The nature and strength of interactions for an anti-HIV drug, Lamivudine, were studied in a pure crystal form of the drug and the ligand-receptor complexes. High-resolution single-crystal X-ray diffraction studies of the tetragonal polymorph allowed the drug's experimental charge density distribution in the solid state to be obtained. The QM/MM calculations were performed for a simplified model of the Lamivudine complex with deoxycytidine kinase (two complexes with different binding modes) to reconstruct the theoretical charge density distribution. The peculiarities of intramolecular interactions were compared with previously reported data for an isolated molecule. Intermolecular interactions were revealed within the quantum theory of 'Atoms in Molecules', and their contributions to the total crystal energy or ligand-receptor binding energy were evaluated. It was demonstrated that the crystal field effect weakened the intramolecular interactions. Overall, the energies of intermolecular interactions in ligand-receptor complexes (320.1-394.8 kJ/mol) were higher than the energies of interactions in the crystal (276.9 kJ/mol) due to the larger number of hydrophilic interactions. In contrast, the sum of the energies of hydrophobic interactions was found to be unchanged. It was demonstrated by means of the Voronoi tessellation that molecular volume remained constant for different molecular conformations (250(13) Å3) and increased up to 399 Å3 and 521(30) Å3 for the Lamivudine phosphate and triphosphate.
A convenient method to access the above perchlorates has been developed, based on the cyclocondensation of 3-aminofurazans with 1,3-diketones in the presence of HClO4. All compounds were fully characterized by multinuclear NMR spectroscopy and X-ray crystal structure determinations. Initial safety testing (impact and friction sensitivity) and thermal stability measurements (DSC/DTA) were also carried out. Energetic performance was calculated by using the PILEM code based on calculated enthalpies of formation and experimental densities at r.t. These salts exhibit excellent burn rates and combustion behavior and are promising ingredients for energetic materials.
Antithyroid Agents , Perchlorates , Friction , Ketones , Nuclear Magnetic Resonance, Biomolecular
Strontium titanate SrTiO3 (STO) is a canonical example of a quantum paraelectric, and its doping with manganese ions unlocks its potential as a quantum multiferroic candidate. However, to date, the specifics of incorporation of the manganese ion into the perovskite lattice and its impact on structure-property relationships are debatable questions. Herein, using high-precision X-ray diffraction of a Mn (2 atom %)-doped STO single crystal, clear fingerprints of the displacement disorder of Mn cations in the perovskite B-sublattice are observed. Moreover, near the temperature of the antiferrodistortive transition, the off-center Mn position splits in two, providing the unequal potential barrier's distribution for possible local atomic hopping. A link with this was found via analysis of the dielectric response that reveals two Arrhenius-type relaxation processes with similar activation energies (35 and 43 meV) and attempt frequencies (1 × 1011 and â¼1.6 × 1010 Hz), suggesting similar dielectric relaxation mechanisms.
Intricate behaviour of one-electron potentials from the Euler equation for electron density and corresponding gradient force fields in crystals was studied. Channels of locally enhanced kinetic potential and corresponding saddle Lagrange points were found between chemically bonded atoms. Superposition of electrostatic Ï e s r and kinetic Ï k r potentials and electron density ρ r allowed partitioning any molecules and crystals into atomic ρ - and potential-based Ï -basins; Ï k -basins explicitly account for the electron exchange effect, which is missed for Ï e s -ones. Phenomena of interatomic charge transfer and related electron exchange were explained in terms of space gaps between zero-flux surfaces of ρ - and Ï -basins. The gap between Ï e s - and ρ -basins represents the charge transfer, while the gap between Ï k - and ρ -basins is a real-space manifestation of sharing the transferred electrons caused by the static exchange and kinetic effects as a response against the electron transfer. The regularity describing relative positions of ρ -, Ï e s -, and Ï k - basin boundaries between interacting atoms was proposed. The position of Ï k -boundary between Ï e s - and ρ -ones within an electron occupier atom determines the extent of transferred electron sharing. The stronger an Hâ â â O hydrogen bond is, the deeper hydrogen atom's Ï k -basin penetrates oxygen atom's ρ -basin, while for covalent bonds a Ï k -boundary closely approaches a Ï e s -one indicating almost complete sharing of the transferred electrons. In the case of ionic bonds, the same region corresponds to electron pairing within the ρ -basin of an electron occupier atom.
A detailed analysis of a complete set of the local potentials that appear in the Euler equation for electron density is carried out for noncovalent interactions in the crystal of a uracil derivative using experimental X-ray charge density. The interplay between the quantum theory of atoms in molecules and crystals and the local potentials and corresponding inner-crystal electronic forces of electrostatic and kinetic origin is explored. Partitioning of crystal space into atomic basins and atomic-like potential basins led us to the definite description of interatomic interaction and charge transfer. Novel physically grounded bonding descriptors derived within the orbital-free quantum crystallography provided the detailed examination of π-stacking and intricate C=Oâ â â π interactions and nonclassical hydrogen bonds present in the crystal. The donor-acceptor character of these interactions is revealed by analysis of Pauli and von Weizsäcker potentials together with well-known functions, e. g., deformation electron density and electron localization function. In this way, our analysis throws light on aspects of these closed-shell interactions hitherto hidden from the description.
