1
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Malloum A, Conradie J. Dimethylformamide clusters: non-covalent bondings, structures and temperature-dependence. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2118188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Alhadji Malloum
- Department of Chemistry, University of the Free State, Bloemfontein, South Africa
- Department of Physics, Faculty of Science, University of Maroua, Maroua, Cameroon
| | - Jeanet Conradie
- Department of Chemistry, University of the Free State, Bloemfontein, South Africa
- Department of Chemistry, UiT – The Arctic University of Norway, Tromsø, Norway
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2
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Haiwang Djefoulna VH, Abia D, Jules Fifen J, Nsangou M, Jaidane NE. Rotational thermodynamic parameters for asymmetric-top molecules: classical vs. quantum approaches and new analytical partition function. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2087565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
| | - Daouda Abia
- Department of Chemistry, Faculty of Science, The University of Ngaoundere, Ngaoundere, Cameroon
| | - Jean Jules Fifen
- Quantum Theory and Aplications Unit, Department of Physics, Faculty of Science, The University of Ngaoundere, Ngaoundere, Cameroon
| | - Mama Nsangou
- Quantum Theory and Aplications Unit, Department of Physics, Faculty of Science, The University of Ngaoundere, Ngaoundere, Cameroon
- University of Maroua, Maroua, Cameroon
| | - Nejm-Eddine Jaidane
- Laboratoire de Spectroscopie Atomique Moléculaire et Applications, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisie
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3
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Schran C, Brieuc F, Marx D. Transferability of machine learning potentials: Protonated water neural network potential applied to the protonated water hexamer. J Chem Phys 2021; 154:051101. [DOI: 10.1063/5.0035438] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Christoph Schran
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Fabien Brieuc
- 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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4
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Djefoulna VHH, Fifen JJ, Malloum A, Jaidane NE. Rotational thermodynamic parameters for symmetric-top, linear-top and spherical-top molecules: classical versus quantum approach and New analytical partition functions. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-02674-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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5
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Niu Z, Tang M, Ge N. Structure, stability, infrared spectra, and bonding of OH m(H 2O) 7 ( m = 0, ±1) clusters: ab initio study combining the particle swarm optimization algorithm. Phys Chem Chem Phys 2020; 22:26487-26501. [PMID: 33185201 DOI: 10.1039/d0cp04332j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The various structural candidates of anionic, neutral, and cationic water clusters OHm(H2O)7 (m = 0, ±1) have been globally predicted by combining the particle swarm optimization method and quantum chemical calculations. Geometry optimization and vibrational analysis for the optimal structures were performed with the MP2/aug-cc-pVDZ method, and the energy profile was further refined at the CCSD(T)/CBS level. Special attention was paid to the relationships between configurations and energies, particularly the first solvation shell coordination number of OH- and OH. For OH-(H2O)7, OH(H2O)7, and OH+(H2O)7 clusters, the most stable species at room temperature are predicted to be the tetra-solvated multi-ring structure A6, the tri-solvated hemibond cage structure N1, and the single five-membered ring structure C2, respectively. The temperature effects on the stability of these three systems were also explored via Gibbs free energies. Furthermore, for the OH-(H2O)7 clusters, the assignments of vibrational transitions in the OH stretching region are in good agreement with the studies of small hydroxide ion-water clusters, and the IR spectra of two isomers (tetra-solvated multi-ring A6 and penta-solvated cage A3) may match future experimental observation well. By topological analysis and reduced density gradient analysis, the structural characteristics and bonding strengths of the studied clusters were investigated. This work indicates the excellent performance of the PSO search algorithm and CALYPSO on water clusters, and may further provide extensive insights into the chemical behavior such as the transport mechanism of OH- ions and OH radicals in the aqueous phase.
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Affiliation(s)
- Zhenwei Niu
- School of National Defense Science & Technology, Southwest University of Science and Technology, Mianyang 621010, P. R. China
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6
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Lebedev AV. The H3O+(H2O)n Reagent Ion: Calculations of the Structure, Thermodynamic Parameters of Hydration, Equilibrium Composition, and Mobility. JOURNAL OF ANALYTICAL CHEMISTRY 2019. [DOI: 10.1134/s1061934819130082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Mishra S, Sahoo DK, Hsu PJ, Matsuda Y, Kuo JL, Biswal HS, Patwari GN. A liquid crucible model for aggregation of phenylacetylene in the gas phase. Phys Chem Chem Phys 2019; 21:13623-13632. [DOI: 10.1039/c8cp07738j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structural transformation from a π-stacked dimer to an aromatic C–H⋯π trimer and a tetramer.
