Crystal structure and Hirshfeld surface analysis of the hydrated 2:1 adduct of piperazine-1,4-diium 3,5-dinitro-2-oxidobenzoate and piperazine

The crystal structure of the adduct piperazine-1,4-diium 3,5-dinitro-2-oxidobenzoate–piperazine–water (2/1/2) shows the existence of a 3,5-dinitrosalicylate dianion (DNSA2−) and a protonated piperazine-1,4-diium cation (PIP2+) along with a piperazine molecule. The formula of the title adduct in the asymmetric unit is 2C4H12N2 2+·2C7H2N2O7 2−·C4H10N2·2H2O with Z = 1. The piperazine ring in the piperazine-1,4-diium cation and in the neutral piperazine molecule adopt chair conformations. All O atoms in the DNSA2− moiety and the water molecule act as hydrogen-bonding acceptors for various intermolecular O—H...O, N—H...O and C—H...O interactions, which stabilize the crystal structure. Various supramolecular architectures formed by the different intermolecular interactions are discussed. The relative contribution of various intermolecular contacts is analysed with the aid of two-dimensional (full and decomposed) fingerprint plots, indicating that H...O/O...H (50.2%) and H...H (36.2%) contacts are the major contributors to the stabilization of the crystal structure.

Crystal structure and Hirshfeld surface analysis of 6,6′-((1E,1′E)-{[1,4-phenylenebis(methylene)]bis(azanylylidene)}bis(methaneylylidene))bis(2-methoxyphenol)

The Schiff base compound, C24H24N2O4, was synthesized by the interaction of 2-hydroxy-3-methoxy benzaldehyde and 1,4-benzene dimethanamine in ethanol, and crystallizes in the monoclinic space group P21/n with Z′ = 0.5. The molecule is not planar, the 1,4-diethylbenzene and the phenol rings are twisted with respect to each other, making a dihedral angle of 74.27 (5)°. The molecular structure is stabilized by an O—H...N hydrogen bond, forming an S(6) ring motif. In the crystal, molecules are linked by C—H...O hydrogen bonds, resulting in the formation of sheets parallel to the bc plane. A Hirshfeld surface analysis was undertaken to investigate the various intermolecular contacts controlling the supramolecular topology, suggesting the H...O (18%) contacts to be the most significant interactions, whereas the H...H (50.5%) and C...H (24.3%) interactions are less significant.

Interactions of Pleiotrophin with a Structurally Defined Heparin Hexasaccharide

Pleiotrophin (PTN) is a potent cytokine that plays an important role in neural generation, angiogenesis, inflammation, and cancers. Its interactions with the polysaccharide glycosaminoglycan (GAG) are crucial to PTN’s biological activities. In this study, we investigated the interaction of selectively protonated PTN with the heparin hexasaccharide ΔUA2S-(GlcNS6S-IdoA2S)2-GlcNS6S using solution NMR. The use of a structurally defined oligosaccharide and selectively protonated PTN enabled us to obtain intermolecular contacts using unfiltered NOESY experiments, significantly increasing the amount of high-resolution structural information obtainable. Our data showed that PTN’s arginines, lysines, and tryptophans in the two structured domains have strong interactions with the 2-O-sulfated uronate protons in the heparin hexasaccharide. Consistent with the NMR data is the observation that 2-O-desulfation and N-desulfation/N-acetylation significantly decreased heparin hexasaccharides’ affinity for PTN, while 6-O-desulfation only modestly affected the interactions with PTN. These results allowed us to hypothesize that PTN has a preference for sulfate clusters centered on the GlcNS6S-IdoA2S disaccharide. Using these data and the fact that PTN domains mostly bind heparin hexasaccharides independently, models of the PTN-heparin complex were constructed.

Roboustness of Hydrogen Bonding in the Construction of Supramolecular Architechures in Protonated Perchlorate Salts

Five new multicomponent salts of perchloric acid with a series of substituted anilines and N-heterocyclic amines namely Diphenylaminium perchlorate (DPAPC) (1), 2, 5-dichloroanilinium perchlorate (25DAP) hydrate (2), 4-Methylanilinium perchlorate (4MAPC) (3), 4-diamino-6-methyl-1, 3, 5-triazin-1-ium hydrogen perchlorate (24DAMTHP) (4) and 8-hydroxyquinolinium hydrogen perchlorate (8HQP) (5) were prepared and structurally characterized. The entire complexes were subjected to FTIR and elemental analysis. A vast family of intermolecular contacts N-H…O, O-H…O, N-H…N and C-H…O were observed, which are key ingredient in the generation of privileged supramolecular self-assemblies appeared as one-dimensional chain, two-dimensional ladder and helix. Cambridge structural Database (CSD) analysis of 52 hits revealed the perchloric acid display higher propensity of ladder architectures. Molecular stability of the complexes were studied by quantum chemical calculations using DFT/B3LYP method with 6-31G(d,p) basis set. Further their relative charge distributions were identified using molecular electrostatic potential map. The use of Hirshfeld surfaces in combination with fingerprint plots was visualized in order to study the closer contacts within the molecule. The relative contribution of whole percentage of interactions associated is highlighted.

