X-ray diffraction studies of crystals under pressure and quantitative experimental charge density analysis are among the most demanding types of crystallographic research. A successful feasibility study of the electron density in the mineral grossular under 1 GPa pressure conducted at the CRISTAL beamline at the SOLEIL synchrotron is presented in this work. A single crystal was placed in a diamond anvil cell, but owing to its special design (wide opening angle), short synchrotron wavelength and the high symmetry of the crystal, data with high completeness and high resolution were collected. This allowed refinement of a full multipole model of experimental electron distribution. Results are consistent with the benchmark measurement conducted without a diamond-anvil cell and also with the literature describing investigations of similar structures. Results of theoretical calculations of electron density distribution on the basis of dynamic structure factors mimic experimental findings very well. Such studies allow for laboratory simulations of processes which take place in the Earth's mantle.
[2]rotaxanes composed of a dibenzo-24-crown-8 wheel (DB24C8) and an axle containing two metal-complexing tetraazamacrocyclic units linked with a p-xylylene bridge, coordinating the same or different metal ions (Ni and/or Cu) are described. A symmetric di-Ni rotaxane crystallizes in the monoclinic P21/c space group with one rotaxane cation and four PF6− counterions in the asymmetric part of the unit cell. In the crystal, the cations and anions of the investigated compound form an intertwined 3D-framework with C–H⋯F and C–H⋯π intermolecular interactions. The NMR ROESY spectrum of the diamagnetic di-Ni rotaxane confirms that at room temperature slow shuttling of the DB24C8 moiety takes place along the symmetric axle. The non-symmetric rotaxane, containing 14- and 16-membered nickel(II)-complexing macrocycles, exists in solution as an equilibrium mixture of two conformers in the ratio of ca. 1 : 7. This rotaxane behaves as a potential-controlled molecular switch: in the major isomer, the DB24C8 moiety is localized in the vicinity of the 14-membered metal-complexing macrocycle, and moves towards the 16-membered unit upon the first oxidation. Reverse translocation occurs after the subsequent oxidation of the 14-membered complex unit. In contrast, no such movements of the DB24C8 moiety were observed upon investigation of the heteronuclear [2]rotaxane, coordinating copper(II) and nickel(II) ions.
The azamacrocyclic complex was used as a platform for the construction of [3]rotaxanes containing two DB24C8 macrocycles per molecule. The complex unit incorporates two electron deficient π-bond systems and two N–H hydrogen bond donating groups which facilitated the formation of a 1 : 2 interlocked structure. Synthesis and properties of such compounds are presented. Structures of the obtained compounds were confirmed by NMR spectroscopy, ESI mass spectrometry, elemental analysis and single crystal X-ray diffraction. Both [3]rotaxanes containing two DB24C8 macrocycles per molecule crystallise in P and P21/n space groups. They have different counterions (PF6− and Cl− anions, respectively) and mostly disordered solvent molecules such as water, methanol and acetone. Both [3]rotaxanes have a flexible axle in which the Cl− salt takes the shape closer to the “S”-letter, while in the PF6− case the axle is more linear. The shape results from respective packing and intra-, and intermolecular interactions among the moieties in the rotaxane and the crystal lattice.
Plants are able to produce various types of crystals through metabolic processes, serving functions ranging from herbivore deterrence to photosynthetic efficiency. However, the structural analysis of these crystals has remained challenging due to their small and often imperfect nature, which renders traditional X-ray diffraction techniques unsuitable. This study explores the use of Microcrystal Electron Diffraction (microED) as a novel method for the structural analysis of plant-derived microcrystals, focusing on Armeria maritima (Milld.), a halophytic plant known for its biomineralisation capabilities. In this study, A. maritima plants were cultivated under controlled laboratory conditions with exposure to cadmium and thallium to induce the formation of crystalline deposits on their leaf surfaces. These deposits were analysed using microED, revealing the presence of sodium chloride (halite), sodium sulphate (thénardite), and calcium sulphate dihydrate (gypsum). Our findings highlight the potential of microED as a versatile tool in plant science, capable of providing detailed structural insights into biomineralisation processes, even from minimal and imperfect crystalline samples. The application of microED in this context not only advances the present understanding of A. maritima’s adaptation to saline environments but also opens new avenues for exploring the structural chemistry of biomineralisation in other plant species. Our study advocates for the broader adoption of microED in botanical research, especially when dealing with challenging crystallographic problems.
30 June 2026 in Journal of Chemical Information and Modeling
Synthetic ligands of retinoic acid receptor γ (RARγ) and vitamin D receptor (VDR) can act as agonists or antagonists by reshaping receptor conformation and cofactor recruitment, yet the structural and energetic determinants of this selectivity remain incompletely defined. Here, we present an integrated structural and thermodynamic analysis combining conformational characterization, molecular dynamics simulations, and molecular mechanics Poisson-Boltzmann surface area calculations to compare representative agonists and antagonists of human RARγ and VDR. Binding free energies and effective enthalpic contributions were evaluated for selected ligands, whereas the apparent entropic term, estimated indirectly as -TΔSapp = ΔGbind - ΔHeff, was used only as a qualitative internal descriptor. The thermodynamic profiles indicate that effective enthalpic stabilization is a more informative comparative descriptor than binding free energy alone, with clear agonist-antagonist separation for RARγ and a directional, less statistically resolved trend for VDR. These energetic patterns were interpreted alongside ligand-dependent stabilization of helix 12 and receptor-ligand interaction networks. Newly determined MicroED structures of AGN194310 and AGN205728 were incorporated as ligand-specific conformational references, improving structural definition without being treated as direct evidence of receptor-bound bioactive conformations. Comparative analysis of RARγ and VDR suggests that functional selectivity is not governed solely by affinity but emerges from the interplay among ligand-binding energetics, interaction networks, and receptor conformational dynamics. These results provide a retrospective mechanistic benchmark for interpreting agonist- and antagonist-associated behavior in nuclear receptors and may guide future studies on functionally selective modulators.