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Matsumoto M, Yagasaki T, Tanaka H. GenIce-core: Efficient algorithm for generation of hydrogen-disordered ice structures. J Chem Phys 2024; 160:094101. [PMID: 38426513 DOI: 10.1063/5.0198056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/09/2024] [Indexed: 03/02/2024] Open
Abstract
Ice is different from ordinary crystals because it contains randomness, which means that statistical treatment based on ensemble averaging is essential. Ice structures are constrained by topological rules known as the ice rules, which give them unique anomalous properties. These properties become more apparent when the system size is large. For this reason, there is a need to produce a large number of sufficiently large crystals that are homogeneously random and satisfy the ice rules. We have developed an algorithm to quickly generate ice structures containing ions and defects. This algorithm is provided as an independent software module that can be incorporated into crystal structure generation software. By doing so, it becomes possible to simulate ice crystals on a previously impossible scale.
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Affiliation(s)
- Masakazu Matsumoto
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
| | - Takuma Yagasaki
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Osaka 560-8531, Japan
| | - Hideki Tanaka
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
- Toyota Physical and Chemical Research Institute, Nagakute 480-1192, Japan
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Yamashita K, Nakayama K, Komatsu K, Ohhara T, Munakata K, Hattori T, Sano-Furukawa A, Kagi H. The hydrogen-bond network in sodium chloride tridecahydrate: analogy with ice VI. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2023; 79:414-426. [PMID: 37703290 DOI: 10.1107/s2052520623007199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 08/16/2023] [Indexed: 09/15/2023]
Abstract
The structure of a recently found hyperhydrated form of sodium chloride (NaCl·13H2O and NaCl·13D2O) has been determined by in situ single-crystal neutron diffraction at 1.7 GPa and 298 K. It has large hydrogen-bond networks and some water molecules have distorted bonding features such as bifurcated hydrogen bonds and five-coordinated water molecules. The hydrogen-bond network has similarities to ice VI in terms of network topology and disordered hydrogen bonds. Assuming the equivalence of network components connected by pseudo-symmetries, the overall network structure of this hydrate can be expressed by breaking it down into smaller structural units which correspond to the ice VI network structure. This hydrogen-bond network contains orientational disorder of water molecules in contrast to the known salt hydrates. An example is presented here for further insights into a hydrogen-bond network containing ionic species.
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Affiliation(s)
- Keishiro Yamashita
- Geochemical Research Center, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kazuya Nakayama
- Geochemical Research Center, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kazuki Komatsu
- Geochemical Research Center, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takashi Ohhara
- J-PARC Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai-mura, Ibaraki 319-1195, Japan
| | - Koji Munakata
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society (CROSS), IQBRC Building, 162-1 Shirakata, Tokai, Naka, Ibaraki 319-1106, Japan
| | - Takanori Hattori
- J-PARC Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai-mura, Ibaraki 319-1195, Japan
| | - Asami Sano-Furukawa
- J-PARC Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai-mura, Ibaraki 319-1195, Japan
| | - Hiroyuki Kagi
- Geochemical Research Center, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Komatsu K. Neutrons meet ice polymorphs. CRYSTALLOGR REV 2022. [DOI: 10.1080/0889311x.2022.2127148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2022]
Affiliation(s)
- Kazuki Komatsu
- Geochemical Research Center, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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Computational Analysis of Hydrogen Bond Vibrations of Ice III in the Far-Infrared Band. CRYSTALS 2022. [DOI: 10.3390/cryst12070910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The hydrogen-disordered structure of ice III makes it difficult to analyze its vibrational spectrum theoretically. To clarify the contribution of hydrogen bonds (HBs), we constructed a 24-molecule supercell to mimic the real structure and performed first-principles density functional theory calculations. The calculated curve of phonon density of states showed good correspondence with the experimental data. Based on the theory of two kinds of HB vibrational modes, we analyzed the distributions of two-bond modes and four-bond modes. The energy splitting of these modes results in a flat vibrational band, which is a common phenomenon in high-pressure ice phases. These findings verified the general rule that there are two types of HB vibrations in ice, thereby furthering our understanding of HB interactions in water ice and their broad role in nature.