The nature and strength of weak interactions with organic fluorine in the solid state are revealed by periodic density functional theory (periodic DFT) calculations coupled with experimental data on the structure and sublimation thermodynamics of crystalline organofluorine compounds. To minimize other intermolecular interactions, several sets of crystals of perfluorinated and partially fluorinated organic molecules are considered. This allows us to establish the theoretical levels providing an adequate description of the metric and electron-density parameters of the C-Fâ¯F-C interactions and the sublimation enthalpy of crystalline perfluorinated compounds. A detailed comparison of the C-Fâ¯F-C and C-Hâ¯F-C interactions is performed using the relaxed molecular geometry in the studied crystals. The change in the crystalline packing of aromatic compounds during their partial fluorination points to the structure-directing role of C-Hâ¯F-C interactions due to the dominant electrostatic contribution to these contacts. C-Hâ¯F-C and C-Hâ¯O interactions are found to be identical in nature and comparable in energy. The factors that determine the contribution of these interactions to the crystal packing are revealed. The reliability of the results is confirmed by considering the superposition of the electrostatic potential and electron density gradient fields in the area of the investigated intermolecular interactions.
Here an approach is presented for reconstructing the distribution of electronic internal quantum pressure in the electronic continuum of solids from the experimental electron density. Using the formalism of the density functional theory, the spatial inner-crystal map of the quantum pressure is obtained. The results are visualized via the indicator of quantum pressure focusing (IQPF) which reveals the regions where the pressure is concentrated or depleted due to quantum effects. IQPF contains all quantum electron-shell structure-forming contributions resulting from kinetic, exchange and correlation effects, and presents a clear picture of the chemical bond features in crystals with different type of bonding mechanisms.
The crystal structures of 1,2-dihydro-1,1'-bi[thiazolo[3,2-a]quinoline]-10a,10a'-diium diiodide hemihydrate, C22H16N2S22+·2I-·0.5H2O, and 1,2-dihydro-1,1'-bi[thiazolo[3,2-a]quinoline]-10a,10a'-diium iodide triiodide, C22H16N2S22+·I-·I3-, obtained during the reaction of 1,4-bis(quinolin-2-ylsulfanyl)but-2-yne (2TQB) with iodine, have been determined at 120â K. The crystalline products contain the dication as a result of the reaction proceeding along the iodocyclization pathway. This is fundamentally different from the previously observed reaction of 1,4-bis(quinolin-8-ylsulfanyl)but-2-yne (8TQB) with iodine under similar conditions. A comparative analysis of the possible conformational states indicates differences in the relative stabilities and free rotation for the 2- and 8-thioquinoline derivatives which lead to a disparity in the convergence of the potential reaction centres for 2TQB and 8TQB.
Single crystals of the multiferroic double-perovskite Pb2MnWO6 have been synthesized and their structural, thermal, magnetic and dielectric properties studied in detail. Pure perovskite-phase formation and stoichiometric chemical composition of the as-grown crystals are confirmed by X-ray single-crystal and powder diffraction techniques as well as energy-dispersive X-ray and inductively coupled plasma mass spectrometry. Detailed structural analyses reveal that the crystals experience a structural phase transition from the cubic space group (s.g.) Fm3Ì m to an orthorhombic structure in s.g. Pn21a at about 460 K. Dielectric data suggest that a ferrielectric phase transition takes place at that same temperature, in contrast to earlier results on polycrystalline samples, which reported a transition to s.g. Pnma and an antiferroelectric low-temperature phase. Magnetic susceptibility measurements indicate that a frustrated antiferromagnetic phase emerges below 8 K. Density functional theory based calculations confirm that the cationic order between Mn and W is favorable. The lowest total energy was found for an antiferromagnetically ordered state. However, analyses of the calculated exchange parameters revealed strongly competing antiferromagnetic interactions. The large distance between the magnetic atoms, together with magnetic frustration, is shown to be the main reason for the low value of the ordering temperature observed experimentally. We discuss the structure-property relationships in Pb2MnWO6 and compare these observations to reported results on related Pb2BWO6 perovskites with different B cations.
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.
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.
Using experimental electron densities, the recent effort of quantifying steric effect within the framework of density functional theory is continued. In this work, steric potential, steric field, and steric charge distributions are systematically examines for diamond and boron nitride crystals. Bader's zero-flux condition has been employed to discuss the atomic contributions of these quantities. Two new concepts, characteristic radius r(s) of steric field and atomic steric charge q(s), are introduced in this work, which are intrinsic properties of a system and thus can be used to characterize atomic properties in a molecule or crystal. We anticipate that these steric effect related quantities together with the new concepts introduced in this work can be applied to characterize variety categories of the chemical bonds or weak interactions and provide in-depth insights to a wide range of organic, inorganic, and biological systems.
