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Latosińska JN, Latosińska M, Seliger J, Žagar V, Apih T. Butterfly Effect in Cytarabine: Combined NMR-NQR Experiment, Solid-State Computational Modeling, Quantitative Structure-Property Relationships and Molecular Docking Study. Pharmaceuticals (Basel) 2024; 17:445. [PMID: 38675407 PMCID: PMC11053780 DOI: 10.3390/ph17040445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/11/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Cytarabine (Ara-C) is a synthetic isomer of cytidine that differs from cytidine and deoxycytidine only in the sugar. The use of arabinose instead of deoxyribose hinders the formation of phosphodiester linkages between pentoses, preventing the DNA chain from elongation and interrupting the DNA synthesis. The minor structural alteration (the inversion of hydroxyl at the 2' positions of the sugar) leads to change of the biological activity from anti-depressant and DNA/RNA block builder to powerful anti-cancer. Our study aimed to determine the molecular nature of this phenomenon. Three 1H-14N NMR-NQR experimental techniques, followed by solid-state computational modelling (Quantum Theory of Atoms in Molecules, Reduced Density Gradient and 3D Hirshfeld surfaces), Quantitative Structure-Property Relationships, Spackman's Hirshfeld surfaces and Molecular Docking were used. Multifaceted analysis-combining experiments, computational modeling and molecular docking-provides deep insight into three-dimensional packing at the atomic and molecular levels, but is challenging. A spectrum with nine lines indicating the existence of three chemically inequivalent nitrogen sites in the Ara-C molecule was recorded, and the lines were assigned to them. The influence of the structural alteration on the NQR parameters was modeled in the solid (GGA/RPBE). For the comprehensive description of the nature of these interactions several factors were considered, including relative reactivity and the involvement of heavy atoms in various non-covalent interactions. The binding modes in the solid state and complex with dCK were investigated using the novel approaches: radial plots, heatmaps and root-mean-square deviation of the binding mode. We identified the intramolecular OH···O hydrogen bond as the key factor responsible for forcing the glycone conformation and strengthening NH···O bonds with Gln97, Asp133 and Ara128, and stacking with Phe137. The titular butterfly effect is associated with both the inversion and the presence of this intramolecular hydrogen bond. Our study elucidates the differences in the binding modes of Ara-C and cytidine, which should guide the design of more potent anti-cancer and anti-viral analogues.
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Affiliation(s)
| | - Magdalena Latosińska
- Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, 61-614 Poznań, Poland
| | - Janez Seliger
- “Jožef Stefan” Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000 Ljubljana, Slovenia
| | - Veselko Žagar
- “Jožef Stefan” Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Tomaž Apih
- “Jožef Stefan” Institute, Jamova 39, 1000 Ljubljana, Slovenia
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Latosińska JN, Latosińska M, Seliger J, Žagar V, Apih T, Grieb P. Elucidating the Role of Noncovalent Interactions in Favipiravir, a Drug Active against Various Human RNA Viruses; a 1H- 14N NQDR/Periodic DFT/QTAIM/RDS/3D Hirshfeld Surfaces Combined Study. Molecules 2023; 28:molecules28083308. [PMID: 37110542 PMCID: PMC10147075 DOI: 10.3390/molecules28083308] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 03/28/2023] [Accepted: 04/01/2023] [Indexed: 04/29/2023] Open
Abstract
Favipiravir (6-fluoro-3-hydroxypyrazine-2-carboxamide, FPV), an active pharmaceutical component of the drug discovered and registered in March 2014 in Japan under the name Avigan, with an indication for pandemic influenza, has been studied. The study of this compound was prompted by the idea that effective processes of recognition and binding of FPV to the nucleic acid are affected predominantly by the propensity to form intra- and intermolecular interactions. Three nuclear quadrupole resonance experimental techniques, namely 1H-14N cross-relaxation, multiple frequency sweeps, and two-frequency irradiation, followed by solid-state computational modelling (density functional theory supplemented by the quantum theory of atoms in molecules, 3D Hirshfeld Surfaces, and reduced density gradient) approaches were applied. The complete NQR spectrum consisting of nine lines indicating the presence of three chemically inequivalent nitrogen sites in the FPV molecule was detected, and the assignment of lines to particular sites was performed. The description of the nearest vicinity of all three nitrogen atoms was used to characterize the nature of the intermolecular interactions from the perspective of the local single atoms and to draw some conclusions on the nature of the interactions required for effective recognition and binding. The propensity to form the electrostatic N-H···O, N-H···N, and C-H···O intermolecular hydrogen bonds competitive with two intramolecular hydrogen bonds, strong O-H···O and very weak N-H···N, closing the 5-member ring and stiffening the structure, as well as π···π and F···F dispersive interactions, were analysed in detail. The hypothesis regarding the similarity of the interaction pattern in the solid and the RNA template was verified. It was discovered that the -NH2 group in the crystal participates in intermolecular hydrogen bonds N-H···N and N-H···O, in the precatalytic state only in N-H···O, while in the active state in N-H···N and N-H···O hydrogen bonds, which is of importance to link FVP to the RNA template. Our study elucidates the binding modes of FVP (in crystal, precatalytic, and active forms) in detail and should guide the design of more potent analogues targeting SARS-CoV-2. Strong direct binding of FVP-RTP to both the active site and cofactor discovered by us suggests a possible alternative, allosteric mechanism of FVP action, which may explain the scattering of the results of clinical trials or the synergistic effect observed in combined treatment against SARS-CoV-2.