Straightforward Regio- and Diastereoselective Synthesis, Molecular Structure, Intermolecular Interactions and Mechanistic Study of Spirooxindole-Engrafted Rhodanine Analogs

Straightforward regio- and diastereoselective synthesis of bi-spirooxindole-engrafted rhodanine analogs 5a–d were achieved by one-pot multicomponent [3 + 2] cycloaddition (32CA) reaction of stabilized azomethine ylide (AYs 3a–d) generated in situ by condensation of L-thioproline and 6-chloro-isatin with (E)-2-(5-(4-chlorobenzylidene)-2,4-dioxothiazolidin-3-yl)-N-(2-morpholinoethyl)acetamide. The bi-spirooxindole-engrafted rhodanine analogs were constructed with excellent diastereo- and regioselectivity along with high chemical yield. X-ray crystallographic investigations for hybrid 5a revealed the presence of four contiguous stereocenters related to C11, C12, C19 and C22 of the spiro structure. Hirshfeld calculations indicated the presence of many short intermolecular contacts such as Cl...C, S...S, S...H, O...H, N...H, H...C, C...C and H...H interactions. These contacts played a very important role in the crystal stability. The polar nature of the 32CA reaction was studied by analysis of the conceptual DFT reactivity indices. Theoretical study of this 32CA reaction indicated that it takes place through a non-concerted two-stage one-step mechanism associated with the nucleophilic attack of AY 3a to the electrophilic ethylene derivative.

Synthesis, X-ray Structure, Conformational Analysis, and DFT Studies of a Giant s-Triazine bis-Schiff Base

The current work involves the synthesis of 2,2′-(6-(piperidin-1-yl)-1,3,5-triazine-2,4-diyl)bis(hydrazin-2-yl-1-ylidene))bis(methanylylidene))diphenol 4, characterization, and the DFT studies of the reported compound. The crystal unit cell parameters of 4 are a = 8.1139(2) Å, b = 11.2637(2) Å, c = 45.7836(8) Å. The unit cell volume is 4184.28(15) Å3 and Z = 4. It crystallized in the orthorhombic crystal system and Pbca space group. The O…H, N…H, C…H, H…H and C…C intermolecular contacts which affect the crystal stability were quantitatively analyzed using Hirshfeld calculations. Their percentages were calculated to be 9.8, 15.8, 23.7, 46.4, and 1.6% from the whole contacts occurred in the crystal, respectively. Conformational analysis was performed using DFT calculations for 17 suggested conformers and the most stable conformer was found to be the one which is stabilized by two intramolecular O-H…N hydrogen bonding interactions. This conclusion was further revealed by natural bond orbital calculations.

Fluorenonophane chlorobenzene solvate: molecular and crystal structures

The title compound, 19 H,79 H-3,5,9,11-tetraoxa-1,7(2,7)-difluorena-4,10(1,3)-dibenzenacyclododecaphane-19,79-dione (fluorenonophane), exists as a solvate with chlorobenzene, C42H28O6·C6H5Cl. The fluorenonophane contains two fluorenone fragments linked by two m-substituted benzene fragments. Some decrease in its macrocyclic cavity leads to a stacking interaction between the tricyclic fluorenone fragments. In the crystal, the fluorenonophane and chlorobenzene molecules are linked by weak C—H...π(ring) interactions and C—H...Cl hydrogen bonds. The Cl atom of chlorobenzene does not form a halogen bond. A Hirshfeld surface analysis and two-dimensional fingerprint plots were used to analyse the intermolecular contacts found in the crystal structure.

Crystal structure and Hirshfeld surface analysis of 2-{[(E)-(3-cyclobutyl-1H-1,2,4-triazol-5-yl)imino]methyl}phenol

The title compound, C13H14N4O, was developed using the reaction of salicylaldehyde and 3-amino-5-cyclobutyl-1,2,4-triazole in ethanol under microwave irradiation. This eco-friendly microwave-promoted method proved to be efficient in the synthesis of 2-{[(E)-(3-cyclobutyl-1H-1,2,4-triazol-5-yl)imino]methyl}phenol in good yields and purity. The title compound is a Schiff base that exists in the phenol–imine tautomeric form and adopts an E configuration. The three independent molecules in the asymmetric unit (A, B and C) are not planar, the cyclobutyl and the phenol-imine rings are twisted to each other making a dihedral angle of 67.8 (4)° in molecule A, 69.1 (2)° in molecule B and 89.1 (2)° in molecule C. In each molecule an intramolecular O—H...N hydrogen bond is present, forming an S(6) ring motif. A Hirshfeld surface analysis was performed to investigate the contributions of the different intermolecular contacts within the supramolecular structure. The major interactions are H...H (53%), C...H (19%) and N...H (17%) for molecule A, H...H (50%), N...H (20%) and C...H (20%) for molecule B and H...H (57%), C...H (14%) and N...H (13%) for molecule C.