Analysis Of Experimental Electron Density Research Articles

Rietveld Refinement and X-ray Absorption Study on the Bonding States of Lanthanum-Based Perovskite-Type Oxides La1−xCexCoO3

Metal-oxygen bonding of the Ce-doped LaCoO3 system remains largely unexplored despite extensive studies on its magnetic properties. Here, we investigate the structure and local structure of nanoscale La1−xCexCoO3, with x = 0, 0.2, and 0.4, using the Rietveld refinement and synchrotron X-ray absorption techniques, complemented by topological analysis of experimental electron density and electron energy distribution. The Rietveld refinement results show that LaCoO3 subject to Ce addition is best interpretable by a model of cubic symmetry in contrast to the pristine LaCoO3, conventionally described by either a monoclinic model or a rhombohedral model. Ce4+/Co2+ are more evidently compatible dopants than Ce3+ for insertion into the main lattice. X-ray absorption data evidence the partially filled La 5d-band of the pristine LaCoO3 in accordance with the presence of La–O bonds with the shared-type atomic interaction. With increasing x, the increased Ce spectroscopic valence and enhanced La–O ionic bonding are noticeable. Characterization of the local structures around Co species also provides evidence to support the findings of the Rietveld refinement analysis.

Crystal engineering of co-crystal of nicotinic acid and pyrogallol: an experimental and theoretical electron density analysis

Experimental electron density analysis by means of high-resolution X-ray diffraction data up to sinθ/λmax = 1.11 Å−1 at 100 (1) K has been performed to analyze the detailed structure and the strength of intermolecular interactions responsible for the formation of a new solid form of nicotinic acid (NA), cocrystallized with pyrogallol (PY). There are two NA–PY units in the asymmetric unit. The experimental results are compared with the results obtained from theoretical structure factors modeled using periodic boundary DFT calculations. Both refinements were carried out using the Hansen and Coppens multipolar formalism (in MoPro program). The non-centrosymmetric and polar nature of the crystal system rendered the multipolar refinement challenging which was addressed by involving the transferability principle. This study highlights the significance of the transferability principle in electron density modeling in non-routine situations. The 2:2 cocrystal of NA–PY exhibits a zigzag, brickwall and sheet-like layered structure in three dimensions and is stabilized by strong intra- and inter-molecular hydrogen bonding through N—H...O and O—H...O bonds, some of them due to the zwitterion nature of NA as well as weak interactions between the PY molecules. Ranking these interactions via topological analysis of the electron density shows the leading role of the NA–NA substructure which drives the organization of the cocrystals. These strong interactions between the NA zwitterions may explain why Z′ = 2.

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...

The Lightest Element Phosphoranylidene: NHC‐Supported Cyclic Borylidene–Phosphorane with Significant B=P Character

AbstractA borylidene–phosphorane, the lightest phosphoranylidene, which is stabilized by an N‐heterocyclic carbene ligand, was synthesized and fully characterized. Experimental electron density analysis and DFT calculations indicate an enhanced ylene character (rather than an ylide character) with an exceptionally strong B→P π‐back bonding related to the less electronegative boron compared to phosphorus.

The Lightest Element Phosphoranylidene: NHC-Supported Cyclic Borylidene-Phosphorane with Significant B=P Character.

A borylidene-phosphorane, the lightest phosphoranylidene, which is stabilized by an N-heterocyclic carbene ligand, was synthesized and fully characterized. Experimental electron density analysis and DFT calculations indicate an enhanced ylene character (rather than an ylide character) with an exceptionally strong B→P π-back bonding related to the less electronegative boron compared to phosphorus.

How Reliable Are Intermolecular Interaction Energies Estimated from Topological Analysis of Experimental Electron Densities?

We examine the reliability of intermolecular interaction energies estimated from intermolecular bond critical point properties of experimental electron densities and show that they are inherently unreliable, typically underestimating but sometimes overestimating more reliable values. Based on these estimates, conclusions regarding the energetic importance of specific intermolecular interactions, especially in the context of crystal packing and crystal engineering, can be misleading.

