-like environments in liquid water at room conditions can be captured by classical water models.
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Affiliation(s)
- Riccardo Capelli
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, I-10129 Torino, Italy
| | - Francesco Muniz-Miranda
- Department of Chemical and Geological Sciences, University of Modena and Reggio-Emilia, Via Campi 103, I-41125 Modena, Italy
| | - Giovanni M. Pavan
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, I-10129 Torino, Italy
- Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Polo Universitario Lugano, Campus Est, Via la Santa 1, CH-6962 Lugano-Viganello, Switzerland
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6
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Faccio C, Benzi M, Zanetti-Polzi L, Daidone I. Low- and high-density forms of liquid water revealed by a new medium-range order descriptor. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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7
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Hydrogen bonding in liquid water at 1 GPa : Molecular dynamics simulation study of TIP4P/2005 water model. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2021.113527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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8
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Modification of local and collective dynamics of water in perchlorate solution, induced by pressure and concentration. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Piskulich ZA, Thompson WH. Examining the Role of Different Molecular Interactions on Activation Energies and Activation Volumes in Liquid Water. J Chem Theory Comput 2021; 17:2659-2671. [PMID: 33819026 DOI: 10.1021/acs.jctc.0c01217] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There are a large number of force fields available to model water in molecular dynamics simulations, which each have their own strengths and weaknesses in describing the behavior of the liquid. One particular weakness in many of these models is their description of dynamics away from ambient conditions, where their ability to reproduce measurements is mixed. To investigate this issue, we use the recently developed fluctuation theory for dynamics to directly evaluate measures of the local temperature and pressure dependence: the activation energy and the activation volume. We examine these activation parameters for hydrogen-bond jump exchange times, OH reorientation times, and diffusion coefficients calculated from the SPC/E, SPC/Fw, TIP3P-PME, TIP3P-PME/Fw, OPC3, TIP4P/2005, TIP4P/Ew, E3B2, and E3B3 water models. Activation energy decompositions available through the fluctuation theory approach provide mechanistic insight into the origins of different temperature dependences between the various models, as well as the influence of three-body effects and flexibility.
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Affiliation(s)
- Zeke A Piskulich
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Ward H Thompson
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
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10
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Linear and Non-Linear Middle Infrared Spectra of Penicillin G in the CO Stretching Mode Region. Symmetry (Basel) 2021. [DOI: 10.3390/sym13010106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In this work we report the linear and non-linear IR spectral response characterization of the CO bonds of PenicillinG sodium salt in D2O and in DMSO−d6 solutions. In order to better characterize the spectral IR features in the CO stretching region, broadband middle infrared pump-probe spectra are recorded. The role of hydrogen bonds in determining the inhomogeneous broadening and in tuning anharmonicity of the different types of oscillators is exploited. Narrow band pump experiments, at the three central frequencies of β−lactam, amide and carboxylate CO stretching modes, identify the couplings between the different types of CO oscillators opening the possibility to gather structural dynamic information. Our results show that the strongest coupling is between the β−lactam and the carboxylate CO vibrational modes.
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11
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Coppola F, Perrella F, Petrone A, Donati G, Rega N. A Not Obvious Correlation Between the Structure of Green Fluorescent Protein Chromophore Pocket and Hydrogen Bond Dynamics: A Choreography From ab initio Molecular Dynamics. Front Mol Biosci 2020; 7:569990. [PMID: 33195416 PMCID: PMC7653547 DOI: 10.3389/fmolb.2020.569990] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/11/2020] [Indexed: 11/23/2022] Open
Abstract
The Green Fluorescent Protein (GFP) is a widely studied chemical system both for its large amount of applications and the complexity of the excited state proton transfer responsible of the change in the protonation state of the chromophore. A detailed investigation on the structure of the chromophore environment and the influence of chromophore form (either neutral or anionic) on it is of crucial importance to understand how these factors could potentially influence the protein function. In this study, we perform a detailed computational investigation based on the analysis of ab-initio molecular dynamics simulations, to disentangle the main structural quantities determining the fine balance in the chromophore environment. We found that specific hydrogen bonds interactions directly involving the chromophore (or not), are correlated to quantities, such as the volume of the cavity in which the chromophore is embedded and that it is importantly affected by the chromophore protonation state. The cross-correlation analysis performed on some of these hydrogen bonds and the cavity volume, demonstrates a direct correlation among them and we also identified the ones specifically involved in this correlation. We also found that specific interactions among residues far in the space are correlated, demonstrating the complexity of the chromophore environment and that many structural quantities have to be taken into account to properly describe and understand the main factors tuning the active site of the protein. From an overall evaluation of the results obtained in this work, it is shown that the residues which a priori are perceived to be spectators play instead an important role in both influencing the chromophore environment (cavity volume) and its dynamics (cross-correlations among spatially distant residues).
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Affiliation(s)
- Federico Coppola
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Fulvio Perrella
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Alessio Petrone
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Greta Donati
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Nadia Rega
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy.,Center for Advanced Biomaterials for Healthcare@CRIB, Naples, Italy
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12
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Donati G, Petrone A, Rega N. Multiresolution continuous wavelet transform for studying coupled solute-solvent vibrations via ab initio molecular dynamics. Phys Chem Chem Phys 2020; 22:22645-22661. [PMID: 33015693 DOI: 10.1039/d0cp02495c] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Vibrational analysis in solution and the theoretical determination of infrared and Raman spectra are of key importance in many fields of chemical interest. Vibrational band dynamics of molecules and their sensitivity to the environment can also be captured by these spectroscopies in their time dependent version. However, it is often difficult to provide an interpretation of the experimental data at the molecular scale, such as molecular mechanisms or the processes hidden behind them. In this work, we present a theoretical-computational protocol based on ab initio molecular dynamics simulations and a combination of normal-like (generalized) mode analysis of solute-solvent clusters with a wavelet transform, for the first time. The case study is the vibrational dynamics of N-methyl-acetamide (NMA) in water solution, a well-known model of hydration of peptides and proteins. Amide modes are typical bands of peptide and protein backbone, and their couplings with the environment are very challenging in terms of the accurate prediction of solvent induced intensity and frequency shifts. The contribution of water molecules surrounding NMA to the composition of generalized and time resolved modes is introduced in our vibrational analysis, showing unequivocally its influence on the amide mode spectra. It is also shown that such mode compositions need the inclusion of the first shell solvent molecules to be accurately described. The wavelet analysis is proven to be strongly recommended to follow the time evolution of the spectra, and to capture vibrational band couplings and frequency shifts over time, preserving at the same time a well-balanced time-frequency resolution. This peculiar feature also allows one to perform a combined structural-vibrational analysis, where the different strengths of hydrogen bond interactions can quantitatively affect the amide bands over time at finite temperature. The proposed method allows for the direct connection between vibrational modes and local structural changes, providing a link from the spectroscopic observable to the structure, in this case the peptide backbone, and its hydration layouts.
