X-ray electron density investigation of chemical bonding in van der Waals materials.

Van der Waals (vdW) solids have attracted great attention ever since the discovery of graphene, with the essential feature being the weak chemical bonding across the vdW gap. The nature of these weak interactions is decisive for many extraordinary properties, but it is a strong challenge for current theory to accurately model long-range electron correlations. Here we use synchrotron X-ray diffraction data to precisely determine the electron density in the archetypal vdW solid, TiS2, and compare the results with density functional theory calculations. Quantitative agreement is observed for the chemical bonding description in the covalent TiS2 slabs, but significant differences are identified for the interactions across the gap, with experiment revealing more electron deformation than theory. The present data provide an experimental benchmark for testing theoretical models of weak chemical bonding.

High-Temperature Crystal Structure and Chemical Bonding in Thermoelectric Germanium Selenide (GeSe).

The discovery of the ultra-high thermoelectric figure of merit of 2.6 in SnSe has drawn attention to other lead-free IV-VI orthorhombic semiconductors. GeSe has been predicted to possess thermoelectric performances comparable to SnSe. Here, a complete structural study is reported of GeSe with temperature by means of high-resolution synchrotron powder X-ray diffraction. In the orthorhombic phase, the evolution of the bond distances with temperature is shown to deviate significantly with respect to SnSe. Analysis of the chemical bonding within the Quantum Theory of Atoms in Molecules shows that GeSe is ionic with van der Waals interlayer interactions. The signature of the N shell lone pair of Ge is also evident from both the electron density Laplacian and the ELF topologies.

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).

Experimental and Theoretical Electron Density Determination for Two Norbornene Derivatives: Topological Analysis Provides Insights on Reactivity.

The electron density distribution of two substituted norbornene derivatives (cis-5-norbornene-endo-2,3-dicarboxylic anhydride (1) and 7-oxabicylo[2.2.1]hept-5-ene-exo-2,3-dicarboxylic anhydride (2) has been determined from low-temperature (20 K) X-ray diffraction data and from DFT calculations with periodic boundary conditions. Topological analysis of the electron density is discussed with respect to exo-selective additions, the partial retro-Diels-Alder (rDA) character of the ground state, and intermolecular interaction energies.

Host perturbation in a ß-hydroquinone clathrate studied by combined X-ray/neutron charge-density analysis: implications for molecular inclusion in supramolecular entities.

X-ray/neutron (X/N) diffraction data measured at very low temperature (15 K) in conjunction with ab initio theoretical calculations were used to model the crystal charge density (CD) of the host-guest complex of hydroquinone (HQ) and acetonitrile. Due to pseudosymmetry, information about the ordering of the acetonitrile molecules within the HQ cavities is present only in almost extinct, very weak diffraction data, which cannot be measured with sufficient accuracy even by using the brightest X-ray and neutron sources available, and the CD model of the guest molecule was ultimately based on theoretical calculations. On the other hand, the CD of the HQ host structure is well determined by the experimental data. The neutron diffraction data provide hydrogen anisotropic thermal parameters and positions, which are important to obtain a reliable CD for this light-atom-only crystal. Atomic displacement parameters obtained independently from the X-ray and neutron diffraction data show excellent agreement with a |ΔU| value of 0.00058 Å(2) indicating outstanding data quality. The CD and especially the derived electrostatic properties clearly reveal increased polarization of the HQ molecules in the host-guest complex compared with the HQ molecules in the empty HQ apohost crystal structure. It was found that the origin of the increased polarization is inclusion of the acetonitrile molecule, whereas the change in geometry of the HQ host structure following inclusion of the guest has very little effect on the electrostatic potential. The fact that guest inclusion has a profound effect on the electrostatic potential suggests that nonpolarizable force fields may be unsuitable for molecular dynamics simulations of host-guest interaction (e.g., in protein-drug complexes), at least for polar molecules.

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.

Experimental and theoretical charge densities of a zinc-containing coordination polymer, Zn(HCOO)2(H2O)2.

We present a combined experimental and theoretical charge density study of the coordination polymer Zn(HCOO)(2)(H(2)O)(2), which serves as a nonmagnetic reference for the isostructural magnetic compounds containing 3d transition metals. The charge density has been modeled using the multipole formalism against a high-resolution single-crystal X-ray diffraction data set collected at 100 K. The theoretical model is based on periodic density functional theory calculations in the experimental geometry. To gauge the degree of systematic bias from the multipole model, the structure factors of the theoretical model were also projected into a multipole model and the two theoretical models are compared with the experimental results. All models, both experiment and theory, show that the Zn atom densities are highly spherical but show small accumulations of charge toward the negative ligands. The metal-ligand interactions are found to be primarily ionic, but there are subtle topological indications of covalent contributions to the bonds. The source function calculated at the bond critical points reveals a rather delocalized picture of the density in the bridging carboxylates, and this presumably reflects the exchange pathway in the magnetic analogues.

Testing the concept of hypervalency: charge density analysis of K2SO4.

One of the most basic concepts in chemical bonding theory is the octet rule, which was introduced by Lewis in 1916, but later challenged by Pauling to explain the bonding of third-row elements. In the third row, the central atom was assumed to exceed the octet by employing d orbitals in double bonding leading to hypervalency. Ever since, polyoxoanions such as SO(4)(2-), PO(4)(3-), and ClO(4)(-) have been paradigmatic examples for the concept of hypervalency in which the double bonds resonate among the oxygen atoms. Here, we examine S-O bonding by investigating the charge density of the sulfate group, SO(4)(2-), within a crystalline environment based both on experimental and theoretical methods. K(2)SO(4) is a high symmetry inorganic solid, where the crystals are strongly affected by extinction effects. Therefore, high quality, very low temperature single crystal X-ray diffraction data were collected using a small crystal (∼30 µm) and a high-energy (30 keV) synchrotron beam. The experimental charge density was determined by multipole modeling, whereas a theoretical density was obtained from periodic ab initio DFT calculations. The chemical bonding was jointly analyzed within the framework of the Quantum Theory of Atoms In Molecules only using quantities derived from an experimental observable (the charge density). The combined evidence suggests a bonding situation where the S-O interactions can be characterized as highly polarized, covalent bonds, with the "single bond" description significantly prevailing over the "double bond" picture. Thus, the study rules out the hypervalent description of the sulfur atom in the sulfate group.

One-step synthesis and functionalization of hydroxyl-decorated magnetite nanoparticles.

Magnetite nanoparticles covered by a layer of omega-hydroxycarboxylic acid were synthesized in one step by high-temperature decomposition of iron(III) omega-hydroxycarboxylates in tri- and tetra-ethylene glycol. The nanoparticles were characterized by TEM, XRD, IR, XPS and NMR techniques in order to show that they comprise a crystalline magnetite core and actually bear on the outer surface terminal hydroxy groups. The latter ones are convenient "handles" for further functionalization as opposed to the chemically-inert aliphatic chains which cover conventionally synthesized nanoparticles. This was shown by several examples in which the hydroxy groups on the nanoparticle surface were easily transformed in other functional groups or reacted with other molecules. For instance, the hydroxyl-decorated nanoparticles were made water soluble by esterification with a PEGylated acetic acid. The reactive behavior of the surfactant monolayer was monitored by degrading the nanoparticles with aqueous acid and isolating the surfactant for NMR characterization. In general, the reactivity of the terminal hydroxyl groups on the nanoparticle surface parallels that observed in the free surfactants. The reported hydroxyl-decorated magnetite nanoparticles can be thus considered as pro-functional nanoparticles, i.e., a convenient starting material to functionalized magnetic nanoparticles.