Thermal-induced transformation of glutamic acid to pyroglutamic acid and self-cocrystallization: a charge–density analysis

Thermal-induced transformation of glutamic acid to pyroglutamic acid is well known. However, confusion remains over the exact temperature at which this happens. Moreover, no diffraction data are available to support the transition. In this article, we make a systematic investigation involving thermal analysis, hot-stage microscopy and single-crystal X-ray diffraction to study a one-pot thermal transition of glutamic acid to pyroglutamic acid and subsequent self-cocrystallization between the product (hydrated pyroglutamic acid) and the unreacted precursor (glutamic acid). The melt upon cooling gave a robust cocrystal, namely, glutamic acid–pyroglutamic acid–water (1/1/1), C5H7NO3·C5H9NO4·H2O, whose structure has been elucidated from single-crystal X-ray diffraction data collected at room temperature. A three-dimensional network of strong hydrogen bonds has been found. A Hirshfeld surface analysis was carried out to make a quantitative estimation of the intermolecular interactions. In order to gain insight into the strength and stability of the cocrystal, the transferability principle was utilized to make a topological analysis and to study the electron-density-derived properties. The transferred model has been found to be superior to the classical independent atom model (IAM). The experimental results have been compared with results from a multipolar refinement carried out using theoretical structure factors generated from density functional theory (DFT) calculations. Very strong classical hydrogen bonds drive the cocrystallization and lend stability to the resulting cocrystal. Important conclusions have been drawn about this transition.

Regioselective synthesis of methyl 5-(N-Boc-cycloaminyl)-1,2-oxazole-4-carboxylates as new amino acid-like building blocks

A convenient and efficient synthesis of novel achiral and chiral heterocyclic amino acid-like building blocks was developed. Regioisomeric methyl 5-(N-Boc-cycloaminyl)-1,2-oxazole-4-carboxylates were prepared by the reaction of β-enamino ketoesters (including azetidine, pyrrolidine or piperidine enamines) with hydroxylamine hydrochloride. Unambiguous structural assignments were based on chiral HPLC analysis, 1H, 13C, and 15N NMR spectroscopy, HRMS, and single-crystal X-ray diffraction data.

Crystal structure from X-ray powder diffraction data, DFT-D calculation, Hirshfeld surface analysis, and energy frameworks of (RS)-trichlormethiazide

The structure of racemic (RS)-trichlormethiazide [systematic name: (RS)-6-chloro-3-(dichloromethyl)-1,1-dioxo-3,4-dihydro-2H-1λ6,2,4-benzothiadiazine-7-sulfonamide], C8H8Cl3N3O4S2 (RS-TCMZ), a diuretic drug used in the treatment of oedema and hypertension, was determined from laboratory X-ray powder diffraction data using DASH [David et al. (2006). J. Appl. Cryst. 39, 910–915.], refined by the Rietveld method with TOPAS-Academic [Coelho (2018). J. Appl. Cryst. 51, 210–218], and optimized using DFT-D calculations. The extended structure consists of head-to-tail dimers connected by π–π interactions which, in turn, are connected by C—Cl...π interactions. They form chains propagating along [101], further connected by N—H...O hydrogen bonds to produce layers parallel to the ac plane that stack along the b-axis direction, connected by additional N—H...O hydrogen bonds. The Hirshfeld surface analysis indicates a major contribution of H...O and H...Cl interactions (32.2 and 21.7%, respectively). Energy framework calculations confirm the major contribution of electrostatic interactions (E elec) to the total energy (E tot). A comparison with the structure of S-TCMZ is also presented.

