Vladimir V. Zhurov

Optimization and evaluation of data quality for charge density studies

Criteria for the evaluation of hardware and software for the collection of charge density diffraction data are presented with examples. Evaluation of charge density studies using area detectors (based on 61 data sets) indicates that, although it is possible to obtain excellent data using such detectors, there are significant shortcomings which need to be addressed.

Importance of the consideration of anharmonic motion in charge‐density studies: a comparison of variable‐temperature studies on two explosives, RDX and HMX

Extremely accurate X-ray data were obtained for the explosive RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) at three different temperatures (20, 120 and 298 K). Collected reflections were integrated using the latest version of the program VIIPP which uses separate Kα(1)/Kα(2) contributions to the profile fitting during integration. For each temperature both anharmonic and harmonic descriptions of the atomic thermal motion were utilized in the model refinements along with the multipole expansion of the electron density. H atoms were refined anisotropically and agree well with a previous neutron study. Topological analysis [Bader (1990). Atoms in Molecules: A Quantum Theory. The International Series of Monographs of Chemistry, edited by J. Halpern & M. L. H. Green. Oxford: Clarendon Press] of the attained electron density followed. For 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane (HMX), old data collected at 20 and 120 K were re-integrated with the new version of VIIPP and refined in the same manner as for RDX. In both cases theoretical structure factors were also calculated based on the 20 K structures, and employed in comparison multipole refinements for the atoms at rest. Limiting the refinement to a harmonic model of the atomic displacements may result in a biased and erroneous electron density, especially when atomic vibrations are significant (as in RDX) and at temperatures higher than obtained by using liquid helium. Given the similarity of the two compounds the effects of anharmonic motion are strikingly more severe in the case of RDX. Our study reinforces the conclusion of Meindl et al. [Acta Cryst. (2010), A66, 362-371] that in certain cases it is necessary to include anharmonic term(s) of the probability density function (or temperature factor) in order to obtain a meaningful electron density suitable for topological analysis, even for compact (high-density) light-atom structures. For RDX it was observed that the oxygen lone-pair concentrations of electrons are located close to perpendicular to the N-O bond vectors, which is typical for explosive materials. Conjugation of the electron density in the -N-NO(2) fragment has been established based on the topological bond orders. Nine moderately strong hydrogen bonds and nine N-N, O-N and O-O bonding interactions were found and described. The RDX molecular electronic energy per mole is 4.02-4.04 a.u., very close to the reported value for HMX.

Charge transfer vibronic transitions in uranyl tetrachloride compounds

The electronic and vibronic interactions of uranyl (UO(2))(2+) in three tetrachloride crystals have been investigated with spectroscopic experiments and theoretical modeling. Analysis and simulation of the absorption and photoluminescence spectra have resulted in a quantitative understanding of the charge transfer vibronic transitions of uranyl in the crystals. The spectra obtained at liquid helium temperature consist of extremely narrow zero-phonon lines (ZPL) and vibronic bands. The observed ZPLs are assigned to the first group of the excited states formed by electronic excitation from the 3σ ground state into the f(δ,ϕ) orbitals of uranyl. The Huang-Rhys theory of vibronic coupling is modified successfully for simulating both the absorption and luminescence spectra. It is shown that only vibronic coupling to the axially symmetric stretching mode is Franck-Condon allowed, whereas other modes are involved through coupling with the symmetric stretching mode. The energies of electronic transitions, vibration frequencies of various local modes, and changes in the O═U═O bond length of uranyl in different electronic states and in different coordination geometries are evaluated in empirical simulations of the optical spectra. Multiple uranyl sites derived from the resolution of a superlattice at low temperature are resolved by crystallographic characterization and time- and energy-resolved spectroscopic studies. The present empirical simulation provides insights into fundamental understanding of uranyl electronic interactions and is useful for quantitative characterization of uranyl coordination.

Characterization of bonding in cesium uranyl chloride: topological analysis of the experimental charge density.

The topological analysis of the charge density distribution in Cs(2)UO(2)Cl(4) obtained from an accurate X-ray diffraction experiment at 20K is reported. Details of the techniques applied during data collection and data refinement are discussed. A split Hansen-Coppens multipole model for uranium and cesium atoms has been used to describe the charge density features associated with valence electrons and core deformations. The analysis of the deformation density distribution, QTAIM space partitioning, the Laplacian of the electron density, and electron localization function are discussed. Local QTAIM descriptors for bonds to uranium and cesium are reported, as well as integrated properties of each individual atom. U(5f), U(6s), U(6p), U(6d), and U(7s) shells were required to describe the aspherical charge density of the uranium pseudoatom. Observed deformation of the cesium atom core was described by applying the multipole model to Cs(5s) and Cs(5p) shells.

