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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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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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Zhabanov YA, Pogonin AE. An alternative approach to structural analysis for gas electron diffraction method. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2017.11.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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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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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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Tikhonov DS, Rykov AN, Grikina OE, Khaikin LS. Gas phase equilibrium structure of histamine. Phys Chem Chem Phys 2016; 18:6092-102. [PMID: 26845147 DOI: 10.1039/c5cp07719b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first gas electron diffraction (GED) experiment for histamine was carried out. The equilibrium structure of histamine in the gas phase was determined on the basis of the data obtained. The refinement was also supported by the rotational constants obtained in previous studies [B. Vogelsanger, et al., J. Am. Chem. Soc., 1991, 113, 7864-7869; P. Godfrey, et al., J. Am. Chem. Soc., 1998, 120, 10724-10732] and quantum chemical calculations. The proposed mechanism of tautomerization by simultaneous intermolecular transfer of hydrogens in a histamine dimer helps to explain the distribution of tautomers in different experiments. The estimations of the conformational interconversion times provided the explanation for the absence of some conformers in the rotational spectroscopy experiments.
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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, Faculty of Chemistry, Department of Physical Chemistry, GSP-1, 1-3 Leninskiye Gory, 119991 Moscow, Russian Federation
| | - Anatolii N Rykov
- M. V. Lomonosov Moscow State University, Faculty of Chemistry, Department of Physical Chemistry, GSP-1, 1-3 Leninskiye Gory, 119991 Moscow, Russian Federation
| | - Olga E Grikina
- M. V. Lomonosov Moscow State University, Faculty of Chemistry, Department of Physical Chemistry, GSP-1, 1-3 Leninskiye Gory, 119991 Moscow, Russian Federation
| | - Leonid S Khaikin
- M. V. Lomonosov Moscow State University, Faculty of Chemistry, Department of Physical Chemistry, GSP-1, 1-3 Leninskiye Gory, 119991 Moscow, Russian Federation
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Kuramshina GM, Vakula OA, Vakula NI, Majouga AG, Senyavin VM, Gorb LG, Leszczynski J. Conformations, vibrational spectra and force field of 1-methyl-2-(2′-pyridyl)benzimidazole: experimental data and density functional theory investigation in comparison with 2-(2′-pyridyl)benzimidazole. Struct Chem 2015. [DOI: 10.1007/s11224-015-0693-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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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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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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Khaikin LS, Tikhonov DS, Grikina OE, Rykov AN, Stepanov NF. Quantum-chemical calculations and electron diffraction study of the equilibrium molecular structure of vitamin K3. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2014. [DOI: 10.1134/s0036024414050112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Khaikin LS, Grikina OE, Kochikov IV, Stepanov NF. Quantum-chemical calculations for silyl- and alkyl-pseudohalides X3YNCZ (X = H or CH3; Y = C or Si; Z = O, S, or Se) and electron diffraction study of the equilibrium molecular structure of (CH3)3SiNCSe. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2014. [DOI: 10.1134/s0036024414040128] [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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Khaikin LS, Grikina OE, Kochikov IV, Stepanov NF. Hexamethylenetetramine (urotropine) C6H12N2: Interpreting the vibrational spectra of -d0 and -d12 isotopomers by scaling the quantum-chemical force field. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2014. [DOI: 10.1134/s0036024414030108] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Khaikin LS, Grikina OE, Karasev NM, Kovtun DM, Kochikov IV. Electron diffraction study of the equilibrium structure of hexamethylenetetramine involving data from quantum chemistry and vibrational spectroscopy. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2014. [DOI: 10.1134/s0036024414040116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Philosophy of scaling the quantum mechanical molecular force field versus philosophy of solving the inverse vibrational problem. J Mol Struct 2002. [DOI: 10.1016/s0022-2860(02)00063-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Kochikov I, Tarasov Y, Vogt N, Spiridonov V. Large-amplitude motion in 1,4-cyclohexadiene and 1,4-dioxin: theoretical background for joint treatment of spectroscopic, electron diffraction and ab initio data. J Mol Struct 2002. [DOI: 10.1016/s0022-2860(01)00914-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Dakkouri M, Kochikov I, Tarasov Y, Vogt N, Vogt J, Bitschenauer R. Equilibrium structure and large amplitude motion investigation of 1,4-disilacyclohexa-2,5-diene by means of electron diffraction, vibrational spectroscopic data, and ab initio calculations. J Mol Struct 2002. [DOI: 10.1016/s0022-2860(01)00915-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Kochikov I, Tarasov Y, Spiridonov V, Kuramshina G, Rankin D, Saakjan A, Yagola A. The equilibrium structure of thiophene by the combined use of electron diffraction, vibrational spectroscopy and microwave spectroscopy guided by theoretical calculations. J Mol Struct 2001. [DOI: 10.1016/s0022-2860(01)00539-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Kochikov I, Tarasov Y, Spiridonov V, Kuramshina G, Saakjan A, Yagola A. The use of ab initio anharmonic force fields in experimental studies of equilibrium molecular geometry. J Mol Struct 2000. [DOI: 10.1016/s0022-2860(00)00504-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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