Experimental Charge Density Analysis Research Articles

Intermolecular interactions, charge-density distribution and the electrostatic properties of pyrazinamide anti-TB drug molecule: an experimental and theoretical charge-density study.

An experimental charge-density analysis of pyrazinamide (a first line antitubercular drug) was performed using high-resolution X-ray diffraction data [(sin θ/λ)max = 1.1 Å(-1)] measured at 100 (2) K. The structure was solved by direct methods using SHELXS97 and refined by SHELXL97. The total electron density of the pyrazinamide molecule was modeled using the Hansen-Coppens multipole formalism implemented in the XD software. The topological properties of electron density determined from the experiment were compared with the theoretical results obtained from CRYSTAL09 at the B3LYP/6-31G** level of theory. The crystal structure was stabilized by N-H...N and N-H...O hydrogen bonds, in which the N3-H3B...N1 and N3-H3A...O1 interactions form two types of dimers in the crystal. Hirshfeld surface analysis was carried out to analyze the intermolecular interactions. The fingerprint plot reveals that the N...H and O...H hydrogen-bonding interactions contribute 26.1 and 18.4%, respectively, of the total Hirshfeld surface. The lattice energy of the molecule was calculated using density functional theory (B3LYP) methods with the 6-31G** basis set. The molecular electrostatic potential of the pyrazinamide molecule exhibits extended electronegative regions around O1, N1 and N2. The existence of a negative electrostatic potential (ESP) region just above the upper and lower surfaces of the pyrazine ring confirm the π-electron cloud.

Exploring cyclopentadienone antiaromaticity: charge density studies of various tetracyclones.

A systematic study of six tetracyclones has been carried out using experimental and theoretical charge density analysis. A three pronged approach based on quantum theory of atoms in molecules (QTAIM), nucleus independent chemical shifts (NICS) criterion, and source function (SF) contributions has been performed to establish the degree of antiaromaticity of the central five-membered ring in all the derivatives. Electrostatic potentials mapped on the isodensity surface show that electron withdrawing substituents turn both C and O atoms of the carbonyl group more electropositive while retaining the direction of polarity.

Topological analysis of electron density and the electrostatic properties of isoniazid: an experimental and theoretical study

Isoniazid (isonicotinohydrazide) is an important first-line antitubercular drug that targets the InhA enzyme which synthesizes the critical component of the mycobacterial cell wall. An experimental charge-density analysis of isoniazid has been performed to understand its structural and electronic properties in the solid state. A high-resolution single-crystal X-ray intensity data has been collected at 90 K. An aspherical multipole refinement was carried out to explore the topological and electrostatic properties of the isoniazid molecule. The experimental results were compared with the theoretical charge-density calculations performed using CRYSTAL09 with the B3LYP/6-31G** method. A topological analysis of the electron density reveals that the Laplacian of electron density of the N-N bond is significantly less negative, which indicates that the charges at the b.c.p. (bond-critical point) of the bond are least accumulated, and so the bond is considered to be weak. As expected, a strong negative electrostatic potential region is present in the vicinity of the O1, N1 and N3 atoms, which are the reactive locations of the molecule. The C-H···N, C-H···O and N-H···N types of intermolecular hydrogen-bonding interactions stabilize the crystal structure. The topological analysis of the electron density on hydrogen bonding shows the strength of intermolecular interactions.

Probing the Zintl–Klemm Concept: A Combined Experimental and Theoretical Charge Density Study of the Zintl Phase CaSi

The nature of the chemical bonds in CaSi, a textbook example of a Zintl phase, was investigated for the first time by means of a combined experimental and theoretical charge density analysis to test the validity of the Zintl-Klemm concept. The presence of covalent Si-Si interactions, which were shown by QTAIM analysis, supports this fundamental bonding concept. However, the use of an experimental charge density study and theoretical band structure analyses give clear evidence that the cation-anion interaction cannot be described as purely ionic, but also has partially covalent character. Integrated QTAIM atomic charges of the atoms contradict the original Zintl-Klemm concept and deliver a possible explanation for the unexpected metallic behavior of CaSi.

Charge density distribution and electrostatic interactions of ethionamide: an inhibitor of the enoyl acyl carrier protein reductase (inhA) enzyme of Mycobacterium tuberculosis

The experimental and theoretical charge density analysis of ethionamide molecule provides the topological and the electrostatic properties, which allows the understanding of the nature of intra- and intermolecular interactions.

