Experimental Charge Density Study Research Articles

Experimental charge density and phase transition studies of a new hybrid perovskite: the complementarity between powder diffraction, single-crystal diffraction and magnetic measurements

Experimental charge density and phase transition studies of a new hybrid perovskite: the complementarity between powder diffraction, single-crystal diffraction and magnetic measurements

Accurate experimental characterization of the labile N–Cl bond inN-chloro-N′-(p-fluorophenyl)-benzamidine crystal at 17.5 K

Very low temperature can preserve the photolabile N–Cl bond in aN-chloro-N-benzamidine derivative long enough to carry on an accurate experimental X-ray charge density study.

An experimental and theoretical charge density study of theophylline and malonic acid cocrystallization.

The pharmaceutical agent theophylline (THEO) is primarily used as a bronchodilator and is commercially available in both tablet and liquid dosage forms. THEO is highly hygroscopic, reducing its stability, overall shelf-life, and therefore usage as a drug. THEO and dicarboxylic acid cocrystals were designed by Trask et al. in an attempt to decrease the hygroscopic behaviour of THEO; cocrystallisation of THEO with malonic acid (MA) did not improve the hygroscopic stability of THEO in simulated atmospheric humidity testing. The current study employed high-resolution X-ray crystallography, and Density Functional Theory (DFT) calculations to examine the electron density distribution (EDD) changes between the cocrystal and its individual components. The EED changes identified the reasons why the THEO:MA cocrystal did not alter the hygroscopic profile of THEO. The cocrystal was equally porous, with atomic packing factors (APF) similar to those of THEO 0.73 vs. 0.71, respectively. The THEO:MA (1) cocrystal structure is held together by an array of interactions; a heterogeneous synthon between the imidazole and a carboxylic fragment stabilising the asymmetric unit, a pyrimidine-imidazole homosynthon, and an aromatic cycle stack between two THEO moieties have been identified, providing 9.7–12.9 kJ mol−1 of stability. These factors did not change the overall relative stability of the cocrystal relative to its individual THEO and MA components, as shown by cocrystal (1) and THEO being equally stable, with calculated lattice energies within 2.5 kJ mol−1 of one other. The hydrogen bond analysis and fragmented atomic charge analysis highlighted that the formation of (1) combined both the EDD of THEO and MA with no net chemical change, suggesting that the reverse reaction — (1) back to THEO and MA — is of equal potential, ultimately producing THEO hydrate formation, in agreement with the work of Trask et al. These results highlight that a review of the EDD change associated with a chemical reaction can aid in understanding cocrystal design. In addition, they indicate that cocrystal design requires further investigation before becoming a reliable process, with particular emphasis on identifying the appropriate balance of synthon engineering, weak interactions, and packing dynamics.

Experimental charge-density analysis towards predictive materials science

The ongoing increase in the number of experimental charge-density studies can be related to both the technological advancements and the wide applicability of the method. Regarding materials science, the understanding of bonding features and their relation to the physical properties of materials can not only provide means to optimize such properties, but also to predict and design new materials with the desired ones. In this tutorial, we describe the steps for a charge-density analysis, emphasizing the most relevant features and briefly discussing the applications of the method.

Insight into the Bonding and Aggregation of Alkyllithiums by Experimental Charge Density Studies and Energy Decomposition Analyses.

In this Article, the organolithiums [((-)-sparteine)LitBu] (1), [(ABCO)LitBu]2 (2), and [(ABCO)2(LiiPr)4] (3) are investigated by means of experimental and theoretical charge density determination to elucidate the nature of the Li-C and Li-N bonds. Furthermore, the valence shell charge concentrations (VSCCs) in the nonbonding region of the deprotonated Cα-atom will provide some insight on the localization of the carbanionic lone pair. Analysis of the electron density (ρ(rBCP)), Laplacian (∇2ρ(rBCP)), and the energy decomposition (EDA) confirmed that the Li-C/N bond exhibits astonishingly similar characteristics, to reveal an increasingly polar contact with decreasing aggregate size. This explains former observations on the incorporation of halide salts in organolithium reagents. Furthermore, it could be shown that the bonding properties of the iPr group are similar to those of the tBu substituent. The accuracy of fit to all previously determined properties in organolithiums is remarkable.