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Affiliation(s)
- Greta Donati
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M. S. Angelo, Via Cintia, I-80126 Napoli, Italy.
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13
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Priyadarsini A, Dasari S, Mallik BS. Thermophysical Properties and Angular Jump Dynamics of Water: A Comparative DFT and DFT-Dispersion-Based Molecular Dynamics Study. J Phys Chem A 2020; 124:6039-6049. [DOI: 10.1021/acs.jpca.0c02909] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Adyasa Priyadarsini
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi 502285, Sangareddy, Telangana, India
| | - Sathish Dasari
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi 502285, Sangareddy, Telangana, India
| | - Bhabani S. Mallik
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi 502285, Sangareddy, Telangana, India
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14
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Taschin A, Bartolini P, Fanetti S, Lapini A, Citroni M, Righini R, Bini R, Torre R. Pressure Effects on Water Dynamics by Time-Resolved Optical Kerr Effect. J Phys Chem Lett 2020; 11:3063-3068. [PMID: 32212735 DOI: 10.1021/acs.jpclett.0c00363] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Despite water being the most common and most widely studied substance in the world, it still presents unknown aspects. In particular, water shows several thermodynamic and dynamical anomalies in the liquid and supercooled metastable phases, and the natures of these phases are still hotly debated. Here, we report measurements of water using the optical Kerr effect as a function of pressure along two isotherms, at 273 K from 0.1 to 750 MPa and at 297 K from 0.1 to 1350 MPa, reaching the supercooled metastable phase. The structural relaxation and the low frequency vibrational dynamics of water show a peculiar pressure dependence similar to that of other dynamical properties. The data analysis suggests the presence in the water phase diagram of a crossover area that divides two regions characterized by different dynamic regimes, which appear to be related to two liquid forms, one dominated by the high density water and the other by the low density water.
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Affiliation(s)
- Andrea Taschin
- European Laboratory for Non-Linear Spectroscopy (LENS), Università di Firenze, via N. Carrara 1, I-50019 Sesto Fiorentino, Firenze, Italy
| | - Paolo Bartolini
- European Laboratory for Non-Linear Spectroscopy (LENS), Università di Firenze, via N. Carrara 1, I-50019 Sesto Fiorentino, Firenze, Italy
| | - Samuele Fanetti
- European Laboratory for Non-Linear Spectroscopy (LENS), Università di Firenze, via N. Carrara 1, I-50019 Sesto Fiorentino, Firenze, Italy
- ICCOM-CNR, Istituto di Chimica dei Composti OrganoMetallici, Consiglio Nazionale delle Ricerche, Via Madonna del Piano 10, I-50019 Sesto Fiorentino, Firenze, Italy
| | - Andrea Lapini
- European Laboratory for Non-Linear Spectroscopy (LENS), Università di Firenze, via N. Carrara 1, I-50019 Sesto Fiorentino, Firenze, Italy
- INRIM, Istituto Nazionale di Ricerca Metrologica, Strada delle Cacce 91, I-10135 Torino, Italy
| | - Margherita Citroni
- European Laboratory for Non-Linear Spectroscopy (LENS), Università di Firenze, via N. Carrara 1, I-50019 Sesto Fiorentino, Firenze, Italy
| | - Roberto Righini
- European Laboratory for Non-Linear Spectroscopy (LENS), Università di Firenze, via N. Carrara 1, I-50019 Sesto Fiorentino, Firenze, Italy
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, via Della Lastruccia 13, I-50019 Sesto Fiorentino, Firenze, Italy
| | - Roberto Bini
- European Laboratory for Non-Linear Spectroscopy (LENS), Università di Firenze, via N. Carrara 1, I-50019 Sesto Fiorentino, Firenze, Italy
- ICCOM-CNR, Istituto di Chimica dei Composti OrganoMetallici, Consiglio Nazionale delle Ricerche, Via Madonna del Piano 10, I-50019 Sesto Fiorentino, Firenze, Italy
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, via Della Lastruccia 13, I-50019 Sesto Fiorentino, Firenze, Italy
| | - Renato Torre
- European Laboratory for Non-Linear Spectroscopy (LENS), Università di Firenze, via N. Carrara 1, I-50019 Sesto Fiorentino, Firenze, Italy
- Dipartimento di Fisica e Astronomia, Università di Firenze, via G. Sansone 1, I-50019 Sesto Fiorentino, Firenze, Italy
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15
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Priyadarshini A, Biswas A, Chakraborty D, Mallik BS. Structural and Thermophysical Anomalies of Liquid Water: A Tale of Molecules in the Instantaneous Low- and High-Density Regions. J Phys Chem B 2020; 124:1071-1081. [DOI: 10.1021/acs.jpcb.9b11596] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Adyasa Priyadarshini
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi-502285 Sangareddy, Telangana, India
| | - Aritri Biswas
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi-502285 Sangareddy, Telangana, India
| | - Debashree Chakraborty
- Department of Chemistry, National Institute of Technology Karnataka, Surathkal, 575025 Mangalore, Karnataka, India
| | - Bhabani S. Mallik
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi-502285 Sangareddy, Telangana, India
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16
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Friant-Michel P, Wax JF, Meyer N, Xu H, Millot C. Translational and Rotational Diffusion in Liquid Water at Very High Pressure: A Simulation Study. J Phys Chem B 2019; 123:10025-10035. [PMID: 31725300 DOI: 10.1021/acs.jpcb.9b06884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Translational and rotational diffusion coefficients of liquid water have been computed from molecular dynamics simulation with a recent polarizable potential at 298, 400, and 550 K at very high pressure. At 298 K, the model reproduces the initial increase and the occurrence of a maximum for the translational and rotational diffusion coefficients when the pressure increases. At 400 and 550 K, translational and rotational diffusion coefficients are found to monotonically decrease when pressure increases in the gigapascal range, with the translational coefficient decreasing faster than the rotational one. At 400 K, such an evolution of the rotational diffusion coefficient contrasts with quasielastic neutron scattering results predicting a near independence of the rotational diffusion with a pressure increase above ≃0.5 GPa. An interpretation is proposed to explain this discrepancy. The pressure dependence of the translation-rotation coupling is analyzed. The anisotropy of rotational diffusion is investigated by computing the rotational diffusion tensor in a molecular system of axes and the reorientational correlation times of rank 1 and rank 2 of the inertia axes and of the OH bond vector. Deviation of the simulation data with respect to the predictions of the isotropic Debye model of rotational diffusion are quantified and can be used to estimate experimental rotational diffusion coefficients from experimental reorientational correlation times.
