A New Crystal Form of the SARS-CoV-2 Receptor Binding Domain: CR3022 Complex—An Ideal Target for In-Crystal Fragment Screening of the ACE2 Binding Site Surface

In-crystal fragment screening is a powerful tool to chemically probe the surfaces used by proteins to interact, and identify the chemical space worth exploring to design protein-protein inhibitors. A crucial prerequisite is the identification of a crystal form where the target area is exposed and accessible to be probed by fragments. Here we report a crystal form of the SARS-CoV-2 Receptor Binding Domain in complex with the CR3022 antibody where the ACE2 binding site on the Receptor Binding Domain is exposed and accessible. This crystal form of the complex is a valuable tool to develop antiviral molecules that could act by blocking the virus entry in cells.

FragMAX: the fragment-screening platform at the MAX IV Laboratory

Advances in synchrotron storage rings and beamline automation have pushed data-collection rates to thousands of data sets per week. With this increase in throughput, massive projects such as in-crystal fragment screening have become accessible to a larger number of research groups. The quality of support offered at large-scale facilities allows medicinal chemistry-focused or biochemistry-focused groups to supplement their research with structural biology. Preparing the experiment, analysing multiple data sets and prospecting for interesting complexes of protein and fragments require, for both newcomers and experienced users, efficient management of the project and extensive computational power for data processing and structure refinement. Here, FragMAX, a new complete platform for fragment screening at the BioMAX beamline of the MAX IV Laboratory, is described. The ways in which users are assisted in X-ray-based fragment screenings and in which the fourth-generation storage ring available at the facility is best exploited are also described.

Quantum-chemical modeling of hydrogen bonds in α-glycine

Quantum chemistry was used to simulate a fragment of α-glycine crystal consisting of 5 and 6 glycine molecules. The α-glycine crystal fragment model was constructed using X-ray diffraction data contained in the Cambridge Crystallographic Database (CCDC). Theoretical IR spectra were obtained. It was shown that in a fragment of a crystal, glycine molecules in zwitterionic form form N-H...O hydrogen bonds of different strength, which correspond to different frequencies of stretching vibrations νst (N-H) of the NH3+ group. Full optimization of glycine crystal fragments consisting of a small number of molecules, regardless of the method of calculation, leads to the agglomeration of the structure. The system forms the maximum possible number of the most durable hydrogen bonds, thereby lowering the overall energy of the system, which leads to disruption of the crystal structure of the fragment, distortion of the parameters of hydrogen bonds in the crystal, and, consequently, to an unsystematic shift in the frequencies of N-H vibrations. To avoid this process, further modeling was performed by partially optimizing the geometry of the crystal fragment, with the positions of heavy nitrogen atoms, carbon and oxygen atoms being fixed, and only the positions of hydrogen atoms involved in the formation of hydrogen bonds were varied. Using the DFT/B3LYP/6-311G** method, the energies of donor–acceptor interaction in a fragment of a crystal, as well as its oscillation frequencies, are calculated. The calculated frequencies are consistent with the three experimental frequencies in the indicated X-ray region. A comparison was made between the calculated and experimental frequencies of the stretching vibrations of the N-H group of the NH3+ group. According to the geometric characteristics of the HB and the energy of donor-acceptor interaction between the lone electron pairs of oxygen atoms and the *(N-H) loosening orbitals, it was found that the hydrogen bonds of N-H...O between molecules in one layer are stronger than between molecules in different layers of a crystal.

Кинетика преципитации в бинарных сплавах вблизи границ зерен

Based on the method of the free energy density functional, the effect of grain boundaries on the precipitation process in binary alloys is considered. A comparative analysis of precipitation kinetics has been carried out for a single-crystal fragment of a solid solution and for a fragment containing a part of the boundary between two grains. We have found the influence of grain boundaries on the kinetics of the average radius of precipitates, their concentration, and nucleation rate for several compositions of the alloy.

