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Barone V. Accurate structures and spectroscopic parameters of α,α-dialkylated α-amino acids in the gas-phase: a joint venture of DFT and wave-function composite methods. Phys Chem Chem Phys 2023; 25:22768-22774. [PMID: 37591810 DOI: 10.1039/d3cp02503a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Accurate computations of structural, conformational and spectroscopic properties in the gas phase have been performed for two α,α-dialkylated α-amino acids, namely aminoisobutyric acid and cyclopropylglycine. Thanks to the integration of modern double hybrid functionals and wave-function methods, several low-energy structures of the title molecules could be analyzed employing standard computer resources. The computed features of all the most stable conformers of the target amino acids closely match the corresponding spectroscopic parameters issued from microwave spectroscopic studies in the gas-phase. Together with their intrinsic interest, the accuracy of the results obtained with reasonable computer times paves the way for accurate investigations of other flexible bricks of life.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
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2
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Vogt N, Savelev D, Giricheva NI, Girichev GV. Accurate equilibrium structure of 3-aminophthalimide from gas electron diffraction and coupled-cluster computations and diverse structural effects due to electron density transfer. Phys Chem Chem Phys 2020; 22:27539-27546. [PMID: 33179653 DOI: 10.1039/d0cp04423g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
For the first time, the molecular structure of 3-aminophthalimide has been determined by the gas electron diffraction (GED) method supported by a mass-spectrometric analysis of the gas phase and results of quantum-chemical computations up to coupled-cluster level of theory, CCSD(T). The semiexperimental equilibrium structure, rsee, has been derived from the GED data by taking into account harmonic and anharmonic vibrational corrections estimated from the quantum-chemical force field (up to cubic terms). High accuracy structures have been exploited for the observation of fine structural effects arising due the presence of the electron-donating amino group and the formation of a hydrogen bond. Natural bond orbital (NBO) analysis and quantum theory of atoms in molecules (QTAIM) have been applied to explain these effects.
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Affiliation(s)
- Natalja Vogt
- Section of Chemical Information Systems, Faculty of Sciences, University of Ulm, 89069 Ulm, Germany.
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3
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Vogt N, Khaikin LS, Rykov AN, Grikina OE, Batiukov AA, Vogt J, Kochikov IV, Shishkov IF. The equilibrium molecular structure of 2-cyanopyridine from combined analysis of gas-phase electron diffraction and microwave data and results of ab initio calculations. Struct Chem 2019. [DOI: 10.1007/s11224-019-01393-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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4
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Belyakov AV, Nikolaenko KO, Oskorbin AA, Vogt N, Rykov AN, Shishkov IF. Semiexperimental equilibrium structure of 1-methylisatin from gas-phase electron diffraction data and structural changes in isatin due to 1-methyl and 5-fluoro substituents as predicted by coupled cluster computations. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1554193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
| | | | | | - Natalja Vogt
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- Section of Chemical Information Systems, University of Ulm, Ulm, Germany
| | - Anatolii N. Rykov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Igor F. Shishkov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
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5
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Khaikin LS, Vogt N, Rykov AN, Grikina OE, Demaison J, Vogt J, Kochikov IV, Shishova YD, Ageeva ES, Shishkov IF. The Equilibrium Molecular Structure of 4-Cyanopyridine According to a Combined Analysis of Gas-Phase Electron Diffraction and Microwave Data and Coupled-Cluster Computations. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2018. [DOI: 10.1134/s0036024418100102] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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6
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Vogt N, Nair KPR, Grabow JU, Demaison J. Microwave rotational spectrum and ab initio computations on 4-cyanopyridine: molecular structure and hyperfine interactions. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1467053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Natalja Vogt
- Section of Chemical Information Systems, Faculty of Sciences, University of Ulm, Ulm, Germany
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russian Federation
| | - K. P. Rajappan Nair