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Affiliation(s)
| | - Magdalena Latosińska
- Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, 61-614 Poznań, Poland
| | - Janez Seliger
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000 Ljubljana, Slovenia
| | - Veselko Žagar
- "Jožef Stefan" Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Tomaž Apih
- "Jožef Stefan" Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Paweł Grieb
- Department of Experimental Pharmacology, Mossakowski Medical Research Institute, Polish Academy of Science, Adolfa Pawińskiego 5, 02-106 Warszawa, Poland
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Seliger J, Žagar V, Apih T, Gregorovič A, Latosińska M, Olejniczak GA, Latosińska JN. Polymorphism and disorder in natural active ingredients. Low and high-temperature phases of anhydrous caffeine: Spectroscopic (1H–14N NMR–NQR/14N NQR) and solid-state computational modelling (DFT/QTAIM/RDS) study. Eur J Pharm Sci 2016; 85:18-30. [DOI: 10.1016/j.ejps.2016.01.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 01/06/2016] [Accepted: 01/24/2016] [Indexed: 10/22/2022]
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Salpin JY, Haldys V, Guillaumont S, Tortajada J, Hurtado M, Lamsabhi AM. Gas-Phase Interactions between Lead(II) Ions and Cytosine: Tandem Mass Spectrometry and Infrared Multiple-Photon Dissociation Spectroscopy Study. Chemphyschem 2014; 15:2959-71. [DOI: 10.1002/cphc.201402369] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Indexed: 12/07/2022]
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Zahedi E. A Theoretical Study of NBO, NICS, and 14N NQR Parameters of Adenine Tautomers in the Gas Phase via DFT. J Heterocycl Chem 2012. [DOI: 10.1002/jhet.857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Ehsan Zahedi
- Department of Chemistry; Shahrood Branch, Islamic Azad University; Shahrood; Iran
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Elmi MM, Kaykhaei AA, Elmi F. Density functional theory study of nitrogen-14 nuclear quadrupole coupling parameters of L-histidine: hydrogen-bonded system. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2012; 50:314-319. [PMID: 22415677 DOI: 10.1002/mrc.3809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2011] [Revised: 01/22/2012] [Accepted: 02/13/2012] [Indexed: 05/31/2023]
Abstract
The calculations of nitrogen-14 nuclear quadrupole parameters, nuclear quadrupole coupling constant, χ, and asymmetry parameter, η, of L-His were done in two distinct environments: one as a free fully optimized molecule, an isolated molecule with the geometrical parameters taken from X-ray, and the other in the orthorhombic and monoclinic solid states. The most probable interacting molecules with the central molecule in the crystalline phase were considered in the hexameric clusters to include hydrogen-bonding effects in the calculations. The computations were performed with PW91P86/6-31++G** and B3LYP6-31++G** methods using the Gaussian 98 program. The good agreement between the nitrogen-14 quadrupole parameters of the free His and imidazole molecules with their microwave available data demonstrates that the applied level of theory and the 6-31++G** basis set are suitable to obtain reliable electric field gradient values. In the solid state, the shifts of quadrupole coupling parameters from the monomer to the solid phase are reasonably well reproduced for the amino and imino sites of imidazole ring in a hexameric cluster. That implies the fact that the hexameric cluster worked effectively to generate the results which are compatible with the experiment. The quadrupole coupling constant values of -N(+) H(3) group are in fair agreement with the experiment. This discrepancy is due to the absences of vibrational effects and the rotation of -N(+) H(3) group around N-C(α) bond.
