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Sameera WMC, Maseras F. Expanding the Range of Force Fields Available for ONIOM Calculations: The SICTWO Interface. J Chem Inf Model 2018; 58:1828-1835. [PMID: 30137980 DOI: 10.1021/acs.jcim.8b00332] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The ONIOM scheme is one of the most popular QM/MM approaches, but its extended application has been so far hindered by the limited availability of force fields in most practical implementations. This paper describes a simple software code to overcome this limitation, and its application to three representative chemical problems. The "Shell Interface for Combining Tinker With ONIOM" (SICTWO) program gives access to all force fields available in the Tinker molecular mechanics program from a Gaussian09 or Gaussian16 calculation. The first application presented is the geometry optimization of dithienobicyclo-[4.4.1]-undeca-3,8-diene-11-one ethylene glycol ketal. A variety of force fields were tested for the MM part, and the molecular structure using the ONIOM(B3LYP:OPLS-AA) method shows good agreement with the experimental results. The second problem is related with enantioselectivity of the vanadium-catalyzed asymmetric oxidation of 1,2-bis( tert-butyl)-disulfide. ONIOM(B3LYP:MM3) results, obtained with SICTWO, are consistent with those of a previous IMOMM(B3LYP:MM3) study. In the third application, we have combined AMOEBA09 polarizable force field with ONIOM to study a water molecule binding on water ice. Calculated ONIOM(ωB97X-D:AMOEBA09) binding energies are consistent with the ωB97X-D results. These studies show SICTWO as an easy-to-use tool that can further expand the use of the multiscale ONIOM method within computational chemistry and computational biology.
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Affiliation(s)
- W M C Sameera
- Institute of Chemical Research of Catalonia (ICIQ) , The Barcelona Institute of Science and Technology , Avgda. Països Catalans 16 , 43007 , Tarragona , Spain.,Institute of Low Temperature Science , Hokkaido University , Sapporo , Hokkaido 060-0819 , Japan
| | - Feliu Maseras
- Institute of Chemical Research of Catalonia (ICIQ) , The Barcelona Institute of Science and Technology , Avgda. Països Catalans 16 , 43007 , Tarragona , Spain.,Departament de Química , Universitat Autònoma de Barcelona , 08193 Bellaterra , Spain
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2
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Larijani HT, Jahanshahi M, Ganji MD, Kiani MH. Computational studies on the interactions of glycine amino acid with graphene, h-BN and h-SiC monolayers. Phys Chem Chem Phys 2017; 19:1896-1908. [DOI: 10.1039/c6cp06672k] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In the present work, the adsorption of glycine amino acid and its zwitterionic form onto three different hexagonal sheets, namely graphene, boron-nitride (h-BN) and silicon carbide (h-SiC), has been investigated within the framework of density functional theory (DFT) calculations.
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Affiliation(s)
- H. Tavassoli Larijani
- Nanotechnology Research Institute
- School of Chemical Engineering
- Babol University of Technology
- Babol
- Iran
| | - M. Jahanshahi
- Nanotechnology Research Institute
- School of Chemical Engineering
- Babol University of Technology
- Babol
- Iran
| | - M. Darvish Ganji
- Department of Nanochemistry
- Faculty of Pharmaceutical Chemistry
- Pharmaceutical Sciences Branch
- Islamic Azad University
- (IAUPS)
| | - M. H. Kiani
- Department of Electrical Engineering
- Faculty of Engineering
- University of Guilan
- Rasht
- Iran
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3
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Delarami HS, Ebrahimi A. Theoretical investigation of the backbone···π and π···π stacking interactions in substituted-benzene||3-methyl-2′-deoxyadenosine: a perspective to the DNA repair. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1118569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Hojat Samareh Delarami
- Computational Quantum Chemistry Laboratory, Department of Chemistry, University of Sistan and Baluchestan, Zahedan, Iran
| | - Ali Ebrahimi
- Computational Quantum Chemistry Laboratory, Department of Chemistry, University of Sistan and Baluchestan, Zahedan, Iran
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Wu LC, Chung WC, Wang CC, Lee GH, Lu SI, Wang Y. A charge density study of π-delocalization and intermolecular interactions. Phys Chem Chem Phys 2015; 17:14177-84. [DOI: 10.1039/c5cp01575h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The location of bond critical points (red dots) and its associated bond path (black line) provide the evidence on the existence of the weak intermolecular interactions of the π–π interactions between triazole rings of atrz molecules in crystal with the close ring distance of 3.17 Å.