Systematic experimental charge density analysis of anion receptor complexes.

The first systematic electronic resolution study of a series of urea-based anion receptor complexes is presented. The hydrogen bonding in these multi-component systems was fully characterised using Bader's Quantum Theory of Atoms In Molecules (QTAIM) with the strength of the various N-H···anion hydrogen bonds quantified and the individual contributions of different intermolecular forces to the overall receptor: anion interaction derived by comparison of the charge densities in the related complexes. The strength of the N-Hanion hydrogen bonds was correlated to the basicity of the anion and related to the structure of the receptors. The geometric criteria used to identify hydrogen bonding interactions in standard resolution X-ray diffraction studies were shown to be valid for stronger interactions. However, these geometric criteria are less reliable and lead to assumptions that are not necessarily upheld when applied to weaker intermolecular interactions. The presence of these could only be confirmed by charge density studies. The effect that changes to the receptor substitution pattern have on the entire supramolecular system is illustrated by the differences in the electrostatic potential distributions and atomic charges across the series. The application of systematic high resolution studies to rationalise a variety of host-guest systems has been demonstrated.

Molecular origins of nonlinear optical activity in zinc tris(thiourea)sulfate revealed by high-resolution x-ray diffraction data andab initiocalculations

Structure-property relationships are established in the nonlinear optical (NLO) material, zinc tris(thiourea)sulfate (ZTS), via an experimental charge-density study, x-ray constrained wave-function refinement, and quantum-mechanical calculations. The molecular charge-transfer characteristics of ZTS, that are important for NLO activity, are topologically analyzed via a multipolar refinement of high-resolution x-ray diffraction data, which is supported by neutron diffraction measurements. The extent to which each chemical bond is ionic or covalent in nature is categorized by Laplacian-based bonding classifiers of the electron density; these include bond ellipticities, energy densities, and the local source function. Correspondingly, the NLO origins of ZTS are judged to best resemble those of organic NLO materials. The molecular dipole moment, ${\mathbit{\ensuremath{\mu}}}_{\mathbf{i}}$, and (hyper)polarizability coefficients, ${\mathbit{\ensuremath{\alpha}}}_{\mathbf{ij}}$ and ${\mathbit{\ensuremath{\beta}}}_{\mathbf{ijk}}$, are calculated from the experimental diffraction data using the x-ray constrained wave-function method. Complementary gas-phase ab initio quantum-mechanical calculations of ${\mathbit{\ensuremath{\mu}}}_{\mathbf{i}}$, ${\mathbit{\ensuremath{\alpha}}}_{\mathbf{ij}}$, and ${\mathbit{\ensuremath{\beta}}}_{\mathbf{ijk}}$ offer a supporting comparison. When taken alone, the experimental charge-density analysis does not fare well in deriving ${\mathbit{\ensuremath{\mu}}}_{\mathbf{i}}$, ${\mathbit{\ensuremath{\alpha}}}_{\mathbf{ij}}$, or ${\mathbit{\ensuremath{\beta}}}_{\mathbf{ijk}}$, which is not entirely surprising given that the associated calculations are only generally valid for organic molecules. However, by refining the x-ray data within the constrained wave-function method, the evaluations of ${\mathbit{\ensuremath{\mu}}}_{\mathbf{i}}$, ${\mathbit{\ensuremath{\alpha}}}_{\mathbf{ij}}$, and ${\mathbit{\ensuremath{\beta}}}_{\mathbf{ijk}}$ are shown to agree very well with those from ab initio calculations and show remarkable normalization to experimental refractive index measurements. The small differences observed between ab initio and x-ray constrained wave-function refinement results can be related directly to gas- versus solid-state phase differences. ${\mathbit{\ensuremath{\mu}}}_{\mathbf{i}}$ is found to be 28.3 Debye (gas phase) and 29.7 Debye (solid state) while ${\mathbit{\ensuremath{\beta}}}_{\mathbf{ijk}}$ coefficients are not only significant but are also markedly three dimensional in form. Accordingly, substantial octupolar as well as dipolar NLO contributions in ZTS are indicated, which challenges the traditional focus on dipolar NLO molecules. This evaluation of NLO properties and their relation to the molecular structure offers several ways by which ZTS may be more widely functionalized as a NLO material. More generally, this case study on ZTS demonstrates how experimental and computational techniques can be combined to understand NLO structure-property relationships, an important tool for the quantum-tailored molecular design of next-generation metalorganic NLO materials.