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Affiliation(s)
| | | | - Nadège Meyer
- Université de Lorraine, LCP-A2MC , F-57000 Metz , France
| | - Hong Xu
- Université de Lorraine, LCP-A2MC , F-57000 Metz , France
| | - Claude Millot
- Université de Lorraine, CNRS, LPCT , F-54000 Nancy , France
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17
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Pagliai M, Macchiagodena M, Procacci P, Cardini G. Evidence of a Low-High Density Turning Point in Liquid Water at Ordinary Temperature under Pressure: A Molecular Dynamics Study. J Phys Chem Lett 2019; 10:6414-6418. [PMID: 31584829 DOI: 10.1021/acs.jpclett.9b02724] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Water has a fundamental role in important processes spanning a wide range of pressure and temperature conditions. Knowledge of structural, dynamic and thermodynamic properties of water at nonstandard conditions is a primary concern since interest in astronomical, geological, and technological processes is continuously growing. Molecular dynamics simulations allow us to study thermodynamic conditions that require sophisticated techniques and instruments, while at the same time offering the interpretation of properties at the atomic level. It is established that the behavior of water is strongly affected by the temperature and pressure conditions, determining the existence of low and high density regimes. For the first time, a thermodynamic property, isothermal compressibility, has been adopted to detect the low-high density turning point at ambient temperature in liquid water due to pressure. Molecular dynamics simulations have been performed with five three-site models, allowing us to characterize the complexity of water nature at these conditions at the atomic level.
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Affiliation(s)
- Marco Pagliai
- Dipartimento di Chimica "Ugo Schiff" , Università degli Studi di Firenze , Via della Lastruccia 3 , 50019 Sesto Fiorentino , Italy
| | - Marina Macchiagodena
- Dipartimento di Chimica "Ugo Schiff" , Università degli Studi di Firenze , Via della Lastruccia 3 , 50019 Sesto Fiorentino , Italy
| | - Piero Procacci
- Dipartimento di Chimica "Ugo Schiff" , Università degli Studi di Firenze , Via della Lastruccia 3 , 50019 Sesto Fiorentino , Italy
| | - Gianni Cardini
- Dipartimento di Chimica "Ugo Schiff" , Università degli Studi di Firenze , Via della Lastruccia 3 , 50019 Sesto Fiorentino , Italy
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18
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Fanetti S, Falsini N, Bartolini P, Citroni M, Lapini A, Taschin A, Bini R. Superheating and Homogeneous Melting Dynamics of Bulk Ice. J Phys Chem Lett 2019; 10:4517-4522. [PMID: 31342749 DOI: 10.1021/acs.jpclett.9b01490] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Homogeneous melting of crystals is a complex multistep process involving the formation of transient states at temperatures considerably higher than the melting point. The nature and persistence of these metastable structures are intimately connected to the melting process, and a precise definition of the temporal boundaries of these phenomena is not yet available. We set up a specifically designed experiment to probe by transient infrared absorption spectroscopy the entire dynamics, ranging from tens of picoseconds to microseconds, of superheating and melting of an ice crystal. In spite of a large excess of energy provided, only about 30% of the micrometric crystal liquefies in the first 20-25 ns because of the long persistence of the superheated metastable phase that extends for more than 100 ns. This behavior is ascribed to the population of low-energy states that trap a large amount of energy, favoring the formation of a metastable, likely plastic, ice phase.
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Affiliation(s)
- Samuele Fanetti
- European Laboratory for Nonlinear Spectroscopy (LENS) , via Nello Carrara 1 , 50019 Sesto Fiorentino (FI), Italy
- ICCOM, Istituto di Chimica dei Composti OrganoMetallici , Via Madonna del Piano 10 , I-50019 Sesto Fiorentino , Firenze , Italy
| | - Naomi Falsini
- European Laboratory for Nonlinear Spectroscopy (LENS) , via Nello Carrara 1 , 50019 Sesto Fiorentino (FI), Italy
| | - Paolo Bartolini
- European Laboratory for Nonlinear Spectroscopy (LENS) , via Nello Carrara 1 , 50019 Sesto Fiorentino (FI), Italy
| | - Margherita Citroni
- European Laboratory for Nonlinear Spectroscopy (LENS) , via Nello Carrara 1 , 50019 Sesto Fiorentino (FI), Italy
| | - Andrea Lapini
- European Laboratory for Nonlinear Spectroscopy (LENS) , via Nello Carrara 1 , 50019 Sesto Fiorentino (FI), Italy
- INRIM, Istituto Nazionale di Ricerca Metrologica , Strada delle Cacce 91 , I-10135 Torino , Italy
| | - Andrea Taschin
- European Laboratory for Nonlinear Spectroscopy (LENS) , via Nello Carrara 1 , 50019 Sesto Fiorentino (FI), Italy
- ENEA, Centro Ricerche Frascati , Via E. Fermi 45 , I-00044 Frascati Roma , Italy
| | - Roberto Bini
- European Laboratory for Nonlinear Spectroscopy (LENS) , via Nello Carrara 1 , 50019 Sesto Fiorentino (FI), Italy
- ICCOM, Istituto di Chimica dei Composti OrganoMetallici , Via Madonna del Piano 10 , I-50019 Sesto Fiorentino , Firenze , Italy
- Dipartimento di Chimica "Ugo Schiff" , Università di Firenze , via della Lastruccia 3 , 50019 Sesto Fiorentino (FI), Italy
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19
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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: 39] [Impact Index Per Article: 7.8] [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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20
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Espinosa YR, Caffarena ER, Grigera JR. The role of hydrophobicity in the cold denaturation of proteins under high pressure: A study on apomyoglobin. J Chem Phys 2019; 150:075102. [PMID: 30795674 DOI: 10.1063/1.5080942] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
An exciting debate arises when microscopic mechanisms involved in the denaturation of proteins at high pressures are explained. In particular, the issue emerges when the hydrophobic effect is invoked, given that hydrophobicity cannot elucidate by itself the volume changes measured during protein unfolding. In this work, we study by the use of molecular dynamics simulations and essential dynamics analysis the relation between the solvation dynamics, volume, and water structure when apomyoglobin is subjected to a hydrostatic pressure regime. Accordingly, the mechanism of cold denaturation of proteins under high-pressure can be related to the disruption of the hydrogen-bond network of water favoring the coexistence of two states, low-density and high-density water, which directly implies in the formation of a molten globule once the threshold of 200 MPa has been overcome.