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Affiliation(s)
- L.-C. Wu
- Department of Chemistry
- National Taiwan University
- Taipei
- Taiwan
| | - W.-C. Chung
- Department of Chemistry
- National Taiwan University
- Taipei
- Taiwan
| | - C.-C. Wang
- Department of Chemistry
- Soochow University
- Taipei
- Taiwan
| | - G.-H. Lee
- Instrumentation Center
- National Taiwan University
- Taipei
- Taiwan
| | - S.-I. Lu
- Department of Chemistry
- Soochow University
- Taipei
- Taiwan
| | - Y. Wang
- Department of Chemistry
- National Taiwan University
- Taipei
- Taiwan
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Roy D, Marianski M, Maitra NT, Dannenberg JJ. Comparison of some dispersion-corrected and traditional functionals with CCSD(T) and MP2 ab initio methods: dispersion, induction, and basis set superposition error. J Chem Phys 2012; 137:134109. [PMID: 23039587 PMCID: PMC3477180 DOI: 10.1063/1.4755990] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 09/17/2012] [Indexed: 11/14/2022] Open
Abstract
We compare dispersion and induction interactions for noble gas dimers and for Ne, methane, and 2-butyne with HF and LiF using a variety of functionals (including some specifically parameterized to evaluate dispersion interactions) with ab initio methods including CCSD(T) and MP2. We see that inductive interactions tend to enhance dispersion and may be accompanied by charge-transfer. We show that the functionals do not generally follow the expected trends in interaction energies, basis set superposition errors (BSSE), and interaction distances as a function of basis set size. The functionals parameterized to treat dispersion interactions often overestimate these interactions, sometimes by quite a lot, when compared to higher level calculations. Which functionals work best depends upon the examples chosen. The B3LYP and X3LYP functionals, which do not describe pure dispersion interactions, appear to describe dispersion mixed with induction about as accurately as those parametrized to treat dispersion. We observed significant differences in high-level wavefunction calculations in a basis set larger than those used to generate the structures in many of the databases. We discuss the implications for highly parameterized functionals based on these databases, as well as the use of simple potential energy for fitting the parameters rather than experimentally determinable thermodynamic state functions that involve consideration of vibrational states.
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Affiliation(s)
- Dipankar Roy
- Departments of Chemistry, City University of New York-Hunter College and the Graduate School, 695 Park Avenue, New York, New York 10065, USA
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Balaji G, Della Pelle AM, Popere BC, Chandrasekaran A, Thayumanavan S. Synthesis and properties of thienopyrrole based heteroacenes – indolodibenzothienopyrrole and dicarbazolodithienopyrrole. Org Biomol Chem 2012; 10:3455-62. [DOI: 10.1039/c2ob25087j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Steinmann SN, Corminboeuf C. Comprehensive Benchmarking of a Density-Dependent Dispersion Correction. J Chem Theory Comput 2011; 7:3567-77. [DOI: 10.1021/ct200602x] [Citation(s) in RCA: 333] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stephan N. Steinmann
- Laboratory for Computational Molecular Design, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Clemence Corminboeuf
- Laboratory for Computational Molecular Design, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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Zeng Y, Hao J, Zheng S, Meng L. Cooperativity between S···π and Rg···π in the OCS···C6H6···Rg (Rg = He, Ne, Ar, and Kr) van der Waals Complexes. J Phys Chem A 2011; 115:11057-66. [DOI: 10.1021/jp206835m] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yanli Zeng
- Institute of Computational Quantum Chemistry, College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang 050016, People's Republic of China
| | - Jing Hao
- Institute of Computational Quantum Chemistry, College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang 050016, People's Republic of China
| | - Shijun Zheng