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Affiliation(s)
- Saurabh Mishra
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai 400 076
- India
| | - Dipak Kumar Sahoo
- Homi Bhabha National Institute
- School of Chemical Sciences
- National Institute of Science Education and Research Bhubaneswar
- Khurda 752050
- India
| | - Po-Jen Hsu
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Yoshiyuki Matsuda
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Himansu S. Biswal
- Homi Bhabha National Institute
- School of Chemical Sciences
- National Institute of Science Education and Research Bhubaneswar
- Khurda 752050
- India
| | - G. Naresh Patwari
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai 400 076
- India
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8
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Malloum A, Fifen JJ, Conradie J. Structures and infrared spectroscopy of large sized protonated ammonia clusters. J Chem Phys 2018; 149:244301. [DOI: 10.1063/1.5053172] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Alhadji Malloum
- Department of Physics, Faculty of Science, The University of Ngaoundere, P.O. Box 454, Ngaoundere, Cameroon
| | - Jean Jules Fifen
- Department of Physics, Faculty of Science, The University of Ngaoundere, P.O. Box 454, Ngaoundere, Cameroon
| | - Jeanet Conradie
- Department of Chemistry, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
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9
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Shi R, Li K, Su Y, Tang L, Huang X, Sai L, Zhao J. Revisit the landscape of protonated water clusters H +(H 2O) n with n = 10-17: An ab initio global search. J Chem Phys 2018; 148:174305. [PMID: 29739201 DOI: 10.1063/1.5026383] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Using a genetic algorithm incorporated with density functional theory, we explore the ground state structures of protonated water clusters H+(H2O)n with n = 10-17. Then we re-optimize the isomers at B97-D/aug-cc-pVDZ level of theory. The extra proton connects with a H2O molecule to form a H3O+ ion in all H+(H2O)10-17 clusters. The lowest-energy structures adopt a monocage form at n = 10-16 and core-shell structure at n = 17 based on the MP2/aug-cc-pVTZ//B97-D/aug-cc-pVDZ+ZPE single-point-energy calculation. Using second-order vibrational perturbation theory, we further calculate the infrared spectra with anharmonic correction for the ground state structures of H+(H2O)10-17 clusters at the PBE0/aug-cc-pVDZ level. The anharmonic correction to the spectra is crucial since it reproduces the experimental results quite well. The extra proton weakens the O-H bond strength in the H3O+ ion since the Wiberg bond order of the O-H bond in the H3O+ ion is smaller than that in H2O molecules, which causes a red shift of the O-H stretching mode in the H3O+ ion.
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Affiliation(s)
- Ruili Shi
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams (Dalian University of Technology), Ministry of Education, Dalian 116024, China
| | - Keyao Li
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams (Dalian University of Technology), Ministry of Education, Dalian 116024, China
| | - Yan Su
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams (Dalian University of Technology), Ministry of Education, Dalian 116024, China
| | - Lingli Tang
- College of Science, Dalian Minzu University, Dalian 116600, China
| | - Xiaoming Huang
- School of Ocean Science and Technology, Dalian University of Technology, Panjin Campus, Panjin 124221, China
| | - Linwei Sai
- Department of Mathematics and Physics, Hohai University, Changzhou 213022, China
| | - Jijun Zhao
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams (Dalian University of Technology), Ministry of Education, Dalian 116024, China
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10
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Fujii A, Sugawara N, Hsu PJ, Shimamori T, Li YC, Hamashima T, Kuo JL. Hydrogen bond network structures of protonated short-chain alcohol clusters. Phys Chem Chem Phys 2018; 20:14971-14991. [DOI: 10.1039/c7cp08072g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protonated alcohol clusters enable extraction of the physical essence of the nature of hydrogen bond networks.