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Affiliation(s)
- Maryam Mitra Elmi
- Cellular and Molecular Biology Research Center, Babol University of Medical Sciences, PO Box: 4717647745, Babol, Iran
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Brzyska A, Woliński K, Jaszuński M. Theoretical studies of the dependence of nuclear quadrupole coupling constants on intermolecular forces. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2011.12.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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Latosińska JN, Seliger J, Zagar V, Burchardt DV. A comparative study of the hydrogen-bonding patterns and prototropism in solid 2-thiocytosine (potential antileukemic agent) and cytosine, as studied by 1H-14N NQDR and QTAIM/ DFT. J Mol Model 2011; 18:11-26. [PMID: 21445709 PMCID: PMC3249547 DOI: 10.1007/s00894-011-1021-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Accepted: 02/13/2011] [Indexed: 02/03/2023]
Abstract
A potential antileukemic and anticancer agent, 2-thiocytosine (2-TC), has been studied experimentally in the solid state by 1H-14N NMR-NQR double resonance (NQDR) and theoretically by the quantum theory of atoms in molecules (QTAIM)/density functional theory (DFT). Eighteen resonance frequencies on 14N were detected at 180 K and assigned to particular nitrogen sites (−NH2, –N=, and –NH–) in 2-thiocytosine. Factors such as the nonequivalence of molecules (connected to the duplication of sites) and possible prototropic tautomerism (capable of modifying the type of site due to proton transfer) were taken into account during frequency assignment. The result of replacing oxygen with sulfur, which leads to changes in the intermolecular interaction pattern and molecular aggregation, is discussed. This study demonstrates the advantages of combining NQDR and DFT to extract detailed information on the H-bonding properties of crystals with complex H-bonding networks. Solid-state properties were found to have a profound impact on the stabilities and reactivities of both compounds. The experimental 1H-14N NQDR spectrum of 2-thiocytosine obtained at T = 180 K by the solid effect technique (left) and 3d distribution of the electron density Laplacian calculated by DFT (right) ![]()
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Seliger J, Žagar V, Latosińska JN. 14N NQR, 1H NMR and DFT/QTAIM study of hydrogen bonding and polymorphism in selected solid 1,3,4-thiadiazole derivatives. Phys Chem Chem Phys 2010; 12:13007-19. [DOI: 10.1039/c0cp00195c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Latosińska J, Latosińska M, Seliger J, Žagar V, Kazimierczuk Z. Electron density distribution in cladribine (2-chloro-2′-deoxyadenosine) – A drug against leukemia and multiple sclerosis – Studied by multinuclear NQR spectroscopy and DFT calculations. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.06.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Savitsky A, Dubinskii AA, Plato M, Grishin YA, Zimmermann H, Möbius K. High-Field EPR and ESEEM Investigation of the Nitrogen Quadrupole Interaction of Nitroxide Spin Labels in Disordered Solids: Toward Differentiation between Polarity and Proticity Matrix Effects on Protein Function. J Phys Chem B 2008; 112:9079-90. [DOI: 10.1021/jp711640p] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A. Savitsky
- Department of Physics, Free University Berlin, Arnimallee 14, D-14195 Berlin, Germany, Semenov Institute of Chemical Physics, Kosygina str. 4, 119991 Moscow, Russia, Institute of Chemical Kinetics and Combustion, Institutskaya str. 3, 630090 Novosibirsk, Russia, and Max-Planck-Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - A. A. Dubinskii
- Department of Physics, Free University Berlin, Arnimallee 14, D-14195 Berlin, Germany, Semenov Institute of Chemical Physics, Kosygina str. 4, 119991 Moscow, Russia, Institute of Chemical Kinetics and Combustion, Institutskaya str. 3, 630090 Novosibirsk, Russia, and Max-Planck-Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - M. Plato
- Department of Physics, Free University Berlin, Arnimallee 14, D-14195 Berlin, Germany, Semenov Institute of Chemical Physics, Kosygina str. 4, 119991 Moscow, Russia, Institute of Chemical Kinetics and Combustion, Institutskaya str. 3, 630090 Novosibirsk, Russia, and Max-Planck-Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Y. A. Grishin
- Department of Physics, Free University Berlin, Arnimallee 14, D-14195 Berlin, Germany, Semenov Institute of Chemical Physics, Kosygina str. 4, 119991 Moscow, Russia, Institute of Chemical Kinetics and Combustion, Institutskaya str. 3, 630090 Novosibirsk, Russia, and Max-Planck-Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - H. Zimmermann
- Department of Physics, Free University Berlin, Arnimallee 14, D-14195 Berlin, Germany, Semenov Institute of Chemical Physics, Kosygina str. 4, 119991 Moscow, Russia, Institute of Chemical Kinetics and Combustion, Institutskaya str. 3, 630090 Novosibirsk, Russia, and Max-Planck-Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - K. Möbius