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Whale TF. Disordering effect of the ammonium cation accounts for anomalous enhancement of heterogeneous ice nucleation. J Chem Phys 2022; 156:144503. [DOI: 10.1063/5.0084635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Heterogeneous nucleation of ice from supercooled water is the process responsible for triggering nearly all ice formation in the natural environment. Understanding of heterogeneous ice nucleation is particularly key for understanding the formation of ice in clouds, which impacts weather and climate. While many effective ice nucleators are known the mechanisms of their actions remain poorly understood. Some inorganic nucleators have been found to nucleate ice at warmer temperatures in dilute ammonium solution than in pure water. This is surprising, analogous to salty water melting at a warmer temperature than pure water. Here, the magnitude of this effect is rationalized as being due to thermodynamically favorable ammonium-induced disordering of the hydrogen bond network of ice critical clusters formed on inorganic ice nucleators. Theoretical calculations are shown to be consistent with new experimental measurements aimed at finding the maximum magnitude of the effect. The implication of this study is that the ice-nucleating sites and surfaces of many inorganic ice nucleators are either polar or charged and therefore tend to induce formation of hydrogen ordered ice clusters. This work corroborates various literature reports indicating that some inorganic ice nucleators are most effective when nominally neutral and implies a commonality in mechanism between a wide range of inorganic ice nucleators.
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Affiliation(s)
- Thomas F Whale
- Department of Chemistry, University of Warwick, United Kingdom
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Sharif Z, Salzmann CG. Comparison of the phase transitions of high-pressure phases of ammonium fluoride and ice at ambient pressure. J Chem Phys 2022; 156:014502. [PMID: 34998346 DOI: 10.1063/5.0077419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The phase diagrams of water and ammonium fluoride (NH4F) display some interesting parallels. Several crystalline NH4F phases have isostructural ice counterparts and one of the famous anomalies of water, the fact that the liquid is denser than ice Ih, is also found for NH4F. Here, we investigate the phase transitions of the pressure-quenched high-pressure phases of NH4F upon heating at ambient pressure with x-ray diffraction and calorimetry, and we compare the results with the corresponding ices. NH4F II transforms to NH4F Isd, which is a stacking-disordered variant of the stable hexagonal NH4F Ih polymorph. Heating NH4F III gives a complex mixture of NH4F II and NH4F Isd, while some NH4F III remains initially. Complete conversion to NH4F Isd is achieved above ∼220 K. The NH4F II obtained from NH4F III persists to much higher temperatures compared to the corresponding pressure-quenched NH4F II. Quantification of the stacking disorder in NH4F Isd reveals a more sluggish conversion to NH4F Ih for NH4F Isd from NH4F III. In general, the presence of stress and strain in the samples appears to have pronounced effects on the phase transition temperatures. NH4F shows a complete lack of amorphous forms at low temperatures either upon low-temperature compression of NH4F Ih or heating NH4F III at ambient pressure. The amorphous forms of ice are often used to explain the anomalies of water. It will, therefore, be interesting to explore if liquid NH4F displays more water-like anomalies despite the apparent lack of amorphous forms at low temperatures.
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Affiliation(s)
- Zainab Sharif
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Christoph G Salzmann
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
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Tanaka H, Yagasaki T, Matsumoto M. On the role of intermolecular vibrational motions for ice polymorphs. III. Mode characteristics associated with negative thermal expansion. J Chem Phys 2021; 155:214502. [PMID: 34879657 DOI: 10.1063/5.0068560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Low-pressure ice forms, such as hexagonal and cubic ice, expand on cooling below temperature 60 K. This negative thermal expansivity has been explored in terms of phonon frequency modulation with varying volume and attributed to the negative Grüneisen parameters unique mostly to tetrahedrally coordinated substances. However, an underlying mechanism for the negative Grüneisen parameters has not been known except some schematic analyses. We investigate in this study the characteristics of the intermolecular vibrational modes whose Grüneisen parameters are negative by examining the individual vibrational modes rigorously. It is found that the low frequency modes below 100 cm-1, which we explicitly show are mostly bending motions of three hydrogen-bonded molecules, necessarily accompany elongation of the hydrogen bond length at peak amplitudes compared with that at the equilibrium position in executing the vibrational motions. The elongation gives rise to a decrease in the repulsive interaction while an increase in the Coulombic one. The decrease in the repulsive interaction is relaxed substantially by expansion due to its steep slope against molecular separation compared with the sluggish increase in the Coulombic one, and therefore, the negative Grüneisen parameters are obtainable. This scenario is tested against some variants of cubic ice with various water potential models. It is demonstrated that four interaction-site models are suitable to describe the intermolecular vibrations and the thermal expansivity because of the moderate tendency to favor the tetrahedral coordination.
