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Rzepiela K, Kaminský J, Buczek A, Broda MA, Kupka T. Electron Correlation or Basis Set Quality: How to Obtain Converged and Accurate NMR Shieldings for the Third-Row Elements? MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238230. [PMID: 36500321 PMCID: PMC9737175 DOI: 10.3390/molecules27238230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022]
Abstract
The quality of theoretical NMR shieldings calculated at the quantum-chemical level depends on various theoretical aspects, of which the basis set type and size are among the most important factors. Nevertheless, not much information is available on the basis set effect on theoretical shieldings of the NMR-active nuclei of the third row. Here, we report on the importance of proper basis set selection to obtain accurate and reliable NMR shielding parameters for nuclei from the third row of the periodic table. All calculations were performed on a set of eleven compounds containing the elements Na, Mg, Al, Si, P, S, or Cl. NMR shielding tensors were calculated using the SCF-HF, DFT-B3LYP, and CCSD(T) methods, combined with the Dunning valence aug-cc-pVXZ, core-valence aug-cc-pCVXZ, Jensen polarized-convergent aug-pcSseg-n and Karlsruhe x2c-Def2 basis set families. We also estimated the complete basis set limit (CBS) values of the NMR parameters. Widely scattered nuclear shieldings were observed for the Dunning polarized-valence basis set, which provides irregular convergence. We show that the use of Dunning core-valence or Jensen basis sets effectively reduces the scatter of theoretical NMR results and leads to their exponential-like convergence to CBS. We also assessed the effect of vibrational, temperature, and relativistic corrections on the predicted shieldings. For systems with single bonds, all corrections are relatively small, amounting to less than 4% of the CCSD(T)/CBS value. Vibrational and temperature corrections were less reliable for H3PO and HSiCH due to the high anharmonicity of the molecules. An abnormally high relativistic correction was observed for phosphorus in PN, reaching ~20% of the CCSD(T)/CBS value, while the correction was less than 7% for other tested molecules.
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Affiliation(s)
- Kacper Rzepiela
- Faculty of Chemistry, University of Opole, 48 Oleska Street, 46-052 Opole, Poland
| | - Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 166 10 Prague, Czech Republic
- Correspondence: (J.K.); (T.K.)
| | - Aneta Buczek
- Faculty of Chemistry, University of Opole, 48 Oleska Street, 46-052 Opole, Poland
| | - Małgorzata A. Broda
- Faculty of Chemistry, University of Opole, 48 Oleska Street, 46-052 Opole, Poland
| | - Teobald Kupka
- Faculty of Chemistry, University of Opole, 48 Oleska Street, 46-052 Opole, Poland
- Correspondence: (J.K.); (T.K.)
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2
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Lo R, Lamanec M, Wang W, Manna D, Bakandritsos A, Dračínský M, Zbořil R, Nachtigallová D, Hobza P. Structure-directed formation of the dative/covalent bonds in complexes with C 70piperidine. Phys Chem Chem Phys 2021; 23:4365-4375. [PMID: 33589890 DOI: 10.1039/d0cp06280d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The combined experimental-computational study has been performed to investigate the complexes formed between C70 carbon allotrope and piperidine. The results of FT-IR, H-NMR, and C-NMR measurements, together with the calculations based on the DFT approach and molecular dynamics simulations, prove the existence of dative/covalent bonding in C70piperidine complexes. The dative bond forms not only at the region of five- and six-membered rings, observed previously with C60, but also at the region formed of six-membered rings. The structure, i.e., nonplanarity, explains the observed dative bond formation. New findings on the character of interaction of secondary amines with C70 bring new aspects for the rational design of modified fullerenes and their applications in electrocatalysis, spintronics, and energy storage.