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Affiliation(s)
- Asuka Fujii
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Natsuko Sugawara
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Po-Jen Hsu
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Takuto Shimamori
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Ying-Cheng Li
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Toru Hamashima
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
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11
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Malloum A, Fifen JJ, Conradie J. Solvation energies of the proton in methanol revisited and temperature effects. Phys Chem Chem Phys 2018; 20:29184-29206. [DOI: 10.1039/c8cp05823g] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Various functionals assessing solvation free energies and enthalpies of the proton in methanol.
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Affiliation(s)
- Alhadji Malloum
- Department of Physics, Faculty of Science
- The University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Jean Jules Fifen
- Department of Physics, Faculty of Science
- The University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Jeanet Conradie
- Department of Chemistry
- University of the Free State
- Bloemfontein
- South Africa
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12
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Katada M, Hsu PJ, Fujii A, Kuo JL. Temperature and Size Dependence of Characteristic Hydrogen-Bonded Network Structures with Ion Core Switching in Protonated (Methanol)6–10–(Water)1 Mixed Clusters: A Revisit. J Phys Chem A 2017; 121:5399-5413. [DOI: 10.1021/acs.jpca.7b03762] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marusu Katada
- Department
of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Po-Jen Hsu
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
| | - Asuka Fujii
- Department
of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Jer-Lai Kuo
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
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13
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Shi R, Huang X, Su Y, Lu HG, Li SD, Tang L, Zhao J. Which Density Functional Should Be Used to Describe Protonated Water Clusters? J Phys Chem A 2017; 121:3117-3127. [DOI: 10.1021/acs.jpca.7b00058] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ruili Shi
- Key
Laboratory of Materials Modification by Laser, Ion and Electron Beams, Dalian University of Technology, Ministry of Education, Dalian, 116024, China
| | - Xiaoming Huang
- School
of Ocean Science and Technology, Dalian University of Technology, Panjin Campus, Panjin, 124221, China
| | - Yan Su
- Key
Laboratory of Materials Modification by Laser, Ion and Electron Beams, Dalian University of Technology, Ministry of Education, Dalian, 116024, China
| | - Hai-Gang Lu
- Key
Laboratory of Chemical Biology and Molecular Engineering of the Education
Ministry, Institute of Molecular Science, Shanxi University, Taiyuan, 030006, China
| | - Si-Dian Li
- Key
Laboratory of Chemical Biology and Molecular Engineering of the Education
Ministry, Institute of Molecular Science, Shanxi University, Taiyuan, 030006, China
| | - Lingli Tang
- College
of Science, Dalian Nationalities University, Dalian 116600, China
| | - Jijun Zhao
- Key
Laboratory of Materials Modification by Laser, Ion and Electron Beams, Dalian University of Technology, Ministry of Education, Dalian, 116024, China
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14
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Malloum A, Fifen JJ, Dhaouadi Z, Nana Engo SG, Jaidane NE. Structures and spectroscopy of medium size protonated ammonia clusters at different temperatures, H+(NH3)10–16. J Chem Phys 2017; 146:044305. [DOI: 10.1063/1.4974179] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15
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Hsu PJ, Ho KL, Lin SH, Kuo JL. Exploration of hydrogen bond networks and potential energy surfaces of methanol clusters using a two-stage clustering algorithm. Phys Chem Chem Phys 2017; 19:544-556. [DOI: 10.1039/c6cp07120a] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A two-stage algorithm based both on the similarity in shape and hydrogen bond network is developed to explore the potential energy surface of methanol clusters.
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Affiliation(s)
- Po-Jen Hsu
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei
- Taiwan
- Department of Applied Chemistry
| | - Kun-Lin Ho
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei
- Taiwan
| | - Sheng-Hsien Lin
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei
- Taiwan
- Department of Applied Chemistry
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei
- Taiwan
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16
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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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17
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Pang R, Yu LJ, Zhang M, Tian ZQ, Wu DY. DFT Study of Hydrogen-Bonding Interaction, Solvation Effect, and Electric-Field Effect on Raman Spectra of Hydrated Proton. J Phys Chem A 2016; 120:8273-8284. [PMID: 27689539 DOI: 10.1021/acs.jpca.6b07064] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Strong hydrogen-bonding interaction and Raman spectra of hydrated proton have been investigated using hybrid density functional theory method B3LYP. The solvation model of density (SMD) approach is employed in the present calculation to simulate hydrated protons in aqueous solution. Focusing on the different hydrogen-bonded Eigen-water and Zundel-water interactions, we present a better assignment of Raman signals of hydrated proton on the basis of vibrational analysis in different environments. Our results showed that B3LYP calculations could give a good prediction for characteristic vibrational frequencies of Eigen and Zundel isomers in liquid phase. The O-H stretching vibrational frequencies from Eigen and Zundel units are very sensitive to hydrogen-bonding interaction with solvent water molecules. Moreover, the solvation effect and the external electric-field effect lead to the proton deviating from the central position of Zundel structure and finally resulting in a transition to Eigen one in aqueous solution. Furthermore, by combining theoretical prediction and Raman scattering theory, we calculate absolute Raman intensities of characteristic signals based on the polarizability tensor derivatives of hydrated proton clusters. This is very helpful to infer the microstructure of hydrated protons in aqueous solution by using Raman measurements.
