Marlena Gryl

Polymorphism of urea–barbituric acid co-crystals

The crystal structures of three polymorphs found for the addition complex of urea and barbituric acid are described and compared. Two polymorphs are monoclinic, space groups P2(1)/c and Cc, whereas the third is triclinic, P1. The displacement of electron density towards the mesomeric forms, corresponding to the tautomeric forms of higher stability, of the barbituric acid molecule seem to influence the type of hydrogen bonds formed, which in turn determines the different packing topology in the polymorphs. While the polymorphic forms can be easily differentiated at the first-level graph-set analysis of their hydrogen-bonding patterns, a higher-level analysis enables important features of the mutual spatial arrangement of the structural components to be revealed.

Charge-density analysis in polymorphs of urea-barbituric acid co-crystals.

High-resolution single-crystal X-ray diffraction measurements at 100 K were performed for the two polymorphs of urea-barbituric acid co-crystals: (I) P2(1)/c and (II) Cc. Experimental and theoretical charge density and its properties were analysed for (I) and (II) in order to confirm the previous observation that in the polymorphs studied the barbituric acid molecules adopt different mesomeric forms, leading to different hydrogen-bond systems. Koch and Popelier criteria were applied to distinguish between hydrogen bonds and van der Waals interactions in the structures presented.

Lidocaine barbiturate: a promising material for second harmonic generation

Lidocaine barbiturate is a novel organic, mechanically and optically stable non-linear optical material, which shows effects higher than that of KDP. The engineered material, which belongs to the group of organic salts containing polarizable components, was characterized by means of X-ray diffraction, optical properties measurements and calculations.

Chelate Ring Size Effect as a Factor of Selective Fluorescent Recognition of Zn(2+) Ions by Pyrrolo[2,3-b]quinoxaline with a Substituted 2-Pyridyl Group Receptor.

Analysis of the spectral properties and structural differences of two turn-on ratiometric fluorescent receptors for Zn(2+) and Cd(2+) ions, derivatives of pyrrolo[2,3-b]quinoxaline (2), and earlier published 3 (Ostrowska et al. CrystEngComm 2015, 17, 498-502) was performed. Both ligands are E/Z push-pull olefins interconverting at room temperature, with barriers to rotation about enamine double bonds, from E to Z isomers of 19.3 ± 0.1 and 16.9 ± 0.3 kcal/mol and from Z to E of 16.9 ± 0.3 and 15.7 ± 0.2 kcal/mol, respectively. Diastereoisomers (E)-2 and (Z)-2 were isolated and characterized by X-ray structural analysis. The formation of complexes by (E/Z)-2 with acetates and acetylacetonates of Zn(2+) and Cd(2+) was monitored by UV-vis, fluorescence, and (1)H NMR titrations in acetonitrile, respectively. X-ray structural analysis for isolated [(E)-2]2Zn in relation to earlier published (E)-3-ZnOAc revealed the formation of a six-coordinated zinc ion with six- and four-membered bis-chelate rings by (E)-2. The chelate effect increases the ligand affinity for Zn(2+) (log β12 = 12.45) and causes the elongation of nitrogen-metal bonds. Extension of the coordination cavity size allows coordination of a cadmium ion. The introduction of a flexible ethylene linker between the fluorophore and ionophore pyridyl groups in 3 significantly affects the selectivity of zinc-ion recognition. The distorted tetrahedral geometry of (E)-3-ZnOAc with a four-coordinated zinc ion appears to be the most preferred because of the short donor-zinc distance with a 1:1 binding mode. The formation of the small coordination cavity size with six-membered bis-chelate rings provides an effective overlap of zinc and donor orbitals, precluding the coordination of a cadmium ion in the same manner as zinc.

The crystal structure and optical properties of a pharmaceutical co-crystal – the case of the melamine–barbital addition compound

The melamine barbital co-crystal is a product of crystal engineering of non-linear optical materials composed of pharmaceutically active ingredients. The resulting crystal phase shows a non-linear effect higher than that of KDP. The material was characterized by means of X-ray diffraction and optical property measurements and calculations.