Carlhintzeite, Ca2AlF7·H2O, from the Gigante granitic pegmatite, Córdoba province, Argentina: description and crystal structure

Carlhintzeite, Ca2AlF7·H2O, has been found at the Gigante pegmatite, Punilla Department, Córdoba Province, Argentina. It occurs as colourless prismatic crystals up to 0.8 mm long, ubiquitously twinned on {001}. Electron microprobe analyses provided the empirical formula Ca1.98Al1.02F6.24(OH)0.76·H1.62O. A crystal fragment used for the collection of structure data provided the triclinic, C1̄ cell: a = 9.4227(4), b = 6.9670(5), c = 9.2671(7) Å, α = 90.974(6), β = 104.802(5), γ = 90.026(6)°, V = 558.08(7) Å3 and Z = 4. The crystal structure, solved by direct methods and refined to R1 = 0.0322 for 723 Fo > 4σF reflections, is made up of linkages of AlF6 octahedra, CaF8 polyhedra and CaF6(H2O)2 polyhedra. The AlF6 octahedra are isolated from one another, but share polyhedral elements with Ca polyhedra. Most notably, the Al1 octahedron shares trans faces with two CaF8 polyhedra and the Al2 octahedron shares trans edges with two CaF6(H2O)2 polyhedra. The linkage of the Ca polyhedra alone can be described as a framework in which edge-sharing chains along b are cross-linked by edge-sharing. Edge-sharing chains of Ca polyhedra along b in the carlhintzeite structure are similar to those along c in the structures of gearksutite, CaAlF4(OH)·(H2O), and prosopite, CaAl2F4(OH)4.

LaI2@(18,3)SWNT: The Unprecedented Structure of a LaI2 “Crystal,” Encapsulated within a Single-Walled Carbon Nanotube

The novel crystallization properties of nano-materials represent a great challenge to researchers across all disciplines of materials science. Simple binary solids can be found to adopt unprecedented structures, when confined into nanometer-sized cavities, such as the inner cylindrical bore of single-walled carbon nanotubes (SWNT). Lanthanum iodide was encapsulated within SWNTs and the resulting encapsulation composite was analyzed using energy-dispersive X-ray microanalysis (EDX) and high-resolution transmission electron microscopy (HRTEM) imaging techniques, to reveal a one-dimensional crystal fragment, with the stoichiometry of LaI2, crystallizing in the structure of LaI3 with one third of the iodine positions unoccupied. A complete characterization of the encapsulation composite was achieved using an enhanced image restoration technique, which restores the object wave from a focal series of HRTEM images, providing information about the precise structural data of both filling material and host SWNT, and thereby enabling the identification of the SWNT chirality.

The surprisingly elusive crystal structure of sodium metabisulfite

The crystal structure of Na2S2O5, a simple and common ionic compound, is reported here for the first time. The crystals form non-merohedral twins, with the twin domains related by a twofold axis which bisects the angle between the a and c axes of each unit cell. The structure was determined from a single-crystal fragment of a twinned crystal that had undergone cleavage along the twin boundary. In addition to the problems associated with twinning, space-group determination proved difficult as well, with the structure initially determined in the P21 space group appearing to be disordered with two rotational conformers of the metabisulfite ion occupying equivalent sites in the lattice. An analysis at low temperature provided new weak reflections which were inconsistent with the original unit cell, but indexed to the correct unit cell, allowing for space group and crystal structure determination. The apparent structure, which appeared disordered in P21, seems to have resulted from an apparently fortuitous superposition of two conformationally inequivalent S2O_5^{2-} anions in the asymmetric unit of the correct structure in the P21/n space group. The metabisulfite ions in this structure do not adopt the Cs geometry observed in previously determined crystal structures containing S2O_5^{2-}. The structures of both ions in the asymmetric unit are effectively conformational mirror images of one another with two of the O atoms on each S atom in the ion approaching an eclipsed geometry. This observation provides further evidence that the structures of sulfur-oxy anions in the solid state are dictated mainly by interionic coulombic forces rather than by intraionic bonding interactions