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Stepanov GO, Penkov NV, Rodionova NN, Petrova AO, Kozachenko AE, Kovalchuk AL, Tarasov SA, Tverdislov VA, Uvarov AV. The heterogeneity of aqueous solutions: the current situation in the context of experiment and theory. Front Chem 2024; 12:1456533. [PMID: 39391834 PMCID: PMC11464478 DOI: 10.3389/fchem.2024.1456533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 09/12/2024] [Indexed: 10/12/2024] Open
Abstract
The advancement of experimental methods has provided new information about the structure and structural fluctuations of water. Despite the appearance of numerous models, which aim to describe a wide range of thermodynamic and electrical characteristics of water, there is a deficit in systemic understanding of structuring in aqueous solutions. A particular challenge is the fact that even pure water is a heterogeneous, multicomponent system composed of molecular and supramolecular structures. The possibility of the existence of such structures and their nature are of fundamental importance for various fields of science. However, great difficulties arise in modeling relatively large supramolecular structures (e.g. extended hydration shells), where the bonds between molecules are characterized by low energy. Generally, such structures may be non-equilibrium but relatively long-lived. Evidently, the short times of water microstructure exchanges do not mean short lifetimes of macrostructures, just as the instability of individual parts does not mean the instability of the entire structure. To explain this paradox, we review the data from experimental and theoretical research. Today, only some of the experimental results on the lifetime of water structures have been confirmed by modeling, so there is not a complete theoretical picture of the structure of water yet. We propose a new hierarchical water macrostructure model to resolve the issue of the stability of water structures. In this model, the structure of water is presented as consisting of many hierarchically related levels (the stratification model). The stratification mechanism is associated with symmetry breaking at the formation of the next level, even with minimal changes in the properties of the previous level. Such a hierarchical relationship can determine the unique physico-chemical properties of water systems and, in the future, provide a complete description of them.
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Affiliation(s)
- German O. Stepanov
- Department of General and Medical biophysics, Medical Biological Faculty, N.I. Pirogov Russian National Research Medical University, Moscow, Russia
- Research and Development Department, OOO "NPF "Materia Medica Holding", Moscow, Russia
| | - Nikita V. Penkov
- Institute of Cell Biophysics RAS, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, Russia
| | - Natalia N. Rodionova
- Research and Development Department, OOO "NPF "Materia Medica Holding", Moscow, Russia
| | - Anastasia O. Petrova
- Research and Development Department, OOO "NPF "Materia Medica Holding", Moscow, Russia
| | | | | | - Sergey A. Tarasov
- Research and Development Department, OOO "NPF "Materia Medica Holding", Moscow, Russia
| | - Vsevolod A. Tverdislov
- Department of Biophysics Faculty of Physics, Lomonosov Moscow State University, Moscow, Russia
| | - Alexander V. Uvarov
- Department of Molecular Processes and Extreme States of Matter, Faculty of Physics, Lomonosov Moscow State University, Moscow, Russia
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Volkov AA, Chuchupal SV. Isochores and Heat Capacity of Liquid Water in Terms of the Ion–Molecular Model. Int J Mol Sci 2023; 24:ijms24065630. [PMID: 36982704 PMCID: PMC10051472 DOI: 10.3390/ijms24065630] [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: 01/31/2023] [Revised: 03/02/2023] [Accepted: 03/08/2023] [Indexed: 03/18/2023] Open
Abstract
Thermodynamics of liquid water in terms of a non-standard approach—the ion–molecular model—is considered. Water is represented as a dense gas of neutral H2O molecules and single charged H3O+ and OH− ions. The molecules and ions perform thermal collisional motion and interconvert due to ion exchange. The energy-rich process—vibrations of an ion in a hydration shell of molecular dipoles—well known to spectroscopists with its dielectric response at 180 cm−1 (5 THz), is suggested to be key for water dynamics. Taking into account this ion–molecular oscillator, we compose an equation of state of liquid water to obtain analytical expressions for the isochores and heat capacity.
