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Trimers formed by formaldehyde with hydrogen fluoride: Structures, energetics, and infrared absorption spectra. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Ohno K, Kodaya Y, Yamakado H. Quantum chemical exploration of formaldehyde clusters (H 2 CO) n (n = 2-4). J Comput Chem 2018; 39:1498-1507. [PMID: 29607516 DOI: 10.1002/jcc.25220] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/13/2018] [Accepted: 03/17/2018] [Indexed: 01/25/2023]
Abstract
Global exploration of equilibrium structures and interconversion pathways on the quantum chemical potential energy surface (PES) is performed for (H2 CO)n (n = 2-4) by using the Scaled Hypersphere Search-Anharmonic Downward Distortion Following (SHS-ADDF) method. Density functional theoretical (DFT) calculations with empirical dispersion corrections (D3) yielded comparable results for formaldehyde dimer in comparison with recent detailed studies at CCSD(T) levels. Based on DFT-D3 calculations, trimer and tetramer structures and their stabilities were studied. For tetramer, a highly symmetrical S4 structure was found as the most stable form in good accordance with experimentally determined tetramer unit in the formaldehyde crystal. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Koichi Ohno
- Institute for Quantum Chemical Exploration, Kaigan 3-9-15, Minato-ku, Tokyo, 108-0022, Japan.,Department of Chemistry Graduate School of Science, Tohoku University, Aramaki Aza-Aoba 6-3, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Yoshitomo Kodaya
- Graduate School of Systems Engineering, Wakayama University, Sakaedani 930, Wakayama, Wakayama, 640-8510, Japan
| | - Hideo Yamakado
- Faculty of Systems Engineering, Wakayama University, Sakaedani 930, Wakayama, Wakayama, 640-8510, Japan
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Karpfen A. On the potential energy surfaces of dimers formed between trans-glyoxal, trans-acrolein and formaldehyde. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Albrecht L, Boyd RJ. Atomic energy analysis of cooperativity, anti-cooperativity, and non-cooperativity in small clusters of methanol, water, and formaldehyde. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.08.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Gopi R, Ramanathan N, Sundararajan K. Experimental evidence for blue-shifted hydrogen bonding in the fluoroform-hydrogen chloride complex: a matrix-isolation infrared and ab initio study. J Phys Chem A 2014; 118:5529-39. [PMID: 24979667 DOI: 10.1021/jp503718v] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The 1:1 hydrogen-bonded complex of fluoroform and hydrogen chloride was studied using matrix-isolation infrared spectroscopy and ab initio computations. Using B3LYP and MP2 levels of theory with 6-311++G(d,p) and aug-cc-pVDZ basis sets, the structures of the complexes and their energies were computed. For the 1:1 CHF3-HCl complexes, ab initio computations showed two minima, one cyclic and the other acyclic. The cyclic complex was found to have C-H · · · Cl and C-F · · · H interactions, where CHF3 and HCl sub-molecules act as proton donor and proton acceptor, respectively. The second minimum corresponded to an acyclic complex stabilized only by the C-F · · · H interaction, in which CHF3 is the proton acceptor. Experimentally, we could trap the 1:1 CHF3-HCl cyclic complex in an argon matrix, where a blue-shift in the C-H stretching mode of the CHF3 sub-molecule was observed. To understand the nature of the interactions, Atoms in Molecules and Natural Bond Orbital analyses were carried out to unravel the reasons for blue-shifting of the C-H stretching frequency in these complexes.
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Affiliation(s)
- R Gopi
- Chemistry Group, Indira Gandhi Centre for Atomic Research , Kalpakkam 603 102, Tamil Nadu, India
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Van Dornshuld E, Holy CM, Tschumper GS. Homogeneous and Heterogeneous Noncovalent Dimers of Formaldehyde and Thioformaldehyde: Structures, Energetics, and Vibrational Frequencies. J Phys Chem A 2014; 118:3376-85. [DOI: 10.1021/jp502588h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Eric Van Dornshuld
- Department of Chemistry and
Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Christina M. Holy
- Department of Chemistry and
Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Gregory S. Tschumper
- Department of Chemistry and
Biochemistry, University of Mississippi, University, Mississippi 38677, United States
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Dolgonos GA. Which isomeric form of formaldehyde dimer is the most stable – a high-level coupled-cluster study. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.08.073] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Thakur TS, Kirchner MT, Bläser D, Boese R, Desiraju GR. Nature and strength of C–H⋯O interactions involving formyl hydrogen atoms: computational and experimental studies of small aldehydes. Phys Chem Chem Phys 2011; 13:14076-91. [DOI: 10.1039/c0cp02236e] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Sato H, Sakaki S, Sakamoto Y, Kawasaki M. Effective Interaction Energies for Weakly Bound Dimers at Room Temperature: (H2O)2, (N2O)2, (CO2)2, and (HCHO)2. CHEM LETT 2010. [DOI: 10.1246/cl.2010.296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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DFT prediction of anomalously large blue shift of the C–H stretching frequency in 2-vinyloxypyridine and -quinoline due to the intramolecular C–H···N hydrogen bonding. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2009.10.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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12
