Molecular Structure of Pyrazinamide: A Critical Assessment of Modern Gas Electron Diffraction Data from Three Laboratories

Otlyotov AA, Girichev, Georgiy V, Rykov AN, Glodde T, Vishnevskiy Y. Molecular Structure of Pyrazinamide: A Critical Assessment of Modern Gas Electron Diffraction Data from Three Laboratories. JOURNAL OF PHYSICAL CHEMISTRY A. 2020;124(25):5204-5211.Accuracy and precision of molecular parameters determined by modern gas electron diffraction have been investigated. Diffraction patterns of gaseous pyrazinamide have been measured independently in three laboratories, in Bielefeld (Germany), Ivanovo (Russia), and Moscow (Russia). All data sets have been analyzed in equal manner using a highly controlled background elimination procedure and flexible restraints in molecular structure refinement. In detailed examination and comparison of the obtained results we have determined the average experimental precision of 0.004 angstrom for bond lengths and 0.2 degrees for angles. The corresponding average deviations of the refined parameters from the ae-CCSD(T)/cc-pwCVTZ theoretical values were 0.003 angstrom and 0.2 degrees. The average precision for refined amplitudes of interatomic vibrations was determined to be 0.005 angstrom. It is recommended to take into account these values in calculations of total errors for refined parameters of other molecules with comparable complexity

Molecular Structure of Pyrazinamide: a Critical Assessment of Modern Gas Electron Diffraction Data from Three Laboratories

Accuracy and precision of molecular parameters determined by modern gas electron diffraction methodhave been investigated. Diffraction patterns of gaseous pyrazinamide have been measured independently in three laboratories, in Bielefeld (Germany), Ivanovo (Russia) and Moscow (Russia). All data sets have been analysed in equal manner using highly controlled background elimination procedure and flexible restraints in molecular structure refinement. In detailed examination and comparison of the obtained results we have determined the average experimental precision of 0.004 Å for bond lengths and 0.2 degrees for angles. The corresponding average deviations of the refined parameters from the ae-CCSD(T)/ccpwCVTZ theoretical values were 0.003 Å and 0.2 degrees. The average precision for refined amplitudes of interatomic vibrations was determined to be 0.005 Å. It is recommended to take into account these values in calculations of total errors for refined parameters of other molecules with comparable complexity.</div

Semi-experimental equilibrium structure of pyrazinamide from gas-phase electron diffraction. How much experimental is it?

Tikhonov DS, Vishnevskiy Y, Rykov AN, Grikina OE, Khaikin LS. Semi-experimental equilibrium structure of pyrazinamide from gas-phase electron diffraction. How much experimental is it? JOURNAL OF MOLECULAR STRUCTURE. 2017;1132:20-27.A semi-experimental equilibrium structure of free molecules of pyrazinamide has been determined for the first time using gas electron diffraction method. The refinement was carried using regularization of geometry by calculated quantum chemical parameters. It is discussed to which extent is the final structure experimental. A numerical approach for estimation of the amount of experimental information in the refined parameters is suggested. The following values of selected internuclear distances were determined (values are in angstrom with 1 sigma in the parentheses): r(e)(C-pyrazine-C-pyrazine)(av) = 1.397(2), r(e)(N-pyrazine-C-pyrazine)(av) = 1.332(3), r(e)(C-pyrazine-C-amide) = 1.493(1), r(e)(N-amide-C-amide) = 1.335(2), r(e)(O-amide-C-amide) = 1.219(1). The given standard deviations represent pure experimental uncertainties without the influence of regularization. (C) 2016 Elsevier B.V. All rights reserved

Molecular Structure of 1,5-Diazabicyclo[3.1.0]hexane as Determined by Gas Electron Diffraction and Quantum-Chemical Calculations

Vishnevskiy YV, Vogt N, Vogt J, et al. Molecular Structure of 1,5-Diazabicyclo[3.1.0]hexane as Determined by Gas Electron Diffraction and Quantum-Chemical Calculations. The Journal of Physical Chemistry A. 2008;112(23):5243-5250.The equilibrium molecular structure and conformation of 1,5-diazabicyclo[3.1.0]hexane (DABH) has been studied by the gas-phase electron-diffraction method at 20 °C and quantum-chemical calculations. Three possible conformations of DABH were considered: boat, chair, and twist. According to the experimental and theoretical results, DABH exists exclusively as a boat conformation of Cs symmetry at the temperature of the experiment. The MP2 calculations predict the stable chair and twist conformations to be 3.8 and 49.5 kcal mol−1 above the boat form, respectively. The most important semi-experimental geometrical parameters of DABH (re, Å and ∠e, deg) are (N1−N5) = 1.506(13), (N1−C6) = 1.442(2), (N1−C2) = 1.469(4), (C2−C3) = 1.524(7), (C6−N1−C2) = 114.8(8), (N5−N1−C2) = 107.7(4), (N1−C2−C3) = 106.5(9), and (C2−C3−C4) = 104.0(10). The natural bond orbital (NBO) analysis has shown that the most important stabilization factor in the boat conformation is the n(N) → σ*(C−C) anomeric effect. The geometry calculations and NBO analysis have been performed also for the bicyclohexane molecule