Comparative study of X-ray charge-density data on CoSb3

CoSb3 is an example of a highly challenging case for experimental charge-density analysis due to the heavy elements (suitability factor of ~0.01), the perfect crystallinity and the high symmetry of the compound. It is part of a family of host-guest structures that are potential candidates for use as high-performance thermoelectric materials. Obtaining and analysing accurate charge densities of the undoped host structure potentially can improve the understanding of the thermoelectric properties of this family of materials. In a previous study, analysis of the electron density gave a picture of covalent Co-Sb and Sb-Sb interactions together with relatively low atomic charges based on state-of-the-art experimental and theoretical data. In the current study, several experimental X-ray diffraction data sets collected on the empty CoSb3 framework are compared in order to probe the experimental requirements for obtaining data of high enough quality for charge-density analysis even in the case of very unsuitable crystals. Furthermore, the quality of the experimental structure factors is tested by comparison with theoretical structure factors obtained from periodic DFT calculations. The results clearly show that, in the current study, the data collected on high-intensity, high-energy synchrotron sources and very small crystals are superior to data collected at conventional sources, and in fact necessary for a meaningful charge-density study, primarily due to greatly diminished effects of extinction and absorption which are difficult to correct for with sufficient accuracy.

Noncovalent Interactions in Crystalline Picolinic Acid N-Oxide: Insights from Experimental and Theoretical Charge Density Analysis

This study provides a detailed description of noncovalent interactions of different types and strengths in the title crystal using a combined experimental and theoretical study of the charge density distribution. The nature of the noncovalent interactions is visualized using information theory and through the superposition of the gradient fields in the electron density and electrostatic potential. The energy of the intramolecular O–H···O bond, intermolecular C–H···O bonds, and π-stacking interactions, Eint, are evaluated from empirical correlations between Eint and geometrical and electron-density bond critical point parameters. The complete set of noncovalent interactions including the strong intramolecular O–H···O (Eint > 90 kJ/mol) and weak C–H···O (Eint < 10 kJ/mol) hydrogen bonds, and π-stacking interactions (Eint < 4 kJ/mol) is quantitatively described. The results from the experimental charge density analysis are compared with periodic quantum calculations using density functional theory with the G...

Charge Density Analysis of Ferulic Acid: Robustness of a Trifurcated C–H···O Hydrogen Bond

The toplogical features of a sporadic trifurcated C–H···O interaction region, where an oxygen atom acts as an acceptor of three weak hydrogen bonds, has been investigated by experimental and theoretical charge density analysis of ferulic acid. The interaction energy of the asymmetric molecular dimer formed by the trifurcated C–H···O motif, based on the multipolar model, is shown to be greater than the corresponding asymmetric O–H···O dimer in this crystal structure. Further, the hydrogen bond energies associated with these interaction motifs have been estimated from the local kinetic and potential energy densities at the bond critical points. The trends suggest that the interaction energy of the trifurcated C–H···O region is comparable to that of a single O–H···O hydrogen bond.

Charge Density Analysis and Topological Properties of Hal3-Synthons and Their Comparison with Competing Hydrogen Bonds

Trimers based on intermolecular halogen-bonding interactions (Hal3-synthons) have been studied in hexachlorobenzene, hexabromobenzene, pentachlorophenol, and pentabromophenol. Attention is paid to the comparison of Cl3- and Br3-synthons and to their competition with hydrogen bonds (HBs), based on the experimental and theoretical charge density analyses in crystal and gas phases. The main differences between Cl3- and Br3-synthons are established coming from the particular structure of the valence shell charge concentration region in Cl and Br atoms. Electrophilic–nucleophilic interactions take place within the intermolecular regions of Hal3-synthons by putting face-to-face charge depletion (CD) and charge concentration (CC) regions belonging to the valence shell of the halogen atoms. The electrostatic interaction follows the electrophilic and nucleophilic power of these regions and is monitored by the negative Laplacian values normalized to charge density unit (L/ρ) at the corresponding topological critica...