- Department of Physics, Free University Berlin, Arnimallee 14, D-14195 Berlin, Germany, Semenov Institute of Chemical Physics, Kosygina str. 4, 119991 Moscow, Russia, Institute of Chemical Kinetics and Combustion, Institutskaya str. 3, 630090 Novosibirsk, Russia, and Max-Planck-Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
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Wu Y, Jin L, Xue Y, Xie DQ, Kim CK, Guo Y, Yan GS. Theoretical study on the hydrolysis mechanism ofN,N-dimethyl-N′-(2-oxo-1, 2-dihydro-pyrimidinyl)formamidine: Water-assisted mechanism and cluster-continuum model. J Comput Chem 2008; 29:1222-32. [DOI: 10.1002/jcc.20883] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Monajjemi M, Honarparvar B, Haeri HH, Heshmat M. An ab initio quantum chemical investigation of solvent-induced effect on 14N-NQR parameters of alanine, glycine, valine, and serine using a polarizable continuum model. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2006. [DOI: 10.1134/s0036024406130073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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Mirzaei M, Elmi F, Hadipour NL. A Systematic Investigation of Hydrogen-Bonding Effects on the 17O, 14N, and 2H Nuclear Quadrupole Resonance Parameters of Anhydrous and Monohydrated Cytosine Crystalline Structures: A Density Functional Theory Study. J Phys Chem B 2006; 110:10991-6. [PMID: 16771352 DOI: 10.1021/jp060301g] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A systematic computational study was carried out to characterize the 17O, 14N, and 2H nuclear quadrupole resonance (NQR) parameters in the anhydrous and monohydrated cytosine crystalline structures. To include the hydrogen-bonding effects in the calculations, the most probable interacting molecules with the central molecule in the crystalline phase were considered in the pentameric clusters of both structures. To calculate the parameters, couples of the methods B3LYP and B3PW91 and the basis sets 6-311++G** and CC-pVTZ were employed. The mentioned methods calculated reliable values of 17O, 14N, and 2H NQR tensors in the pentameric clusters, which are in good agreements with the experiment. The different influences of various hydrogen-bonding interactions types, N-H...N, N-H...O, and O-H...O, were observed on the 17O, 14N, and 2H NQR tensors. Lower values of quadrupole coupling constants and higher values of asymmetry parameters in the crystalline monohydrated cytosine indicate the presence of stronger hydrogen-bonding interactions in the monohydrated form rather than that of crystalline anhydrous cytosine.
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Affiliation(s)
- Mahmoud Mirzaei
- Department of Chemistry, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
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Latosińska JN. Structure-activity study of thiazides by magnetic resonance methods (NQR, NMR, EPR) and DFT calculations. J Mol Graph Model 2005; 23:329-37. [PMID: 15670953 DOI: 10.1016/j.jmgm.2004.11.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2004] [Revised: 10/26/2004] [Accepted: 11/03/2004] [Indexed: 10/26/2022]
Abstract
The paper presents a comprehensive analysis of the relationship between the electronic structure of thiazides and their biological activity. The compounds of interest were studied in solid state by the resonance methods nuclear quadrupole resonance (NQR), nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) and quantum chemistry (ab inito and DFT) methods. Detailed parallel analysis of the spectroscopic parameters such as quadrupole coupling constant (QCC) NQR chemical shift (delta), chemical shift anisotropy (CSA), asymmetry parameter (eta), NMR and hyperfine coupling constant (A), EPR was performed and the electronic effects (polarisation and delocalisation) were revealed and compared. Biological activity of thiazides has been found to depend on many factors, but mainly on the physico-chemical properties whose assessment was possible on the basis of electron density determination in the molecules performed by experimental and theoretical methods.
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Affiliation(s)
- J N Latosińska
- Department of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznań, Poland.
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A correlation of spectroscopic parameters from different magnetic resonance spectroscopies for thiazides: a study by NQR, NMR, EPR and DFT methods. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.09.088] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Latosińska J, Pajzderska A, Wąsicki J. Barriers for cation reorientation in pyridinium iodide studied by an atom–atom and DFT methods. J Mol Struct 2004. [DOI: 10.1016/j.molstruc.2004.05.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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