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Affiliation(s)
- Ran Pang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
| | - Li-Juan Yu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
| | - Meng Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
| | - Zhong-Qun Tian
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
| | - De-Yin Wu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
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18
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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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19
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Crespo Y, Hassanali A. Characterizing the local solvation environment of OH(-) in water clusters with AIMD. J Chem Phys 2016; 144:074304. [PMID: 26896983 DOI: 10.1063/1.4941107] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In this work, we use ab initio molecular dynamics coupled with metadynamics to explore and characterize the glassy potential energy landscape of the OH(-) in a 20 and 48 water cluster. The structural, energetic, and topological properties of OH(-) are characterized for both clusters and the molecular origins of the IR signatures are examined. We find that in both the small and large clusters, the OH(-) can donate or accept a varying number of hydrogen bonds confirming that the amphiphilic character does not depend on cluster size. However, we highlight some important differences found between the energetic and topological properties of both families of clusters which may have implications on understanding the changes in the solvation structure of OH(-) between bulk and interfacial environments. By studying the IR spectra of smaller subsets of molecules within the 20 water molecule cluster, we find that the IR spectrum of the bare OH(-) as well as the water molecule donating a strong hydrogen bond to it exhibits characteristic absorption along the amphiphilic band between 1500 and 3000 cm(-1) at positions very similar to those found for the entire hydroxide cluster. The results presented here will be useful in the calibration and improvement of both ab initio and semi-empirical methods to model this complex anion.
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Affiliation(s)
- Yanier Crespo
- International Institute of Physics (IIP), Av. Odilon Gomes de Lima, 1722-Capim Macio, 59078-400 Natal-RN, Brazil
| | - Ali Hassanali
- The Abdus Salam ICTP, Strada Costiera 11, I-34151 Trieste, Italy
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20
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Nakai Y, Hidaka H, Watanabe N, Kojima TM. Stepwise formation of H3O(+)(H2O)n in an ion drift tube: Empirical effective temperature of association/dissociation reaction equilibrium in an electric field. J Chem Phys 2016; 144:224306. [PMID: 27306006 DOI: 10.1063/1.4953416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We measured equilibrium constants for H3O(+)(H2O)n-1 + H2O↔H3O(+)(H2O)n (n = 4-9) reactions taking place in an ion drift tube with various applied electric fields at gas temperatures of 238-330 K. The zero-field reaction equilibrium constants were determined by extrapolation of those obtained at non-zero electric fields. From the zero-field reaction equilibrium constants, the standard enthalpy and entropy changes, ΔHn,n-1 (0) and ΔSn,n-1 (0), of stepwise association for n = 4-8 were derived and were in reasonable agreement with those measured in previous studies. We also examined the electric field dependence of the reaction equilibrium constants at non-zero electric fields for n = 4-8. An effective temperature for the reaction equilibrium constants at non-zero electric field was empirically obtained using a parameter describing the electric field dependence of the reaction equilibrium constants. Furthermore, the size dependence of the parameter was thought to reflect the evolution of the hydrogen-bond structure of H3O(+)(H2O)n with the cluster size. The reflection of structural information in the electric field dependence of the reaction equilibria is particularly noteworthy.
