1
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Hong D, Liu Y, Liu H, Hu Y. Development of
dual‐model
classical density functional theory and its application to gas adsorption in porous materials. AIChE J 2021. [DOI: 10.1002/aic.17120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Dandan Hong
- State Key Laboratory of Chemical Engineering and School of Chemistry & Molecular Engineering East China University of Science and Technology Shanghai China
| | - Yu Liu
- State Key Laboratory of Chemical Engineering and School of Chemistry & Molecular Engineering East China University of Science and Technology Shanghai China
- School of Chemical Engineering and Technology Sun Yat‐sen University Zhuhai China
| | - Honglai Liu
- State Key Laboratory of Chemical Engineering and School of Chemistry & Molecular Engineering East China University of Science and Technology Shanghai China
| | - Ying Hu
- State Key Laboratory of Chemical Engineering and School of Chemistry & Molecular Engineering East China University of Science and Technology Shanghai China
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2
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Onuki A. Long-range correlations of polarization and number densities in dilute electrolytes. J Chem Phys 2020; 153:234501. [DOI: 10.1063/5.0030763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Akira Onuki
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
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3
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New RRC, Bui TTT, Bogus M. Binding Interactions of Peptide Aptamers. Molecules 2020; 25:molecules25246055. [PMID: 33371475 PMCID: PMC7767479 DOI: 10.3390/molecules25246055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/11/2020] [Accepted: 12/16/2020] [Indexed: 11/17/2022] Open
Abstract
Peptide aptamers are short amino acid chains that are capable of binding specifically to ligands in the same way as their much larger counterparts, antibodies. Ligands of therapeutic interest that can be targeted are other peptide chains or loops located on the surface of protein receptors (e.g., GCPR), which take part in cell-to-cell communications either directly or via the intermediary of hormones or signalling molecules. To confer on aptamers the same sort of conformational rigidity that characterises an antibody binding site, aptamers are often constructed in the form of cyclic peptides, on the assumption that this will encourage stronger binding interactions than would occur if the aptamers were simply linear chains. However, no formal studies have been conducted to confirm the hypothesis that linear peptides will engage in stronger binding interactions with cyclic peptides than with other linear peptides. In this study, the interaction of a model cyclic decamer with a series of linear peptide constructs was compared with that of a linear peptide with the same sequence, showing that the cyclic configuration does confer benefits by increasing the strength of binding.
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Affiliation(s)
- Roger R. C. New
- Vaxcine (UK) Limited, London Bioscience Innovation Centre, London NW1 0NH, UK;
- Faculty of Science & Technology, Middlesex University, Hendon, London NW4 4BT, UK
- Correspondence: or
| | - Tam T. T. Bui
- Centre for Biomolecular Spectroscopy and Institute of Pharmaceutical Science, King’s College, London SE1 1UL, UK;
| | - Michal Bogus
- Vaxcine (UK) Limited, London Bioscience Innovation Centre, London NW1 0NH, UK;
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4
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Liu H, Liu Y, Shang Y, Liu H. Toxicant Deposition and Transport in Alveolus: A Classical Density Functional Prediction. Chem Res Toxicol 2018; 31:1398-1404. [PMID: 30479130 DOI: 10.1021/acs.chemrestox.8b00272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The deposition and transport of toxicants on pulmonary surfactant are important processes in human health and medical care. We have introduced classical density functional theory (CDFT) to provide insight into this process. Nine typical toxicants in PM2.5 were considered, and their free energy and structural information have been examined. The free energy profile indicates that PbO, As2O3, and CdO are the three toxicants most easily deposited in the pulmonary alveolus, which is consistent with survey data. CuO appears to be the easiest toxicant to transport through the surfactant. Structural analysis indicates that the toxicants tend to pass through the surfactant with rotation. The configuration of the pulmonary surfactant was examined by extending our previous work to polymer systems, and it appears that both the configurational entropy and the direct interaction between the surfactant and the toxicant dominate the configuration of the pulmonary surfactant.
