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Kochikov IV, Tarasov YI. Application of statistical criteria in the presence of systematic errors in GED. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.140013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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2
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Demaison J, Vogt N, Nguyen HVL. Determination of rotational constants in the presence of methyl internal rotation: 2-acetylfuran and 2-acetylthiophene as examples. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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3
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Tikhonov DS. A simplistic computational procedure for tunneling splittings caused by proton transfer. Struct Chem 2021. [DOI: 10.1007/s11224-021-01845-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AbstractIn this manuscript, we present an approach for computing tunneling splittings for large amplitude motions. The core of the approach is a solution of an effective one-dimensional Schrödinger equation with an effective mass and an effective potential energy surface composed of electronic and harmonic zero-point vibrational energies of small amplitude motions in the molecule. The method has been shown to work in cases of three model motions: nitrogen inversion in ammonia, single proton transfer in malonaldehyde, and double proton transfer in the formic acid dimer. In the current work, we also investigate the performance of different DFT and post-Hartree–Fock methods for prediction of the proton transfer tunneling splittings, quality of the effective Schrödinger equation parameters upon the isotopic substitution, and possibility of a complete basis set (CBS) extrapolation for the resulting tunneling splittings.
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Ageev GG, Rykov AN, Grikina OE, Shishkov IF, Kochikov IV, Kuznetsov VV, Makhova NN, Bukalov SS. Equilibrium Molecular Structure of 3,3,6-trimethyl-1,5-diazabicyclo[3.1.0]hexane: the joint analysis of the gas-phase electron diffraction data and quantum chemical simulations. Struct Chem 2021. [DOI: 10.1007/s11224-021-01828-5] [Citation(s) in RCA: 2] [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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5
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Altova EP, Rykov AN, Vogt N, Shishkov IF. Equilibrium molecular structure of orotic acid from gas-phase electron diffraction data and quantum-chemical calculations. MENDELEEV COMMUNICATIONS 2021. [DOI: 10.1016/j.mencom.2021.01.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Khaikin LS, Ageev GG, Rykov AN, Grikina OE, Shishkov IF, Kochikov IV, Kuznetsov VV, Makhova NN, Bukalov SS, Leites LA. Equilibrium molecular structure and spectra of 6-methyl-1,5-diazabicyclo[3.1.0]hexane: joint analysis of gas phase electron diffraction, quantum chemistry, and spectroscopic data. Phys Chem Chem Phys 2020; 22:22477-22492. [PMID: 32996973 DOI: 10.1039/d0cp04005c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The equilibrium geometry of the boat conformation (Cs point group symmetry) of the 6-methyl-1,5-diazabicyclo[3.1.0]hexane (MDABH) molecule, absolutely dominating under normal conditions, was studied by the gas-phase electron diffraction (GED) method at 20 °C with the involvement of NMR, IR, and Raman spectroscopic data and quantum chemical calculations. The potential function of ring-puckering deformation for the MDABH bicyclic system was calculated at the MP2/aug-cc-pVTZ and B3LYP/cc-pVTZ levels. It was found by MP2 calculation that the total energy of the boat conformation is 3.52 kcal mol-1 lower than that of the chair conformation. For the first time, we recorded the IR and Raman spectra for liquid samples of MDABH and assigned their peculiarities only to boat conformation vibrations using the Pulay technique of scaling quantum chemical force fields. In the case of the chair form, transferability of the refined scale factors was used for reliable prediction of the location of its fundamental frequencies. According to the joint structural analysis of the above data, the most important equilibrium geometric re-parameters for the boat conformation of the MDABH molecule were determined to be (bond lengths in Å; angles in degrees, Cs symmetry): C2N1 = 1.466(2), C2C3 = 1.523(2), N1N5 = 1.512(2), C6N1 = 1.440(2), C6C7 = 1.487(2), ∠C2N1N5 = 106.1(2), ∠N1C2C3) = 110.2(4), ∠C2C3C4 = 99.9(4), ∠N1N5C6 = 58.3(1), ∠N1C6N5 = 63.3(1), ∠N1C6C7 = 114.9(6), ∠C6N1C2 = 111.8(1), ∠N5N1C2C3 = 17.3(1), ∠N1C2C3C4 = -26.8(2), θ = C2C3C4/C2N1N5C4 = -26.2(3), φ = N1C6N5/C2N1N5C4 = 74.0(1). Comparison of these and earlier results showed that the NN bond length in the diaziridine ring is very weakly dependent on the cis- or trans-arrangement of substituents at the nitrogen atoms.
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Affiliation(s)
- Leonid S Khaikin
- Chemistry Department, M. V. Lomonosov Moscow State University, 1 Leninsky Gory, 119991, Moscow, Russia.
