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Bento-Oliveira A, Moita MLCJ, de Almeida RFM, Starosta R. Unraveling environmental effects in the absorption and fluorescence spectra of p-methoxyphenylpiperazine derivatives. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 306:123583. [PMID: 37913739 DOI: 10.1016/j.saa.2023.123583] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/16/2023] [Accepted: 10/26/2023] [Indexed: 11/03/2023]
Abstract
The p-methoxyphenylpiperazine motif can be found in many biologically active molecules, including approved drugs. It is characterized by a relatively weak fluorescence, which can be employed in different types of studies involving molecules with this motif. In this work, a thorough analysis of the absorption, excitation and emission spectra of the diphenyl(aminomethyl)phosphine and tris(aminomethyl)phosphine derivatives of p-methoxyphenylpiperazine, supported by the DFT calculations (ωB97XD/6-311++G(d,p)) with NBO and QTAIM analysis also for different model molecules (e.g. 1-(4-methoxyphenyl)-4-methylpiperazine) enabled determination of the mechanisms underlying beneath the electronic transitions and allowed to rationalize mixed solvent effects observed in electronic spectra of the studied compounds. Electronic transition from the ground state to the first excited state can be regarded as the n,π → π* transition with no solvatochromic effects, however the hydrogen bonds between the HBD solvent molecules and the nitrogen atom bound directly to the aromatic ring (N(4)) are shifting strongly the 1st absorption or excitation band maxima to the higher energies. Fluorescence band, as a result of the electron transition from the equilibrated 1st excited state to the ground state, can be described as the π*→π with positive solvatochromism. N(4) in the excited states adopts a sp2 hybridization and is no longer able to form HBs. On the other hand, increased electron density on the aromatic ring makes the emission processes vulnerable to its direct environment.
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Affiliation(s)
- Andreia Bento-Oliveira
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Maria-Luísa C J Moita
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Rodrigo F M de Almeida
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Radosław Starosta
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland.
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Jindal S, Hsu PJ, Phan HT, Tsou PK, Kuo JL. Capturing the potential energy landscape of large size molecular clusters from atomic interactions up to a 4-body system using deep learning. Phys Chem Chem Phys 2022; 24:27263-27276. [DOI: 10.1039/d2cp04441b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We propose a new method that utilizes the database of stable conformers and borrow the fragmentation concept of many-body-expansion (MBE) methods in ab initio methods to train a deep-learning machine learning (ML) model using SchNet.
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Affiliation(s)
- Shweta Jindal
- Institute of Atomic and Molecular Sciences, Academia Sinica, No. 1 Roosevelt Road, Section 4, Daan District, Taipei City 10617, Taiwan
| | - Po-Jen Hsu
- Institute of Atomic and Molecular Sciences, Academia Sinica, No. 1 Roosevelt Road, Section 4, Daan District, Taipei City 10617, Taiwan
| | - Huu Trong Phan
- Institute of Atomic and Molecular Sciences, Academia Sinica, No. 1 Roosevelt Road, Section 4, Daan District, Taipei City 10617, Taiwan
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Pei-Kang Tsou
- Institute of Atomic and Molecular Sciences, Academia Sinica, No. 1 Roosevelt Road, Section 4, Daan District, Taipei City 10617, Taiwan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, No. 1 Roosevelt Road, Section 4, Daan District, Taipei City 10617, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
- Molecular Science and Technology, National Taiwan University, Section 4, Daan District, Taipei City 10617, Taiwan
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Yoshida Y, Sato H, Morgan JW, Wales DJ. Potential energy landscapes of tetragonal pyramid molecules. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.09.058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Gadre SR, Yeole SD, Sahu N. Quantum chemical investigations on molecular clusters. Chem Rev 2014; 114:12132-73. [PMID: 25341561 DOI: 10.1021/cr4006632] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Shridhar R Gadre
- Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur 208 016, India