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Affiliation(s)
- Rabindranath Lo
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námstí 542/2, 16000 Prague, Czech Republic. and CATRIN, Palacký University, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Maximilián Lamanec
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námstí 542/2, 16000 Prague, Czech Republic. and Department of Physical Chemistry, Palacký University Olomouc, Tr. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Weizhou Wang
- College of Chemistry and Chemical Engineering, and Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang Normal University, Luoyang 471934, China
| | - Debashree Manna
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námstí 542/2, 16000 Prague, Czech Republic. and CATRIN, Palacký University, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Aristides Bakandritsos
- CATRIN, Palacký University, Šlechtitelů 27, 78371 Olomouc, Czech Republic and Regional Centre of Advanced Technologies and Materials, Palacký University, Olomouc, Šlechtitelů 27, 78371, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námstí 542/2, 16000 Prague, Czech Republic.
| | - Radek Zbořil
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námstí 542/2, 16000 Prague, Czech Republic. and CATRIN, Palacký University, Šlechtitelů 27, 78371 Olomouc, Czech Republic and Regional Centre of Advanced Technologies and Materials, Palacký University, Olomouc, Šlechtitelů 27, 78371, Czech Republic and Nanotechnology Centre, VŠB-Technical University of Ostrava, 17. Listopadu 2172/15, 708 00 Ostrava-Poruba, Czech Republic
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námstí 542/2, 16000 Prague, Czech Republic. and CATRIN, Palacký University, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námstí 542/2, 16000 Prague, Czech Republic. and CATRIN, Palacký University, Šlechtitelů 27, 78371 Olomouc, Czech Republic
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3
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Chen D, Szczepanik DW, Zhu J, Muñoz-Castro A, Solà M. Aromaticity Survival in Hydrofullerenes: The Case of C 66 H 4 with Its π-Aromatic Circuits. Chemistry 2021; 27:802-808. [PMID: 33089913 DOI: 10.1002/chem.202004322] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/19/2020] [Indexed: 11/08/2022]
Abstract
The isolated-pentagon rule (IPR) is a determining structural feature that accounts for hollow fullerene stabilization and properties related to Cn (n≥60) cages. The recent characterization of an unprecedented non-IPR hydrofullerene, C2v C66 H4 , bearing two heptagons with adjacent fused-pentagon motifs, largely dismisses this feature. Herein, employing DFT calculations, the 13 C NMR spectroscopy and aromatic behavior of C2v C66 H4 are explored. The results show the presence of three π-aromatic circuits at the bottom boat section of C66 H4 , indicating the unique features of this hydrofullerene in comparison to those of pristine C60 . In addition, under specific orientations of the external field, certain π-aromatic circuits are enabled, resulting in a more aromatic fullerene than that of C60 , but lower than that of the spherical aromatic C60 6- fulleride. Notably, under a field aligned with the saturated carbon atoms, nonaromatic characteristics are exposed. This reveals that spherical-like cages can involve a complex magnetic response that heavily depends on the orientation of the applied field.
