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Abstract
The existence of a two-center, three-electron hemibond in the first solvation shell of •OH(aq) has long been a matter of debate. The hemibond manifests in ab initio molecular dynamics simulations as a small-r feature in the oxygen radial distribution function (RDF) for H2O···•OH, but that feature disappears when semilocal density functionals are replaced with hybrids, suggesting a self-interaction artifact. Using periodic simulations at the PBE0+D3 level, we demonstrate that the hemibond is actually still present (as evidenced by delocalization of the spin density) but is obscured by the hydrogen-bonded feature in the RDF due to a slight elongation of the hemibond. Computed electronic spectra for •OH(aq) are in excellent agreement with experiment and confirm that hemibond-like configurations play an outsized role in the spectroscopy due to an intense charge-transfer transition that is strongly attenuated in hydrogen-bonded configurations. Apparently, 25% exact exchange (as in PBE0) is insufficient to eliminate delocalization of unpaired spins.
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Affiliation(s)
- Bhaskar Rana
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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Liu JM, Nishigori T, Maeyama T, Huang QR, Katada M, Kuo JL, Fujii A. Infrared Spectroscopy and Anharmonic Vibrational Analysis of (H 2O-Kr n) + ( n = 1-3): Hemibond Formation of the Water Radical Cation. J Phys Chem Lett 2021; 12:7997-8002. [PMID: 34433278 DOI: 10.1021/acs.jpclett.1c02164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The hemibond is a nonclassical covalent bond formed between a radical (cation) and a closed shell molecule. The hemibond formation ability of water has attracted great interest, concerning its role in ionization of water. While many computational studies on the water hemibond have been performed, clear experimental evidence has been hardly reported because the hydrogen bond formation overwhelms the hemibond formation. In the present study, infrared photodissociation spectroscopy is applied to (H2O-Krn)+ (n = 1-3) radical cation clusters. The observed spectra of (H2O-Krn)+ are well reproduced by the anharmonic vibrational simulations based on the hemibonded isomer structures. The firm evidence of the hemibond formation ability of water is revealed.
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Affiliation(s)
- Jing-Min Liu
- Institute of Atomic and Molecular Sciences, Academia Sinica, 1 Roosevelt Rd., Sec. 4, Taipei 10617, Taiwan
| | - Tomoki Nishigori
- Department of Chemistry, Graduate School of Science, Tohoku University, Aramaki-Aza-Aoba 6-3, Aoba-Ku, Sendai 980-8578, Japan
| | - Toshihiko Maeyama
- Department of Chemistry, Graduate School of Science, Tohoku University, Aramaki-Aza-Aoba 6-3, Aoba-Ku, Sendai 980-8578, Japan
| | - Qian-Rui Huang
- Institute of Atomic and Molecular Sciences, Academia Sinica, 1 Roosevelt Rd., Sec. 4, Taipei 10617, Taiwan
| | - Marusu Katada
- Department of Chemistry, Graduate School of Science, Tohoku University, Aramaki-Aza-Aoba 6-3, Aoba-Ku, Sendai 980-8578, Japan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, 1 Roosevelt Rd., Sec. 4, Taipei 10617, Taiwan
| | - Asuka Fujii
- Department of Chemistry, Graduate School of Science, Tohoku University, Aramaki-Aza-Aoba 6-3, Aoba-Ku, Sendai 980-8578, Japan
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3
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Nayarisseri A, Khandelwal R, Madhavi M, Selvaraj C, Panwar U, Sharma K, Hussain T, Singh SK. Shape-based Machine Learning Models for the Potential Novel COVID-19 Protease Inhibitors Assisted by Molecular Dynamics Simulation. Curr Top Med Chem 2020; 20:2146-2167. [PMID: 32621718 DOI: 10.2174/1568026620666200704135327] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/20/2020] [Accepted: 04/25/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND The vast geographical expansion of novel coronavirus and an increasing number of COVID-19 affected cases have overwhelmed health and public health services. Artificial Intelligence (AI) and Machine Learning (ML) algorithms have extended their major role in tracking disease patterns, and in identifying possible treatments. OBJECTIVE This study aims to identify potential COVID-19 protease inhibitors through shape-based Machine Learning assisted by Molecular Docking and Molecular Dynamics simulations. METHODS 31 Repurposed compounds have been selected targeting the main coronavirus protease (6LU7) and a machine learning approach was employed to generate shape-based molecules starting from the 3D shape to the pharmacophoric features of their seed compound. Ligand-Receptor Docking was performed with Optimized Potential for Liquid Simulations (OPLS) algorithms to identify