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Kazachenko S, Bulusu S, Thakkar AJ. Methanol clusters (CH3OH)n: Putative global minimum-energy structures from model potentials and dispersion-corrected density functional theory. J Chem Phys 2013; 138:224303. [DOI: 10.1063/1.4809528] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Fifen JJ, Nsangou M, Dhaouadi Z, Motapon O, Jaidane NE. Solvation Energies of the Proton in Methanol. J Chem Theory Comput 2013; 9:1173-81. [PMID: 26588760 DOI: 10.1021/ct300669v] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
pKa's, proton affinities, and proton dissociation free energies characterize numerous properties of drugs and the antioxidant activity of some chemical compounds. Even with a higher computational level of theory, the uncertainty in the proton solvation free energy limits the accuracy of these parameters. We investigated the thermochemistry of the solvation of the proton in methanol within the cluster-continuum model. The scheme used involves up to nine explicit methanol molecules, using the IEF-PCM and the strategy based on thermodynamic cycles. All computations were performed at B3LYP/6-31++G(dp) and M062X/6-31++G(dp) levels of theory. It comes out from our calculations that the functional M062X is better than B3LYP, on the evaluation of gas phase clustering energies of protonated methanol clusters, per methanol stabilization of neutral methanol clusters and solvation energies of the proton in methanol. The solvation free energy and enthalpy of the proton in methanol were obtained after converging the partial solvation free energy of the proton in methanol and the clustering free energy of protonated methanol clusters, as the cluster size increases. Finally, the recommended values for the solvation free energy and enthalpy of the proton in methanol are -257 and -252 kcal/mol, respectively.
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Affiliation(s)
- Jean Jules Fifen
- University of Ngaoundere, Faculty of Science, P.O. Box 454, Ngaoundere, Cameroon.,Fundamental Physics Lab, Graduate Training Unit in Physics and Engineering Sciences, Faculty of Science, University of Douala, P.O. Box 24157, Douala, Cameroon
| | - Mama Nsangou
- University of Ngaoundere, Faculty of Science, P.O. Box 454, Ngaoundere, Cameroon.,University of Maroua, P.O. Box 46, Maroua, Cameroon
| | - Zoubeida Dhaouadi
- Laboratoire de Spectroscopie Atomique et Moléculaire, Faculté des Sciences de Tunis, Université de Tunis El Manar, Campus Universitaire 1060, Tunis, Tunisia
| | - Ousmanou Motapon
- Fundamental Physics Lab, Graduate Training Unit in Physics and Engineering Sciences, Faculty of Science, University of Douala, P.O. Box 24157, Douala, Cameroon
| | - Nejm-Eddine Jaidane
- Laboratoire de Spectroscopie Atomique et Moléculaire, Faculté des Sciences de Tunis, Université de Tunis El Manar, Campus Universitaire 1060, Tunis, Tunisia
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Ploetz EA, Smith PE. A Kirkwood-Buff force field for the aromatic amino acids. Phys Chem Chem Phys 2011; 13:18154-67. [PMID: 21931889 DOI: 10.1039/c1cp21883b] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In a continuation of our efforts to develop a united atom non-polarizable protein force field based upon the solution theory of Kirkwood and Buff i.e., the Kirkwood-Buff Force Field (KBFF) approach, we present KBFF models for the side chains of phenylalanine, tyrosine, tryptophan, and histidine, including both tautomers of neutral histidine and doubly-protonated histidine. The force fields were specifically designed to reproduce the thermodynamic properties of mixtures over the full composition range in an attempt to provide an improved description of intermolecular interactions. The models were developed by careful parameterization of the solution phase partial charges to reproduce the experimental Kirkwood-Buff integrals for mixtures of solutes representative of the amino acid sidechains in solution. The KBFF parameters and simulated thermodynamic and structural properties are presented for the following eleven binary mixtures: benzene + methanol, benzene + toluene, toluene + methanol, toluene + phenol, toluene + p-cresol, pyrrole + methanol, indole + methanol, pyridine + methanol, pyridine + water, histidine + water, and histidine hydrochloride + water. It is argued that the present approach and models provide a reasonable description of intermolecular interactions which ensures that the required balance between solute-solute, solute-solvent, and solvent-solvent distributions is obtained.