- Institut für Physikalische Chemie und Elektrochemie, Wilhelm-Gottfried-Leibniz-Universität Hannover, Hannover, Germany
| | - Jens-Uwe Grabow
- Institut für Physikalische Chemie und Elektrochemie, Wilhelm-Gottfried-Leibniz-Universität Hannover, Hannover, Germany
| | - Jean Demaison
- Section of Chemical Information Systems, Faculty of Sciences, University of Ulm, Ulm, Germany
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7
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Khaikin LS, Vogt N, Rykov AN, Grikina OE, Vogt J, Kochikov IV, Ageeva ES, Shishkov IF. The equilibrium molecular structure of 3-cyanopyridine according to gas-phase electron diffraction and microwave data and the results of quantum-chemical calculations. MENDELEEV COMMUNICATIONS 2018. [DOI: 10.1016/j.mencom.2018.05.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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Vogt N, Marochkin II, Rykov AN. Experiment and theory at the convergence limit: accurate equilibrium structure of picolinic acid by gas-phase electron diffraction and coupled-cluster computations. Phys Chem Chem Phys 2018; 20:9787-9795. [PMID: 29564453 DOI: 10.1039/c8cp00310f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The accurate molecular structure of picolinic acid has been determined from experimental data and computed at the coupled cluster level of theory. Only one conformer with the O[double bond, length as m-dash]C-C-N and H-O-C[double bond, length as m-dash]O fragments in antiperiplanar (ap) positions, ap-ap, has been detected under conditions of the gas-phase electron diffraction (GED) experiment (Tnozzle = 375(3) K). The semiexperimental equilibrium structure, rsee, of this conformer has been derived from the GED data taking into account the anharmonic vibrational effects estimated from the ab initio force field. The equilibrium structures of the two lowest-energy conformers, ap-ap and ap-sp (with the synperiplanar H-O-C[double bond, length as m-dash]O fragment), have been fully optimized at the CCSD(T)_ae level of theory in conjunction with the triple-ζ basis set (cc-pwCVTZ). The quality of the optimized structures has been improved due to extrapolation to the quadruple-ζ basis set. The high accuracy of both GED determination and CCSD(T) computations has been disclosed by a correct comparison of structures having the same physical meaning. The ap-ap conformer has been found to be stabilized by the relatively strong NH-O hydrogen bond of 1.973(27) Å (GED) and predicted to be lower in energy by 16 kJ mol-1 with respect to the ap-sp conformer without a hydrogen bond. The influence of this bond on the structure of picolinic acid has been analyzed within the Natural Bond Orbital model. The possibility of the decarboxylation of picolinic acid has been considered in the GED analysis, but no significant amounts of pyridine and carbon dioxide could be detected. To reveal the structural changes reflecting the mesomeric and inductive effects due to the carboxylic substituent, the accurate structure of pyridine has been also computed at the CCSD(T)_ae level with basis sets from triple- to 5-ζ quality. The comprehensive structure computations for pyridine as well as for carbon dioxide have been used to examine the convergence with respect to the basis set size.
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Affiliation(s)
- Natalja Vogt
- Section of Chemical Information Systems, University of Ulm, 89069 Ulm, Germany. and Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ilya I Marochkin
- Section of Chemical Information Systems, University of Ulm, 89069 Ulm, Germany. and Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Anatolii N Rykov
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
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9
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Vallejo-López M, Écija P, Vogt N, Demaison J, Lesarri A, Basterretxea FJ, Cocinero EJ. N-Methyl Inversion and Accurate Equilibrium Structures in Alkaloids: Pseudopelletierine. Chemistry 2017; 23:16491-16496. [PMID: 28759141 DOI: 10.1002/chem.201702232] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Indexed: 11/06/2022]
Abstract
A rotational spectroscopy investigation has resolved the conformational equilibrium and structural properties of the alkaloid pseudopelletierine. Two different conformers, which originate from inversion of the N-methyl group from an axial to an equatorial position, have been unambiguously identified in the gas phase, and nine independent isotopologues have been recorded by Fourier-transform microwave spectroscopy in a jet expansion. Both conformers share a chair-chair configuration of the two bridged six-membered rings. The conformational equilibrium is displaced towards the axial form, with a relative population in the supersonic jet of Naxial /Nequatorial ≈2/1. An accurate equilibrium structure has been determined by using the semiexperimental mixed-estimation method and alternatively computed by quantum-chemical methods up to the coupled-cluster level of theory. A comparison with the N-methyl inversion equilibria in related tropanes is also presented.