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Affiliation(s)
- Dandan Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Fujian Provincial Key Laboratory of Theoretical and Computational, Chemistry and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, P.R. China.,Institute of Computational Chemistry and Catalysis and Department of, Chemistry, University of Girona, C/M. Aurèlia Capmany, 69, 17003, Girona, Catalonia, Spain
| | - Dariusz W Szczepanik
- Institute of Computational Chemistry and Catalysis and Department of, Chemistry, University of Girona, C/M. Aurèlia Capmany, 69, 17003, Girona, Catalonia, Spain.,K. Guminski Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa, 2, 30-387, Kraków, Poland
| | - Jun Zhu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Fujian Provincial Key Laboratory of Theoretical and Computational, Chemistry and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, P.R. China
| | - Alvaro Muñoz-Castro
- Grupo de Química Inorgánica y Materiales Moleculares, Facultad de Ingeniería, Universidad Autónoma de Chile, El Llano Subercaseaux, 2801, Santiago, Chile
| | - Miquel Solà
- Institute of Computational Chemistry and Catalysis and Department of, Chemistry, University of Girona, C/M. Aurèlia Capmany, 69, 17003, Girona, Catalonia, Spain
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4
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Muñoz-Castro A, King RB. Th@C 86, Th@C 82, Th@C 80, and Th@C 76: role of thorium encapsulation in determining spherical aromatic and bonding properties on medium-sized endohedral metallofullerenes. Phys Chem Chem Phys 2020; 22:23920-23928. [PMID: 33073794 DOI: 10.1039/d0cp03784b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thorium encapsulated metallofullerenes (Th-EMFs) with external C76, C80, C82, and C86 cages have been synthesized, with the 13C-NMR spectrum recorded for Th@C82. Here, we explore computationally the chemical bonding, NMR and spherical aromaticity of Th@C82 and related thorium-encapsulated metallofullerenes. Our results show that these Th-EMFs are new examples of spherical aromatic structures, representing interesting low-symmetry exceptions to the Hirsch 2(N + 1)2 rule of spherical aromaticity. Their electronic structures are based on π-electron counts of 80, 84, 86, and 90, respectively, with a shell structure ranging from S2P6D10F14G18H22I8 to S2P6D10F14G18H22I18, where the partially filled I-shell remains as a frontier orbital. Their behavior is comparable to that of the spherical aromatic alkali-C606- phases, which in addition to the favorable endohedral Th-fullerene bonding account for their particular abundance exhibiting the ability to sustain a long-range shielding cone as a result of the favorable metal-cage bonding. This rationalization of such species as neutral spherical aromatic EMFs suggests the possibility of an extensive series of aromatic fullerenes with nuclearity larger than C60 buckminsterfullerene as stable building blocks towards nanostructured metal-organic materials.
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Affiliation(s)
- Alvaro Muñoz-Castro
- Laboratorio de Química Inorgánica y Materiales Moleculares, Universidad Autonoma de Chile, Llano Subercaseaux 2801, San Miguel, Santiago, Chile.
| | - R Bruce King
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA.
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6
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Liosi K, Romero-Rivera A, Semivrazhskaya O, Caniglia CD, Garcia-Borràs M, Trapp N, Osuna S, Yamakoshi Y. Site-Selectivity of Prato Additions to C 70: Experimental and Theoretical Studies of a New Thermodynamic Product at the dd-[5,6]-Junction. Org Lett 2019; 21:5162-5166. [PMID: 31199152 DOI: 10.1021/acs.orglett.9b01756] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Three Prato monoadduct isomers were synthesized and structurally characterized by 1H, 13C NMR spectra and single-crystal X-ray diffraction, and one adduct on the dd-[5,6]-bond was found as the first example of a Prato [5,6]-adduct of C70. To investigate the mechanism in the generation of this dd-[5,6]-adduct, computational studies were employed to show that it was thermodynamically obtained by sigmatropic rearrangement from the presumed initial kinetic product de-[6,6]-adduct.
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Affiliation(s)
- Korinne Liosi
- Laboratorium für Organische Chemie , ETH Zürich , Vladimir-Prelog-Weg 3 , CH-8093 Zürich , Switzerland
| | - Adrian Romero-Rivera
- CompBioLab group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química , Universitat de Girona , Campus Montilivi , 17071 Girona , Catalonia , Spain
| | - Olesya Semivrazhskaya
- Laboratorium für Organische Chemie , ETH Zürich , Vladimir-Prelog-Weg 3 , CH-8093 Zürich , Switzerland
| | - Caravaggio D Caniglia
- Laboratorium für Organische Chemie , ETH Zürich , Vladimir-Prelog-Weg 3 , CH-8093 Zürich , Switzerland
| | - Marc Garcia-Borràs
- CompBioLab group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química , Universitat de Girona , Campus Montilivi , 17071 Girona , Catalonia , Spain
| | - Nils Trapp
- Laboratorium für Organische Chemie , ETH Zürich , Vladimir-Prelog-Weg 3 , CH-8093 Zürich , Switzerland
| | - Sílvia Osuna
- CompBioLab group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química , Universitat de Girona , Campus Montilivi , 17071 Girona , Catalonia , Spain.,ICREA , Pg. Lluís Companys 23 , 08010 Barcelona , Catalonia , Spain
| | - Yoko Yamakoshi
- Laboratorium für Organische Chemie , ETH Zürich , Vladimir-Prelog-Weg 3 , CH-8093 Zürich , Switzerland
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7
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Abstract
The potential energy surfaces for the interior rotation of a series of pairs of noble gas atoms encapsulated in the C70 cavity have been explored.