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5
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Sun CQ. Aqueous charge injection: solvation bonding dynamics, molecular nonbond interactions, and extraordinary solute capabilities. INT REV PHYS CHEM 2018. [DOI: 10.1080/0144235x.2018.1544446] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Chang Q. Sun
- EBEAM, Yangtze Normal University, Chongqing, People's Republic of China
- NOVITAS, EEE, Nanyang Technological University, Singapore, Singapore
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6
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Leong KY, Wang F. A molecular dynamics investigation of the surface tension of water nanodroplets and a new technique for local pressure determination through density correlation. J Chem Phys 2018; 148:144503. [DOI: 10.1063/1.5004985] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Kai-Yang Leong
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Feng Wang
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA
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7
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Besford QA, Christofferson AJ, Liu M, Yarovsky I. Long-range dipolar order and dispersion forces in polar liquids. J Chem Phys 2017; 147:194503. [DOI: 10.1063/1.5005581] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
| | | | - Maoyuan Liu
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University, Victoria 3001, Australia
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8
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Sheng S, Miller M, Wu J. Molecular Theory of Hydration at Different Temperatures. J Phys Chem B 2017; 121:6898-6908. [DOI: 10.1021/acs.jpcb.7b04264] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shijie Sheng
- Department of Chemical and
Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Michael Miller
- Department of Chemical and
Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Jianzhong Wu
- Department of Chemical and
Environmental Engineering, University of California, Riverside, California 92521, United States
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9
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Henchman RH. Water's dual nature and its continuously changing hydrogen bonds. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:384001. [PMID: 27447299 DOI: 10.1088/0953-8984/28/38/384001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A model is proposed for liquid water that is a continuum between the ordered state with predominantly tetrahedral coordination, linear hydrogen bonds and activated dynamics and a disordered state with a continuous distribution of multiple coordinations, multiple types of hydrogen bond, and diffusive dynamics, similar to that of normal liquids. Central to water's heterogeneous structure is the ability of hydrogen to donate to either one acceptor in a conventional linear hydrogen bond or to multiple acceptors as a furcated hydrogen. Linear hydrogen bonds are marked by slow, activated kinetics for hydrogen-bond switching to more crowded acceptors and sharp first peaks in the hydrogen-oxygen radial distribution function. Furcated hydrogens, equivalent to free, broken, dangling or distorted hydrogens, have barrierless, rapid kinetics and poorly defined first peaks in their hydrogen-oxygen radial distribution function. They involve the weakest donor in a local excess of donors, such that barrierless whole-molecule vibration rapidly swaps them between the linear and furcated forms. Despite the low number of furcated hydrogens and their transient existence, they are readily created in a single hydrogen-bond switch and free up the dynamics of numerous surrounding molecules, bringing about the disordered state. Hydrogens in the ordered state switch with activated dynamics to make the non-tetrahedral coordinations of the disordered state, which can also combine to make the ordered state. Consequently, the ordered and disordered states are both connected by diffusive dynamics and differentiated by activated dynamics, bringing about water's continuous heterogeneity.
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Affiliation(s)
- Richard H Henchman
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK. School of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
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10
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Baul U, Kanth JMP, Anishetty R, Vemparala S. Effect of simple solutes on the long range dipolar correlations in liquid water. J Chem Phys 2016; 144:104502. [DOI: 10.1063/1.4943097] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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11
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Affiliation(s)
- Shijie Sheng
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
| | - Jianzhong Wu
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
- Department of Mathematics, University of California, Riverside, CA, USA
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12
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Henao A, Busch S, Guàrdia E, Tamarit JL, Pardo LC. The structure of liquid water beyond the first hydration shell. Phys Chem Chem Phys 2016; 18:19420-5. [DOI: 10.1039/c6cp00720a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Distance dependent excess entropy calculations reveal that water is tetrahedrally structured up to long distances.