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Affiliation(s)
- Yanis R Espinosa
- Instituto de Física de Líquidos y Sistemas Biológicos (CONICET-UNLP), Calle 59 Nro 789, B1900BTE La Plata, Argentina
| | - Ernesto R Caffarena
- Programa de Computação Científica (PROCC), Fundação Oswaldo Cruz, Manguinhos, CEP 21040-360 Rio de Janeiro, Brazil
| | - J Raúl Grigera
- CEQUINOR, Universidad de La Plata and CONICET, 47 y 115, B1900 La Plata, Argentina
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21
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Imoto S, Marx D. Pressure response of the THz spectrum of bulk liquid water revealed by intermolecular instantaneous normal mode analysis. J Chem Phys 2019; 150:084502. [PMID: 30823759 DOI: 10.1063/1.5080381] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The radial distribution functions of liquid water are known to change significantly their shape upon hydrostatic compression from ambient conditions deep into the kbar pressure regime. It has been shown that despite their eye-catching changes, the fundamental locally tetrahedral fourfold H-bonding pattern that characterizes ambient water is preserved up to about 10 kbar (1 GPa), which is the stability limit of liquid water at 300 K. The observed increase in coordination number comes from pushing water molecules into the first coordination sphere without establishing an H-bond, resulting in roughly two such additional interstitial molecules at 10 kbar. THz spectroscopy has been firmly established as a powerful experimental technique to analyze H-bonding in aqueous solutions given that it directly probes the far-infrared lineshape and thus the prominent H-bond network mode around 180 cm-1. We, therefore, set out to assess pressure effects on the THz response of liquid water at 10 kbar in comparison to the 1 bar (0.1 MPa) reference, both at 300 K, with the aim to trace back the related lineshape changes to the structural level. To this end, we employ the instantaneous normal mode approximation to rigorously separate the H-bonding peak from the large background arising from the pronounced librational tail. By exactly decomposing the total molecular dynamics into hindered translations, hindered rotations, and intramolecular vibrations, we find that the H-bonding peak arises from translation-translation and translation-rotation correlations, which are successively decomposed down to the level of distinct local H-bond environments. Our utmost detailed analysis based on molecular pair classifications unveils that H-bonded double-donor water pairs contribute most to the THz response around 180 cm-1, whereas interstitial waters are negligible. Moreover, short double-donor H-bonds have their peak maximum significantly shifted toward higher frequencies with respect to such long H-bonds. In conjunction with an increasing relative population of these short H-bonds versus the long ones (while the population of other water pair classes is essentially pressure insensitive), this explains not only the blue-shift of the H-bonding peak by about 20-30 cm-1 in total from 1 bar to 10 kbar but also the filling of the shallow local minimum of the THz lineshape located in between the network peak and the red-wing of the librational band at 1 bar. Based on the changing populations as a function of pressure, we are also able to roughly estimate the pressure-dependence of the H-bond network mode and find that its pressure response and thus the blue-shifting are most pronounced at low kbar pressures.
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Affiliation(s)
- Sho Imoto
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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22
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Koga Y. The effect of temperature on fluctuation functions in pure H2O and n-hexane: Wavelength (extensity) vs. amplitude (intensity). J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.04.114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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23
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The solvent side of proteinaceous membrane-less organelles in light of aqueous two-phase systems. Int J Biol Macromol 2018; 117:1224-1251. [PMID: 29890250 DOI: 10.1016/j.ijbiomac.2018.06.030] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 06/07/2018] [Indexed: 12/29/2022]
Abstract
Water represents a common denominator for liquid-liquid phase transitions leading to the formation of the polymer-based aqueous two-phase systems (ATPSs) and a set of the proteinaceous membrane-less organelles (PMLOs). ATPSs have a broad range of biotechnological applications, whereas PMLOs play a number of crucial roles in cellular compartmentalization and often represent a cellular response to the stress. Since ATPSs and PMLOs contain high concentrations of polymers (such as polyethylene glycol (PEG), polypropylene glycol (PPG), Ucon, and polyvinylpyrrolidone (PVP), Dextran, or Ficoll) or biopolymers (peptides, proteins and nucleic acids), it is expected that the separated phases of these systems are characterized by the noticeable changes in the solvent properties of water. These changes in solvent properties can drive partitioning of various compounds (proteins, nucleic acids, organic low-molecular weight molecules, metal ions, etc.) between the phases of ATPSs or between the PMLOs and their surroundings. Although there is a sizable literature on the properties of the ATPS phases, much less is currently known about PMLOs. In this perspective article, we first represent liquid-liquid phase transitions in water, discuss different types of biphasic (or multiphasic) systems in water, and introduce various PMLOs and some of their properties. Then, some basic characteristics of polymer-based ATPSs are presented, with the major focus being on the current understanding of various properties of ATPS phases and solvent properties of water inside them. Finally, similarities and differences between the polymer-based ATPSs and biological PMLOs are discussed.