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Affiliation(s)
- Sara Gómez
- Scuola Normale Superiore
- Classe di Scienze
- 56126 Pisa
- Italy
| | - Albeiro Restrepo
- Instituto de Química
- Universidad de Antioquia UdeA
- Medellín
- Colombia
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8
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Lukyanov DA, Konev AS, Amsharov K, Khlebnikov AF, Hirsch A. Diastereospecific and Highly Site-Selective Functionalization of C 70 Fullerene by a Reaction with Diethyl N-Arylaziridine-2,3-dicarboxylates. J Org Chem 2018; 83:14146-14151. [PMID: 30362752 DOI: 10.1021/acs.joc.8b02240] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The diastereospecific and highly site-selective cycloaddition of N-arylazomethine ylides generated in situ from diethyl N-arylaziridine-2,3-dicarboxylates to C70 fullerene is reported. The reaction provides C70 fulleropyrrolidines in up to hundreds on a milligram scale as α- and β-adducts in a 4:1 ratio with a controlled stereochemical outcome: cis-aziridines give exclusively trans-adducts, and trans-aziridines give only cis-adducts. The 1H and 13C{1H} NMR spectra for different isomeric adducts were recorded and analyzed to identify some characteristic features, which permit an easy identification of isomeric adducts of this type.
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Affiliation(s)
- Daniil A Lukyanov
- Institute of Chemistry , Saint Petersburg State University , 7/9 Universitetskaya nab. , St. Petersburg 199034 , Russia
| | - Alexander S Konev
- Institute of Chemistry , Saint Petersburg State University , 7/9 Universitetskaya nab. , St. Petersburg 199034 , Russia
| | - Konstantin Amsharov
- The Institute of Organic Chemistry , University of Erlangen-Nurnberg , Nikolaus-Fiebiger Str. 10 , Erlangen D-91058 , Germany
| | - Alexander F Khlebnikov
- Institute of Chemistry , Saint Petersburg State University , 7/9 Universitetskaya nab. , St. Petersburg 199034 , Russia
| | - Andreas Hirsch
- The Institute of Organic Chemistry , University of Erlangen-Nurnberg , Nikolaus-Fiebiger Str. 10 , Erlangen D-91058 , Germany
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Miralrio A, Sansores LE, King B, Muñoz-Castro A. C50Cl10, a planar aromatic fullerene. Computational study of 13C-NMR chemical shift anisotropy patterns and aromatic properties. Phys Chem Chem Phys 2018; 20:26325-26332. [DOI: 10.1039/c8cp04938f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The structural characterization of D5h-C50Cl10 as an IPR-violating fullerene provides an interesting case of an oblate structure displaying a planar-aromatic character provided by the face-to-face disposition of two IPR structural motifs, as unraveled by DFT calculations.