Pyrrolo[2,3-b]quinoxaline with 2-(2-aminoethyl)pyridine chain highly selective fluorescent receptor for Zn2+ exhibiting a dual fluorescence and AIEE in crystalline state

This article describes the synthesis of a selective dual emissive intramolecular charge transfer (ICT) receptor for zinc ion in acetonitrile, exhibiting aggregation induced emission enhancement (AIEE) in the solid state due to the formation of inter- or intra-molecular hydrogen bonds and aromatic donor–acceptor interaction with H- or J-aggregation.

N-(5-Nitro­pyridin-2-yl)-5H-dibenzo[d,f][1,3]diazepine-6-carboxamide

The title compound, C19H13N5O3, can be obtained from the corresponding α-amido-α-aminonitrone in a reaction with biphenyl-2,2′-diamine. The amido–amidine core has distinctive geometrical parameters including: an outstandingly long Csp 2—Csp 2 single bond of 1.5276 (13) Å and an amidine N—C—N angle of 130.55 (9)°. Intramolecular N—H⋯O, N—H⋯N and C—H⋯O hydrogen bonds occur. In the crystal, molecules form layers parallel to (001) via weak intermolecular C—H⋯N interactions. The layers are linked via N—H⋯O hydrogen bonds and π–π interactions along [001] [benzene–pyridine centroid–centroid distance = 3.672 (2) Å].

Rubidium 2,4,6-trioxo-1,3-diazinan-5-ide–1,3-diazinane-2,4,6-trione–water (1/1/1)

The asymmetric unit of the title compound, Rb+·C4H3N2O3 −·C4H4N2O3·H2O, consists of one rubidium cation, a barbituric acid molecule, a barbiturate anion and one water molecule. The rubidium ion has seven close-contact interactions with O atoms, with Rb⋯O distances ranging from 2.8594 (16) to 3.2641 (14) Å. These seven O atoms together with an eighth O atom at 3.492 (2) Å away from Rb form a distorted polyhedron with shape intermediate between an antiprism and a dodecahedron. The Rb+ ions connect layers built of organic components and water molecules linked via N—H⋯O and O—H⋯O hydrogen bonds.

New tetraaza[14]annulene receptors derived from 2,3-diaminonaphthalene: synthesis and crystal structures

The first synthesis of the bis(2-hydroxybenzoyl)dinaphthotetraaza[14]annulene ligand and its O,O-bis-alkylated derivatives containing a decanedioxy bridging moiety, pendant bis-alkoxy groups as well as dicationic butoxypyridinium substituents is reported. The synthetic procedures, full analytical and spectroscopic characterisation (NMR, MS and IR) and crystal structures of the new products are described. The crystal structures show that naphthylene moieties incorporated into the investigated derivatives provide additional opportunities for non-covalent interactions between the molecules.

Unmasking the Mechanism of Structural Para- to Ferroelectric Phase Transition in (NH4)2SO4

New nontoxic and biocompatible ferroelectric materials are a subject undergoing intense study. One of the most promising research branches is focused on H-bonded organic or hybrid ferroelectrics. The engineering of these materials is based on mimicking the phase transition mechanisms of the well-known inorganic ferroelectrics. In our study, a coupled experimental and theoretical methodology was used for a precise investigation of the ferroelectric phase transition mechanism in ammonium sulfate (AS). A series of single-crystal X-ray diffraction measurements were performed in the temperature range between 273 and 163 K. The detailed inspection of the obtained static structural data, in the above-mentioned temperature range, allowed us to reveal dynamical effects at the ferroelectric phase transition. Accurate analysis of all geometrical features within the obtained crystal structures was carried out. The results were discussed in the view of previously discovered physical properties. X-ray studies were complemented by the use of quantum theory of atoms in molecules calculations and Hirshfeld surface analysis. Valence shell charge concentration analysis allowed us to find the subtle changes between charge density distribution within SO42- in para- and ferroelectric phases. H-bond interactions, geometrically classified in both AS phases, were all confirmed by the appropriate critical points. The interaction energies were estimated for the structures at 273, 233, 213, 183, and 163 K. Correlation between the geometrical approach and the results of theoretical calculations enabled us to discover the differences in interaction equilibrium between the AS phases. The mechanism of the phase transition originates from the disruption of the vibrational lattice mode between sulfate anions. Our studies resolved the problem, which was under discussion for more than 60 years.