Conformational and Bonding Properties of 3,3-Dimethyl- and 6,6-Dimethyl-1,5-diazabicyclo[3.1.0]hexane: A Case Study Employing the Monte Carlo Method in Gas Electron Diffraction

Gas-phase structures of two isomers of dimethyl-substituted 1,5-diazabicyclo[3.1.0]­hexanes, namely, 3,3-dimethyl- and 6,6-dimethyl-1,5-diazabicyclo[3.1.0]­hexane molecules, have been determined by gas electron diffraction method. A new approach based on the Monte Carlo method has been developed and used for the analysis of precision and accuracy of the refined structures. It was found that at 57 °C 3,3-dimethyl derivative exists as a mixture of chair and boat conformers with abundances 68(8)% and 32(8)%, respectively. 6,6-Dimethyl-1,5-diazabicyclo[3.1.0]­hexane at 50 °C has only one stable conformation with planar 5-ring within error limits. Theoretical calculations predict that the 6,6-dimethyl isomer is more stable in comparison to the 3,3-dimethyl isomer with energy difference 3–5 kcal mol^–1. In order to explain the relative stability and bonding properties of different structures the natural bond orbitals (NBO), atoms in molecules (AIM), and interacting quantum atoms (IQA) analyses were performed

Molecular structure, conformation, potential to internal rotation, and ideal gas thermodynamic properties of 3-fluoroanisole and 3,5-difluoroanisole as studied by gas-phase electron diffraction and quantum chemical calculations

Dorofeeva OV, Vishnevskiy YV, Rykov AN, et al. Molecular structure, conformation, potential to internal rotation, and ideal gas thermodynamic properties of 3-fluoroanisole and 3,5-difluoroanisole as studied by gas-phase electron diffraction and quantum chemical calculations. Journal of Molecular Structure. 2006;789(1-3):100-111

Structure and Bonding Nature of the Strained Lewis Acid 3-Methyl-1-boraadamantane: A Case Study Employing a New Data-Analysis Procedure in Gas Electron Diffraction

Vishnevskiy Y, Abaev MA, Rykov AN, et al. Structure and Bonding Nature of the Strained Lewis Acid 3-Methyl-1-boraadamantane: A Case Study Employing a New Data-Analysis Procedure in Gas Electron Diffraction. Chemistry. 2012;18(34):10585-10594.Base-free 3-methyl-1-boraadamantane was synthesized by starting from its known THF adduct, transforming it to a butylate-complex with n-butyllithium, cleaving the cage with acetyl chloride to give 3-n-butyl-5-methyl-7-methylene-3-borabicyclo[3.3.1]nonane and closing the cage again by reacting the latter with dicyclohexylborane. The identity of 3-methyl-1-boraadamantane was proven by 1H, 11B and 13C NMR spectroscopy and elemental analysis. The experimental equilibrium structure of the free 3-methyl-1-boraadamantane molecules has been determined at 100 degrees C by using gas-phase electron diffraction. For this structure determination, an improved method for data analysis has been introduced and tested: the structural refinement versus gas-phase electron diffraction data (in terms of Cartesian coordinates) with a set of quantum-chemically derived regularization constraints for the complete structure under optimization of a regularization constant, which maximizes the contribution of experimental data while retaining a stable refinement. The detailed analysis of parameter errors shows that the new approach allows obtaining more reliable results. The most important structural parameters are: re(B-C)av=1.556(5) angstrom, ${\angle }$e(C-B-C)av=116.5(2)degrees. The configuration of the boron atom is pyramidal with ${\sum \angle }$(C-B-C)=349.4(4)degrees. The nature of bonding was analyzed further by applying the natural bond orbital (NBO) and atoms in molecules (AIM) approaches. The experimentally observed shortening of the B?C bonds and elongation of the adjacent C?C bonds can be explained by the s(C-C)?p(B) hyperconjugation model. Both NBO and AIM analyses predict that the B?C bonds are significantly bent in the direction out of the cage

Nitroxoline Molecule: Planar or Not? A Story of Battle between π–π Conjugation and Interatomic Repulsion

The conformational properties of the nitro group in nitroxoline (8-hydroxy-5-nitroquinoline, NXN) were investigated in the gas phase by means of gas electron diffraction (GED) and quantum chemical calculations, and also with solid-state analysis performed using terahertz time-domain spectroscopy (THz-TDS). The results of the GED refinement show that in the equilibrium structure the NO₂ group is twisted by angle ϕ = 8 ± 3° with respect to the 8-hydroxyoquinoline plane. This is the result of interatomic repulsion of oxygen in the NO₂ group from the closest hydrogen, which overcomes the energy gain from the π–π conjugation of the nitro group and aromatic system of 8-hydroxyoquinoline. The computation of equilibrium geometry using MP2/cc-pVXZ (X = T, Q) shows a large overestimation of the ϕ value, while DFT with the cc-pVTZ basis set performs reasonably well. On the other hand, DFT computations with double-ζ basis sets yield a planar structure of NXN. The refined potential energy surface of the torsion vibration the of nitro group in the condensed phase derived from the THz-TDS data indicates the NXN molecule to be planar. This result stays in good agreement with the previous X-ray structure determination. The strength of the π-system conjugation for the NO₂ group and 8-hydroxyoquinoline is discussed using NBO analysis, being further supported by comparison of the refined semiexperimental gas-phase structure of NXN from GED with other nitrocompounds