Investigation of bond topological and electrostatic properties of plumbagin molecule: An experimental and theoretical charge density study

Plumbagin is a naturally occurring derivative with several medicinal properties including antioxidants, antifungal, antimalarial, leprosy and antitumor properties; their structural and electrostatic properties are yet to be determined. The crystal structure of plumbagin has been solved; it shows that the compound crystallizes in P21/c space group with two molecules in the asymmetric unit. The electron density distribution of both molecules have determined from multipole model refinement. Among all the C–O bonds of both molecules (I & II), the OH group connected C–O bond and the methyl group connected C–C bond exhibits less electron density and the negative Laplacian of electron density as well. Further, the electrostatic potential (ESP) surface of two plumbagin molecules show some difference in their electronegative regions. The carbonyl O-atoms exhibit high electronegative ESP regions which are the key reactive locations of plumbagin when bind with the active site of target protein and in the ESP map, an aromatic π-cloud also observed in one of the molecule. The electron density distribution of O–H⋅⋅⋅O intermolecular interactions between the molecules I and II, reveals that these interactions are found very stronger than the other interactions in the crystal.

Charge density studies of energetic material: RDX

Experimental charge density study has been carried out for Cyclotrimethylene-trinitramine (space group Pbca), an explosive material from a low temperature X-ray diffraction experiment. The electron density was modeled using the Hansen-Coppens multipole model and refined to R=0.032 for 6226 unique observed reflections. The electron density, laplacian and electrostatic potential distributions are reported and discussed, especially, the properties of the bond (3,-1) critical points, which are thought to play a key role in the decomposition of the molecule. From the bond topological analysis of all the bonds, it is observed that the N–N bond is the weakest. The dominating nature of the oxygen atoms was clearly well understood from isosurface electrostatic potential of isolated and symmetrically sitting molecules in the crystal.

X-ray Charge Density Study of the Drug Methimazole with Z′ = 2: Differences in the Electronic Structure of the Thiourea Core due to Crystal Packing Effects

Herein we present a detailed experimental charge-density study for the low-temperature polymorph of antithyroid drug methimazole crystallized with two crystallographically independent molecules lacking conformational freedom. Quantum-topological analysis of experimental electron density allowed us to detect the distinctive differences in the electron distribution within their thiourea groups, arising primarily from crystal packing effects. Sulfur atom S(1a) features two separate regions of positive deformation density, whilst the other atom S(1b) is found to be more diffuse with positive density taking a toroidal form. In contrast to S(1a), the couple of the lone pairs of S(1b) derived by non-bonding charge concentrations takes a more significant turn relative to the molecular plane and proves to be distorted. We also report an ambiguous electronic structure of the heteroatoms, i.e. appearance of “false” Laplacian CPs (3, +3) or splitting of true ones, which is caused by neglecting or excessive use of Gra...

Role of Staple Molecules in the Formation of S···S Contact in Thioamides: Experimental Charge Density and Theoretical Studies

The reasons behind the formation of S···S contacts in thioamides, the most important compounds with terminal sulfur atoms, were investigated by means of experimental charge density studies and theo...

Featuring I···N Halogen Bond and Weaker Interactions in Iodoperfluoroalkylimidazoles: An Experimental and Theoretical Charge Density Study

The experimental charge density distribution of two new iodoperfluoroalkylimidazole derivatives has been determined with the aspherical atom model against single-crystal X-ray diffracted intensities and analyzed by means of the Bader Quantum Theory of Atoms In Molecules. The compounds self-assemble in the solid state forming infinite chains through strong I···N halogen bonds. The topological and energetic features of these interactions have been determined and compared with those of a previously reported I···N interaction formed by an iodoperfluoroarene derivative, allowing elucidation of the role of hybridization of the carbon atom bonded to the halogen atom in the nature of the halogen bonding interaction. The weaker interactions present in the crystal structures have been investigated as well, with particular attention to F···F interactions. They have also been analyzed through the Interacting Quantum Atoms approach in order to elucidate their role in stabilizing the crystal structure.