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Crow MB, Gilchrist A, Hancock G, Peverall R, Richmond G, Ritchie GAD, Taylor SR. High-resolution absorption studies of the A(1)A2-X(1)A1 2(0)(2)4(0)(1) band of formaldehyde. J Phys Chem A 2009; 113:6689-96. [PMID: 19459699 DOI: 10.1021/jp9023475] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Absolute peak absorption cross sections and pressure broadening coefficients have been recorded with sub-Doppler limited instrumental resolution for selected rotational lines in the 2(0)(2)4(0)(1) vibronic band of the formaldehyde A(1)A2-X(1)A1 electronic transition. The measured absorption cross sections range between (0.18 +/- 0.01) and (10.1 +/- 0.08) x 10(-19) cm2 molecule(-1) and are considerably larger than values from the literature recorded using apparatus where instrumental broadening was significant. However, comparisons with spectral simulations with equivalent resolution from Smith et al. (J. Phys. Chem. A 2006, 110, 11645-11653) are in excellent agreement. Pressure broadening was studied for the collision partners CH2O, CO2, N2, O2, Ne, Kr, Ar, and He, and the resulting broadening coefficients were found to be reduced in comparison to equivalent values measured in infrared regions, consistent with the reduced dipole moment of the upper state probed in this work. Cavity-enhanced absorption spectroscopy (CEAS) measurements were undertaken using calibrated low concentration (2.9-4.6 ppmv) samples from a permeation source and demonstrate a noise equivalent absorption of 1.2 x 10(-6) cm(-1) Hz(-1/2). This implies a minimum detectable formaldehyde concentration with the current system in atmospheric air of 172 ppbv Hz(-1/2).
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Affiliation(s)
- Martin B Crow
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
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Oliveira B, Araújo RD, Ramos M. A theoretical study of blue-shifting hydrogen bonds in π weakly bound complexes. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.05.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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A chemometrical study of intermolecular properties of hydrogen-bonded complexes formed by C2H4O⋅⋅⋅HX and C2H5N⋅⋅⋅HX with X = F, CN, NC, and CCH. J Mol Model 2008; 15:421-32. [DOI: 10.1007/s00894-008-0422-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Accepted: 11/13/2008] [Indexed: 10/21/2022]
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Dedíková P, Pitoňák M, Neogrády P, Černušák I, Urban M. Toward More Efficient CCSD(T) Calculations of Intermolecular Interactions in Model Hydrogen-Bonded and Stacked Dimers. J Phys Chem A 2008; 112:7115-23. [DOI: 10.1021/jp8033903] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pavlína Dedíková
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina, SK-842 15 Bratislava, Slovakia, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, CZ-16610 Prague, Czech Republic
| | - Michal Pitoňák
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina, SK-842 15 Bratislava, Slovakia, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, CZ-16610 Prague, Czech Republic
| | - Pavel Neogrády
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina, SK-842 15 Bratislava, Slovakia, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, CZ-16610 Prague, Czech Republic
| | - Ivan Černušák
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina, SK-842 15 Bratislava, Slovakia, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, CZ-16610 Prague, Czech Republic
| | - Miroslav Urban
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina, SK-842 15 Bratislava, Slovakia, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, CZ-16610 Prague, Czech Republic
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Li Q, Liu H, An X, Gong B, Cheng J. Effect of methyl group on the cooperativity of CH···O blue-shifted hydrogen bond in HCHO–HCHO–HCHO cyclic complex. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.theochem.2008.04.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Rivelino R. Lewis acid-base interactions in weakly bound formaldehyde complexes with CO2, HCN, and FCN: considerations on the cooperative H-bonding effects. J Phys Chem A 2007; 112:161-5. [PMID: 18154278 DOI: 10.1021/jp7105154] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ab initio quantum chemistry calculations reveal that HCN and mainly FCN can form Lewis acid-base complexes with formaldehyde associated with cooperative H bonds, as first noticed by Wallen et al. (Blatchford, M. A.; Raveendran, P.; Wallen, S. L. J. Am. Chem. Soc. 2002, 124, 14818-14819) for CO2-philic materials under supercritical conditions. The present results, obtained with MP2(Full)/aug-cc-pVDZ calculations, show that the degeneracy of the nu(2) mode in free HCN or FCN is removed upon complexation in the same fashion as that of CO2. The splitting of these bands along with the electron structure analysis provides substantial evidence of the interaction of electron lone pairs of the carbonyl oxygen with the electron-deficient carbon atom of the cyanides. Also, this work investigates the role of H bonds acting as additional stabilizing interactions in the complexes by performing the energetic and geometric characterization.
