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

The gas-phase structure of octaphenyloctasilsesquioxane Si₈O₁₂Ph₈ and the crystal structures of Si₈O₁₂(<em>p</em>-tolyl)₈ and Si₈O₁₂(<em>p</em>-ClCH₂C₆H₄)₈

The equilibrium molecular structure of octaphenyloctasilsesquioxane Si8O12Ph8 in the gas phase has been determined by electron diffraction. It was found to have D4 point-group symmetry, with Si–O bond lengths of 1.634(15)–1.645(19) Å, and a narrow range [147.5(45)–149.8(24)°] of Si–O–Si angles. The structures of Si8O12(p-tolyl)8 and Si8O12(p-ClCH2C6H4)8 have been determined by X-ray diffraction and are found to have Si8O12 cages significantly distorted from the symmetry found for Si8O12Ph8 in the gas phase. Thus, Si–O–Si angles range between 144.2(2)–151.64(16)° for Si8O12(p-tolyl)8, and between 138.8(2)–164.2(2)° for Si8O12(p-ClCH2C6H4)8. These three structures show how much a Si8O12 cage may be distorted away from an ideal structure, free from intermolecular forces, by packing forces in a crystalline lattice.</p

Cyclic Dimers of 4-n-Propyloxybenzoic Acid with Hydrogen Bonds in the Gaseous State

A comprehensive study of saturated vapors of 4-n-propyloxybenzoic acid (POBA) by gas electron diffraction (GED) and mass spectrometric (MS) methods supplemented by quantum chemical (QC) calculations was carried out for the first time. An attempt was made to detect dimeric forms of the acid in the gaseous state. It has been established that at the temperature of GED experiment, vapor over a solid sample contains up to 20 mol.% of cyclic dimers with two O-H...O hydrogen bonds. The main geometrical parameters of gaseous monomers and dimers of POBA are obtained. The distance r(O…O) = 2.574(12) Å in the cyclic fragment of the gaseous dimer is close to that in the crystal structure (2.611 Å). In the mass spectrum of the POBA recorded the ions of low intensity with a mass exceeding the molecular mass of the monomer were detected. The presence of ions, whose elemental composition corresponds to the dissociative ionization of the dimer, confirms the results of the GED experiment on the presence of POBA dimers in the gas state. The results of GED studies of acetic acid, benzoic acid, and POBA were compared. It is shown that the COOH fragment saves its geometric structure in monomers, as well as the COOH...HOOC fragment with two hydrogen bonds in dimers of different acids. The intermolecular interaction energy in considered acid dimers was estimated using QC calculations (B97D/6-311++G **). The significant value of last (>84 kJ/mol) is the reason for the noticeable presence of dimers in the gas phase

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

Tautomeric Properties and Gas-Phase Structure of Acetylacetone

The tautomeric and structural properties of acetylacetone, CH₃C­(O)­CH₂C­(O)­CH₃, have been studied by gas-phase electron diffraction (GED) and quantum chemical calculations (B3LYP and MP2 approximation with different basis sets up to aug-cc-pVTZ). The analysis of GED intensities resulted in the presence of 100(3)% of the enol tautomer at 300(5) K and 64(5)% of the enol at 671(7) K. The enol tautomer possesses <i>C</i>_<i>s</i> symmetry with a planar ring and strongly asymmetric hydrogen bond. The diketo form possesses <i>C</i>₂ symmetry. The experimental geometric parameters of both tautomeric forms are reproduced very closely by B3LYP/aug-cc-pVTZ and MP2/cc-pVTZ methods

Gas phase structures of potassium tetrakis(hexafluoroacetyl-ace-to-nato)-lanthanate(III) complexes [KLn(C5HF6O2)4] (Ln = La, Gd, Lu)

Girichev GV, Giricheva NI, Khochenkov AE, Sliznev VV, Belova NV, Mitzel NW. Gas phase structures of potassium tetrakis(hexafluoroacetyl-ace-to-nato)-lanthanate(III) complexes [KLn(C5HF6O2)4] (Ln = La, Gd, Lu). Chemistry - A European Journal. 2021;27(3):1103-1112.The molecular structures of potassium tetrakis(hexafluoro-acetylacetonato)lanthanate(III) complexes [KLn(hfa) 4 ] (Ln = La, Gd, Lu; hfa = C 5 HF 6 O 2 ,) were studied by synchronous gas-phase electron diffraction / mass spectrometry (GED/MS) supported by quantum-chemical (DFT/PBE0) calculations. The compounds sublimate congruently and the vapors contain single molecular species: the heterobinuclear complex [KLn(hfa) 4 ]. All molecules are of C 1 symmetry with the lanthanide atom in the center of a coordination polyhedron LnO 8 , while the potassium atom is coordinated by three ligands under formation of three K-O and three K-F bonds. Topological analysis of the electron density distributions confirms the existence of ionic-type K-O and K-F bonding. The presence of the potassium ion distorts the coordination polyhedron LnO 8 and takes influence on the structure of the ligands. The structures of the free [KLn(hfa) 4 ] molecules are compared with those of the related compounds [KDy(hfa) 4 ] and [KEr(hfa) 4 ] in their crystalline state. The complex nature of chemical bonding is discussed on the basis of electron density topology analyses. © 2020 Wiley-VCH GmbH

The Perfluoro-o-phenylene-mercury Trimer [Hg(o-C6F4)]3 - a Textbook Example of Phase-Dependent Structural Differences

Giricheva N, Tverdova NV, Otlyotov AA, Girichev GV, Lamm J-H, Mitzel NW. The Perfluoro-o-phenylene-mercury Trimer [Hg(o-C6F4)]3 - a Textbook Example of Phase-Dependent Structural Differences. Chemistry. 2024.The geometric and electronic structure of [Hg(o-C6F4)]3 (1) in the gas phase, i.e. free of intermolecular interactions, was deter-mined by a synchronous gas-phase electron diffraction/mass spec-trometry experiment (GED/MS), complemented by quantum chemi-cal calculations. 1 is stable up to 498 K and the gas phase contains a single molecular form: the trimer [Hg(o-C6F4)]3. It has a planar structure of D3h sym-metry with a Hg-C distance of 2.075(5) A and a Hg-Hg distance of 3.614(7) A (both rh1). Structural differences between the crystalline and gaseous state have been analyzed. Different DFT functio-nal-basis combi-na-tions were tested, demon-stra-ting the importance to consider the relativistic effects of the mercury atoms. The combi-na-tion PBE0/-MWB(Hg),cc-pVTZ(C,F) turned out to be the most appro-priate for the geometry optimization of such organomercurials. The elec-tronic structure of 1, the nature of the chemical bonding in C-Hg-C fragments and the nature of the Hg···Hg inter-actions have been analyzed in terms of the Natural Bond Orbital (NBO) and Quantum Theory of Atoms in Molecules (QTAIM) approaches. The influence of the nature of halogen substi-tution on the structure of the molecules in the series [Hg(o-C6H4)]3, [Hg(o-C6F4)]3, [Hg(o-C6Cl4)]3, [Hg(o-C6Br4)]3 was also analyzed. © 2024 Wiley‐VCH GmbH