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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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Ab initio molecular force fields fitted in Cartesian coordinates to experimental frequencies of isotopic species using symmetry constraints: application to indole and pyrrole molecules. Struct Chem 2019. [DOI: 10.1007/s11224-018-1262-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Khaikin LS, Kochikov IV, Rykov AN, Grikina OE, Ageev GG, Shishkov IF, Kuznetsov VV, Makhova NN. Equilibrium structures of the tetramezine diastereomers and their ratio: joint analysis of gas phase electron diffraction, quantum chemistry, and spectroscopic data. Phys Chem Chem Phys 2019; 21:5598-5613. [PMID: 30785435 DOI: 10.1039/c8cp07607c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
For the first time, we applied a gas-phase electron diffraction (GED) method together with vibrational spectroscopy and quantum chemical calculations to investigate the equilibrium geometries of achiral meso and enantiomeric diastereomers of tetramezine [1,2-bis-(3,3-dimethyldiaziridin-1-yl)ethane] and their ratio in the mixture. In the joint structural analysis of these data, a new approach based on PES parameters is used in the framework of a static molecular model (small amplitude motion approximation). The agreement between the theoretical and experimental molecular intensities is characterized by a divergence factor Rf of 5.9%. The experimental re-parameters of tetramezine diastereomers agreed with our B3LYP/cc-pVTZ and MP2/cc-pVTZ calculations, which predicted the total energy of the meso form (Ci point group symmetry) to be lower than that of the enantiomeric form (C2 point group symmetry), by 6.4 and 4.7 kJ mol-1, respectively. The experimentally measured percentages of the meso and both enantiomeric diastereoisomers at 360 K were 70% and 30%, respectively. We characterized the meso form using 2D NMR spectra. Our GED data are in good agreement with the X-ray diffraction analysis of the meso form. This result reflects the weak effect of intermolecular interactions in the crystal. We assigned the IR spectrum bands of the crystalline meso form using the Pulay technique of scaling quantum chemical force fields. In the case of the enantiomeric form calculated at the same level, transferability of the refined scale factors was used for more reliable prediction of the mutual location and interpretation of its fundamental frequencies.
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Affiliation(s)
- Leonid S Khaikin
- Chemistry Department, M. V. Lomonosov Moscow State University, 119991 Moscow, Russia.
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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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Tarasov YI, Kochikov IV. Pseudo-conformer models for linear molecules: Joint treatment of spectroscopic, electron diffraction and ab initio data for the C 3 O 2 molecule. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.02.095] [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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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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Tarasov YI, Kochikov IV, Bazhanova ZG. Internal Rotation and Equilibrium Structure of the Bromonitromethane Molecule According to Gas Electron Diffraction Data and Quantum Chemical Calculations. J STRUCT CHEM+ 2018. [DOI: 10.1134/s0022476618030034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Tikhonov DS, Sharapa DI, Schwabedissen J, Rybkin VV. Application of classical simulations for the computation of vibrational properties of free molecules. Phys Chem Chem Phys 2018; 18:28325-28338. [PMID: 27722605 DOI: 10.1039/c6cp05849c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, we investigate the ability of classical molecular dynamics (MD) and Monte-Carlo (MC) simulations for modeling the intramolecular vibrational motion. These simulations were used to compute thermally-averaged geometrical structures and infrared vibrational intensities for a benchmark set previously studied by gas electron diffraction (GED): CS2, benzene, chloromethylthiocyanate, pyrazinamide and 9,12-I2-1,2-closo-C2B10H10. The MD sampling of NVT ensembles was performed using chains of Nose-Hoover thermostats (NH) as well as the generalized Langevin equation thermostat (GLE). The performance of the theoretical models based on the classical MD and MC simulations was compared with the experimental data and also with the alternative computational techniques: a conventional approach based on the Taylor expansion of potential energy surface, path-integral MD and MD with quantum-thermal bath (QTB) based on the generalized Langevin equation (GLE). A straightforward application of the classical simulations resulted, as expected, in poor accuracy of the calculated observables due to the complete neglect of quantum effects. However, the introduction of a posteriori quantum corrections significantly improved the situation. The application of these corrections for MD simulations of the systems with large-amplitude motions was demonstrated for chloromethylthiocyanate. The comparison of the theoretical vibrational spectra has revealed that the GLE thermostat used in this work is not applicable for this purpose. On the other hand, the NH chains yielded reasonably good results.