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Affiliation(s)
- Hideki Tanaka
- Toyota Physical and Chemical Research Institute, Nagakute 480-1192, Japan
| | - Takuma Yagasaki
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Osaka 560-8531, Japan
| | - Masakazu Matsumoto
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
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Conway LJ, Brown K, Loveday JS, Hermann A. Ammonium fluoride's analogy to ice: Possibilities and limitations. J Chem Phys 2021; 154:204501. [PMID: 34241159 DOI: 10.1063/5.0048516] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ammonium fluoride, NH4F, is often seen as an analog to ice, with several of its solid phases closely resembling known ice phases. While its ionic and hydrogen-ordered nature puts topological constraints on the ice-like network structures it can form, it is not clear what consequences these constraints have for NH4F compound formation and evolution. Here, we explore computationally the reach and eventual limits of the ice analogy for ammonium fluoride. By combining data mining of known and hypothetical ice networks with crystal structure prediction and density functional calculations, we explore the high-pressure phase diagram of NH4F and host-guest compounds of its hydrides. Pure NH4F departs from ice-like behavior above 80 GPa with the emergence of close-packed ionic structures. The predicted stability of NH4F hydrides shows that NH4F can act as a host to small guest species, albeit in a topologically severely constraint configuration space. Finally, we explore the binary NH3-HF chemical space, where we find candidate structures for several unsolved polyfluoride phases; among them is the chemical analog to H2O2 dihydrate.
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Affiliation(s)
- L J Conway
- SUPA, School of Physics and Astronomy and Centre for Science at Extreme Conditions, The University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
| | - K Brown
- SUPA, School of Physics and Astronomy and Centre for Science at Extreme Conditions, The University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
| | - J S Loveday
- SUPA, School of Physics and Astronomy and Centre for Science at Extreme Conditions, The University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
| | - A Hermann
- SUPA, School of Physics and Astronomy and Centre for Science at Extreme Conditions, The University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
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Salzmann CG, Rosu-Finsen A, Sharif Z, Radaelli PG, Finney JL. Detailed crystallographic analysis of the ice V to ice XIII hydrogen-ordering phase transition. J Chem Phys 2021; 154:134504. [PMID: 33832256 DOI: 10.1063/5.0045443] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ice V is a structurally highly complex material with 28 water molecules in its monoclinic unit cell. It is classified as a hydrogen-disordered phase of ice. Yet, some of its hydrogen-bonded water molecules display significant orientational order. Upon cooling pure ice V, additional orientational ordering cannot be achieved on the experimental time scale. Doping with hydrochloric acid has been shown to be most effective in enabling the phase transition of ice V to its hydrogen-ordered counterpart ice XIII. Here, we present a detailed crystallographic study of this phase transition investigating the effects of hydrochloric and hydrofluoric acid as well as lithium and potassium hydroxide doping. The magnitudes of the stepwise changes in the lattice constants during the phase transition are found to be more sensitive indicators for the extent of hydrogen order in ice XIII than the appearance of new Bragg peaks. Hydrofluoric acid and lithium hydroxide doping enable similar ordering processes as hydrochloric acid but with slower kinetics. The various possible space groups and ordered configurations of ice XIII are examined systematically, and the previously determined P21/a structure is confirmed. Interestingly, the partial hydrogen order already present in ice V is found to perpetuate into ice XIII, and these ordering processes are found to be independent of pressure. Overall, the hydrogen ordering goes along with a small increase in volume, which appears to be the origin of the slower hydrogen-ordering kinetics under pressure. Heating pressure-quenched samples at ambient pressure revealed low-temperature "transient ordering" features in both diffraction and calorimetry.
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Affiliation(s)
- Christoph G Salzmann
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Alexander Rosu-Finsen
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Zainab Sharif
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Paolo G Radaelli
- Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom
| | - John L Finney
- Department of Physics and Astronomy and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT, United Kingdom
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