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24
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Fanetti S, Citroni M, Dziubek K, Nobrega MM, Bini R. The role of H-bond in the high-pressure chemistry of model molecules. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:094001. [PMID: 29345624 DOI: 10.1088/1361-648x/aaa8cf] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Pressure is an extraordinary tool to modify direction and strength of intermolecular interactions with important consequences on the chemical stability of molecular materials. The decrease of the distance among nearest neighbour molecules can give rise to reactive configurations reflecting the crystal arrangement and leading to association processes. In this context, the role of the H-bonds is very peculiar because their usual strengthening with rising pressure does not necessarily configure a decrease of the reaction activation energy but, on the contrary, can give rise to an anomalous stability of the system. In spite of this central role, the mechanisms by which a chemical reaction is favoured or prevented by H-bonding under high pressure conditions is a poorly explored field. Here we review a few studies where the chemical behaviour of simple molecular systems under static compression was related to the H-bonding evolution with pressure. These results are able to clarify a wealth of changes of the chemical and physical properties caused by the strengthening with pressure of the H-bonding network and provide additional tools to understand the mechanisms of high-pressure reactivity, a mandatory step to make these synthetic methods of potential interest for applicative purposes.
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Affiliation(s)
- Samuele Fanetti
- LENS, European Laboratory for Non-linear Spectroscopy, Via N. Carrara 1, I-50019 Sesto Fiorentino, Firenze, Italy. Dipartimento di Chimica 'Ugo Schiff' dell'Università degli Studi di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Firenze, Italy
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25
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Biswas S, Chakraborty D, Mallik BS. Interstitial Voids and Resultant Density of Liquid Water: A First-Principles Molecular Dynamics Study. ACS OMEGA 2018; 3:2010-2017. [PMID: 31458509 PMCID: PMC6641304 DOI: 10.1021/acsomega.7b01996] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 02/07/2018] [Indexed: 05/31/2023]
Abstract
Many anomalous properties of water can be explained on the basis of the coexistence of more than one density states: high-density water (HDW) and low-density water (LDW). We investigated these two phases of water molecules through first-principles molecular dynamics simulations using density functional theory (DFT) in conjunction with various van der Waals-corrected exchange and correlation functionals. Different density regions were found to exist due to the difference in short-range and long-range forces present in DFT potentials. These density regions were identified and analyzed on the basis of the distribution of molecules and voids present. We defined a local structure index to distinguish and find the probability of occurrence of these different states. HDW and LDW arise due to the presence of "interstitial water" molecules in between the first and second coordination shells. The population of interstitial water molecules is found to affect the overall dynamics of the system as they change the hydrogen bond pattern.
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Affiliation(s)
- Sohag Biswas
- Department
of Chemistry, Indian Institute of Technology
Hyderabad, Kandi, 502285 Sangareddy, Telangana, India
| | - Debashree Chakraborty
- Department
of Chemistry, National Institute of Technology
Karnataka, Surathkal, Mangalore 575025, Karnataka, India
| | - Bhabani S. Mallik
- Department
of Chemistry, Indian Institute of Technology
Hyderabad, Kandi, 502285 Sangareddy, Telangana, India
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26
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Espinosa YR, Caffarena ER, Martínez YB, Grigera JR. Pressure effect on micellization of non-ionic surfactant Triton X-100. J Chem Phys 2018; 148:074901. [DOI: 10.1063/1.5003358] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- Yanis R. Espinosa
- Instituto de Física de Líquidos y Sistemas Biológicos (CONICET-UNLP), Calle 59 Nro 789, B1900BTE La Plata, Argentina
| | - Ernesto R. Caffarena
- Programa de Computação Científica (PROCC), Fundação Oswaldo Cruz. Manguinhos, CEP 21040-360 Rio de Janeiro, Brazil
| | | | - J. Raúl Grigera
- CEQUINOR, Universidad de La Plata and CONICET, 47 y 115, B1900 La Plata, Argentina
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27
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Espinosa YR, Grigera JR, Caffarena ER. Essential dynamics of the cold denaturation: pressure and temperature effects in yeast frataxin. Proteins 2017; 85:125-136. [PMID: 27802581 DOI: 10.1002/prot.25205] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/19/2016] [Accepted: 10/25/2016] [Indexed: 11/09/2022]
Abstract
The cold denaturation of globular proteins is a process that can be caused by increasing pressure or decreasing the temperature. Currently, the action mechanism of this process has not been clearly understood, raising an interesting debate on the matter. We have studied the process of cold denaturation using molecular dynamics simulations of the frataxin system Yfh1, which has a dynamic experimental characterization of unfolding at low and high temperatures. The frataxin model here studied allows a comparative analysis using experimental data. Furthermore, we monitored the cold denaturation process of frataxin and also investigated the effect under the high-pressure regime. For a better understanding of the dynamics and structural properties of the cold denaturation, we also analyzed the MD trajectories using essentials dynamic. The results indicate that changes in the structure of water by the effect of pressure and low temperatures destabilize the hydrophobic interaction modifying the solvation and the system volume leading to protein denaturation. Proteins 2016; 85:125-136. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Yanis R Espinosa
- CEQUINOR (CONICET-UNLP), 120 e/61 y 62, Universidad Nacional de La Plata, La Plata, 1900, Argentina
| | - J Raúl Grigera
- CEQUINOR (CONICET-UNLP), 120 e/61 y 62, Universidad Nacional de La Plata, La Plata, 1900, Argentina
- Departmento de Biología, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, 1900, Argentina
| | - Ernesto R Caffarena
- Fundação Oswaldo Cruz., Rio de Janeiro, Programa de Computação Científica (PROCC), CEP, 21040-360, Rio de Janeiro, Brazil
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28
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Evidence of low-density water to high-density water structural transformation in milk during high-pressure processing. INNOV FOOD SCI EMERG 2016. [DOI: 10.1016/j.ifset.2016.10.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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29
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Knake L, Vondracek H, Havenith M. A novel set-up to investigate the low-frequency spectra of aqueous solutions at high hydrostatic pressure. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2016; 87:104101. [PMID: 27802710 DOI: 10.1063/1.4964099] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We present a novel setup to investigate the low frequency (THz/FIR) spectra of an aqueous solution under high hydrostatic pressure (HHP). By integration of a diamond anvil cell into a THz Fourier transform spectrometer, we are able to record the absorption of bulk water in the pressure range from 1 bar to 10 kbar. The difference in intensity can directly be compared to the difference in extinction coefficients. The spectroscopic data reveal a blue shift of the H-bond stretch vibration at 180 cm-1, which is evidence of changes in the H-bond network dynamics.