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Affiliation(s)
- Andrés Henao
- Grup de Caracterització de Materials
- Departament de Física
- ETSEIB
- Universitat Politècnica de Catalunya
- E-08028 Barcelona
| | - Sebastian Busch
- German Engineering Materials Science Centre (GEMS) at Heinz Maier-Leibnitz Zentrum (MLZ)
- Helmholtz-Zentrum Geesthacht GmbH
- 85747 Garching bei München
- Germany
| | - Elvira Guàrdia
- Grup de Simulació per Ordinador en Matèria Condensada
- Departament de Física
- B4-B5 Campus Nord
- Universitat Politècnica de Catalunya
- E-08034 Barcelona
| | - Josep Lluis Tamarit
- Grup de Caracterització de Materials
- Departament de Física
- ETSEIB
- Universitat Politècnica de Catalunya
- E-08028 Barcelona
| | - Luis Carlos Pardo
- Grup de Caracterització de Materials
- Departament de Física
- ETSEIB
- Universitat Politècnica de Catalunya
- E-08028 Barcelona
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13
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Shelton DP. Long-range orientation correlation in dipolar liquids probed by hyper-Rayleigh scattering. J Chem Phys 2015; 143:134503. [DOI: 10.1063/1.4931973] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- David P. Shelton
- Department of Physics and Astronomy, University of Nevada, Las Vegas, Nevada 89154-4002, USA
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14
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Huang YL, Zhang X, Ma Z, Zhou G, Sun CQ, Gong YY. Potential Paths for the Hydrogen-Bond Relaxing With (H 2O) NCluster Size. J Phys Chem A 2015. [DOI: 10.1021/acs.jpca.5b03921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Huang YL, Zhang X, Ma Z, Zhou G, Sun CQ, Gong YY. Potential Paths for the Hydrogen-Bond Relaxing With (H 2O) N Cluster Size. J Phys Chem A 2015; 119:16962-16971. [PMID: 26119068 DOI: 10.1021/acs.jpcc.5b03921] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Relaxation of the inter- and intra-molecular interactions for the hydrogen bond (O:H-O) between undercoordinated molecules determines the unusual behavior of water nanodroplets and nanobubbles. However, probing such potentials remains unreality. Here we show that the Lagrangian solution [Huang et al., J. Phys. Chem. B, 2013. 117: 13639] transforms the observed H-O bond (x = H) and O:H nonbond (x = L) lengths and phonon frequencies (dx, x) [Sun et al., J. Phys. Chem. Lett., 2013. 4: 2565] into the respective force constants and bond energies (kx, Ex) and hence enables the mapping of the potential paths for the O:H-O bond relaxing with water cluster size. Results show that molecular undercoordination not only reduces the molecular size (dH) with enhanced H-O energy from the bulk value of 3.97 to 5.10 eV for a H2O monomer, but also enlarges the molecular separation (dL) with reduced O:H energy from 95 to 35 meV for a dimer. The H-O energy gain raises the melting point from bulk value 273 to 310 K for the skin and the O:H energy loss lowers the freezing temperature from bulk value 258 to 202 K for 1.4 nm sized droplet, by dispersing the quasisolid phase boundaries.
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16
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Abstract
Strong short-range intermolecular interactions result in position and orientation correlations between nearest neighbour molecules in isotropic liquids, but it is generally assumed that such correlations extend at most a few molecular diameters. Results from second-harmonic light scattering experiments presented here reveal long-range molecular orientation correlations in liquid water, where the molecular dipole orientation distribution has the form of a nearly pure transverse vector field. Spatial scales in the range 200-2000 nm are probed by the angle-dependent measurements and the observed correlations are thought to result from rotation-translation coupling in acoustic phonons in the liquid.
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Affiliation(s)
- David P Shelton
- Department of Physics and Astronomy, University of Nevada, Las Vegas, Nevada 89154-4002, USA
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17
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18
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19
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Zhang X, Yan T, Huang Y, Ma Z, Liu X, Zou B, Sun CQ. Mediating relaxation and polarization of hydrogen-bonds in water by NaCl salting and heating. Phys Chem Chem Phys 2014; 16:24666-71. [PMID: 25325235 DOI: 10.1039/c4cp04080e] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Infrared spectroscopy and contact-angle measurements revealed that NaCl salting has the same effect as heating on O:H phonon softening and H-O phonon stiffening, but has the opposite effect on skin polarization of liquid water. The mechanics of thermal modulation of O-O Coulomb repulsion [Sun, et al., J. Phys. Chem. Lett., 2013, 4, 3238] may suggest a possible mechanism for this NaCl involved Hofmeister effect, aqueous solution modulated surface tension and its abilities in protein dissolution, from the perspective of Coulomb mediation of interaction within the O:H-O bond.