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Vila A, Mosquera RA. Atoms in molecules interpretation of the anomeric effect in the OCO unit. J Comput Chem 2007; 28:1516-1530. [PMID: 17330885 DOI: 10.1002/jcc.20585] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The conformational preferences of two model compounds for the O--CH2--O anomeric unit: methanediol and dimethoxymethane analyzed within the framework of the QTAIM theory provide a new interpretation of the anomeric effect. The characteristic stabilization of the gauche conformers of these compounds is accompanied by a progressive reduction of the electron population of the hydrogens of the central methylene as the number of their gauche interactions to lone pairs rises. The electron population removed from these atoms during the conformational change is gained in the gauche conformers by atoms of larger atomic number, which results in a more negative molecular energy. Also, the variations displayed by atomic populations and the QTAIM delocalization indexes are not keeping in line with the hyperconjugative model of the anomeric effect.
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Affiliation(s)
- Antonio Vila
- Departamento de Química Física, Universidade de Vigo, Facultade de Química, 36310-Vigo, Galicia, Spain
| | - Ricardo A Mosquera
- Departamento de Química Física, Universidade de Vigo, Facultade de Química, 36310-Vigo, Galicia, Spain
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Hydrogen bonds in alcohols:water complexes: A theoretical study about new intramolecular interactions via CHELPG and AIM calculations. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.theochem.2006.06.018] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Lorenzo L, Gonzalez Moa MJ, Mandado M, Mosquera RA. Do the Neighboring Residues in a Polypeptide Affect the Electron Distribution of an Amino Acid Significantly? A Quantitative Study Using the Quantum Theory of Atoms in Molecules (QTAIM). J Chem Inf Model 2006; 46:2056-65. [PMID: 16995736 DOI: 10.1021/ci600184t] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Geometries, as well as bond and atomic properties obtained with the atoms-in-molecules theory applied on B3LYP/6-31++G//B3LYP/6-31G charge densities, of the N-formyl amides of the nine tripeptides obtained by combining glycine, alanine, and serine around a central glycine residue were analyzed to check how the properties of the central residue are modified by other amino acids bonded to it. All of the molecules were optimized from an alpha-helix conformation that was also displayed by the optimized structure. Significant variations of the geometry (especially remarkable for dihedral angles) and atomic properties of the central glycine residue are observed when it is attached to a serine residue whose side chain is involved in a hydrogen bond.
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Affiliation(s)
- Luis Lorenzo
- Departamento de Química Física, Facultade de Química, Universidade de Vigo, Lagoas-Marcosende s/n 36310-Vigo, Galicia, Spain
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Hermida-Ramón JM, Graña AM. Blue-shifting hydrogen bond in the benzene–benzene and benzene–naphthalene complexes. J Comput Chem 2006; 28:540-6. [PMID: 17186487 DOI: 10.1002/jcc.20568] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Ab initio complete optimizations at MP2/6-31++G** level have been performed in the T-shaped geometry of the benzene-benzene and benzene-naphthalene complexes. To check the effect of the basis set superposition error (BSSE), optimizations have been done in the BSSE corrected and BSSE uncorrected potential energy surfaces. The BSSE effect in the calculation of the Hessian has also been evaluated to check its influence in the frequency values. Quantum theory atoms in molecules (QTAIM) calculations have also been performed on both dimers. Intermolecular energies differ around a 25% when the optimization is performed with or without counterpoise corrected gradients. The influence of BSSE is also noticeable in the distances. Frequency shifts show big changes because of the BSSE. Thus, uncorrected values are up 350% larger than corrected ones. The hypotheses given in the literature to explain the origin of the blue-shifting hydrogen bond do not seem to give a suitable explanation for all characteristics of the behavior found in the studied systems.
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Affiliation(s)
- Jose M Hermida-Ramón
- Departamento de Química Física, Facultade de Química, Universidade de Vigo, Campus Lagoas Marcosende s/n, 36200 Vigo, Galicia, Spain.
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Vila A, Mosquera RA. Quantum Theory of Atoms in Molecules Analysis on the Conformational Preferences of Vinyl Alcohol and Related Ethers. J Phys Chem A 2005; 109:6985-9. [PMID: 16834058 DOI: 10.1021/jp052673f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Vinyl alcohol, methyl vinyl ether, and tert-butyl vinyl ether were studied within the framework of the quantum theory of atoms in molecules at the B3LYP/6-311++G(2d,2p) level. Local and integrated properties of the charge density indicate that the anti conformational preference of the tert-butyl derivative is not due to a differing resonance contribution with regard to the less bulky vinyl ethers but to steric effects. There is a small delocalization of charge density, either total or pi, between oxygen and the terminal vinyl carbon, which does not support the resonance picture of vinyl compounds.
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Affiliation(s)
- Antonio Vila
- Departamento de Química Física, Universidade de Vigo, Facultade de Química, 36310 Vigo, Galicia, Spain
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Vila A, Mosquera RA. On the different origin of the stabilisation of oxygen versus sulphur H-bond complexes with water. Chem Phys 2003. [DOI: 10.1016/s0301-0104(03)00185-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Barry HR, Corner L, Hancock G, Peverall R, Ranson TL, Ritchie GAD. Measurements of pressure broadening coefficients of selected transitions in the 2ν5band of formaldehyde. Phys Chem Chem Phys 2003. [DOI: 10.1039/b304139p] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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