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Affiliation(s)
- L Knake
- Department of Physical Chemistry II, Ruhr-University Bochum, 44780 Bochum, Germany
| | - H Vondracek
- Department of Physical Chemistry II, Ruhr-University Bochum, 44780 Bochum, Germany
| | - M Havenith
- Department of Physical Chemistry II, Ruhr-University Bochum, 44780 Bochum, Germany
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30
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Lapini A, Pagliai M, Fanetti S, Citroni M, Scandolo S, Bini R, Righini R. Pressure Dependence of Hydrogen-Bond Dynamics in Liquid Water Probed by Ultrafast Infrared Spectroscopy. J Phys Chem Lett 2016; 7:3579-3584. [PMID: 27560355 DOI: 10.1021/acs.jpclett.6b01375] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Clarifying the structure/dynamics relation of water hydrogen-bond network has been the aim of extensive research over many decades. By joining anvil cell high-pressure technology, femtosecond 2D infrared spectroscopy, and molecular dynamics simulations, we studied, for the first time, the spectral diffusion of the stretching frequency of an HOD impurity in liquid water as a function of pressure. Our experimental and simulation results concordantly demonstrate that the rate of spectral diffusion is almost insensitive to the applied pressure. This behavior is in contrast with the previously reported pressure-induced speed up of the orientational dynamics, which can be rationalized in terms of large angular jumps involving sudden switching between two hydrogen-bonded configurations. The different trend of the spectral diffusion can be, instead, inferred considering that the first solvation shell preserves the tetrahedral structure with pressure and the OD stretching frequency is only slight perturbed.
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Affiliation(s)
- Andrea Lapini
- LENS, European Laboratory for Nonlinear Spectroscopy , Via N. Carrara 1, I-50019 Sesto Fiorentino, Firenze, Italy
- Dipartimento di Chimica "Ugo Schiff" dell'Università degli Studi di Firenze , Via della Lastruccia 3, I-50019 Sesto Fiorentino, Firenze, Italy
- Istituto Nazionale di Ottica INO-CNR , Largo Fermi 6, 50125 Firenze, Italy
| | - Marco Pagliai
- Dipartimento di Chimica "Ugo Schiff" dell'Università degli Studi di Firenze , Via della Lastruccia 3, I-50019 Sesto Fiorentino, Firenze, Italy
| | - Samuele Fanetti
- Istituto di Chimica dei Composti Organometallici ICCOM-CNR , Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
| | - Margherita Citroni
- LENS, European Laboratory for Nonlinear Spectroscopy , Via N. Carrara 1, I-50019 Sesto Fiorentino, Firenze, Italy
- Dipartimento di Chimica "Ugo Schiff" dell'Università degli Studi di Firenze , Via della Lastruccia 3, I-50019 Sesto Fiorentino, Firenze, Italy
| | - Sandro Scandolo
- The Abdus Salam International Centre for Theoretical Physics (ICTP) , I-34151 Trieste, Italy
| | - Roberto Bini
- LENS, European Laboratory for Nonlinear Spectroscopy , Via N. Carrara 1, I-50019 Sesto Fiorentino, Firenze, Italy
- Dipartimento di Chimica "Ugo Schiff" dell'Università degli Studi di Firenze , Via della Lastruccia 3, I-50019 Sesto Fiorentino, Firenze, Italy
| | - Roberto Righini
- LENS, European Laboratory for Nonlinear Spectroscopy , Via N. Carrara 1, I-50019 Sesto Fiorentino, Firenze, Italy
- Dipartimento di Chimica "Ugo Schiff" dell'Università degli Studi di Firenze , Via della Lastruccia 3, I-50019 Sesto Fiorentino, Firenze, Italy
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31
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Ranieri U, Giura P, Gorelli FA, Santoro M, Klotz S, Gillet P, Paolasini L, Koza MM, Bove LE. Dynamical Crossover in Hot Dense Water: The Hydrogen Bond Role. J Phys Chem B 2016; 120:9051-9. [DOI: 10.1021/acs.jpcb.6b04142] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Umbertoluca Ranieri
- EPSL, ICMP, École
polytechnique fédérale de Lausanne (EPFL), Station 3, CH-1015 Lausanne, Switzerland
- Institut Laue Langevin, 71, avenue
des Martyrs, B.P. 156, 38042 Grenoble, Cedex 9, France
| | - Paola Giura
- Institut
de Minéralogie, de Physique des Matériaux et de Cosmochimie,
CNRS UMR 7590, Université Pierre et Marie Curie, 4 Place
Jussieu, F-75252 Paris, France
| | - Federico A. Gorelli
- Istituto Nazionale di Ottica, CNR-INO, via N. Carrara 1, 50019 Sesto Fiorentino, Italy
- European Laboratory
for Non Linear Optics, LENS, via N.
Carrara 1, 50019 Sesto Fiorentino, Italy
| | - Mario Santoro
- Istituto Nazionale di Ottica, CNR-INO, via N. Carrara 1, 50019 Sesto Fiorentino, Italy
- European Laboratory
for Non Linear Optics, LENS, via N.