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Affiliation(s)
- Denis S Tikhonov
- Universität Bielefeld, Lehrstuhl für Anorganische Chemie und Strukturchemie, Universitätsstrasse 25, 33615, Bielefeld, Germany. and M. V. Lomonosov Moscow State University, Department of Physical Chemistry, GSP-1, 1-3 Leninskiye Gory, 119991 Moscow, Russia
| | - Dmitry I Sharapa
- Computer-Chemie-Centrum and Interdisciplinary Center for Molecular Materials, Department Chemie und Pharmazie, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Jan Schwabedissen
- Universität Bielefeld, Lehrstuhl für Anorganische Chemie und Strukturchemie, Universitätsstrasse 25, 33615, Bielefeld, Germany.
| | - Vladimir V Rybkin
- ETH Zurich, Department of Materials, Wolfgang-Pauli-Strasse 27, CH-8093 Zurich, Switzerland.
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Ischenko AA, Weber PM, Miller RJD. Capturing Chemistry in Action with Electrons: Realization of Atomically Resolved Reaction Dynamics. Chem Rev 2017; 117:11066-11124. [DOI: 10.1021/acs.chemrev.6b00770] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Anatoly A. Ischenko
- Institute
of Fine Chemical Technologies, Moscow Technological University, Vernadskogo
86, 119571 Moscow, Russia
| | - Peter M. Weber
- Department
of Chemistry, Brown University, 324 Brook Street, 02912 Providence, Rhode Island, United States
| | - R. J. Dwayne Miller
- The Max Planck Institute for the Structure and Dynamics of Matter, Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Departments
of Chemistry and Physics, University of Toronto, 80 St. George, M5S 3H6 Toronto, Canada
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Tarasov YI, Kochikov IV, Kovtun DM, Polenov EA, Ivanov AA. Internal rotation and equilibrium structure of the 2-methyl-2-nitropropane molecule from joint processing of gas phase electron diffraction data, vibrational and microwave spectroscopy data, and quantum chemical calculation results. J STRUCT CHEM+ 2017. [DOI: 10.1134/s0022476617030106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Tikhonov DS, Vishnevskiy YV, Rykov AN, Grikina OE, Khaikin LS. Semi-experimental equilibrium structure of pyrazinamide from gas-phase electron diffraction. How much experimental is it? J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.05.090] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Kochikov IV, Kovtun DM, Tarasov YI. Electron diffraction analysis for the molecules with degenerate large amplitude motions: Intramolecular dynamics in arsenic pentafluoride. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.09.064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Internal rotation and equilibrium structure of 2-chloro-3-nitrothiophene from gas electron diffraction and quantum chemistry. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.07.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Ischenko AA. Effect of vibronic interactions on molecular structures determined by gas electron diffraction. Struct Chem 2015. [DOI: 10.1007/s11224-015-0667-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Khaikin LS, Kochikov IV, Grikina OE, Tikhonov DS, Baskir EG. IR spectra of nitrobenzene and nitrobenzene-15N in the gas phase, ab initio analysis of vibrational spectra and reliable force fields of nitrobenzene and 1,3,5-trinitrobenzene. Investigation of equilibrium geometry and internal rotation in these simplest aromatic nitro compounds with one and three rotors by means of electron diffraction, spectroscopic, and quantum chemistry data. Struct Chem 2015. [DOI: 10.1007/s11224-015-0613-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Khaikin LS, Kochikov IV, Tikhonov DS, Grikina OE. Analysis of electron diffraction data for several symmetric coordinates of large-amplitude motions in the case of the 1,3,5-trinitrobenzene molecule. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2015. [DOI: 10.1134/s0036024415060163] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Kovtun DM, Kochikov IV, Tarasov YI. Electron Diffraction Analysis for the Molecules with Multiple Large-Amplitude Motions. 3-Nitrostyrene—A Molecule with Two Internal Rotors. J Phys Chem A 2015; 119:1657-65. [DOI: 10.1021/jp5082774] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dmitry M. Kovtun
- Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia
| | - Igor V. Kochikov
- Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia
| | - Yury I. Tarasov
- Lomonosov Moscow State University of Fine Chemical Technologies, Vernadskogo Prospect 86, 119571 Moscow, Russia
- Joint Institute for High Temperatures of the Russian Academy of Sciences, Izhorskaya Street 13, Building 2, 125412 Moscow, Russia
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Internal rotation and equilibrium structure of 2-nitropropane from gas electron diffraction and quantum chemistry. J Mol Struct 2009. [DOI: 10.1016/j.molstruc.2008.12.071] [Citation(s) in RCA: 11] [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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25
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Tarasov Y, Kochikov I, Vogt N, Stepanova A, Kovtun D, Ivanov A, Rykov A, Deyanov R, Novosadov B, Vogt J. Electron diffraction and quantum chemical study of the structure and internal rotation in nitroethane. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2007.02.038] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Novosadov BK, Kochikov IV, Tarasov YI. Theory and calculations of second-order anharmonic corrections to the radial distribution function of polyatomic molecules. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2006. [DOI: 10.1134/s003602440608019x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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