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Affiliation(s)
- Xi Zhang
- Center for Coordination Bond and Electronic Engineering, College of Materials Science and Engineering, China Jiliang University, Hangzhou 310018, China
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20
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Huang Y, Ma Z, Zhang X, Zhou G, Zhou Y, Sun CQ. Hydrogen Bond Asymmetric Local Potentials in Compressed Ice. J Phys Chem B 2013; 117:13639-45. [PMID: 24090472 DOI: 10.1021/jp407836n] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Yongli Huang
- Key
Laboratory of Low-dimensional Materials and Application Technology
(Ministry of Education) and Faculty of Materials, Optoelectronics
and Physics, Xiangtan University, Xiangtan 411105, China
| | - Zengsheng Ma
- Key
Laboratory of Low-dimensional Materials and Application Technology
(Ministry of Education) and Faculty of Materials, Optoelectronics
and Physics, Xiangtan University, Xiangtan 411105, China
| | - Xi Zhang
- NOVITAS,
School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798
- Center
for Coordination Bond and Electronic Engineering, College of Materials
Science and Engineering, China Jiliang University, Hangzhou 310018, China
| | - Guanghui Zhou
- Department
of Physics and Key Laboratory for Low-Dimensional Structures and Quantum
Manipulation (Ministry of Education), Hunan Normal University, Changsha 410081, China
| | - Yichun Zhou
- Key
Laboratory of Low-dimensional Materials and Application Technology
(Ministry of Education) and Faculty of Materials, Optoelectronics
and Physics, Xiangtan University, Xiangtan 411105, China
| | - Chang Q. Sun
- Key
Laboratory of Low-dimensional Materials and Application Technology
(Ministry of Education) and Faculty of Materials, Optoelectronics
and Physics, Xiangtan University, Xiangtan 411105, China
- NOVITAS,
School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798
- Center
for Coordination Bond and Electronic Engineering, College of Materials
Science and Engineering, China Jiliang University, Hangzhou 310018, China
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21
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Huang Y, Zhang X, Ma Z, Li W, Zhou Y, Zhou J, Zheng W, Sun CQ. Size, separation, structural order, and mass density of molecules packing in water and ice. Sci Rep 2013; 3:3005. [PMID: 24141643 PMCID: PMC3801132 DOI: 10.1038/srep03005] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 10/07/2013] [Indexed: 11/28/2022] Open
Abstract
The structural symmetry and molecular separation in water and ice remain uncertain. We present herewith a solution to unifying the density, the structure order and symmetry, the size (H-O length dH), and the separation (d(OO) = d(L) + d(H) or the O:H length d(L)) of molecules packing in water and ice in terms of statistic mean. This solution reconciles: i) the d(L) and the d(H) symmetrization of the O:H-O bond in compressed ice, ii) the d(OO) relaxation of cooling water and ice and, iii) the d(OO) expansion of a dimer and between molecules at water surface. With any one of the d(OO), the density ρ(g·cm⁻³), the d(L), and the d(H), as a known input, one can resolve the rest quantities using this solution that is probing conditions or methods independent. We clarified that: i) liquid water prefers statistically the mono-phase of tetrahedrally-coordinated structure with fluctuation, ii) the low-density phase (supersolid phase as it is strongly polarized with even lower density) exists only in regions consisting molecules with fewer than four neighbors and, iii) repulsion between electron pairs on adjacent oxygen atoms dictates the cooperative relaxation of the segmented O:H-O bond, which is responsible for the performance of water and ice.
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Affiliation(s)
- Yongli Huang
- Key Laboratory of Low-Dimensional Materials and Application Technologies (Ministry of Education) and Faculty of Materials, Optoelectronics and Physics, Xiangtan University, Hunan 411105, China
- These authors contributed equally to this work
| | - Xi Zhang
- NOVITAS, School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798
- Center for Coordination Bond and Electronic Engineering, College of Materials Science and Engineering, China Jiliang University, Hangzhou 310018, China
- These authors contributed equally to this work
| | - Zengsheng Ma
- Key Laboratory of Low-Dimensional Materials and Application Technologies (Ministry of Education) and Faculty of Materials, Optoelectronics and Physics, Xiangtan University, Hunan 411105, China
| | - Wen Li
- Key Laboratory of Low-Dimensional Materials and Application Technologies (Ministry of Education) and Faculty of Materials, Optoelectronics and Physics, Xiangtan University, Hunan 411105, China
| | - Yichun Zhou
- Key Laboratory of Low-Dimensional Materials and Application Technologies (Ministry of Education) and Faculty of Materials, Optoelectronics and Physics, Xiangtan University, Hunan 411105, China
| | - Ji Zhou
- State Key Laboratory of New Ceramics and Fine Processing, Department of Materials Science and Engineering, Tsinghua University, Beijing 100084, China
| | - Weitao Zheng
- School of Materials Science, Jilin University, Changchun 130012, China
| | - Chang Q. Sun
- Key Laboratory of Low-Dimensional Materials and Application Technologies (Ministry of Education) and Faculty of Materials, Optoelectronics and Physics, Xiangtan University, Hunan 411105, China
- NOVITAS, School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798
- Center for Coordination Bond and Electronic Engineering, College of Materials Science and Engineering, China Jiliang University, Hangzhou 310018, China
- School of Materials Science, Jilin University, Changchun 130012, China
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