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Affiliation(s)
- Alan Miralrio
- Departamento de Física y Química Teórica
- DEPg. Facultad de Química
- Universidad Nacional Autónoma de México
- UNAM
- Ciudad de México 04510
| | - Luis E. Sansores
- Departamento de Materiales de Baja Dimensionalidad
- Instituto de Investigaciones en Materiales
- UNAM
- Ciudad de México 04510
- Mexico
| | - Bruce King
- Department of Chemistry
- University of Georgia
- Athens
- USA
| | - Alvaro Muñoz-Castro
- Grupo de Química Inorgánica y Materiales Moleculares
- Universidad Autonoma de Chile
- Santiago
- Chile
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Muñoz-Castro A, King RB. Formation of Spherical Aromatic Endohedral Metallic Fullerenes. Evaluation of Magnetic Properties of M@C 28 (M = Ti, Zr, and Hf) from DFT calculations. Inorg Chem 2017; 56:15251-15258. [PMID: 29166009 DOI: 10.1021/acs.inorgchem.7b02611] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The small C28 cage has been shown experimentally to encapsulate titanium, zirconium, and hafnium (M), among other elements. Here, we explore computationally its magnetic response properties accounting for both global and local shielding tensors. Our results exhibit a continuous shielding region for M@C28 for an orientation-averaged applied field thereby differing from that observed for the hollow C28 structure. Moreover, under a specific orientation of the applied field a long-ranged shielding cone is obtained supporting the spherical aromatic behavior expected by the 2(N + 1)2 Hirsch rule for M@C28, standing for its particular abundance. The comparison between the hollow and endohedral C28 fullerenes exhibits a characteristic long-range behavior at the outside region of the structure. The particular shape of the local chemical shift anisotropy tensor at a representative carbon atom exhibits inherent patterns as a consequence of the spherical aromatic behavior. This shows the capabilities from NMR experiments to account for the nonaromatic → aromatic variation. We envisage that the current approach will be beneficial in comparative studies of aromatic and electronic structure properties, to gain a deeper understanding of the geometrical and electronic structure situation in other endohedral species beyond that available from the information provided by routine NMR measurements.
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Affiliation(s)
- Alvaro Muñoz-Castro
- Laboratorio de Química Inorgánica y Materiales Moleculares, Universidad Autonoma de Chile , Llano Subercaseaux 2801, San Miguel, Santiago, Chile.,Relativistic Molecular Physics Group, Universidad Andres Bello , Republica 275, Santiago, Chile
| | - R Bruce King
- Department of Chemistry, University of Georgia , Athens, Georgia 30602, United States
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11
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Raich I, Lövyová Z, Trnka L, Parkan K, Kessler J, Pohl R, Kaminský J. Limitations in the description of conformational preferences of C-disaccharides: The (1 → 3)-C-mannobiose case. Carbohydr Res 2017; 451:42-50. [PMID: 28950209 DOI: 10.1016/j.carres.2017.09.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 09/07/2017] [Accepted: 09/11/2017] [Indexed: 11/19/2022]
Abstract
Conformational preferences of two C-glycosyl analogues of Manp-(1 → 3)-Manp, were studied using a combined method of theoretical and experimental chemistry. Molecular dynamics was utilized to provide conformational behavior along C-glycosidic bonds of methyl 3-deoxy-3-C-[(α-d-mannopyranosyl)methyl]-α-d- and l-mannopyranosides. The OPLS2005 and Glycam06 force fields were used. Simulations were performed with explicit water (TIP3P) and methanol. Results were compared with a complete conformational scan at the MM4 level with the dielectric constant corresponding to methanol. In order to verify predicted conformational preferences, vicinal 3JHH NMR coupling constants were calculated by the Karplus equation on simulated potential energy surfaces (PES). A set of new parameters for the Karplus equation was also designed. Predicted 3JHH were compared with experimental data. We also used reverse methodology, in which the 3JHH coupling constants were calculated at the DFT level for each family of (ϕ, ψ)-conformers separately and then experimental values were decomposed onto calculated 3JHH couplings in order to obtain experimentally derived populations of conformers. As an alternative method of evaluation of preferred conformers, analysis of sensitive 13C chemical shifts was introduced. We were able to thoroughly discuss several fundamental issues in predictions of preferred conformers of C-saccharides, such as the solvent effect, reliability of the force field, character of empirical Karplus equation or applicability of NMR parameters in predictions of conformational preferences in general.