Advances in Understanding of Chemical Bonding: Inputs from Experimental and Theoretical Charge Density Analysis

The development of charge density analysis has undergone a major renaissance in the last two decades. In recent years, the characterization of bonding features associated with atoms in molecules and in crystals has been explored using high-resolution X-ray diffraction data (laboratory or synchrotron) complemented by high level ab initio theoretical calculations. The extraction of one electron topological properties, namely, electrostatic charges, dipole moment and higher moments, electrostatic potential, electric field gradients, in addition to evaluation of the local kinetic and potential energy densities, have contributed toward an understanding of the electron density distributions in molecular solids. New topological descriptors, namely, the source function (SF) and electron localization function (ELF) provide additional information as regards characterization of the topology of the electron density. In addition, delocalization indices have also been developed to account for bonding features pertinent to M-M bonds. The evaluation of these properties have contributed significantly toward the understanding of intra- and intermolecular bonding features in organic, inorganic, and biomolecules in the crystalline phase, with concomitant applications in the understanding of chemical reactivity and material/biological properties. In recent years, the focus has strongly shifted toward the understanding of structure-property relationships in organometallic complexes containing labile M-C bonds in the crystal structure with subsequent implications in catalysis. This perspective aims to highlight the major developments in electron density measurements in the past few years and provides pointers directed toward the potential use of this technique in future applications for an improved understanding of chemical bonding in systems that have been unexplored.

Experimental charge density analysis of the nature of C—Br...N=C interactions in biologically active compound

Experimental charge density analysis of the nature of C—Br...N=C interactions in biologically active compound

Topological features and electronic structure of 4-chloro-1H-pyrrolo[2,3-b]pyridine: experimental charge density analysis and DFT studies

The experimental charge density distribution in 4-chloro-1H-pyrrolo[2,3-b]pyridine has been carried out using high resolution X-ray diffraction data collected at 100(2) K. Multipole refinement based on the Hansen–Coppens formalism coupled with an estimation of anisotropic displacement parameters (ADPs) of hydrogen atoms converged to R(F) = 0.0353 for 5700 reflections with I > 3σ(I) and sin θ/λ ≤ 1.08 A−1. The topology of the bonding scheme within the molecule as well as of the intermolecular N–H⋯N and C–H⋯Cl hydrogen bonds has been investigated. The covalent nature of N–C and C–C bonds in the pyrrolopyridine skeleton of the molecule has been established by (3, −1) bond critical points associated with relatively large electron densities [2.07(2)–2.74(3) e A−3] and highly negative Laplacian values [−11.37(4) to −19.20(10) e A−5]. The topological parameters corresponding to H⋯N and H⋯Cl critical points indicate a moderately strong intermolecular N–H⋯N hydrogen bond and a weak C–H⋯Cl closed-shell interaction. The electronic structure of the title compound has been calculated by density functional theory (DFT) at the BLYP level. A large HOMO–LUMO energy gap (3.59 eV; HOMO is the highest occupied molecular orbital and LUMO is the lowest unoccupied molecular orbital) implies a high kinetic stability of the title compound.

Analysis of supramolecular architectures: beyond molecular packing diagrams

Current trends in crystal engineering are critically discussed based on experimental charge density analysis for quantifying various interatomic interactions, from weak van der Waals to coordinate bonds, as applied to the design of crystalline materials.

On the Unusual Weak Intramolecular C...C Interactions in Ru3(CO)12: A Case of Bond Path Artifacts Introduced by the Multipole Model?

In a recent publication in this journal, an experimental charge density analysis on the triruthenium cluster Ru(3)(CO)(12) showed unusual C...C bond paths linking the axial carbonyl ligands [Gervasio, G.; Marabello, D.; Bianchi, R.; Forni, A. J. Phys. Chem. A 2010, 114, 9368, hereafter GMBF]. These were also observed in one theoretical DFT calculation, and are associated with very low values of ρ(r(b)) and ∇(2)ρ(r(b)). Our independent experimental charge density analysis on Ru(3)(CO)(12) is entirely consistent with GMBF and confirms the presence of these apparent weak interactions in the multipole model density. However, we conclusively demonstrate that these unusual C...C bond paths between the axial carbonyl ligands are in fact artifacts arising from the Hansen-Coppens multipole model, which is used to analyze the experimental data. Numerous relativistic and nonrelativistic gas-phase DFT calculations, using very extensive basis sets and with corrections for dispersion effects, uniformly fail to reproduce these intramolecular features in the QTAIM topology of the electron density. Moreover, multipole fitting of theoretical static structure factors computed from these quantum electron densities results in the reappearance of the C...C bond paths between the axial carbonyl ligands in the derived molecular graphs. On the other hand, using the experimental structure factors to generate "experimental" X-ray constrained DFT wave functions once again yields molecular graphs which do not show these secondary C...C bond paths. The evidence therefore strongly implicates the multipole model as the source of these spurious features and in turn suggests that great caution should be applied in the interpretation of bond paths where the values of ρ(r(b)) and ∇(2)ρ(r(b)) are very low.