Unconstrained and X-ray constrained extremely localized molecular orbitals: analysis of the reconstructed electron density

The recently developed X-ray constrained extremely localized molecular orbital (XC-ELMO) technique is a potentially useful tool for the determination and analysis of experimental electron densities. Molecular orbitals strictly localized on atoms, bonds or functional groups allow one to combine the quantum-mechanical rigour of the wavefunction-based approaches with the easy chemical interpretability typical of the traditional multipole models. In this paper, using very high quality X-ray diffraction data for the glycylglycine crystal, a detailed assessment of the capabilities and limitations of this new method is given. In particular, the effects of constraining the ELMO wavefunctions to experimental X-ray structure-factor amplitudes and the ability of the method to reproduce benchmark electron distributions have been accurately investigated. Topological analysis of the XC-ELMO electron densities and of the zero-flux surface-integrated charges and dipole moments shows that the new strategy is already reliable, provided that sufficiently flexible basis sets are used. These analyses also raise new questions and call for further improvements of the method.

From “Loose” to “Dense” Crystalline Phases of Calcium Carbonate through “Repulsive” Interactions: An Experimental Charge‐Density Study

Anion-anion interactions in an eggshell: experimental electron density analysis for two polymorphs of calcium carbonate revealed why the less stable form, aragonite, has higher density than the most stable form, calcite. Although believed to be exclusively repulsive, the interactions between anions cause them to bind more tightly in a crystal and thus make the aragonite phase denser than its calcite counterpart.

A Stable Doubly Hydrogen-Bridged Butterfly-Shaped Diborane(4) Compound

In contrast to the common multiple bonding between carbon atoms, multiply bonded boron compounds have still been a synthetic challenge due to the electron deficiency of boron. We now report that a stable doubly hydrogen-bridged diborane(4), EindB(mu-H)(2)BEind, is produced by the two-electron oxidation of a hydrogen-substituted diborane(4) dianion [Li(+)(thf)](2)[Eind(H)BB(H)Eind](2-), where Eind denotes the 1,1,3,3,5,5,7,7-octaethyl-s-hydrindacen-4-yl. The X-ray crystallography reveals a short B-B distance of 1.4879(7) A in comparison with the normal B-B single bond length (1.72 A), the presence of two hydrogen atoms bridged perpendicular to the B-B bond with a butterfly shape having a dihedral angle of the two BHB triangles of 113(1) degrees, and a linear geometry around the B-B bond with a C-B-B bond angle of 178.92(4) degrees. These structural data, experimental electron density analysis, and computational studies confirm the 3-fold bonding (a sigma and two pi-like bonds) between the two boron atoms incorporating the two bridging hydrogen atoms.

A Favorable Case Where an Experimental Electron Density Analysis Offers a Lead for Understanding a Specific Fluxional Process Observed in Solution

A topological analysis of the electron density in the ketene complex (eta(5)-MeC(5)H(4))(CO)(2)Mn[eta(2)-O=C=C((mu-eta(2)-CCPh)Co(2)(CO)(6))Ph] indicates a predisposition for the carbene component of the ketene ligand to bind the neighboring C atom of the adjacent CO ligand.

Atomic interactions in ethylenebis(1-indenyl)zirconium dichloride as derived by experimental electron density analysis

A topological analysis of the experimental electron density in racemic ethylenebis(1-indenyl)zirconium dichloride, C20H16Cl2Zr, measured at 100 (1) K, has been performed. The atomic charges calculated by the numerical integration of the electron density over the zero-flux atomic basins demonstrate the charge transfer of 2.25 e from the Zr atom to the two indenyl ligands (0.19 e to each) and two Cl atoms (0.93 e to each). All the atomic interactions were quantitatively characterized in terms of the electron density and the electronic energy-density features at the bond critical points. The Zr-C2 bond paths significantly curved towards the C1-C2 bond were found; no other bond paths connecting the Zr atom and indenyl ligand were located. At the same time, the pi-electrons of the C1-C2 bond are significantly involved in the metal-ligand interaction. The electron density features indicate that the indenyl coordination can be approximately described as eta1 with slippage towards eta2. The ;ligand-opposed' charge concentrations around the Zr atom were revealed using the Laplacian of the electron density and the one-particle potential; they were linked to the orbital representations. Bonds in the indenyl ligand were characterized using the Cioslowski-Mixon bond-order indices calculated directly from the experimental electron density.

Can topological analysis of intermolecular interactions explain differences in the physico-chemical properties of related chiral compounds?