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Affiliation(s)
- Ivan Raich
- University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic
| | - Zuzana Lövyová
- University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic
| | - Ladislav Trnka
- University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic
| | - Kamil Parkan
- University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic; Institute of Organic Chemistry and Biochemistry AS CR, Gilead Sciences & IOCB Research Center, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Jiří Kessler
- Institute of Organic Chemistry and Biochemistry AS CR, Gilead Sciences & IOCB Research Center, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry AS CR, Gilead Sciences & IOCB Research Center, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry AS CR, Gilead Sciences & IOCB Research Center, Flemingovo nám. 2, 166 10 Prague, Czech Republic.
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12
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Kaminský J, Vícha J, Bouř P, Straka M. Properties of the Only Thorium Fullerene, Th@C84, Uncovered. J Phys Chem A 2017; 121:3128-3135. [DOI: 10.1021/acs.jpca.7b00346] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo náměstí
2, 166 10 Prague, Czech Republic
| | - Jan Vícha
- Center
of Polymer Systems, University Institute, Tomáš Bat’a University in Zlín, Třída T. Bati, 5678, CZ-76001, Zlín, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo náměstí
2, 166 10 Prague, Czech Republic
| | - Michal Straka
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo náměstí
2, 166 10 Prague, Czech Republic
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13
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Muñoz-Castro A, Caimanque-Aguilar W, Morales-Verdejo C. Computational Study of 13C NMR Chemical Shift Anisotropy Patterns in C20H10 and [C20H10]4–. Insights into Their Variation upon Planarization and Formation of Concentric Aromatic Species in the Smaller Isolated-Pentagon Structural Motif. J Phys Chem A 2017; 121:2698-2703. [DOI: 10.1021/acs.jpca.7b01477] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alvaro Muñoz-Castro
- Grupo de Química
Inorgánica y Materiales Moleculares, Universidad Autonoma de Chile, El Llano
Subercaseaux 2801, Santiago, Chile
- Doctorado en Fisicoquímica Molecular, Universidad Andres Bello, Av. Republica 275, 8370146 Santiago, Chile
| | - Wilson Caimanque-Aguilar
- Doctorado en Fisicoquímica Molecular, Universidad Andres Bello, Av. Republica 275, 8370146 Santiago, Chile
| | - Cesar Morales-Verdejo
- Universidad Bernardo OHiggins, Laboratorio
de Bionanotecnología, Departamento de Ciencias Quimicas y Biologicas, General Gana 1702, Santiago, Chile
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Kupka T, Stachów M, Stobiński L, Kaminský J. DFT study of zigzag (n, 0) single-walled carbon nanotubes: 13C NMR chemical shifts. J Mol Graph Model 2016; 67:14-9. [DOI: 10.1016/j.jmgm.2016.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 04/14/2016] [Accepted: 04/19/2016] [Indexed: 10/21/2022]
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15
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Chikayama E, Shimbo Y, Komatsu K, Kikuchi J. The Effect of Molecular Conformation on the Accuracy of Theoretical (1)H and (13)C Chemical Shifts Calculated by Ab Initio Methods for Metabolic Mixture Analysis. J Phys Chem B 2016; 120:3479-87. [PMID: 26963288 DOI: 10.1021/acs.jpcb.5b12748] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
NMR spectroscopy is a powerful method for analyzing metabolic mixtures. The information obtained from an NMR spectrum is in the form of physical parameters, such as chemical shifts, and construction of databases for many metabolites will be useful for data interpretation. To increase the accuracy of theoretical chemical shifts for development of a database for a variety of metabolites, the effects of sets of conformations (structural ensembles) and the levels of theory on computations of theoretical chemical shifts were systematically investigated for a set of 29 small molecules in the present study. For each of the 29 compounds, 101 structures were generated by classical molecular dynamics at 298.15 K, and then theoretical chemical shifts for 164 (1)H and 123 (13)C atoms were calculated by ab initio quantum chemical methods. Six levels of theory were used by pairing Hartree-Fock, B3LYP (density functional theory), or second order Møller-Plesset perturbation with 6-31G or aug-cc-pVDZ basis set. The six average fluctuations in the (1)H chemical shift were ±0.63, ± 0.59, ± 0.70, ± 0.62, ± 0.75, and ±0.66 ppm for the structural ensembles, and the six average errors were ±0.34, ± 0.27, ± 0.32, ± 0.25, ± 0.32, and ±0.25 ppm. The results showed that chemical shift fluctuations with changes in the conformation because of molecular motion were larger than the differences between computed and experimental chemical shifts for all six levels of theory. In conclusion, selection of an appropriate structural ensemble should be performed before theoretical chemical shift calculations for development of an accurate database for a variety of metabolites.