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Affiliation(s)
- Yoichi Nakai
- Radioactive Isotope Physics Laboratory, RIKEN Nishina Center, Wako, Saitama 351-0198, Japan
| | - Hiroshi Hidaka
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Hokkaido 060-0819, Japan
| | - Naoki Watanabe
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Hokkaido 060-0819, Japan
| | - Takao M Kojima
- Atomic Physics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
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21
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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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22
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Fifen JJ, Agmon N. Structure and Spectroscopy of Hydrated Sodium Ions at Different Temperatures and the Cluster Stability Rules. J Chem Theory Comput 2016; 12:1656-73. [DOI: 10.1021/acs.jctc.6b00038] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jean Jules Fifen
- The
Fritz Haber Research Center, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Department
of Physics, Faculty of Science, The University of Ngaoundere, P.O. Box 454, Ngaoundere, Cameroon
| | - Noam Agmon
- The
Fritz Haber Research Center, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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23
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Malloum A, Fifen JJ, Dhaouadi Z, Nana Engo SG, Jaidane NE. Structures and spectroscopy of protonated ammonia clusters at different temperatures. Phys Chem Chem Phys 2016; 18:26827-26843. [DOI: 10.1039/c6cp03240k] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protonated ammonia clusters are all Eigen structures and the first solvation shell of the related ammonium ion core is saturated by four ammonia molecules.
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Affiliation(s)
- Alhadji Malloum
- Department of Physics
- Faculty of Science
- The University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Jean Jules Fifen
- Department of Physics
- Faculty of Science
- The University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Zoubeida Dhaouadi
- Laboratoire de Spectroscopie Atomique Moléculaire et Applications
- Faculté des Sciences de Tunis
- Université de Tunis El Manar
- Campus Universitaire
- Tunis
| | - Serge Guy Nana Engo
- Department of Physics
- Faculty of Science
- The University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Nejm-Eddine Jaidane
- Laboratoire de Spectroscopie Atomique Moléculaire et Applications
- Faculté des Sciences de Tunis
- Université de Tunis El Manar
- Campus Universitaire
- Tunis
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24
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Heine N, Fagiani MR, Asmis KR. Disentangling the Contribution of Multiple Isomers to the Infrared Spectrum of the Protonated Water Heptamer. J Phys Chem Lett 2015; 6:2298-2304. [PMID: 26266608 DOI: 10.1021/acs.jpclett.5b00879] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We use infrared/infrared double-resonance population labeling (IR(2)MS(2)) spectroscopy in the spectral region of the free and hydrogen-bonded OH stretching fundamentals (2880-3850 cm(-1)) to identify the number and to isolate the vibrational signatures of individual isomers contributing to the gas-phase IR spectra of the cryogenically cooled protonated water clusters H(+)(H2O)n·H2/D2 with n = 7-10. For n = 7, four isomers are identified and assigned. Surprisingly, the IR(2)MS(2) spectra of the protonated water octa-, nona-, and decamer show no evidence for multiple isomers. The present spectra support the prediction that the quasi-2D to 3D structural transition occurs in between n = 8 and 9 in the cold cluster regime. However, the same models have difficulty explaining the remarkable size dependence of the isomer population reported here.
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Affiliation(s)
- Nadja Heine
- †Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| | - Matias R Fagiani
- †Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
- §Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstrasse 2, D-04103 Leipzig, Germany
| | - Knut R Asmis
- §Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstrasse 2, D-04103 Leipzig, Germany
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25
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Malloum A, Fifen JJ, Dhaouadi Z, Engo SGN, Jaidane NE. Structures and relative stabilities of ammonia clusters at different temperatures: DFT vs. ab initio. Phys Chem Chem Phys 2015; 17:29226-42. [DOI: 10.1039/c5cp03374h] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The global minimum energy structures of (NH3)n=2–10are pointed out for the first time at a given temperature.