Carrara 1, 50019 Sesto Fiorentino, Italy
| | - Stefan Klotz
- Institut
de Minéralogie, de Physique des Matériaux et de Cosmochimie,
CNRS UMR 7590, Université Pierre et Marie Curie, 4 Place
Jussieu, F-75252 Paris, France
| | - Philippe Gillet
- EPSL, ICMP, École
polytechnique fédérale de Lausanne (EPFL), Station 3, CH-1015 Lausanne, Switzerland
| | - Luigi Paolasini
- ESRF - The European Synchrotron, 71, avenue des Martyrs, CS 40220 38043 Grenoble Cedex 9, France
| | - Michael Marek Koza
- Institut Laue Langevin, 71, avenue
des Martyrs, B.P. 156, 38042 Grenoble, Cedex 9, France
| | - Livia E. Bove
- EPSL, ICMP, École
polytechnique fédérale de Lausanne (EPFL), Station 3, CH-1015 Lausanne, Switzerland
- Institut
de Minéralogie, de Physique des Matériaux et de Cosmochimie,
CNRS UMR 7590, Université Pierre et Marie Curie, 4 Place
Jussieu, F-75252 Paris, France
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32
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Amann-Winkel K, Bellissent-Funel MC, Bove LE, Loerting T, Nilsson A, Paciaroni A, Schlesinger D, Skinner L. X-ray and Neutron Scattering of Water. Chem Rev 2016; 116:7570-89. [DOI: 10.1021/acs.chemrev.5b00663] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Katrin Amann-Winkel
- Department
of Physics, AlbaNova University Center, Stockholm University, SE-106
91, Stockholm, Sweden
| | | | - Livia E. Bove
- IMPMC, CNRS-UMR 7590, Université P&M Curie, 75252 Paris, France
- Institute
of Condensed Matter Physics, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Thomas Loerting
- Institute
of Physical Chemistry, University of Innsbruck, 6020 Innsbruck, Austria
| | - Anders Nilsson
- Department
of Physics, AlbaNova University Center, Stockholm University, SE-106
91, Stockholm, Sweden
| | - Alessandro Paciaroni
- Dipartimento
di Fisica e Geologia, Università di Perugia, Via Alessandro
Pascoli, I-06123 Perugia, Italy
| | - Daniel Schlesinger
- Department
of Physics, AlbaNova University Center, Stockholm University, SE-106
91, Stockholm, Sweden
| | - Lawrie Skinner
- Mineral
Physics Institute, Stony Brook University, Stony Brook, New York 11794-2100, United States
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33
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Towey JJ, Soper AK, Dougan L. Low-Density Water Structure Observed in a Nanosegregated Cryoprotectant Solution at Low Temperatures from 285 to 238 K. J Phys Chem B 2016; 120:4439-48. [DOI: 10.1021/acs.jpcb.6b01185] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J. J. Towey
- Faculty
of Engineering, University of Nottingham, Nottingham NG7 2NR, U.K
| | - A. K. Soper
- ISIS
Facility, Rutherford Appleton Laboratory, Chilton, Didcot, Oxon OX11 OQX, U.K
| | - L. Dougan
- School
of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, U.K
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Shen B, Wang ZY, Dong F, Guo YR, Zhang RJ, Zheng YX, Wang SY, Wang CZ, Ho KM, Chen LY. Dynamics and Diffusion Mechanism of Low-Density Liquid Silicon. J Phys Chem B 2015; 119:14945-51. [PMID: 26540341 DOI: 10.1021/acs.jpcb.5b09138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A first-order phase transition from a high-density liquid to a low-density liquid has been proposed to explain the various thermodynamic anomies of water. It also has been proposed that such liquid-liquid phase transition would exist in supercooled silicon. Computer simulation studies show that, across the transition, the diffusivity drops roughly 2 orders of magnitude, and the structures exhibit considerable tetrahedral ordering. The resulting phase is a highly viscous, low-density liquid silicon. Investigations on the atomic diffusion of such a novel form of liquid silicon are of high interest. Here we report such diffusion results from molecular dynamics simulations using the classical Stillinger-Weber (SW) potential of silicon. We show that the atomic diffusion of the low-density liquid is highly correlated with local tetrahedral geometries. We also show that atoms diffuse through hopping processes within short ranges, which gradually accumulate to an overall random motion for long ranges as in normal liquids. There is a close relationship between dynamical heterogeneity and hopping process. We point out that the above diffusion mechanism is closely related to the strong directional bonding nature of the distorted tetrahedral network. Our work offers new insights into the complex behavior of the highly viscous low density liquid silicon, suggesting similar diffusion behaviors in other tetrahedral coordinated liquids that exhibit liquid-liquid phase transition such as carbon and germanium.
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Affiliation(s)
- B Shen
- Key Laboratory of Micro and Nano Photonic Structures (MoE) and Department of Optical Science and Engineering, Fudan University , Shanghai, 200433, China.,Ames Laboratory, U.S. Department of Energy and Department of Physics and Astronomy, Iowa State University , Ames, Iowa 50011, United States
| | - Z Y Wang
- Key Laboratory of Micro and Nano Photonic Structures (MoE) and Department of Optical Science and Engineering, Fudan University , Shanghai, 200433, China
| | - F Dong
- Key Laboratory of Micro and Nano Photonic Structures (MoE) and Department of Optical Science and Engineering, Fudan University , Shanghai, 200433, China
| | - Y R Guo
- Key Laboratory of Micro and Nano Photonic Structures (MoE) and Department of Optical Science and Engineering, Fudan University , Shanghai, 200433, China
| | - R J Zhang
- Key Laboratory of Micro and Nano Photonic Structures (MoE) and Department of Optical Science and Engineering, Fudan University , Shanghai, 200433, China
| | - Y X Zheng
- Key Laboratory of Micro and Nano Photonic Structures (MoE) and Department of Optical Science and Engineering, Fudan University , Shanghai, 200433, China
| | - S Y Wang
- Key Laboratory of Micro and Nano Photonic Structures (MoE) and Department of Optical Science and Engineering, Fudan University , Shanghai, 200433, China.,Ames Laboratory, U.S. Department of Energy and Department of Physics and Astronomy, Iowa State University , Ames, Iowa 50011, United States.,Key Laboratory for Information Science of Electromagnetic Waves (MoE) , Shanghai, 200433, China
| | - C Z Wang
- Ames Laboratory, U.S. Department of Energy and Department of Physics and Astronomy, Iowa State University , Ames, Iowa 50011, United States
| | - K M Ho
- Ames Laboratory, U.S. Department of Energy and Department of Physics and Astronomy, Iowa State University , Ames, Iowa 50011, United States
| | - L Y Chen
- Key Laboratory of Micro and Nano Photonic Structures (MoE) and Department of Optical Science and Engineering, Fudan University , Shanghai, 200433, China
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Imoto S, Forbert H, Marx D. Water structure and solvation of osmolytes at high hydrostatic pressure: pure water and TMAO solutions at 10 kbar versus 1 bar. Phys Chem Chem Phys 2015; 17:24224-37. [DOI: 10.1039/c5cp03069b] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Solvation structures of trimethylamine N-oxide change drastically due to the increase in the hydrostatic pressure.