Interactions between chiral molecules play a fundamental role for the most biological and many chemical processes. Due to the complexity of the interactions that range from normal hydrogen bonds to weaker interactions like C-H—O hydrogen bonds and stacking, it can be difficult to relate overall thermodynamic properties to the nature of the intermolecular interactions. The topological analysis developed by R.W. Bader for theoretical electron densities has proven to be a powerful tool to analyse intermolecular interactions in crystals based on an analysis of experimental electron densities obtained from accurate high resolution X-ray diffraction data. Our recent investigations of the molecular crystal naphthalene revealed that the topological analysis could reveal and characterize unexpected interatomic interactions [1]. The two pentose epimers xylitol and ribitol differ in the physico-chemical properties, the acentric xylitol being the higher melting and the less dense than ribitol. All possible hydrogen bond donors participate in the hydrogen bond interactions in both compounds, and the topological analysis confirms the energetic similarity of these interactions. The investigations suggest that the origin of the differences in physico-chemical properties is related to differences in the weaker intermolecular interactions and in the entropy. Crystallization of a racemate may lead to racemic compound composed of equal amounts of the two enantiomers or to a spontaneous resolution of crystals that are formed by the pure enantiomers, and the outcome of the process depends on differences in enthalpy and entropy. We have investigated the intermolecular interactions in closely related crystal structures, e.g. a racemic para-fluoromandelic acid and its corresponding enantiomer. The racemic para-fluoromandelic acid showing the unusual behaviour of being the higher melting. An earlier investigation showed that the two forms have an identical hydrogen bond pattern. This was confirmed by the topological analyses based on accurate X-ray diffraction data. Though additional features were revealed from the topological analysis it also showed the significance of supplementing the investigations with theoretical calculations.

Investigation of Zr−C, Zr−N, and Potential Agostic Interactions in an Organozirconium Complex by Experimental Electron Density Analysis

The crystal structure and electron density (ED) distribution of an imine coupling product with an open zirconocene, Zr(2,4-C(7)H(11))[(i-Pr)NCHPhCH(2)CMe=CHCMe=CH(2)] (C(7)H(11) = dimethylpentadienyl), have been derived from accurate synchrotron X-ray diffraction measurements. The molecular structure reveals asymmetric coordination of Zr by the pentadienyl (2,4-C(7)H(11)) ligand (<Zr-C> = 2.56(6) A), the butadiene fragment (<Zr-C> = 2.43(5) A), and the amide nitrogen atom (Zr-N = 2.0312(5) A) of the second ligand. The study of the ED and its topological analysis affords new insight into the bonding and electronic structure of the title zirconium complex. The interactions between the metal center and the ligands are represented by a Zr-N bond path and one Zr-C bond path with each of the pentadienyl and butadiene moieties, contrary to the usually depicted global metal-ligand bonding. The butadiene and pentadienyl groups exhibit a polarization of the corresponding pi-like ED in the C-Zr directions, indicating that the whole conjugated systems are nonetheless involved. The 4d atomic orbitals of Zr exhibit unusual populations according to ligand field considerations, which reveal a high degree of sigma-donation from the conjugated pi systems of both ligands. As deduced from numerical integration over the topologically defined atomic basins, the Zr to ligand charge transfer is 1.48 e to the C(17)NH(24) ligand and 0.68 e to dimethylpentadienyl. Topological analysis of a short intramolecular Zr.(C,H) contact provides no indication of the presence of agostic interactions, despite a small Zr-N-C angle of 102.87(4) degrees. Thus, no bond path and BCP (bond critical point) of the ED are found in the Zr.(C,H) region, which would have provided evidence for such direct interactions, nor is there any evidence for charge accumulation between the Zr and H atoms, or for lengthening of the C-H bond involved in the putative interaction. These characteristics, similar to those in other distorted situations, may be common for other electron-deficient d(0) complexes.

Topological analysis of experimental electron densities

Practical computing algorithms are described for analysing the topology of experimental electron density distributions represented as either three-dimensional grid densities or multipolar pseudoatom superpositions. The algorithms are implemented in the programNEWPROP, results from which are illustrated with applications to twoN-acetyl,C-methylamide blocked amino acid crystal structures.

Hydrogen bond energetics from topological analysis of experimental electron densities: Recognising the importance of the promolecule

In a recent paper [E. Espinosa, E. Molins, C. Lecomte, Chem. Phys. Lett. 285 (1998) 170] the kinetic energy density G( r c) and potential energy density V( r c) at the bond critical point r c in X–H⋯O hydrogen bonds were deduced from topological analyses of experimental electron distributions extracted from accurate X-ray diffraction experiments. We show that the promolecule, a model of non-interacting overlapping spherical atomic electron densities, can explain many of the observed results as well as the exponential dependence on the H⋯O distance. This raises the question of whether present experimental results differ from a simple reference model for weak interactions.