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Affiliation(s)
- Alhadji Malloum
- Department of Physics
- Faculty of Science
- University of Ngaoundere
- Ngaoundere 454
- Cameroon
| | - Jean Jules Fifen
- Department of Physics
- Faculty of Science
- University of Ngaoundere
- Ngaoundere 454
- Cameroon
| | - Zoubeida Dhaouadi
- Laboratoire de Spectroscopie Atomique Moléculaire et Applications
- Faculté des Sciences de Tunis
- Université de Tunis El Manar
- Tunis
- Tunisie
| | - Serge Guy Nana Engo
- Department of Physics
- Faculty of Science
- University of Ngaoundere
- Ngaoundere 454
- Cameroon
| | - Nejm-Eddine Jaidane
- Laboratoire de Spectroscopie Atomique Moléculaire et Applications
- Faculté des Sciences de Tunis
- Université de Tunis El Manar
- Tunis
- Tunisie
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26
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Shishido R, Li YC, Tsai CW, Bing D, Fujii A, Kuo JL. An infrared spectroscopic and theoretical study on (CH3)3N–H+–(H2O)n, n = 1–22: highly polarized hydrogen bond networks of hydrated clusters. Phys Chem Chem Phys 2015; 17:25863-76. [DOI: 10.1039/c5cp01487e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Highly polarized water networks are found in the micro hydaration of protonated trimethylamine.
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Affiliation(s)
- Ryunosuke Shishido
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Ying-Cheng Li
- Department of Physics
- National Taiwan University
- Taipei 10617
- Taiwan
- Institute of Atomic and Molecular Sciences
| | - Chen-Wei Tsai
- Department of Physics
- National Taiwan University
- Taipei 10617
- Taiwan
- Institute of Atomic and Molecular Sciences
| | - Dan Bing
- Pujiang Institute
- Nanjing Tech University
- Nanjing
- China
| | - Asuka Fujii
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei
- Taiwan
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27
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Lin RJ, Nguyen QC, Ong YS, Takahashi K, Kuo JL. Temperature dependent structural variations of OH−(H2O)n, n = 4–7: effects on vibrational and photoelectron spectra. Phys Chem Chem Phys 2015; 17:19162-72. [DOI: 10.1039/c5cp02604k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this work, we identified a large number of structurally distinct isomers of midsized deprotonated water clusters using first-principles methods.
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Affiliation(s)
- Ren-Jie Lin
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Quoc Chinh Nguyen
- Singapore Institute of Manufacturing Technology
- Agency for Science
- Technology and Research (A*STAR)
- Singapore
| | - Yew-Soon Ong
- School of Computer Engineering
- Nanyang Technological University
- Singapore
| | - Kaito Takahashi
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
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28
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Li YC, Hamashima T, Yamazaki R, Kobayashi T, Suzuki Y, Mizuse K, Fujii A, Kuo JL. Hydrogen-bonded ring closing and opening of protonated methanol clusters H+(CH3OH)n (n = 4–8) with the inert gas tagging. Phys Chem Chem Phys 2015; 17:22042-53. [DOI: 10.1039/c5cp03379a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Temperature dependence of hydrogen bond network structures of protonated methanol clusters is explored by IR spectroscopy and DFT simulations.
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Affiliation(s)
- Ying-Cheng Li
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taiwan
| | - Toru Hamashima
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Ryoko Yamazaki
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Tomohiro Kobayashi
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Yuta Suzuki
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Kenta Mizuse
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Asuka Fujii
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taiwan
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29
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Akase D, Teramae H, Aida M. A comprehensive search of topologically distinct local minimum structures of protonated water octamer and the classification of OH topological types. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2014.10.071] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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30
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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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31
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Structure and thermodynamics of H3O+(H2O)8 clusters: A combined molecular dynamics and quantum mechanics approach. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.07.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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32
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Mizuse K, Fujii A. Infrared spectroscopy of large protonated water clusters H+(H2O)20–50 cooled by inert gas attachment. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2012.07.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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33
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Fifen JJ, Nsangou M, Dhaouadi Z, Motapon O, Jaidane NE. Structures of protonated methanol clusters and temperature effects. J Chem Phys 2013; 138:184301. [DOI: 10.1063/1.4802480] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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34
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Lee HM, Kim KS. Dynamics and structural changes of small water clusters on ionization. J Comput Chem 2013; 34:1589-97. [DOI: 10.1002/jcc.23296] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 03/19/2013] [Accepted: 03/22/2013] [Indexed: 01/02/2023]
Affiliation(s)
- Han Myoung Lee