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.
Estradiol/chemistry , Estrogens/chemistry , Crystallography , Estradiol/pharmacology , Estrogens/pharmacology , Models, Molecular , Molecular Structure , Static Electricity
The atomic and molecular interactions in a crystal of dinitrogen tetraoxide, alpha-N2O4, have been studied in terms of the quantum topological theory of molecular structure using high-resolution, low-temperature X-ray diffraction data. The experimental electron density and electrostatic potential have been reconstructed with the Hansen-Coppens multipole model. In addition, the three-dimensional periodic electron density of crystalline alpha-N2O4 has been calculated at the B3LYP/cc-pVDZ level of theory with and without the geometry optimization. The application of the quantum theory of atoms in molecules and crystals (QTAIMC) recovered the two types of intermolecular bond paths between O atoms in crystalline alpha-N2O4, one measuring 3.094, the other 3.116 A. The three-dimensional distribution of the Laplacian of the electron density around the O atoms showed that the lumps in the negative Laplacian fit the holes on the O atoms in the adjacent molecules, both atoms being linked by the intermolecular bond paths. This shows that the Lewis-type molecular complementarity contributes significantly to intermolecular bonding in crystalline N2O4. Partial overlap of atomic-like basins created by zero-flux surfaces in both the electron density and the electrostatic potential show that attractive electrostatic interaction exists between O atoms even though they carry the same net formal charge. The exchange and correlation contributions to the potential energy density were also computed by means of the model functionals, which use the experimental electron density and its derivatives. It was found that the intermolecular interactions in alpha-N2O4 are accompanied by the correlation energy-density ;bridges' lowering the local potential energy along the intermolecular O...O bond paths in the electron density, while the exchange energy density governs the shape of bounded molecules.
The crystal structure of the title compound, α-PbTeO(3) (PTO), has been reported previously by Mariolacos [Anz. Oesterr. Akad. Wiss. Math. Naturwiss. Kl. (1969), 106, 128-130], refined on powder data. The current determination at room temperature from data obtained from single crystals grown by the Czochralski method shows a significant improvement in the precision of the geometric parameters when all atoms have been refined anisotropically. The selection of a centrosymmetric (C2/c) structure model was confirmed by the second harmonic generation test. The asymmetric unit contains three formula units. The structure of PTO is built up of three types of distorted [PbO(x)] polyhedra (x = 7 and 9) which share their O atoms with TeO(3) pyramidal units. These main anionic polyhedra are responsible for establishing the two types of tunnel required for the stereochemical activity of the lone pairs of the Pb(2+) and Te(4+) cations.
As part of a structural investigation of strontium tellurate(IV) (STO), SrTeO(3), with particular emphasis on the crystal chemistry and phase transitions, the structure of the δ-phase has been determined at 780â K using a single-crystal analysis. Both structural and non-linear optical measurements indicate that STO undergoes a γâδ second-order ferroelectric phase transition at 633â K from the C2 (γ) to the C2/m (δ) modification. Systematic differences between the similar γ- and δ-phase structures were determined and it was found that this phase transformation can be described by a displacive mechanism.
The electron density and related properties of the red-colored energetic material 1,3,4-trinitro-7,8-diazapentalene (space group Pca2(1)) have been determined from a low-temperature [90.0 (1) K] X-ray diffraction experiment. Intensity data were measured with a 2 K CCD Bruker diffractometer using Ag Kalpha radiation. One detector setting, several varphi settings, 0.15 degrees omega scans and 96 s exposure time per frame gave R(int) = 0.0188 for 31 952 (10 283 unique) reflections and (sin theta/lambda)(max) = 1.15 A(-1). The electron density was modeled using the Hansen-Coppens [(1978), Acta Cryst. A34, 909-921] multipole model and refined to R = 0.026 for 9455 unique observed reflections. The electron density, Laplacian and electrostatic potential distributions are reported and discussed. The properties of the bond (3,-1) critical points are analyzed. All results are indicative of multiple bonds in the five-membered rings. In addition, a significant number of weak intermolecular interactions (O...H, O...O, O...N, O...C) have also been characterized by the properties of their critical points. A comparison of experimental results with those obtained from theoretical calculations (periodic, CRYSTAL98; single molecule, GAUSSIAN98) is also reported.
We present an approach for the determination of covalent bond orders from the experimental electron density and its derivatives at the bond critical points. An application of this method to a series of organic compounds has shown that it provides a bonding quantification that is in reasonable agreement with that obtained by orbital theory. The 'experimental' atomic valence indices are also defined and their significance for the characterization of chemical problems is discussed.
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.
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.