Experimental charge density study on FLPs and a FLP reaction product

AbstractThe charge density distribution of the intramolecular frustrated Lewis pair (FLP) Mes2PCH2CH2B(C6F5)2(1), the phosphinimine HNPMes2CH2CH2B(C6F5)2(2), as well as a FLP homologue with nitrogen NEt2CHPhCH2B(C6F5)2(3) were investigated with Bader’s quantum theory of atoms in molecules (QTAIM). The charge densities were derived from both experimental high-resolution X-ray diffraction data (2,3) and theoretical calculations (1,3). The QTAIM analysis for the FLPs1and3showed the prominent B-pnictogen interaction to be weak dative bonds without significant charge-transfer. This holds also true for the B–N–bond of2. The nitrogen atom is negatively charged, due to a charge transfer from phosphorous and shows features of a sp2-hybridization. The bond is therefore best described as a non-hypervalent Pδ+–Nδ−moiety.

Experimental charge-density studies: improvements in data processing

Experimental charge-density studies: improvements in data processing

Short is strong: experimental electron density in a very short N···I halogen bond

Abstract2,3,5,6-Tetrafluoro-1,4-diiodobenzene and 4-(dimethylamino)pyridine co-crystallize in 1:2 stoichiometry. A diffraction experiment at standard resolution was already conducted in 2010 and revealed one of the shortest N···I contacts ever reported. We collected X-ray intensities at 100 K up to a very high resolution of 1.23 Å−1. These experimental data allowed to refine a structure model based on atom-centered multipoles according to the Hansen-Coppens approach and provided an experimental electron density. A subsequent analysis with the help of Bader’s atoms in molecules theory showed a strong interaction between the pyridine N atom and theσhole of its closest iodine neighbor on the halogenated benzene. This contact is characterized by a distance of 2.6622(4) Å and associated with a remarkably large electron density of 0.359(5)e⋅Å−3in the (3, −1) critical point, unprecedented for a secondary interaction. This bona fide shortest halogen bond ever investigated by an experimental charge density study is associated with a significantly negative total energy density in the bond critical point and thus can reliably be classified as strong. Both the electron density and the position of the bond critical point suggest to compare the short N···I contact to coordinative or covalent bonds rather than toσhole interactions.

Behind the Scenes of Group 4 Metallocene Catalysis: Examination of the Metal–Carbon Bond

This contribution provides the first detailed analysis of the nature of the M–C σ-bond of three alkylated, isostructural group 4 (M = Ti, Zr, Hf) metallocenes, thereby elucidating individual peculiarities of each metal center in the catalytic conversion of olefins. Therefore, the subtle electronic differences of the individual M–C σ-bonds, which are considered crucial for several subprocesses in the coordinative polymerization of olefins, were examined by detailed experimental charge density studies. These studies provided measures of the increasing ionic character of the M–C bonds along the group 4 elements (Ti–C < Zr–C < Hf–C). These results are further supported by high-pressure diffraction studies showing that the predominantly ionic Hf–C bond is more compressible than the more covalent Zr–C bond in line with a smaller degree of electron localization in the valence shell of the hafnium relative to the zirconium atom along the M–C bond directions. The Ti–C bond displays the largest degree of electron l...

Protonated nucleobases are not fully ionized in their chloride salt crystals and form metastable base pairs further stabilized by the surrounding anions.

This paper presents experimental charge-density studies of cytosinium chloride, adeninium chloride hemihydrate and guaninium dichloride crystals based on ultra-high-resolution X-ray diffraction data and extensive theoretical calculations. The results confirm that the cohesive energies of the studied systems are dominated by contributions from intermolecular electrostatic interactions, as expected for ionic crystals. Electrostatic interaction energies (Ees) usually constitute 95% of the total interaction energy. The Ees energies in this study were several times larger in absolute value when compared, for example, with dimers of neutral nucleobases. However, they were not as large as some theoretical calculations have predicted. This was because the molecules appeared not to be fully ionized in the studied crystals. Apart from charge transfer from chlorine to the protonated nucleobases, small but visible charge redistribution within the nucleobase cations was observed. Some dimers of singly protonated bases in the studied crystals, namely a cytosinium-cytosinium trans sugar/sugar edge pair and an adeninium-adeninium trans Hoogsteen/Hoogsteen edge pair, exhibited attractive interactions (negative values of Ees) or unusually low repulsion despite identical molecular charges. The pairs are metastable as a result of strong hydrogen bonding between bases which overcompensates the overall cation-cation repulsion, the latter being weakened due to charge transfer and molecular charge-density polarization.