- Department of Chemistry; Center for Superfunctional Materials, Pohang University of Science and Technology; San 31, Hyojadong; Namgu; Pohang; 790-784; Korea
| | - Kwang S. Kim
- Department of Chemistry; Center for Superfunctional Materials, Pohang University of Science and Technology; San 31, Hyojadong; Namgu; Pohang; 790-784; Korea
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35
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Mizuse K, Fujii A. Characterization of a solvent-separated ion-radical pair in cationized water networks: infrared photodissociation and Ar-attachment experiments for water cluster radical cations (H2O)n+(n = 3-8). J Phys Chem A 2013; 117:929-38. [PMID: 23330841 DOI: 10.1021/jp311909h] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We present infrared spectra of nominal water cluster radical cations (H(2)O)(n)(+) (n = 3-8), or to be precise, ion-radical complexes H(+)(H(2)O)(n-1)(OH), with and without an Ar tag. These clusters are closely related to the ionizing radiation-induced processes in water and are a good model to characterize solvation structures of the ion-radical pair. The spectra of Ar-tagged species show narrower bandwidths relative to those of the bare clusters due to the reduced internal energy via an Ar-attachment. The observed spectra are analyzed by comparing with those of the similar system, H(+)(H(2)O)(n), and calculated ones. We find that the observed spectra are attributable to ion-radical-separated motifs in n ≥ 5, as reported in the previous study (Mizuse et al. Chem. Sci.2011, 2, 868-876). Beyond the structural trends found in the previous study, we characterize isomeric structures and determine the number of water molecules between the charged site and the OH radical in each cluster size. In all of the characterized cluster structures (n = 5-8), the most favorable position of OH radical is the next neighbor of the charged site (H(3)O(+) or H(5)O(2)(+)). The positions and cluster structures are governed by the balance among the hydrogen-bonding abilities of the charged site, H(2)O, and OH radical. These findings on the ionized water networks lead to understanding of the detailed processes of ionizing radiation-initiated reactions in liquid water and aqueous solutions.
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Affiliation(s)
- Kenta Mizuse
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
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36
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Kobayashi T, Shishido R, Mizuse K, Fujii A, Kuo JL. Structures of hydrogen bond networks formed by a few tens of methanol molecules in the gas phase: size-selective infrared spectroscopy of neutral and protonated methanol clusters. Phys Chem Chem Phys 2013; 15:9523-30. [DOI: 10.1039/c3cp50985k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Hamashima T, Li YC, Wu MCH, Mizuse K, Kobayashi T, Fujii A, Kuo JL. Folding of the Hydrogen Bond Network of H+(CH3OH)7 with Rare Gas Tagging. J Phys Chem A 2012; 117:101-7. [DOI: 10.1021/jp3114545] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Toru Hamashima
- Department of Chemistry, Graduate
School of Science, Tohoku University, Sendai
980-8578, Japan
| | - Ying-Cheng Li
- Department
of Physics, National Taiwan University,
Taipei 10617, Taiwan
- Institute
of Atomic and Molecular
Sciences, Academia Sinica, Taipei, 10617,
Taiwan
| | - Michael C. H. Wu
- Institute
of Atomic and Molecular
Sciences, Academia Sinica, Taipei, 10617,
Taiwan
| | - Kenta Mizuse
- Department of Chemistry, Graduate
School of Science, Tohoku University, Sendai
980-8578, Japan
| | - Tomohiro Kobayashi
- Department of Chemistry, Graduate
School of Science, Tohoku University, Sendai
980-8578, Japan
| | - Asuka Fujii
- Department of Chemistry, Graduate
School of Science, Tohoku University, Sendai
980-8578, Japan
| | - Jer-Lai Kuo
- Institute
of Atomic and Molecular
Sciences, Academia Sinica, Taipei, 10617,
Taiwan
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38
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ELLABAAN MOSTAFAMH, ONG YEWSOON, NGUYEN QC, KUO JERLAI. EVOLUTIONARY DISCOVERY OF TRANSITION STATES IN WATER CLUSTERS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2012. [DOI: 10.1142/s0219633612500654] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
As a basic Aristotle element, water is the most abundant and more importantly crucial substance on earth. Without water, there would not be any form of life as we know. Understanding many phenomena in water such as water evaporation and ice melting and formation requires a deep understanding of hydrogen bond breaking and formation. In particular transition states play a key role in the understanding of such hydrogen bond behavior. Transition states, unlike other metastable states, are energy maxima along the minimum energy path connecting two isomers of molecular clusters. Geometry optimization of transition state structures, however, is a difficult task, and becomes even more arduous, especially when dealing with complex biochemical systems using first-principles calculations. In this paper, a novel molecular memetic algorithm (MOL-MA) composing of specially designed molecular-based water evolutionary operators coupled with a transition-state-local search solver and valley adaptive clearing scheme for the discovery of multiple precise transition states structures is proposed. The transition states of water clusters up to four water molecules uncovered using MOL-MA are reported. MOL-MA is shown not only to reproduce previously found transition states in water clusters, but also established newly discovered transition states for sizes 2–4 water molecules. The search performance of MOL-MA is also shown to outperform its compeers when pitted against those reported in the literature for finding transition states as well as recent advances in niching algorithms in terms of solution precision, computational effort, and number of transition states uncovered.