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Affiliation(s)
- Eisuke Chikayama
- RIKEN Center for Sustainable Resource Science , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,Department of Information Systems, Niigata University of International and Information Studies , 3-1-1 Mizukino, Nishi-ku, Niigata, Niigata 950-2292, Japan
| | - Yudai Shimbo
- NEC Solution Innovators, Ltd. , 2-2-41 Ekimae, Kashiwazaki, Niigata 945-0055, Japan
| | - Keiko Komatsu
- RIKEN Center for Sustainable Resource Science , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,Graduate School of Medical Life Science, Yokohama City University , 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,Graduate School of Bioagricultural Sciences, Nagoya University , 1 Furo-cho, Chikusa-ku, Nagoya, Aichi 464-0810, Japan
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16
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Faber R, Kaminsky J, Sauer SPA. Rovibrational and Temperature Effects in Theoretical Studies of NMR Parameters. GAS PHASE NMR 2016. [DOI: 10.1039/9781782623816-00218] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The demand for high precision calculations of NMR shieldings (or their related values, chemical shifts δ) and spin–spin coupling constants facilitating and supporting detailed interpretations of NMR spectra increases hand in hand with the development of computational techniques and hardware resources. Highly sophisticated calculations including even relativistic effects are nowadays possible for these properties. However, NMR parameters depend not only on molecular structure and environment but also on molecular flexibility and temperature and the apparent success of theoretical predictions for molecular equilibrium geometries creates a demand for zero-point vibrational and temperature corrections. In this chapter we describe briefly the theory behind rovibrational corrections and review then some important contributions to this field.
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Affiliation(s)
- Rasmus Faber
- Department of Chemistry, University of Copenhagen Universitetsparken 5 DK-2100 Copenhagen Ø Denmark
| | - Jakub Kaminsky
- Department of Molecular Spectroscopy, Institute of Organic Chemistry and Biochemistry 166 10 Prague Czech Republic
| | - Stephan P. A. Sauer
- Department of Chemistry, University of Copenhagen Universitetsparken 5 DK-2100 Copenhagen Ø Denmark
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17
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18
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Toomsalu E, Burk P. Critical test of some computational methods for prediction of NMR 1H and 13C chemical shifts. J Mol Model 2015; 21:244. [DOI: 10.1007/s00894-015-2787-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/11/2015] [Indexed: 11/24/2022]
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19
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Jankowska M, Kupka T, Stobiński L, Kaminský J. DFT studies on armchair (5, 5) SWCNT functionalization. Modification of selected structural and spectroscopic parameters upon two-atom molecule attachment. J Mol Graph Model 2015; 55:105-14. [DOI: 10.1016/j.jmgm.2014.11.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 09/19/2014] [Accepted: 11/07/2014] [Indexed: 12/01/2022]
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20
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Straka M, Štěpánek P, Coriani S, Vaara J. Nuclear spin circular dichroism in fullerenes: a computational study. Chem Commun (Camb) 2014; 50:15228-31. [PMID: 25341745 DOI: 10.1039/c4cc07271e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Chemically different carbons in C70 give distinct signals in nuclear spin circular dichroism spectroscopy, a novel candidate for high-resolution identification of chemical compounds.