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.

Experimental charge-density studies: data reduction and model quality: the more the better?

In this review, recent developments concerning data and model quality in experimental charge-density investigations from a personal view-point are described. Data quality is not only achieved by the high resolution, high I/σ(I) values, low merging R values and high multiplicity. The quality of the innermost reflections especially is crucial for mapping the density distribution of the outermost valence electrons and can be monitored by (I/σ)asymptotic. New detector technologies seem to be promising improvements. Empirical corrections to correct for low-energy contamination of mirror-focused X-ray data and for resolution- and temperature-dependent errors caused by factors such as thermal diffuse scattering are described. Shashlik-like residual density patterns can indicate the need for an anharmonic description of the thermal motion of individual atoms. The physical reliability of the derived model must be thoroughly analysed. The derived probability density functions for the mean-squared atomic vibrational displacements especially should have only small negative values. The treatment of H atoms has been improved by methods to estimate anisotropic thermal motion. For very high resolution data, the polarization of the core density cannot be neglected. Several tools to detect systematic errors are described. A validation tool is presented that easily detects when the refinement of additional parameters yields a real improvement in the model or simply overfits the given data. In all investigated structures, it is proved that the multipole parameters of atoms with a comparable chemical environment should be constrained to be identical. The use of restraints could be a promising alternative.

Is Hexachloro-cyclo-triphosphazene Aromatic? Evidence from Experimental Charge Density Analysis.

Experimental charge density studies of hexachloro-cyclo-triphosphazene (1) and the boat conformation of octachloro-cyclo-tetraphosphazene (2 a) were performed to unambiguously describe the origin of the electron delocalization in the P3 N3 ring in 1. The obtained results were compared to DFT studies in the solid state and the gas phase. Electron density analysis revealed a highly polarized nature of the P-N bonds and a modular structure of the P3 N3 and P4 N4 rings, which can be separated into independent Cl2 PN units with a perfect transferability between the compounds. Further analysis of the source function experimentally proves the presence of negative hyperconjugation involving both out-of-plane and in-plane nitrogen electrons as well as electrons of the chlorine atoms. Finally, these results discard the presence of pseudoaromatic delocalization in the nearly planar P3 N3 ring.

Charge density and optical properties of multicomponent crystals containing active pharmaceutical ingredients or their analogues.

Active pharmaceutical ingredients (APIs), through their favourable donor/acceptor spatial distribution and synthon formation flexibility, are attractive building blocks in modern materials crystallography. The optical properties of a crystal strongly depend on two factors, i.e. the spatial distribution of molecules in the crystal structure and the electronic properties of molecular building blocks (dipole moments, polarizabilities, hyperpolarizabilities). Although the latter are easy to predict through ab initio calculations, the former are not. Only a combination of experimental and theoretical charge density studies together with prediction and measurement of optical properties enable full analysis of the obtained functional material in terms of its usefulness in practical applications. This article presents design strategies of optical materials based on selected pharmaceutical molecules. Factors that contribute to molecular recognition in the four selected polar/chiral crystal phases (derived through charge density and Hirshfeld surfaces analysis) have been determined. Theoretically predicted optical properties of the molecular/ionic building blocks as well as bulk effects have been confirmed experimentally. This research is a first step in the design of novel optical materials based on push-pull molecules and APIs.

Directionality of intermolecular C–F···F–C interactions in crystals: experimental and theoretical charge density study

Bonding intermolecular F···F interactions were analyzed in crystal of a fluorinated benzene derivative using topological analysis of experimental charge density distribution. It was found that the values of electron density and potential energy density in bond critical points of the F···F interactions in crystal depended on the distance between the fluorine atoms, rather than on the corresponding C–F···F angles. The directionality of these F···F interactions was demonstrated by DFT-D and MP2 calculations for model hexafluorobenzene dimers. Possible discrepancies between dimerization energies computed by ab initio methods and via empirical correlations are discussed.