Experimental Charge-Density Study of the Intra- and Intermolecular Bonding in TKX-50.

The intra- and intermolecular bonding in the known phase of dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate, TKX-50, has been analyzed on the basis of the experimentally determined charge density distribution from high-resolution X-ray diffraction data obtained at 20 K. This was compared to the charge density obtained from DFT calculations with periodic boundary conditions using both direct calculations and derived structure factors. Results of topological analysis of the electron density corroborate that TKX-50 is best described as a layered structure linked primarily by a number of hydrogen bonds as well as by a variety of other interactions. Additional bonding interactions were identified, including a pair of equivalent 1,5-type intramolecular closed-shell interactions in the dianion. Refinement of anharmonic motion was shown to be essential for obtaining an adequate model, despite the low temperature of the study. Although generally unusual, the implementation of anharmonic refinement provided a significant improvement compared to harmonic refinement of both traditional and split-core multipole models.

Charge Density and Electrostatic Potential Study of 16α,17ß-Estriol and the Binding of Estrogen Molecules to the Estrogen Receptors ERα and ERß.

An accurate X-ray diffraction study at 20 K combined with DFT theoretical calculations has been performed for the estriol crystal with two conformationally different molecules in the asymmetric unit. The electron density has been modeled via a multipole expansion, using both experimental and theoretical structure factors, and a topological analysis has been performed. The experimental molecular geometry, hydrogen bonding, atomic charges, dipole moments, and other topological characteristics are compared with those calculated theoretically. In particular, the molecular electrostatic potential has been extracted and compared with those reported for other estrogen molecules exhibiting different binding affinities to the estrogen receptors (ERα and ERß).

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.

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.

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.

17Alpha-estradiol x 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 Bader's 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 ESP's 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 Meldrum's 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.

Variable temperature neutron diffraction and X-ray charge density studies of tetraacetylethane.

Single crystal neutron diffraction data have been collected on a sample of enolized 3,4-diacetyl-2,5-hexanedione (tetraacetylethane, TAE) at five temperatures between 20 and 298 K to characterize the temperature-dependent behavior of the short, strong, intramolecular hydrogen bond. Upon decreasing the temperature from 298 K to 20 K, the O2-H1 distance decreases from 1.171(11) to 1.081(2) A and the O1...H1 distance increases from 1.327(10) to 1.416(6) A. The convergence of the C-O bond lengths from inequivalent distances at low temperature to identical values (1.285(4) A) at 298 K is consistent with a resonance-assisted hydrogen bond. However, a rigid bond analysis indicates that the structure at 298 K is disordered. The disorder vanishes at lower temperatures. Short intermolecular C-H...O contacts may be responsible for the ordering at low temperature. The intramolecular O...O distance (2.432 +/- 0.006 A) does not change with temperature. X-ray data at 20 K were measured to analyze the charge density and to gain additional insight into the nature of the strong hydrogen bond. Quantum mechanical calculations demonstrate that periodic boundary conditions provide significant enhancement over gas phase models in that superior agreement with the experimental structure is achieved when applying periodicity. One-dimensional potential energy calculations followed by quantum treatment of the proton reproduce the location of the proton nearer to the O2 site reasonably well, although they overestimate the O-H distance at low temperatures. The choice of the single-point energy calculation strategy for the proton potential is justified by the fact that the proton is preferably located nearer to O2 rather than being equally distant to O1 and O2 or evenly distributed (disordered) between them.

Binding of genistein to the estrogen receptor based on an experimental electron density study.

In a continuing effort to determine a relationship between the biological function and the electronic properties of steroidal and nonsteroidal estrogens by analysis of the submolecular properties, an experimental charge density study has been pursued on the nonsteroidal phytoestrogen, genistein. X-ray diffraction data were obtained using a Rigaku R-Axis Rapid high-power rotating anode diffractometer with a curved image plate detector at 20(1) K. The total electron density was modeled using the Hansen-Coppens multipole model. Genistein packs in puckered sheets characterized by intra- and intermolecular hydrogen bonds while weaker intermolecular hydrogen bonds (O...H-C) exist between the sheets. A topological analysis of the electron density of genistein was then completed to characterize all covalent bonds, three O...H-O and four O...H-C intermolecular hydrogen bonds. Two O...H-O hydrogen bonds are incipient (partially covalent) type bonds, while the other O...H-O hydrogen bond and O...H-C hydrogen bonds are of the pure closed-shell interaction type. In addition, two intermolecular H...H interactions have also been characterized from the topology of the electron density. The binding of genistein to the estrogen receptor is discussed in terms of the electrostatic potential derived from the electron density distribution.

Structure and bonding in beta-HMX-characterization of a trans-annular N...N interaction.

Chemical bonding in the beta-phase of the 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane (HMX) crystal based on the experimental electron density obtained from X-ray diffraction data at 20 K, and solid state theoretical calculations, has been analyzed in terms of the quantum theory of atoms in molecules. Features of the intra- and intermolecular bond critical points and the oxygen atom lone-pair locations are discussed. An unusual N...N bonding interaction across the 8-membered ring has been discovered and characterized. Hydrogen bonding, O...O and O...C intermolecular interactions are reported. Atomic charges and features of the electrostatic potential are discussed.

Experimental charge density study of estrogens: 17beta-estradiol.urea.

To relate the molecular electrostatic potential to the biological activities of estrogens, a comparative charge density study of different derivatives has been initiated. The second completed charge density analysis of this series for 17beta-estradiol*urea is presented here. This is a large organic system with 52 atoms in a noncentrosymmetric space group, therefore special tools such as an optimal coordinate system and slow, initially constrained refinement have been used to accomplish this study. Our results for the urea molecule reasonably agree with previous experimental and theoretical results. In the 17beta-estradiol molecule, the oxygen atoms appear to be close to sp3 in shape, exhibiting two consistent, distinct lone pairs despite different chemical environments. No significant interaction of the hydroxyl group oxygen with the orbitals of the aromatic ring is observed. Analysis of the electrostatic potential revealed that the negative potential in the lone pair region of the two oxygen atoms is quite different. The topological analysis of the electron density has been performed, and the atomic charges have been estimated.