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Affiliation(s)
- Elizabeth A Ploetz
- Department of Chemistry, 213 CBC Building, Kansas State University, Manhattan, KS 66506-0401, USA
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Laksmono H, Tanimura S, Allen HC, Wilemski G, Zahniser MS, Shorter JH, Nelson DD, McManus JB, Wyslouzil BE. Monomer, clusters, liquid: an integrated spectroscopic study of methanol condensation. Phys Chem Chem Phys 2011; 13:5855-71. [DOI: 10.1039/c0cp02485f] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Billes F, Mohammed-Ziegler I, Mikosch H. Methanol in its own gravy. A PCM study for simulation of vibrational spectra. Phys Chem Chem Phys 2011; 13:7760-72. [DOI: 10.1039/c0cp01297a] [Citation(s) in RCA: 9] [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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Mones L, Rossky PJ, Turi L. Analysis of localization sites for an excess electron in neutral methanol clusters using approximate pseudopotential quantum-mechanical calculations. J Chem Phys 2010; 133:144510. [PMID: 20950020 DOI: 10.1063/1.3503506] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Letif Mones
- Department of Physical Chemistry, Eötvös Loránd University, Budapest 112, P. O. Box 32, H-1518, Hungary.
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Marchal R, Carbonnière P, Pouchan C. A global search algorithm of minima exploration for the investigation of low lying isomers of clusters from density functional theory-based potential energy surfaces: The example of Sin (n=3,15) as a test case. J Chem Phys 2009; 131:114105. [DOI: 10.1063/1.3216382] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Lubombo C, Curotto E, Janeiro Barral PE, Mella M. Thermodynamic properties of ammonia clusters (NH3)n n=2–11: Comparing classical and quantum simulation results for hydrogen bonded species. J Chem Phys 2009; 131:034312. [DOI: 10.1063/1.3159398] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Mahmoud H, Germanenko IN, Wright D, El-Shall MS. Chemistry of Styrene (Water)n Clusters, n = 1−5: Spectroscopy and Structure of the Neutral Clusters, Deprotonation of Styrene Dimer Cation, and Implication to the Inhibition of Cationic Polymerization. J Phys Chem A 2005; 109:4474-83. [PMID: 16833783 DOI: 10.1021/jp050594y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The styrene-water binary clusters SW(n), with n = 1-5 have been studied by the (one-color) resonant two-photon ionization technique using the resonance of styrene. The structures and energetics of the neutral clusters are investigated using a search technique that employs Monte Carlo procedure. The strong tendency for water molecules to form cyclic hydrogen-bonded structures is clearly observed in the SW(n) structures starting from n =3. The results indicate that the spectral shifts correlate with the interaction energies between styrene and the water subcluster (W(n)) within the SW(n) clusters. Evidence is presented that points to (1) the formation of a covalent bonded styrene radical cation dimer following the 193 nm MPI of styrene neutral clusters, (2) proton transfer from the styrene dimer cation to the water or methanol subcluster, resulting in the formation of protonated water or methanol clusters and a styrene dimer radical, and (3) extensive solvation of the styrene dimer radical within the protonated solvent molecules. The proton-transfer reactions may explain the strong inhibition effects exerted by small concentrations of water or methanol on the cationic polymerization of styrene. These results provide a molecular level view of the inhibition mechanism exerted by protic solvents on the cationic polymerization of styrene.