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Affiliation(s)
- Michal Straka
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6, Czech Republic
| | - Petr Štěpánek
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6, Czech Republic
| | - Sonia Coriani
- Dipartimento di Scienze Chimiche e Farmaceutiche
- Università degli Studi di Trieste
- I-34127 Trieste, Italy
| | - Juha Vaara
- NMR Research Group
- Department of Physics and Chemistry
- , Finland
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21
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Kupka T, Stachów M, Nieradka M, Radula-Janik K, Stobiński L, Kaminský J. From small to medium and beyond: a pragmatic approach in predicting properties of Ne containing structures. Mol Phys 2013. [DOI: 10.1080/00268976.2013.848301] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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22
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Kupka T, Nieradka M, Kaminský J, Stobiński L. Modeling 21Ne NMR parameters for carbon nanosystems. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2013; 51:676-681. [PMID: 23970499 DOI: 10.1002/mrc.3999] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 06/18/2013] [Accepted: 07/18/2013] [Indexed: 06/02/2023]
Abstract
The potential of nuclear magnetic resonance (NMR) technique in probing the structure of porous systems including carbon nanostructures filled with inert gases is analysed theoretically using accurate calculations of neon ((21) Ne) nuclear magnetic shieldings. The CBS estimates of (21) Ne NMR parameters were performed for single atom, its dimer and neon interacting with acetylene, ethylene and 1,3-cyclopentadiene. Several levels of theory including restricted Hartree-Fock (RHF), Møller-Plesset perturbation theory to the second order (MP2), density functional theory (DFT) with van Voorhis and Scuseria's t-dependent gradient-corrected correlation functional (VSXC), coupled cluster with single and doubles excitations (CCSD), with single, doubles and triples included in a perturbative way (CCSD(T)) and single, doubles and tripes excitations (CCSDT) combined with polarization-consistent aug-pcS-n series of basis sets were employed. The impact of neon confinement inside selected fullerene cages used as an NMR probe was studied at the RHF/pcS-2 level of theory. A sensitivity of neon probe to the proximity of multiple CC bonds in C2 H2 , C2 H4 , C5 H6 and inside C28 , C30 , C32 , C34 and C60 fullerenes was predicted from (21) Ne NMR parameters' changes. Copyright © 2013 John Wiley & Sons, Ltd.
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Affiliation(s)
- Teobald Kupka
- Faculty of Chemistry, University of Opole, 48 Oleska Street, 45-052, Opole, Poland
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23
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Kupka T, Stachów M, Chełmecka E, Pasterny K, Stobińska M, Stobiński L, Kaminský J. Efficient Modeling of NMR Parameters in Carbon Nanosystems. J Chem Theory Comput 2013; 9:4275-86. [DOI: 10.1021/ct4002812] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Teobald Kupka
- University of Opole, Faculty of Chemistry,
48, Oleska Street, 45-052 Opole, Poland
| | - Michał Stachów
- University of Opole, Faculty of Chemistry,
48, Oleska Street, 45-052 Opole, Poland
| | - Elżbieta Chełmecka
- Division of Statistics, Department
of Instrumental Analysis, Medical University of Silesia, 30 Ostrogórska Street, 41-200 Sosnowiec, Poland
| | - Karol Pasterny
- A. Chełkowski Institute of
Physics, University of Silesia, 4 Uniwersytecka
Street, 40-007 Katowice, Poland
| | - Magdalena Stobińska
- Institute of Theoretical Physics and Astrophysics, University of Gdańsk, 57 Wita Stwosza Street, 80-952 Gdańsk,
Poland
- Institute of Physics, Polish Academy of Sciences, 32/46, al. Lotników,
02-668 Warsaw, Poland
| | - Leszek Stobiński
- Institute
of Physical Chemistry, Polish Academy of Sciences, 44/52 Kasprzaka Street, 01-224 Warsaw, Poland
| | - Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nam. 2., 166
10 Prague, Czech Republic
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