Atoms-in-molecules study of intra- and intermolecular bonding in the pentaerythritol tetranitrate crystal.

Chemical bonding in the pentaerythritol tetranitrate crystal based on the experimental electron density obtained from X-ray diffraction data at 100 K and theoretical calculations at the experimental molecular geometry have been analyzed in terms of the Quantum Theory of Atoms in Molecules. Features of the intra- and intermolecular bond critical points and the oxygen atom lone-pair locations are discussed. Numerous intermolecular bonding interactions, including O...H and O...O, have been found and characterized. Atomic charges and atomic energies were integrated and compared with those for similar compounds. The N-O topological bond orders have been calculated for the first time, and the PETN atomic valences have been estimated.

Experimental and theoretical electron density study of estrone.

The electron density and the electrostatic potential (ESP) distributions of estrone have been determined using X-ray diffraction analysis and compared with theoretical calculations in the solid and gas phases. X-ray diffraction measurements are performed with a Rigaku Rapid rotating anode diffractometer at 20 K. The electron density in the estrone crystal has been described with the multipole model, which allowed extensive topological analysis and calculation of the ESP. From DFT calculations in the solid state a theoretical X-ray diffraction data set has been produced and treated in the same way as the experimental data. Two sets of single molecule DFT calculations were performed: (a) An electron density distribution was obtained via a single-point calculation with a large basis set at the experimental geometry and subsequently analyzed according to the quantum theory of atoms in molecules (AIM) to obtain the bond and most atomic properties, and (b) another electron density distribution was obtained with a smaller basis set, but at a geometry optimized using the same basis set for the analysis of atomic energies. An interesting locally stabilizing hydrogen-hydrogen bond path linking H(1) and H(11B) is found which represents the first characterization of such bonding in a steroid molecule. AIM delocalization indices were shown to be well correlated to the experimental electron density at the bond critical points through an exponential relationship. The aromaticity of ring A, chemical bonding, the O(1)...O(2) distance necessary for estrogenic activity, and the electrostatic potential features are also discussed.

Chemical bonding in pentaerythritol at very low temperature or at high pressure: an experimental and theoretical study.

Chemical bonding in the pentaerythritol crystal based on the experimental electron density at 15 (1) K, and theoretical calculations at the experimental molecular geometries obtained at room and low (15 K) temperatures have been analyzed and compared in terms of the topological analysis. Topological electron-density features corresponding to the high-pressure (1.15 GPa) geometry are also reported. In addition to the bond critical points (CPs) within the molecular layers, CPs between the atoms of different molecular layers have been located and the bonding character of these relatively weak interactions discussed. Atomic charges and energies have been integrated over the atomic basins delimited by the zero-flux surfaces, and the intermolecular interaction energies have been calculated. The interaction between molecular layers in the crystal becomes stronger both at very low temperature and high pressure, as demonstrated by the more negative intermolecular interaction energies, higher electron density and energy density values at the CPs, and sharper electronic-energy density profiles.

Electron density and energy density view on the atomic interactions in SrTiO3.

The results of topological analysis of the electron density in an SrTiO3 crystal based on the experimental (at 145 K) and theoretical data are presented and discussed. The features of the electron density lead to the conclusion that the Ti-O interaction is of the partly polar covalent (or intermediate) type. Complicated atomic shapes defined by the zero-flux surfaces in the electron density are revealed. It is found that, in general, they are far from spherical and have very slight asphericity in the close-packed layers. The topological coordination numbers of Sr and Ti are the same as the geometrical numbers, whereas the topological coordination for the O atom (6) differs from the geometrical value (12). The latter results from the specific shape of the Ti-atom basin, which prevents bond-path formation between the O atoms. The analysis of the kinetic and potential energy densities derived from the electron density using the density functional theory formulae revealed the stabilizing crystal-forming role of the O atoms in SrTiO3. Structural homeomorphism between the experimental electron density and the potential and kinetic energy densities is observed.

Chemical bonding in biguanidinium dinitramide and biguanidinium bis-dinitramide from experimental X-ray diffraction data.

The electron density and related properties of biguanidinium dinitramide (BIGH)(DN) and biguanidinium bis-dinitramide (BIGH(2))(DN)(2) crystals (space groups P1 and C2/c) have been determined from low-temperature (90(1) K) X-ray diffraction experiments. The Hansen-Coppens multipole model as implemented in the XD program gave R = 0.0247 and 0.0201 (all reflections) which allowed the calculation of the electron density and Laplacian distributions. The bonding (3,-1) critical points were also found. The analysis of the results shows that Bader's topological theory provides a more useful description of the chemical bonding in the studied crystals as compared to the classical analysis of deformation densities. The hydrogen bonding in the crystals was analyzed. The atomic charges were integrated over the atomic basins.

Characterizing the oxygen-oxygen interaction in the dinitramide anion.

Atomic interactions between oxygen atoms have been analyzed in terms of the Theory of Atoms in Molecules for the biguanidium dinitramide and biguanidium bis-dinitramide crystals. The electron density has been derived from X-ray diffraction data obtained at 90 K, and the potential energy density has been calculated using the density functional approach. Bond critical points have been found on the O(1)...O(4) interatomic line in both the electron density and potential energy density gradient fields. The bond path and its associated virial path have been obtained. The interaction has been identified as a bonding closed-shell type interaction.