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Affiliation(s)
- H Mahmoud
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, USA
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Jia YX, Guo XY, Zhong B. Effects of n-hexane on methanol desorption from copper surface: Monte Carlo simulation. J Supercrit Fluids 2004. [DOI: 10.1016/j.supflu.2004.01.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Rusyniak MJ, Ibrahim YM, Wright DL, Khanna SN, El-Shall MS. Gas-Phase Ion Mobilities and Structures of Benzene Cluster Cations (C6H6)n+, n = 2−6. J Am Chem Soc 2003; 125:12001-13. [PMID: 14505422 DOI: 10.1021/ja035504m] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Benzene clusters are generated by pulsed supersonic beam expansion, ionized by electron impact, mass-selected and then injected into a drift cell for ion mobility measurements in a helium buffer gas. The measured collision cross sections and theoretical calculations are used to determine the structures of the cluster cations (C(6)H(6))(n)(+) with n = 2-6. Density functional theory calculation, at an all-electron level and without any symmetry constraint, predicts that the dimer cation has two nearly degenerate ground state structures with the sandwich configuration more stable than the T-configuration by only 0.07 eV. The ion mobility experiment indicates that only one structure is observed for the mass-selected dimer cation at room temperature. The calculated cross section for the sandwich structure agrees very well (within 2.4%) with the experimental value. For the n = 3-6 clusters, the experiments suggest the presence of at least two structural isomers for each cluster. A Monte Carlo minimum-energy search technique using the 12-site OPLS potential for benzene is used to determine the structures of the lowest-energy isomers. The calculated cross sections for the two lowest-energy isomers of the n = 3-6 clusters agree well with the experimental results. The clusters' structures reveal two different growth patterns involving a sandwich dimer core or a pancake trimer stack core. The lowest-energy isomers of the n = 3-6 clusters incorporate the pancake trimer stack as the cluster's core. The trimer stack allows the charge to hop between two dimers, thus maximizing charge resonance interaction in the clusters. For larger clusters, the appearance of magic numbers at n = 14, 20, 24, 27, and 30 is consistent with the incorporation of a sandwich dimer cation within icosahedral, double icosahedral, and interpenetrating icosahedral structures. On the basis of the ion mobility results and the structural calculations, the parallel-stacked motif among charged aromatic-aromatic interactions is expected to play a major role in determining the structures of multi aromatic components. This conclusion may provide new insights for experimental and theoretical studies of molecular design and recognition involving aromatic systems.
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Affiliation(s)
- Mark J Rusyniak
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, USA
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El-Shall MS, Wright D, Ibrahim Y, Mahmoud H. Theoretical Study of Styrene (Methanol)n Clusters, n = 1−9. Comparison with Methanol Clusters. J Phys Chem A 2003. [DOI: 10.1021/jp030176y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- M. S. El-Shall
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006
| | - D. Wright
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006
| | - Y. Ibrahim
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006
| | - H. Mahmoud
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006
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Mahmoud H, Germanenko IN, Ibrahim Y, El-Shall MS. Resonant Two-Photon Ionization Spectroscopy of Styrene (Methanol)n Clusters, n = 1−9. J Phys Chem A 2003. [DOI: 10.1021/jp0301756] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- H. Mahmoud
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006
| | - I. N. Germanenko
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006
| | - Y. Ibrahim
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006
| | - M. S. El-Shall
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006
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Zhou Y, Karplus M, Ball KD, Berry RS. The distance fluctuation criterion for melting: Comparison of square-well and Morse potential models for clusters and homopolymers. J Chem Phys 2002. [DOI: 10.1063/1.1426419] [Citation(s) in RCA: 189] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Canepa C. A statistical mechanics/density functional approach to the thermodynamics of liquids. J Chem Phys 2001. [DOI: 10.1063/1.1402984] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Buck U, Huisken F. Infrared spectroscopy of size-selected water and methanol clusters. Chem Rev 2000; 100:3863-90. [PMID: 11749332 DOI: 10.1021/cr990054v] [Citation(s) in RCA: 484] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- U Buck
- Max-Planck-Institut für Strömungsforschung, Bunsenstrasse 10, D-37073 Göttingen, Germany
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Zakharov VV, Brodskaya EN, Laaksonen A. Molecular dynamics simulation of methanol clusters. J Chem Phys 1998. [DOI: 10.1063/1.477610] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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25
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Spectroscopy and quantum dynamics of hydrogen fluoride clusters. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s1063-5467(98)80009-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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