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

DFT Study of Molecular and Electronic Structure of Ca(II) and Zn(II) Complexes with Porphyrazine and tetrakis(1,2,5-thiadiazole)porphyrazine

Electronic and geometric structures of Ca(II) and Zn(II) complexes with porphyrazine (Pz) and tetrakis(1,2,5-thiadiazole)porphyrazine (TTDPz) were investigated by density functional theory (DFT) calculations and compared. The perimeter of the coordination cavity was found to be practically independent on the nature of a metal and a ligand. According to the results of the natural bond orbital (NBO) analysis and quantum theory of atoms in molecules (QTAIM) calculations, Ca–N bonds possess larger ionic contributions as compared to Zn–N. The model electronic absorption spectra obtained with the use of time-dependent density functional theory (TDDFT) calculations indicate a strong bathochromic shift (~70 nm) of the Q-band with a change of Pz ligand by TTDPz for both Ca and Zn complexes. Additionally, CaTTDPz was synthesized and its electronic absorption spectrum was recorded in pyridine and acetone

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

DFT Study of the Molecular and Electronic Structure of Metal-Free Tetrabenzoporphyrin and Its Metal Complexes with Zn, Cd, Al, Ga, In

The electronic and molecular structures of metal-free tetrabenzoporphyrin (H2TBP) and its complexes with zinc, cadmium, aluminum, gallium and indium were investigated by density functional theory (DFT) calculations with a def2-TZVP basis set. A geometrical structure of ZnTBP and CdTBP was found to possess D4h symmetry; AlClTBP, GaClTBP and InClTBP were non-planar complexes with C4v symmetry. The molecular structure of H2TBP belonged to the point symmetry group of D2h. According to the results of the natural bond orbital (NBO) analysis, the M-N bonds had a substantial ionic character in the cases of the Zn(II) and Cd(II) complexes, with a noticeably increased covalent contribution for Al(III), Ga(III) and In(III) complexes with an axial &ndash;Cl ligand. The lowest excited states were computed with the use of time-dependent density functional theory (TDDFT) calculations. The model electronic absorption spectra indicated a weak influence of the nature of the metal on the Q-band position

Iron(II) Complexes with Porphyrin and Tetrabenzoporphyrin: CASSCF/MCQDPT2 Study of the Electronic Structures and UV–Vis Spectra by sTD-DFT

The geometry and electronic structures of iron(II) complexes with porphyrin (FeP) and tetrabenzoporphyrin (FeTBP) in ground and low-lying excited electronic states are determined by DFT (PBE0/def2-TZVP) calculations and the complete active space self-consistent field (CASSCF) method, followed by the multiconfigurational quasi-degenerate second-order perturbation theory (MCQDPT2) approach to determine the dynamic electron correlation. The minima on the potential energy surfaces (PESs) of the ground (3A2g) and low-lying, high-spin (5A1g) electronic states correspond to the planar structures of FeP and FeTBP with D4h symmetry. According to the results of the MCQDPT2 calculations, the wave functions of the 3A2g and 5A1g electronic states are single determinant. The electronic absorption (UV–Vis) spectra of FeP and FeTBP are simulated within the framework of the simplified time-dependent density functional theory (sTDDFT) approach with the use of the long-range corrected CAM-B3LYP function. The most intensive bands of the UV–Vis spectra of FeP and FeTBP occur in the Soret near-UV region of 370–390 nm

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

Accurate single crystal and gas-phase molecular structures of acenaphthene: a starting point in the search for the longest C–C bond

Vishnevskiy Y, Otlyotov AA, Lamm J-H, Stammler H-G, Girichev GV, Mitzel NW. Accurate single crystal and gas-phase molecular structures of acenaphthene: a starting point in the search for the longest C–C bond. Physical Chemistry Chemical Physics. 2023.The molecular structure of acenaphthene has been determined experimentally in the gas phase using gas electron diffraction intensities and literature-available rotational constants. Supplementary high-level quantum-chemical calculations were utilized in refinements of the semi-empirical equilibrium structure. In this work we investigate on how different schemes of GED data averaging and weighting can be used for obtaining the most accurate and precise structural parameters. Single-crystal X-ray diffraction experiments at different temperatures have been performed and the solid-state structure of acenaphthene has been determined. Both gas and solid-state acenaphthene molecules are planar and possess a non-twisted ethylene bridge. The aliphatic C–C bond in the ethylene fragment is elongated to 1.560(4) Å in the gas phase and 1.5640(4) Å in the solid phase. Based on the experimental data several theoretical approximations have been calibrated and predictions for other molecules were made, taking into account dispersion and electrostatic interactions. Particular derivatives of acenaphthene may potentially have significantly elongated C–C bonds up to 1.725 Å. However, among the experimental gas-phase structures available to date probably the longest C–C bond (re,(av)= 1.750(28) Å atw= 0.93) was determined in a carbaborane derivative 1,2-(SeH)2-closo-1,2-C2B10H10