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Affiliation(s)
- MOSTAFA M. H. ELLABAAN
- Center of Computational Intelligence, School of Computer Engineering, Nanyang Technological University, Singapore
| | - YEW SOON ONG
- Center of Computational Intelligence, School of Computer Engineering, Nanyang Technological University, Singapore
| | - Q. C. NGUYEN
- Singapore Institute of Manufacturing Technology, A*Star, Singapore
| | - JER-LAI KUO
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan
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39
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Mizuse K, Kuo JL, Fujii A. Structural trends of ionized water networks: Infrared spectroscopy of watercluster radical cations (H2O)n+ (n = 3–11). Chem Sci 2011. [DOI: 10.1039/c0sc00604a] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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40
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Mizuse K, Fujii A. Infrared photodissociation spectroscopy of H+(H2O)6·Mm (M = Ne, Ar, Kr, Xe, H2, N2, and CH4): messenger-dependent balance between H3O+ and H5O2+ core isomers. Phys Chem Chem Phys 2011; 13:7129-35. [DOI: 10.1039/c1cp20207c] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Hamashima T, Mizuse K, Fujii A. Spectral Signatures of Four-Coordinated Sites in Water Clusters: Infrared Spectroscopy of Phenol−(H2O)n (∼20 ≤ n ≤ ∼50). J Phys Chem A 2010; 115:620-5. [DOI: 10.1021/jp111586p] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Toru Hamashima
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Kenta Mizuse
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Asuka Fujii
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
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42
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Torrent-Sucarrat M, Anglada JM. Anharmonicity and the Eigen-Zundel Dilemma in the IR Spectrum of the Protonated 21 Water Cluster. J Chem Theory Comput 2010; 7:467-72. [DOI: 10.1021/ct100692x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Miquel Torrent-Sucarrat
- Departament de Química Biològica i Modelització Molecular, Institut de Química Avançada de Catalunya (IQAC−CSIC), c/Jordi Girona 18, E-08034 Barcelona, Spain
| | - Josep M. Anglada
- Departament de Química Biològica i Modelització Molecular, Institut de Química Avançada de Catalunya (IQAC−CSIC), c/Jordi Girona 18, E-08034 Barcelona, Spain
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43
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Bing D, Hamashima T, Fujii A, Kuo JL. Anticooperative Effect Induced by Mixed Solvation in H+(CH3OH)m(H2O)n (m + n = 5 and 6): A Theoretical and Infrared Spectroscopic Study. J Phys Chem A 2010; 114:8170-7. [DOI: 10.1021/jp104931t] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Dan Bing
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore, Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan, and Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
| | - Toru Hamashima
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore, Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan, and Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
| | - Asuka Fujii
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore, Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan, and Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
| | - Jer-Lai Kuo
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore, Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan, and Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
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Ong YS, Lim M, Chen X. Memetic Computation—Past, Present & Future [Research Frontier. IEEE COMPUT INTELL M 2010. [DOI: 10.1109/mci.2010.936309] [Citation(s) in RCA: 344] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Bing D, Hamashima T, Nguyen QC, Fujii A, Kuo JL. Comprehensive Analysis on the Structure and Proton Switch in H+(CH3OH)m(H2O)n (m + n = 5 and 6). J Phys Chem A 2009; 114:3096-102. [DOI: 10.1021/jp9082689] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Dan Bing
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore, Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan, and Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
| | - Toru Hamashima
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore, Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan, and Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
| | - Quoc Chinh Nguyen
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore, Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan, and Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
| | - Asuka Fujii
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore, Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan, and Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
| | - Jer-Lai Kuo
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore, Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan, and Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
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