highaffinity compounds from the list of selected candidates for 6LU7, which were subjected to Molecular Dynamic Simulations followed by ADMET studies and other analyses. RESULTS Shape-based Machine learning reported remdesivir, valrubicin, aprepitant, and fulvestrant as the best therapeutic agents with the highest affinity for the target protein. Among the best shape-based compounds, a novel compound identified was not indexed in any chemical databases (PubChem, Zinc, or ChEMBL). Hence, the novel compound was named 'nCorv-EMBS'. Further, toxicity analysis showed nCorv-EMBS to be suitable for further consideration as the main protease inhibitor in COVID-19. CONCLUSION Effective ACE-II, GAK, AAK1, and protease 3C blockers can serve as a novel therapeutic approach to block the binding and attachment of the main COVID-19 protease (PDB ID: 6LU7) to the host cell and thus inhibit the infection at AT2 receptors in the lung. The novel compound nCorv- EMBS herein proposed stands as a promising inhibitor to be evaluated further for COVID-19 treatment.
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Affiliation(s)
- Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore-452010, Madhya Pradesh, India,Bioinformatics Research Laboratory, LeGene Biosciences Pvt Ltd., Mahalakshmi Nagar, Indore-452010, Madhya
Pradesh, India,Research Chair for Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King
Saud University, Riyadh, Saudi Arabia,Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
| | - Ravina Khandelwal
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore-452010, Madhya Pradesh, India
| | - Maddala Madhavi
- Department of Zoology, Nizam College, Osmania University, Hyderabad-500001, Telangana State, India
| | - Chandrabose Selvaraj
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
| | - Umesh Panwar
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
| | - Khushboo Sharma
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore-452010, Madhya Pradesh, India
| | - Tajamul Hussain
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia,Research Chair for Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King
Saud University, Riyadh, Saudi Arabia
| | - Sanjeev Kumar Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
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Ab initio investigation of cationic water cluster (H2O)+13 via particle swarm optimization algorithm. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2464-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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5
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Ab initio investigation of the lower-energy candidate structures for (H2O)10+ water cluster. Struct Chem 2018. [DOI: 10.1007/s11224-018-1109-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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Ab initio study of cationic water cluster (H 2 O) 9 + via particle swarm optimization algorithm. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.09.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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7
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Tang M, Hu CE, Lv ZL, Chen XR, Cai LC. Ab Initio Study of Ionized Water Radical Cation (H 2O) 8+ in Combination with the Particle Swarm Optimization Method. J Phys Chem A 2016; 120:9489-9499. [PMID: 27934325 DOI: 10.1021/acs.jpca.6b09866] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The structures of cationic water clusters (H2O)8+ have been globally explored by the particle swarm optimization method in combination with quantum chemical calculations. Geometry optimization and vibrational analysis for the 15 most interesting clusters were computed at the MP2/aug-cc-pVDZ level and infrared spectrum calculation at MPW1K/6-311++G** level. Special attention was paid to the relationships between their configurations and energies. Both MP2 and B3LYP-D3 calculations revealed that the cage-like structure is the most stable, which is different from a five-membered ring lowest energy structure but agrees well with a cage-like structure in the literature. Furthermore, our obtained cage-like structure is more stable by 0.87 and 1.23 kcal/mol than the previously reported structures at MP2 and B3LYP-D3 levels, respectively. Interestingly, on the basis of their relative Gibbs free energies and the temperature dependence of populations, the cage-like structure predominates only at very low temperatures, and the most dominating species transforms into a newfound four-membered ring structure from 100 to 400 K, which can contribute greatly to the experimental infrared spectrum. By topological analysis and reduced density gradient analysis, we also investigated the structural characteristics and bonding strengths of these water cluster radical cations.