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Affiliation(s)
- Montserrat Vallejo-López
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Apartado 644, 48080, Bilbao, Spain
| | - Patricia Écija
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Apartado 644, 48080, Bilbao, Spain
| | - Natalja Vogt
- Chemical Information Systems, Faculty of Sciences, University of Ulm, 89069, Ulm, Germany
| | - Jean Demaison
- Chemical Information Systems, Faculty of Sciences, University of Ulm, 89069, Ulm, Germany
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias, Universidad de Valladolid, 47011, Valladolid, Spain
| | - Francisco J Basterretxea
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Apartado 644, 48080, Bilbao, Spain
| | - Emilio J Cocinero
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Apartado 644, 48080, Bilbao, Spain
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Vogt N, Demaison J, Krasnoshchekov SV, Stepanov NF, Rudolph HD. Determination of accurate semiexperimental equilibrium structure of proline using efficient transformations of anharmonic force fields among the series of isotopologues. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1292370] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Natalja Vogt
- Section of Chemical Information Systems, Faculty of Sciences, University of Ulm, Ulm, Germany
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Jean Demaison
- Section of Chemical Information Systems, Faculty of Sciences, University of Ulm, Ulm, Germany
| | | | - Nikolay F. Stepanov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Heinz Dieter Rudolph
- Section of Chemical Information Systems, Faculty of Sciences, University of Ulm, Ulm, Germany
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11
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Xu C, Xu J. An expeditious method to synthesize difluoroboron complexes of β-keto amides from β-keto nitriles and BF3·OEt2. Org Biomol Chem 2017; 15:6375-6383. [DOI: 10.1039/c7ob01356f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
An expeditious and convenient method has been developed to synthesize difluoroboron complexes of β-keto amides from β-keto nitriles and BF3·OEt2.
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Affiliation(s)
- Chuangchuang Xu
- State Key Laboratory of Chemical Resource Engineering
- Department of Organic Chemistry
- Faculty of Science
- Beijing University of Chemical Technology
- Beijing 100029
| | - Jiaxi Xu
- State Key Laboratory of Chemical Resource Engineering
- Department of Organic Chemistry
- Faculty of Science
- Beijing University of Chemical Technology
- Beijing 100029
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12
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Vogt N, Savelyev DS, Giricheva NI, Islyaikin MK, Girichev GV. Accurate Determination of Equilibrium Structure of 3-Aminophthalonitrile by Gas Electron Diffraction and Coupled-Cluster Computations: Structural Effects Due to Intramolecular Charge Transfer. J Phys Chem A 2016; 120:8853-8861. [DOI: 10.1021/acs.jpca.6b08241] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Natalja Vogt
- Section
of Chemical Information Systems, Faculty of Sciences, University of Ulm, 89069 Ulm, Germany
- Department
of Chemistry, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Denis S. Savelyev
- Section
of Chemical Information Systems, Faculty of Sciences, University of Ulm, 89069 Ulm, Germany
- Department
of Physics, Ivanovo State University of Chemical Technology, 153025 Ivanovo, Russia
| | - Nina I. Giricheva
- Department
of Organic and Physical Chemistry, Ivanovo State University, 153000 Ivanovo, Russia
| | - Mikhail K. Islyaikin
- Department
of Fine Organic Synthesis Technology, Ivanovo State University of Chemical Technology, 153000 Ivanovo, Russia
| | - Georgiy V. Girichev
- Department
of Physics, Ivanovo State University of Chemical Technology, 153025 Ivanovo, Russia
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