Synthesis and crystal structure of cytotoxic copper(II) complex with 1,10-phenanthroline-5,6-dione and isothiazole derivative

Oligopyridine based copper(II) complexes are of interest to scientists as possible anticancer agents due to promising cytotoxic and DNA binding/cleaving properties. In this study, copper(II) complex [Cu(phendione)L2]·C2H5OH with 1,10-phenanthroline-5,6-dione (phendione) and 4,5-dichloro-isothiazole-3-carboxylic acid (HL) was synthesized and characterized by elemental analysis, IR-spectroscopy, X-ray powder diffraction and single-crystal X-ray diffraction. According to X-ray diffraction data, obtained compound is mononuclear complex with square pyramidal coordination environment of the central atom which is surrounded by two isothiazolate molecules and one phendione ligand. The X-ray diffraction data are confirmed by IR-spectroscopy data showing the presence of characteristic stretching vibration bands of the carbonyl and carboxyl groups of oligopyridine ligand and isothiazolate ions, respectively. Density functional theory (DFT) calculations for complex were carried out using the ADF software package to perform geometry optimization and frequency calculations that were in a good agreement with experimental IR spectrum. Cytotoxicity of complex and initial reagents was tested in vitro against HepG2 (human hepatocellular carcinoma) and MCF-7 (human breast adenocarcinoma) cell lines. The complex showed high dose-dependent cytotoxic activity with the IC50 values of 0.60±0.03 µM and 0.96±0.13 µM, respectively, which is higher than the activity of cisplatin against these cell lines. The activity of the complex is due to the presence of phendione ligand, which exhibits a similar cytotoxic activity.

B-factor accuracy in protein crystal structures

The accuracy of B factors in protein crystal structures has been determined by comparing the same atoms in numerous, independent crystal structures of Gallus gallus lysozyme. Both B-factor absolute differences and normal probability plots indicate that the estimated B-factor errors are quite large, close to 9 Å2 in ambient-temperature structures and to 6 Å2 in low-temperature structures, and surprisingly are comparable to values estimated two decades ago. It is well known that B factors are not due to local movements only but reflect several, additional factors from crystal defects, large-scale disorder, diffraction data quality etc. It therefore remains essential to normalize B factors when comparing different crystal structures, although it has clearly been shown that they provide useful information about protein dynamics. Improved, quantitative analyses of raw B factors require novel experimental and computational tools that are able to disaggregate local movements from other features and properties that affect B factors.

Two states of a light-sensitive membrane protein captured at room temperature using thin-film sample mounts

Room-temperature diffraction methods are highly desirable for dynamic studies of biological macromolecules, since they allow high-resolution structural data to be collected as proteins undergo conformational changes. For crystals grown in lipidic cubic phase (LCP), an extruder is commonly used to pass a stream of microcrystals through the X-ray beam; however, the sample quantities required for this method may be difficult to produce for many membrane proteins. A more sample-efficient environment was created using two layers of low X-ray transmittance polymer films to mount crystals of the archaerhodopsin-3 (AR3) photoreceptor and room-temperature diffraction data were acquired. By using transparent and opaque polymer films, two structures, one corresponding to the desensitized, dark-adapted (DA) state and the other to the ground or light-adapted (LA) state, were solved to better than 1.9 Å resolution. All of the key structural features of AR3 were resolved, including the retinal chromophore, which is present as the 13-cis isomer in the DA state and as the all-trans isomer in the LA state. The film-sandwich sample environment enables diffraction data to be recorded at room temperature in both illuminated and dark conditions, which more closely approximate those in vivo. This simple approach is applicable to a wide range of membrane proteins crystallized in LCP and light-sensitive samples in general at synchrotron and laboratory X-ray sources.

X-ray powder diffraction data for rivaroxaban, C19H18ClN3O5S

X-ray powder diffraction data, unit-cell parameters, and space group for rivaroxaban, C19H18ClN3O5S, are reported [a = 9.010(3) Å, b = 10.986(6) Å, c = 11.230(1) Å, α = 63.439(5)°, β = 74.355(4)°, γ = 78.133(3)°, unit-cell volume V = 952.87 Å3, Z = 2, ρcal = 1.519 g cm−3, and space group P1]. All measured lines were indexed and are consistent with the P1 space group. No detectable impurities were observed.