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Affiliation(s)
- Mei Tang
- Institute of Atomic and Molecular Physics, College of Physical Science and Technology, Sichuan University , Chengdu 610065, China
| | - Cui-E Hu
- College of Physics and Electronic Engineering, Chongqing Normal University , Chongqing 400047, China
| | - Zhen-Long Lv
- Institute of Atomic and Molecular Physics, College of Physical Science and Technology, Sichuan University , Chengdu 610065, China
| | - Xiang-Rong Chen
- Institute of Atomic and Molecular Physics, College of Physical Science and Technology, Sichuan University , Chengdu 610065, China
| | - Ling-Cang Cai
- National Key Laboratory for Shock Wave and Detonation Physics Research, Institute of Fluid Physics, Chinese Academy of Engineering Physics , Mianyang 621900, China
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8
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Affiliation(s)
- Daniel M. Chipman
- Radiation Laboratory, University of Notre Dame, Notre
Dame, Indiana 46556-5674, United States
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9
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Liu L, Hu CE, Tang M, Chen XR, Cai LC. Ab initio investigation of structure, stability, thermal behavior, bonding, and infrared spectra of ionized water cluster (H 2O) 6. J Chem Phys 2016; 145:154307. [PMID: 27782468 DOI: 10.1063/1.4964860] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The low-lying isomers of cationic water cluster (H2O)6+ have been globally explored by using particle swarm optimization algorithm in conjunction with quantum chemical calculations. Compared with previous results, our searching method covers a wide range of structural isomers of (H2O)6+ and therefore turns out to be more effective. With these local minima, geometry optimization and vibrational analysis are performed for the most interesting clusters at second-order Møller-Plesset (MP2)/aug-cc-pVDZ level, and their energies are further refined at MP2/aug-cc-pVTZ and coupled-cluster theory with single, double, and perturbative triple excitations/aug-cc-pVDZ level. The interaction energies using the complete basis set limits at MP2 level are also reported. The relationships between their structure arrangement and their energies are discussed. Based on the results of thermal simulation, structural change from a four-numbered ring to a tree-like structure occurs at T ≈ 45 K, and the relative population of six lowest-free-energy isomers is found to exceed 4% at some point within the studied temperature range. Studies reveal that, among these six isomers, two new-found isomers constitute 10% of isomer population at 180 K, and the experimental spectra can be better explained with inclusions of the two isomers. The molecular orbitals for six representative cationic water clusters are also studied. Through topological and reduced density gradient analysis, we investigated the structural characteristics and the bonding strengths of these water cluster radical cations.
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Affiliation(s)
- Lei Liu
- Institute of Atomic and Molecular Physics, College of Physical Science and Technology, Sichuan University, Chengdu 610064, China
| | - Cui-E Hu
- College of Physics and Electronic Engineering, Chongqing Normal University, Chongqing 400047, China
| | - Mei Tang
- Institute of Atomic and Molecular Physics, College of Physical Science and Technology, Sichuan University, Chengdu 610064, China
| | - Xiang-Rong Chen
- Institute of Atomic and Molecular Physics, College of Physical Science and Technology, Sichuan University, Chengdu 610064, China
| | - Ling-Cang Cai
- National Key Laboratory for Shock Wave and Detonation Physics Research, Institute of Fluid Physics, CAEP, Mianyang 621900, China
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Pan PR, Lu EP, Kuo JL, Tsai MK. The Spectroscopic Features of Ionized Water Medium: Theoretical Characterization and Implication Using (H 2O) n+, n=3-4, Cluster Model. J CHIN CHEM SOC-TAIP 2016. [DOI: 10.1002/jccs.201600030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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11
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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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12
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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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13
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Lin LC, Liang JM, Lu EP, Tsai MK. Response of the hydrogen bond network to the ionization of bulk water: ab initio molecular dynamic simulations using H2S(aq). Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.04.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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14
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Lv ZL, Cheng Y, Chen XR, Cai LC. Structural exploration and properties of (H2O)4+ cluster via ab initio in combination with particle swarm optimization method. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2015.02.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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Abstract
A proton transfer process is usually dominant in several biological phenomena such as the energy relaxation of photo-excited DNA base pairs and a charge relay process in Ser-His-Glu.