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Offei-Danso A, Hassanali A, Rodriguez A. High-Dimensional Fluctuations in Liquid Water: Combining Chemical Intuition with Unsupervised Learning. J Chem Theory Comput 2022; 18:3136-3150. [PMID: 35472272 DOI: 10.1021/acs.jctc.1c01292] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The microscopic description of the local structure of water remains an open challenge. Here, we adopt an agnostic approach to understanding water's hydrogen bond network using data harvested from molecular dynamics simulations of an empirical water model. A battery of state-of-the-art unsupervised data-science techniques are used to characterize the free-energy landscape of water starting from encoding the water environment using local atomic descriptors, through dimensionality reduction and finally the use of advanced clustering techniques. Analysis of the free energy under ambient conditions was found to be consistent with a rough single basin and independent of the choice of the water model. We find that the fluctuations of the water network occur in a high-dimensional space, which we characterize using a combination of both atomic descriptors and chemical-intuition-based coordinates. We demonstrate that a combination of both types of variables is needed in order to adequately capture the complexity of the fluctuations in the hydrogen bond network at different length scales both at room temperature and also close to the critical point of water. Our results provide a general framework for examining fluctuations in water under different conditions.
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Affiliation(s)
- Adu Offei-Danso
- The Abdus Salam International Center for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy.,SISSA─International School for Advanced Studies, Via Bonomea 265, 34136 Trieste, Italy
| | - Ali Hassanali
- The Abdus Salam International Center for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - Alex Rodriguez
- The Abdus Salam International Center for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
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Vasin AA, Volkov AA. The Current Understanding of the Properties of Liquid Water: A Possible Alternative Solution. Biophysics (Nagoya-shi) 2021. [DOI: 10.1134/s0006350921050262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Kikutsuji T, Kim K, Matubayasi N. Transition pathway of hydrogen bond switching in supercooled water analyzed by the Markov state model. J Chem Phys 2021; 154:234501. [PMID: 34241244 DOI: 10.1063/5.0055531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In this work, we examine hydrogen-bond (H-bond) switching by employing the Markov State Model (MSM). During the H-bond switching, a water hydrogen initially H-bonded with water oxygen becomes H-bonded to a different water oxygen. MSM analysis was applied to trajectories generated from molecular dynamics simulations of the TIP4P/2005 model from a room-temperature state to a supercooled state. We defined four basis states to characterize the configuration between two water molecules: H-bonded ("H"), unbound ("U"), weakly H-bonded ("w"), and alternative H-bonded ("a") states. A 16 × 16 MSM matrix was constructed, describing the transition probability between states composed of three water molecules. The mean first-passage time of the H-bond switching was estimated by calculating the total flux from the HU to UH states. It is demonstrated that the temperature dependence of the mean first-passage time is in accordance with that of the H-bond lifetime determined from the H-bond correlation function. Furthermore, the flux for the H-bond switching is decomposed into individual pathways that are characterized by different forms of H-bond configurations of trimers. The dominant pathway of the H-bond switching is found to be a direct one without passing through such intermediate states as "w" and "a," the existence of which becomes evident in supercooled water. The pathway through "w" indicates a large reorientation of the donor molecule. In contrast, the pathway through "a" utilizes the tetrahedral H-bond network, which is revealed by the further decomposition based on the H-bond number of the acceptor molecule.
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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
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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Consistency of geometrical definitions of hydrogen bonds based on the two-dimensional potential of mean force with respect to the time correlation in liquid water over a wide range of temperatures. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111603] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Probing hydrogen bond strength in liquid water by resonant inelastic X-ray scattering. Nat Commun 2019; 10:1013. [PMID: 30833573 PMCID: PMC6399250 DOI: 10.1038/s41467-019-08979-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 02/13/2019] [Indexed: 11/09/2022] Open
Abstract
Local probes of the electronic ground state are essential for understanding hydrogen bonding in aqueous environments. When tuned to the dissociative core-excited state at the O1s pre-edge of water, resonant inelastic X-ray scattering back to the electronic ground state exhibits a long vibrational progression due to ultrafast nuclear dynamics. We show how the coherent evolution of the OH bonds around the core-excited oxygen provides access to high vibrational levels in liquid water. The OH bonds stretch into the long-range part of the potential energy curve, which makes the X-ray probe more sensitive than infra-red spectroscopy to the local environment. We exploit this property to effectively probe hydrogen bond strength via the distribution of intramolecular OH potentials derived from measurements. In contrast, the dynamical splitting in the spectral feature of the lowest valence-excited state arises from the short-range part of the OH potential curve and is rather insensitive to hydrogen bonding.
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Kikutsuji T, Kim K, Matubayasi N. How do hydrogen bonds break in supercooled water?: Detecting pathways not going through saddle point of two-dimensional potential of mean force. J Chem Phys 2018; 148:244501. [DOI: 10.1063/1.5033419] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] 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
| | - 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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