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Affiliation(s)
- Sho Imoto
- Ruhr-Universität Bochum
- D-44780 Bochum
- Germany
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36
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Citroni M, Fanetti S, Guigue B, Bartolini P, Taschin A, Lapini A, Foggi P, Bini R. Picosecond optical parametric generator and amplifier for large temperature-jump. OPTICS EXPRESS 2014; 22:30047-30052. [PMID: 25606934 DOI: 10.1364/oe.22.030047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
An optical parametric generator and amplifier producing 15 ps pulses at wavelengths tunable around 2 μm, with energies up to 15 mJ/pulse, has been realized and characterized. The output wavelength is chosen to match a vibrational combination band of water. By measuring the induced birefringence changes we prove that a single pulse is able to completely melt samples of ice in the 10⁻⁶ cm³ volume range, both at room pressure (263 K) and at high pressure (298 K, 1 GPa) in a sapphire anvil cell. This source opens the possibility of studying melting and freezing processes by spectroscopic probes in water or water solutions in a wide range of conditions as found in natural environments.
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Fanetti S, Pagliai M, Citroni M, Lapini A, Scandolo S, Righini R, Bini R. Connecting the Water Phase Diagram to the Metastable Domain: High-Pressure Studies in the Supercooled Regime. J Phys Chem Lett 2014; 5:3804-3809. [PMID: 26278751 DOI: 10.1021/jz501971h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Pressure is extremely efficient to tune intermolecular interactions, allowing the study of the mechanisms regulating, at the molecular level, the structure and dynamics of condensed phases. Among the simplest molecules, water represents in many respects a mystery despite its primary role in ruling most of the biological, physical, and chemical processes occurring in nature. Here we report a careful characterization of the dynamic regime change associated with low-density and high-density forms of liquid water by measuring the line shape of the OD stretching mode of HOD in liquid water along different isotherms as a function of pressure. Remarkably, the high-pressure studies have been here extended down to 240 K, well inside the supercooled regime. Supported by molecular dynamics simulations, a correlation among amorphous and crystalline solids and the two different liquid water forms is attempted to provide a unified picture of the metastable and thermodynamic regimes of water.
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Affiliation(s)
- Samuele Fanetti
- †LENS, European Laboratory for Nonlinear Spectroscopy, Via N. Carrara 1, I-50019 Sesto Fiorentino, Firenze, Italy
| | - Marco Pagliai
- ‡Dipartimento di Chimica "Ugo Schiff" dell'Università degli Studi di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Firenze, Italy
| | - Margherita Citroni
- †LENS, European Laboratory for Nonlinear Spectroscopy, Via N. Carrara 1, I-50019 Sesto Fiorentino, Firenze, Italy
- ‡Dipartimento di Chimica "Ugo Schiff" dell'Università degli Studi di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Firenze, Italy
| | - Andrea Lapini
- †LENS, European Laboratory for Nonlinear Spectroscopy, Via N. Carrara 1, I-50019 Sesto Fiorentino, Firenze, Italy
- ‡Dipartimento di Chimica "Ugo Schiff" dell'Università degli Studi di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Firenze, Italy
| | - Sandro Scandolo
- §The Abdus Salam International Centre for Theoretical Physics (ICTP), ICTP - Strada Costiera, 11, I-34151 Trieste, Italy
| | - Roberto Righini
- †LENS, European Laboratory for Nonlinear Spectroscopy, Via N. Carrara 1, I-50019 Sesto Fiorentino, Firenze, Italy
- ‡Dipartimento di Chimica "Ugo Schiff" dell'Università degli Studi di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Firenze, Italy
| | - Roberto Bini
- †LENS, European Laboratory for Nonlinear Spectroscopy, Via N. Carrara 1, I-50019 Sesto Fiorentino, Firenze, Italy
- ‡Dipartimento di Chimica "Ugo Schiff" dell'Università degli Studi di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Firenze, Italy
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Woods KN. The glassy state of crambin and the THz time scale protein-solvent fluctuations possibly related to protein function. BMC BIOPHYSICS 2014; 7:8. [PMID: 25184036 PMCID: PMC4143578 DOI: 10.1186/s13628-014-0008-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 08/04/2014] [Indexed: 11/17/2022]
Abstract
BACKGROUND THz experiments have been used to characterize the picosecond time scale fluctuations taking place in the model, globular protein crambin. RESULTS Using both hydration and temperature as an experimental parameter, we have identified collective fluctuations (<= 200 cm(-1)) in the protein. Observation of the protein dynamics in the THz spectrum from both below and above the glass transition temperature (Tg) has provided unique insight into the microscopic interactions and modes that permit the solvent to effectively couple to the protein thermal fluctuations. CONCLUSIONS Our findings suggest that the solvent dynamics on the picosecond time scale not only contribute to protein flexibility but may also delineate the types of fluctuations that are able to form within the protein structure.
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Affiliation(s)
- Kristina N Woods
- Physics Department, Carnegie Mellon University, Pittsburgh 15213, PA, USA
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Hidalgo Baltasar E, Taravillo M, Sanz PD, Baonza VG, Guignon B. Role of water structure on the high pressure micellization and phase transformations of sodium dodecanoate aqueous solutions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:7343-7352. [PMID: 24903603 DOI: 10.1021/la501659x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The aim of this work is to study the micelle formation and possible subsequent transformations of sodium dodecanoate aggregates in aqueous solutions at pressures up to 700 MPa. This pressure range is much larger than in most available studies on surfactant solutions and allows for evaluating the possible effect of the low-density to high-density water transformation on the aggregative behavior of the surfactant. The speed-of-sound and attenuation coefficient were determined at 298.15 K as a function of pressure at concentrations up to 0.13 mol kg(-1) in water. The speed-of-sound behavior with concentration is maintained up to pressures around 350 MPa. The attenuation coefficient, initially insensitive to pressure, exhibits a sudden increase around 250 MPa, reaching a maximum around 350 MPa and a plateau above 500 MPa in the case of the highest studied surfactant concentrations. From the analysis of the changes observed in these properties, it was possible to extend the concentration-pressure phase diagram of sodium dodecanoate at constant temperature. Some peculiarities found were: (1) the critical micellar concentration reaches a maximum around 170 MPa, (2) the micellar phase disappears above 400 MPa, (3) a phase transformation starts around 250 MPa, setting the solubility limit of the surfactant at concentrations around 0.06 mol kg(-1) in this pressure region, and (4) further transformations occur between 350 and 500 MPa. We discuss in length the possibility that such transformations might be driven by structural changes linked to the so-called low-density-water to high-density-water transition.
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Affiliation(s)
- Eduardo Hidalgo Baltasar
- MALTA Consolider TEAM, Departamento de Química Física I, Facultad de Ciencias Químicas, Universidad Complutenese de Madrid , 28040-Madrid, Spain
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