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Affiliation(s)
- Hiroto Tachikawa
- Division of Materials Chemistry
- Graduate School of Engineering
- Hokkaido University
- Sapporo 060-8628
- Japan
| | - Tomoya Takada
- Department of Material Chemistry
- Asahikawa National College of Technology
- Asahikawa 071-8142
- Japan
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16
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Lv ZL, Xu K, Cheng Y, Chen XR, Cai LC. Ab initioinvestigation of the lower energy candidate structures for (H2O)5+water cluster. J Chem Phys 2014; 141:054309. [DOI: 10.1063/1.4891721] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Zhen-Long Lv
- Institute of Atomic and Molecular Physics, College of Physical Science and Technology, Sichuan University, Chengdu 610064, China
- School of Physics and Engineering, Henan University of Science and Technology, Luoyang 471023, China
| | - Kai Xu
- Institute of Atomic and Molecular Physics, College of Physical Science and Technology, Sichuan University, Chengdu 610064, China
| | - Yan Cheng
- Institute of Atomic and Molecular Physics, College of Physical Science and Technology, Sichuan University, Chengdu 610064, China
| | - Xiang-Rong Chen
- Institute of Atomic and Molecular Physics, College of Physical Science and Technology, Sichuan University, Chengdu 610064, China
| | - Ling-Cang Cai
- National Key Laboratory for Shock Wave and Detonation Physics Research, Institute of Fluid Physics, Chinese Academy of Engineering Physics, Mianyang 621900, China
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17
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Structures and stabilities of asymmetrical dimer radical cation systems (AH3–H2O)+ (A=N, P, As). Struct Chem 2014. [DOI: 10.1007/s11224-014-0472-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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18
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19
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Lu EP, Pan PR, Li YC, Tsai MK, Kuo JL. Structural evolution and solvation of the OH radical in ionized water radical cations (H2O)n+, n = 5–8. Phys Chem Chem Phys 2014; 16:18888-95. [DOI: 10.1039/c4cp02293a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Structural evolution of ionized water radical cations (H2O)n+, n = 5–8, is studied by ab intio methods.
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Affiliation(s)
- En-Ping Lu
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617, Taiwan
| | - Piin-Ruey Pan
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617, Taiwan
| | - Ying-Cheng Li
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617, Taiwan
| | - Ming-Kang Tsai
- Department of Chemistry
- National Taiwan Normal University
- Taipei 10677, Taiwan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617, Taiwan
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20
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Azamat J, Sardroodi JJ, Rastkar A. Water desalination through armchair carbon nanotubes: a molecular dynamics study. RSC Adv 2014. [DOI: 10.1039/c4ra08249d] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Separation of ions from water using armchair carbon nanotubes.
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Affiliation(s)
- J. Azamat
- Molecular Simulations Lab
- Azarbaijan Shahid Madani University
- Tabriz, Iran
| | - J. J. Sardroodi
- Molecular Simulations Lab
- Azarbaijan Shahid Madani University
- Tabriz, Iran
| | - A. Rastkar
- Molecular Simulations Lab
- Azarbaijan Shahid Madani University
- Tabriz, Iran
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21
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Matsuda Y, Nakayama Y, Mikami N, Fujii A. Isomer-selective infrared spectroscopy of the cationic trimethylamine dimer to reveal its charge sharing and enhanced acidity of the methyl groups. Phys Chem Chem Phys 2014; 16:9619-24. [DOI: 10.1039/c4cp00659c] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The isomer-selective infrared spectroscopy revealed the charge-shared (hemibond) and the C⋯HN hydrogen-bond structures of the trimethylamine dimer cation.
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Affiliation(s)
- Yoshiyuki Matsuda
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai, Japan
- Center for the Advancement of Higher Education
| | - Yuichiro Nakayama
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai, Japan
| | - Naohiko Mikami
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai, Japan
| | - Asuka Fujii
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai, Japan
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22
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Durá G, Carrión MC, Jalón FA, Manzano BR, Rodríguez AM. Dinuclear Species versus Zigzag or Helical Polymers in Palladium, Zinc, and Copper Complexes with Ditopic Bis(pyrazolyl)methane Ligands. Eur J Inorg Chem 2013. [DOI: 10.1002/ejic.201300948] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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23
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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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24
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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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Do H, Besley NA. Proton transfer or hemibonding? The structure and stability of radical cation clusters. Phys Chem Chem Phys 2013; 15:16214-9. [DOI: 10.1039/c3cp52922c] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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