- Institute of Computational Quantum Chemistry, College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang 050016, People's Republic of China
| | - Lingpeng Meng
- Institute of Computational Quantum Chemistry, College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang 050016, People's Republic of China
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Hesselmann A. Comparison of Intermolecular Interaction Energies from SAPT and DFT Including Empirical Dispersion Contributions. J Phys Chem A 2011; 115:11321-30. [DOI: 10.1021/jp205031e] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Andreas Hesselmann
- Lehrstuhl für Theoretische Chemie, Universität Erlangen-Nürnberg, Egerlandstrasse 3, D-91058 Erlangen
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de Wergifosse M, Champagne B. Electron correlation effects on the first hyperpolarizability of push–pull π-conjugated systems. J Chem Phys 2011; 134:074113. [DOI: 10.1063/1.3549814] [Citation(s) in RCA: 156] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Grimme S, Djukic JP. Cation−Cation “Attraction”: When London Dispersion Attraction Wins over Coulomb Repulsion. Inorg Chem 2011; 50:2619-28. [DOI: 10.1021/ic102489k] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Stefan Grimme
- Organisch-Chemisches Institut, Westfälische Wilhelms Universität, Corrensstrasse 40, D-48149 Münster, Germany
| | - Jean-Pierre Djukic
- Institut de Chimie, UMR 7177 CNRS, Université de Strasbourg, 4 rue Blaise Pascal, F-67000 Strasbourg, France
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Rajaraman G, Caneschi A, Gatteschi D, Totti F. A periodic mixed gaussians–plane waves DFT study on simple thiols on Au(111): adsorbate species, surface reconstruction, and thiols functionalization. Phys Chem Chem Phys 2011; 13:3886-95. [DOI: 10.1039/c0cp02042g] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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13
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Sameera WMC, Maseras F. Quantum mechanics/molecular mechanics methods can be more accurate than full quantum mechanics in systems involving dispersion correlations. Phys Chem Chem Phys 2011; 13:10520-6. [DOI: 10.1039/c0cp02957b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Moellmann J, Grimme S. Importance of London dispersion effects for the packing of molecular crystals: a case study for intramolecular stacking in a bis-thiophene derivative. Phys Chem Chem Phys 2010; 12:8500-4. [PMID: 20603666 DOI: 10.1039/c003432k] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The influence of London dispersion effects in density functional theory for the computation of molecular crystals is investigated. The structure of dithienobicyclo[4.4.1]-undeca-3,8-dien-11-one ethylene glycol ketal (Resvan) that has been studied previously under isolated molecule conditions is considered as an example. The intramolecular stacking of the two thiophene rings is strongly influenced by non-covalent interactions. Previous investigations revealed significant deviations between computed molecular and experimentally observed crystal sulfur-sulfur distances. The influence of the crystal environment on this distance is estimated by calculating potential energy curves for the "gas phase" and in the crystal using the periodic plane-wave code VASP. With three common dispersion corrected (DFT-D3) density functionals (PBE, revPBE and PBEsol), an average shortening of the sulfur-sulfur distance by 0.10 A ("packing" effect) is computed which leads to a corrected "experimental" gas-phase value of R(S-S) = 4.19 A. This value is in good agreement with the results of reliable quantum chemical methods and serves as a challenging benchmark for electronic structure methods. Overall the crystal environment leads to a widening of the molecular structure due to intermolecular dispersion interaction. This is opposite to uncorrected DFT that suggest a compression due to Pauli exchange repulsion. In the crystal the intra- and inter-molecular dispersion effects are large but of opposite sign and their effect almost cancels out so that in this example dispersion-uncorrected DFT yields reasonable solid state structures. This is different for the computation of the lattice energy for which reasonable values are obtained only at the DFT-D3 level.