Molecular Structure of Nickel Octamethylporphyrin&mdash;Rare Experimental Evidence of a Ruffling Effect in Gas Phase

The structure of a free nickel (II) octamethylporphyrin (NiOMP) molecule was determined for the first time through a combined gas-phase electron diffraction (GED) and mass spectrometry (MS) experiment, as well as through quantum chemical (QC) calculations. Density functional theory (DFT) calculations do not provide an unambiguous answer about the planarity or non-planar distortion of the NiOMP skeleton. The GED refinement in such cases is non-trivial. Several approaches to the inverse problem solution were used. The obtained results allow us to argue that the ruffling effect is manifested in the NiOMP molecule. The minimal critical distance between the central atom of the metal and nitrogen atoms of the coordination cavity that provokes ruffling distortion in metal porphyrins is about 1.96 &Aring;

1,8-Bis(phenylethynyl)anthracene - gas and solid phase structures

Lamm J-H, Horstmann J, Stammler H-G, et al. 1,8-Bis(phenylethynyl)anthracene - gas and solid phase structures. Organic &amp; Biomolecular Chemistry. 2015;13(33):8893-8905.1,8-Bis(phenylethynyl) anthracene (1,8-BPEA) was synthesized by a twofold Kumada cross-coupling reaction. The molecular structure of 1,8-BPEA was determined using a combination of gas-phase electron diffraction (GED), mass spectrometry (MS), quantum chemical calculations (QC) and single-crystal X-ray diffraction (XRD). Five rotamers of the molecule with different orientations of phenylethynyl groups were investigated by DFT calculations. According to these, molecules of C-2 symmetry with co-directional rotation of the phenylethynyl groups are predicted to exist in the gas phase at 498 K. This was confirmed by a GED/MS experiment at this temperature. The bonding of this conformer was studied and described in terms of an NBO-analysis. Dispersion interactions in the solid state structure and in the free molecule are discussed. In the solid this symmetry is broken; the asymmetric unit of the single crystal contains 3.5 molecules and a herringbone packing motif of pi-stacked dimers and trimers. The pi-stacking in the dimers is between the anthracene units, and the trimers are linked by pi-stacking between phenyl and anthracene units. The interaction between these stacks can be described in terms of sigma(C-H)center dot center dot center dot pi interactions

Gas-phase structure of 1,8-bis[(trimethylsilyl)ethynyl]anthracene: cog-wheel-type vs. independent internal rotation and influence of dispersion interactions

Otlyotov AA, Lamm J-H, Blomeyer S, et al. Gas-phase structure of 1,8-bis[(trimethylsilyl)ethynyl]anthracene: cog-wheel-type vs. independent internal rotation and influence of dispersion interactions. PHYSICAL CHEMISTRY CHEMICAL PHYSICS. 2017;19(20):13093-13100.The gas-phase structure of 1,8-bis[(trimethylsilyl) ethynyl]anthracene (1,8-BTMSA) was determined by a combined gas electron diffraction (GED)/mass spectrometry (MS) experiment as well as by quantum-chemical calculations (QC). DFT and dispersion corrected DFT calculations (DFT-D3) predicted two slightly different structures for 1,8-BTMSA concerning the mutual orientation of the two -C-C C-SiMe3 units: away from one another or both bent to the same side. An attempt was made to distinguish these structures by GED structural analysis. To probe the structural rigidity, a set of Born-Oppenheimer molecular dynamics (BOMD) calculations has been performed at the DFT-D level. Vibrational corrections Delta r = r(a) - r(e) were calculated by two BOMD approaches: a microcanonically (NVE) sampled ensemble of 20 trajectories (BOMD(NVE)) and a canonical (NVT) trajectory thermostated by the Noose-Hoover algorithm (BOMD(NVT)). In addition, the conventional approach with both, rectilinear and curvilinear approximations (SHRINK program), was also applied. Radial distribution curves obtained with models using both MD approaches provide a better description of the experimental data than those obtained using the rectilinear (SHRINK) approximation, while the curvilinear approach turned out to lead to physically inacceptable results. The electronic structure of 1,8-BTMSA was investigated in terms of an NBO analysis and was compared with that of the earlier studied 1,8-bis(phenylethynyl) anthracene. Theoretical and experimental results lead to the conclusion that the (trimethylsilyl) ethynyl (TMSE) groups in 1,8-BTMSA are neither restricted in rotation nor in bending at the temperature of the GED experiment