Molecular and crystal properties of ethyl 4,6‐dimethyl‐2‐thioxo‐1,2,3,4‐tetrahydropyrimidine‐5‐carboxylate from experimental and theoretical electron densities

The electron density and electronic energy densities in ethyl 4,6-dimethyl-2-thioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate have been studied from accurate X-ray diffraction measurements at 110 K and theoretical single-molecule and periodic crystal calculations. The Quantum Theory of Atoms in Molecules and Crystals (QTAMC) was applied to analyze the electron-density and electronic energy-density features to estimate their reproducibility in molecules and crystals. It was found that the local electron-density values at the bond critical points derived by different methods are in reasonable agreement, while the Laplacian of the electron density computed from wavefunctions, and electron densities derived from experimental or theoretical structure factors in terms of the Hansen-Coppens multipole model differ significantly. This disagreement results from insufficient flexibility of the multipole model to describe the longitudinal electron-density curvature in the case of shared atomic interactions. This deficiency runs through all the existing QTAMC bonding descriptors which contain the Laplacian term. The integrated atomic characteristics, however, suffer noticeably less from the aforementioned shortcoming. We conclude that the electron-density and electronic energy QTAMC characteristics derived from wavefunctions, especially the integrated quantities, are nowadays the most suitable candidates for analysis of the transferability of atoms and atomic groups in similar compounds.

Chemical Bonding in Cesium Uranyl Chloride Based on the Experimental Electron Density Distribution

Details of the electron density distribution in Cs(2)UO(2)Cl(4) have been obtained from an accurate X-ray diffraction experiment at 20 K. The electron density was described with the Hansen-Coppens multipole model. Topological analysis of the electron density confirms that the U-O bond is probably a triple bond, the U-Cl bonds are incipient covalent interactions, and the Cs-Cl and Cs-O interactions are of the closed-shell type. The results obtained serve as a proof of principle that electron density features related to chemical bonding may be obtained from X-ray data for even the heaviest elements.

Inter- and Intramolecular Interactions in Crystalline 2-Nitrobenzoic Acid—An Experimental and Theoretical QTAIM Analysis

We have quantified the inter- and intramolecular interactions in crystalline 2-nitrobenzoic acid from QTAIM analysis of the topology of the electron density distribution obtained from both a low temperature (20 K) X-ray diffraction experiment and from theoretical calculations. The covalent bonds have been characterized by the properties at their (3,-1) bond critical points; in particular the nature of the aromatic/nitro group C-N bond is discussed. All noncovalent bonds of the type O···H (both strong and weak), C···C, O···O, and O···C have also been characterized. Intermolecular interactions may be roughly divided into three types, the formation of a classical carboxylic acid hydrogen bonded dimer, an unusual ribbon of O···O interactions parallel to a, and a number of predominantly O···H interactions perpendicular to a. Integrated atomic charges (in particular for the acidic hydrogen, ∼+0.6) and the derived molecular dipole moment are reported.

17α-Estradiol·1/2 H2O: Super-Structural Ordering, Electronic Properties, Chemical Bonding, and Biological Activity in Comparison with Other Estrogens

The biological function of steroidal estrogens is related to their electronic properties. An experimental charge density study has been carried out on 17alpha-estradiol and compared to similar studies on more potent estrogens. High accuracy X-ray data were measured with a Rigaku rotating anode diffractometer equipped with an R-Axis Rapid curved image plate detector at 20 K. The total electron density in the 17alpha-estradiol x 1/2 H(2)O crystal was modeled using the Hansen-Coppens multipole model. Topological analysis of the electron density based on Baders QTAIM theory was performed. The crystal structure, chemical bonding, and molecular properties, including the electrostatic potential (ESP), are reported and discussed. Observed disordering of hydroxyl and water hydrogen atom positions are interpreted as a superstructural ordering in a lower symmetry space group. The ESPs for the resulting four conformers are compared with each other and with that of 17beta-estradiol. The relative binding affinities are discussed in terms of the observed potentials.

Chemical Bonding and Structure−Reactivity Correlation in Meldrum’s Acid: A Combined Experimental and Theoretical Electron Density Study

Chemical bonding in Meldrums acid (MA) based on the experimental electron density obtained from high-resolution X-ray diffraction data at 20 K and from solid state theoretical calculations at the experimental molecular geometry have been analyzed by using the Quantum Theory of Atoms in Molecules. The total electron density was modeled with use of the Hansen-Coppens multipole formalism, and features associated with both intra- and intermolecular bond critical points, topological bond orders, atomic charges, and the electrostatic potential have been characterized and used to understand structure-reactivity relationships. The acidic methylene hydrogen atoms carry modest positive charges. A notable feature is the presence of an intramolecular H...H interaction that imparts stability to the boat conformation. A correlation between the topological bond order and the nature of the chemical bonds in MA illustrates the fact that elimination of carbon dioxide/acetone is an important feature of the chemistry of MA. The surface electrostatic potential and the charge distribution rationalize the sites of nucleophilic/electrophilic attack.

Electron density study of KNiF3 by the vacuum-camera-imaging plate method.

The electron density measurements of KNiF(3), nickel potassium trifluoride, by the vacuum-camera-imaging plate (VCIP) method and using a four-circle diffractometer with scintillation counter, are performed and compared. In the IP (imaging plate) case evacuation allowed the background around peaks to be reduced 50 times, which significantly increased the accuracy of the data, especially for high-angle reflections. A new VIIPP program for visualizing and integration of IP data was designed to treat the data, in which the correction for oblique incidence was applied. The resulting electron density reproduces all the features of the accurate conventional measurement.