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Affiliation(s)
- Jonas Moellmann
- Universität Münster Organisch-Chemisches Institut, Corrensstr. 40, D-48149 Münster, Germany
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Li W, Gahungu G, Zhang J, Hao L. Design of an Organic Zeolite toward the Selective Adsorption of Small Molecules at the Dispersion Corrected Density Functional Theory Level. J Phys Chem B 2009; 113:16472-8. [DOI: 10.1021/jp905471d] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Wenliang Li
- Faculty of Chemistry, Northeast Normal University, Changchun 130024, China, and Key Laboratory for Applied Statistics of MOE, Northeast Normal University, Changchun 130024, China
| | - Godefroid Gahungu
- Faculty of Chemistry, Northeast Normal University, Changchun 130024, China, and Key Laboratory for Applied Statistics of MOE, Northeast Normal University, Changchun 130024, China
| | - Jingping Zhang
- Faculty of Chemistry, Northeast Normal University, Changchun 130024, China, and Key Laboratory for Applied Statistics of MOE, Northeast Normal University, Changchun 130024, China
| | - Lizhu Hao
- Faculty of Chemistry, Northeast Normal University, Changchun 130024, China, and Key Laboratory for Applied Statistics of MOE, Northeast Normal University, Changchun 130024, China
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Aquilante F, Gagliardi L, Pedersen TB, Lindh R. Atomic Cholesky decompositions: a route to unbiased auxiliary basis sets for density fitting approximation with tunable accuracy and efficiency. J Chem Phys 2009; 130:154107. [PMID: 19388736 DOI: 10.1063/1.3116784] [Citation(s) in RCA: 169] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Cholesky decomposition of the atomic two-electron integral matrix has recently been proposed as a procedure for automated generation of auxiliary basis sets for the density fitting approximation [F. Aquilante et al., J. Chem. Phys. 127, 114107 (2007)]. In order to increase computational performance while maintaining accuracy, we propose here to reduce the number of primitive Gaussian functions of the contracted auxiliary basis functions by means of a second Cholesky decomposition. Test calculations show that this procedure is most beneficial in conjunction with highly contracted atomic orbital basis sets such as atomic natural orbitals, and that the error resulting from the second decomposition is negligible. We also demonstrate theoretically as well as computationally that the locality of the fitting coefficients can be controlled by means of the decomposition threshold even with the long-ranged Coulomb metric. Cholesky decomposition-based auxiliary basis sets are thus ideally suited for local density fitting approximations.
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Affiliation(s)
- Francesco Aquilante
- Department of Physical Chemistry, Université de Genève-Science II, 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland.
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Pedersen TB, Aquilante F, Lindh R. Density fitting with auxiliary basis sets from Cholesky decompositions. Theor Chem Acc 2009. [DOI: 10.1007/s00214-009-0608-y] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Shimizu A, Mori T, Inoue Y, Yamada S. Combined Experimental and Quantum Chemical Investigation of Chiroptical Properties of Nicotinamide Derivatives with and without Intramolecular Cation−π Interactions. J Phys Chem A 2009; 113:8754-64. [DOI: 10.1021/jp904243w] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Akinori Shimizu
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan, and Department of Chemistry, Graduate School of Science, Ochanomizu University, Tokyo 112-8610, Japan
| | - Tadashi Mori
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan, and Department of Chemistry, Graduate School of Science, Ochanomizu University, Tokyo 112-8610, Japan
| | - Yoshihisa Inoue
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan, and Department of Chemistry, Graduate School of Science, Ochanomizu University, Tokyo 112-8610, Japan
| | - Shinji Yamada
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan, and Department of Chemistry, Graduate School of Science, Ochanomizu University, Tokyo 112-8610, Japan
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Zelený T, Hobza P, Kabelác M. Microhydration of guanine...cytosine base pairs, a theoretical Study on the role of water in stability, structure and tautomeric equilibrium. Phys Chem Chem Phys 2009; 11:3430-5. [PMID: 19421545 DOI: 10.1039/b819350a] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The potential energy surfaces of guanine...cytosine complexes and microhydrated guanine...cytosine (one and two water molecules) were investigated by the molecular dynamics/quenching method (MD/Q), using the empirical potential Parm94 force field, implemented in the Amber program package. The calculations were conducted for all the possible combinations of the four most stable tautomers of guanine and three of cytosine (covering the canonical forms in both cases). The obtained structures were sorted by their structural motifs into three main groups: planar hydrogen-bonded; stacked; and T-shaped structures. The most stable structures found at the empirical potential energy surfaces were fully reoptimised at the second-order Møller-Plesset perturbation theory as well as using the density functional method with an empirical dispersion term (DFT-D). A combination of the canonical form of guanine and cytosine and canonical cytosine with a guanine tautomer where the hydrogen is switched from position N9 to N7 are energetically preferred in microsolvated systems as well as those without the presence of a solvent. The rising number of water molecules leads to smaller differences between the stability of the various combinations of the tautomers of bases in the base pairs. For some of the tautomer combinations (mainly the enol-enol combination), two water molecules are sufficient for the preference of stacked structures over the H-bonded ones. The interaction energies and geometries obtained by the second-order Møller-Plesset perturbation theory method and the much less computationally demanding DFT-D method are comparable, except for stacked complexes, where the interaction energies are overestimated on average by 3 kcal mol(-1) at the MP2 level.
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Affiliation(s)
- Tomás Zelený
- Department of Physical Chemistry, Faculty of Sciences, Palacky University, tr. Svobody 26, 771 46, Olomouc, Czech Republic.
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