Experimental Charge Density Analysis of a Gallium(I) N-Heterocyclic Carbene Analogue

The experimental electron density of the only known example of a four-membered Ga(I) N-heterocyclic carbene analogue has been determined by multipole modeling of 90 K X-ray diffraction data and compared to theoretical data. In order to obtain a satisfactory model, it is necessary to modify the radial dependency of the core electrons of Ga using two separate scaling parameters for s,p- and d-electrons. Evidence for significant lone-pair density on Ga is found in the electron density and derived properties despite the partial positive charge of this atom. Static deformation density and molecular electrostatic potential clearly show a directional lone pair on Ga, whereas the Laplacian of the total electron density does not; this feature is, however, present in the Laplacian of the valence-only density. The Ga center also acts as an acceptor in four intramolecular C-H···Ga contacts, whose nature is probed by density properties. Substantial covalent character is apparent in the Ga-N bonds, but no sign of donation from filled N p-orbitals to empty Ga p-orbitals is found, whereas π-delocalization over the organic ligand is evident. This study highlights the utility of experimental charge density analysis as a technique to investigate the unusual bonding and electronic characteristics of low oxidation state/low coordinate p-block complexes.

R-free factor and experimental charge-density analysis of 1-(2′-aminophenyl)-2-methyl-4-nitroimidazole: a crystal structure withZ′ = 2

The experimental charge-density distribution was determined for 1-(2'-aminophenyl)-2-methyl-4-nitro-1H-imidazole crystals. An anharmonic model was applied to the N atoms of both amino groups and to one nitro group in order to account for high residual peaks after harmonic multipole refinement and to obtain a better charge-density model. Free R-factor calculations [Brünger (1992). Nature, 355, 472-475] with restrained models implemented in MoPro were used to determine the degree of similarity of the two symmetry-independent molecules in the unit cell. The results are compared with 1-phenyl-4-nitroimidazole in order to analyze the influence of the amine and methyl functional groups. The asymmetric unit contains two symmetry-independent molecules giving rise to a dimer connected via strong N-H···N hydrogen bonds; these dimers are the building blocks of the crystal. In the crystal structure there are also weaker interactions and many short directional contacts (C-H···O, C-H···N and C-H···π), for which the Koch-Popelier topological criteria were applied. This analysis revealed that the C-H···π interactions lie at the border between weak hydrogen bonds and van der Waals interactions. Special attention was also paid to stabilizing H···H interactions. It turned out that the electron density, Laplacian and density energies at the critical points show an exponential dependence on the contact distance, similar to the relation found for other interactions.

Halogen Bonding in 2,5-Dichloro-1,4-benzoquinone: Insights from Experimental and Theoretical Charge Density Analysis

Experimental charge density distribution in 2, 5-dichloro-1, 4-benzoquinone has been carried out using high resolution X-ray diffraction data at 90 K to quantitatively evaluate the nature of C−Cl···O═C halogen bond in molecular crystals. Additionally, the halogen bond is studied from geometrical point of view and the same has been visualized using Hirshfeld surface analysis. The obtained results from experimental charge density analysis are compared with periodic quantum calculations using B3LYP 6-31G(d,p) level of theory. The topological values at bond critical point, three-dimensional static deformation density features and electrostatic potential isosurfaces unequivocally establish the attractive nature of C−Cl···O═C halogen bond in crystalline lattice.

Nature of Cl···Cl Intermolecular Interactions via Experimental and Theoretical Charge Density Analysis: Correlation of Polar Flattening Effects with Geometry

The experimental charge density distribution in three compounds, 2-chloro-3-quinolinyl methanol, 2-chloro-3-hydroxypyridine, and 2-chloro-3-chloromethyl-8-methylquinoline, has been obtained using high-resolution X-ray diffraction data collected at 100 K based on the aspherical multipole modeling of electron density. These compounds represent type I (cis), type I (trans), and type II geometries, respectively, as defined for short Cl···Cl interactions. The experimental results are compared with the theoretical charge densities using theoretical structure factors obtained from a periodic quantum calculation at the B3LYP/6-31G** level. The topological features derived from the Bader's theory of atoms in molecules (AIM) approach unequivocally suggest that both cis and trans type I geometries show decreased repulsion, whereas type II geometry is attractive based on the nature of polar flattening of the electron density around the Cl atom.