Denis S. Tikhonov

Analysis of electron diffraction data for several symmetric coordinates of large-amplitude motions in the case of the 1,3,5-trinitrobenzene molecule

A brief description of a solution of the problem on electron diffraction analysis using the potential procedure for nonrigid molecules with large-amplitude motions along several symmetric internal coordinates was given. The efficiency of the approach was demonstrated for determination of the equilibrium geometry of the 1,3,5-trinitrobenzene molecule with three equivalent internal rotation coordinates of NO2 groups. The results of the electron diffraction experiment and quantum-chemical calculation at the MP2(full)/cc-pVTZ level were considered along with the vibrational spectra of 1,3,5-trinitrobenzene and a planar equilibrium D3hsymmetry conformation for the molecule was found reliably for the first time. The geometrical parameters of the molecule were determined (re, the bond lengths are given in Å, the angles in deg): CC 1.387(2), CN 1.474(4), NO 1.220(1), CH 1.072(31), ONO 125.8(2), CC(H)C 116.6(3), HCC* 121.7(1), CC(N)C* 123.4(3), NCC* 118.3(1), and CNO* 117.1(1); the asterisk marks the dependent parameters.

Influence of Antipodally Coupled Iodine and Carbon Atoms on the Cage Structure of 9,12-I2-closo-1,2-C2B10H10: An Electron Diffraction and Computational Study

Because of the comparable electron scattering abilities of carbon and boron, the electron diffraction structure of the C2v-symmetric molecule closo-1,2-C2B10H12 (1), one of the building blocks of boron cluster chemistry, is not as accurate as it could be. On that basis, we have prepared the known diiodo derivative of 1, 9,12-I2-closo-1,2-C2B10H10 (2), which has the same point-group symmetry as 1 but in which the presence of iodine atoms, with their much stronger ability to scatter electrons, ensures much better structural characterization of the C2B10 icosahedral core. Furthermore, the influence on the C2B10 geometry in 2 of the antipodally positioned iodine substituents with respect to both carbon atoms has been examined using the concerted application of gas electron diffraction and quantum chemical calculations at the MP2 and density functional theory (DFT) levels. The experimental and computed molecular geometries are in good overall agreement. Molecular dynamics simulations used to obtain vibrational parameters, which are needed for analyzing the electron diffraction data, have been performed for the first time for this class of compound. According to DFT calculations at the ZORA-SO/BP86 level, the (11)B chemical shifts of the boron atoms to which the iodine substituents are bonded are dominated by spin-orbit coupling. Magnetically induced currents within 2 have been calculated and compared to those for [B12H12](2-), the latter adopting a regular icosahedral structure with Ih point-group symmetry. Similar total current strengths are found but with a certain anisotropy, suggesting that spherical aromaticity is present; electron delocalization in the plane of the hetero atoms in 2 is slightly hindered compared to that for [B12H12](2-), presumably because of the departure from ideal icosahedral symmetry.

Quantum corrections to parameters of interatomic distance distributions in molecular dynamics simulations

The problem of computation of interatomic distance distributions is considered in the context of gas electron diffraction method. A new theoretical approach has been developed for calculation of mean square amplitudes, corrections for interatomic distances and asymmetry parameters on the basis of ab initio molecular dynamics simulations with a posteriori quantum corrections. Several approximations have been evolved, and corresponding algorithms have been coded. Their testing has been performed by calculation of parameters for a set of diatomic molecules, ethane and 9,12-I2-1,2-dicarba-closo-dodecaborane. Comparison of the obtained amplitudes and distance corrections with those calculated by conventional methods demonstrates the superiority of the new approach. By contrast, asymmetry parameters remain numerically unstable after introduction quantum corrections. The best of the assessed approximations, termed MDC(5), is recommended for routine application to large molecules with small-amplitude vibrations.

Application of classical simulations for the computation of vibrational properties of free molecules

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.

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.

Tetranitromethane: A Nightmare of Molecular Flexibility in the Gaseous and Solid States.

After numerous attempts over the last seven decades to obtain a structure for the simple, highly symmetric molecule tetranitromethane (C(NO2 )4 , TNM) that is consistent with results from diffraction experiments and spectroscopic analysis, the structure has now been determined in the gas phase and the solid state. For the gas phase, a new approach based on a four-dimensional dynamic model for describing the correlated torsional dynamics of the four C-NO2 units was necessary to describe the experimental gas-phase electron diffraction intensities. A model describing a highly disordered high-temperature crystalline phase was also established, and the structure of an ordered low-temperature phase was determined by X-ray diffraction. TNM is a prime example of molecular flexibility, bringing structural methods to the limits of their applicability.

Simple posterior frequency correction for vibrational spectra from molecular dynamics

Vibrational spectra computed from molecular dynamics simulations with large integration time steps suffer from nonphysical frequency shifts of signals [M. Praprotnik and D. Janežič, J. Chem. Phys. 122, 174103 (2005)]. A simple posterior correction technique was developed for compensation of this behavior. It performs through replacement of abscissa in the calculated spectra using following formula: νcorrected=2⋅1-cos(2π⋅Δt⋅νinitial)2π⋅Δt, where ν are initial and corrected frequencies and Δt is the MD simulation time step. Applicability of this method was tested on gaseous infrared spectra of hydrogen fluoride and formic acid.

Planar aromaticity of DNh-symmetrical systems as a perturbed two-dimensional (2D) rigid rotor

Energy levels for DNh-symmetrical cyclic polyenes with planar aromaticity were obtained using two-dimensional (2D) rigid rotor as the zeroth approximation. The addition of nuclei was simulated by the cosine-type potential and treated at the first-order perturbation theory. The result is qualitatively equivalent to that obtained using Hückel’s molecular orbital theory. As an addition, the energetic shift between σ and π orbitals is obtained using the model of electron oscillating around the center of a positively charged ring.

Quantum-chemical calculations and electron diffraction study of the equilibrium molecular structure of vitamin K3

The equilibrium molecular structure of 2-methyl-1,4-naphthoquinone (vitamin K3) having Cs symmetry is experimentally characterized for the first time by means of gas-phase electron diffraction using quantum-chemical calculations and data on the vibrational spectra of related compounds.