N-(4-Amino-1,2,5-oxa­diazol-3-yl)formamide

α-D-2'-Deoxyribonucleosides are products of the γ-irradiation of DNA under oxygen-free conditions and are constituents of anomeric DNA. They are not found as natural building blocks of canonical DNA. Reports on their conformational properties are limited. Herein, the single-crystal X-ray structure of α-D-2'-deoxyadenosine (α-dA), C10H13N5O3, and its conformational parameters were determined. In the crystalline state, α-dA forms two conformers in the asymmetric unit which are connected by hydrogen bonds. The sugar moiety of each conformer is arranged in a `clamp'-like fashion with respect to the other conformer, forming hydrogen bonds to its nucleobase and sugar residue. For both conformers, a syn conformation of the nucleobase with respect to the sugar moiety was found. This is contrary to the anti conformation usually preferred by α-nucleosides. The sugar conformation of both conformers is C2'-endo, and the 5'-hydroxyl groups are in a +sc orientation, probably due to the hydrogen bonds formed by the conformers. The formation of the supramolecular assembly of α-dA is controlled by hydrogen bonding and stacking interactions, which was verified by a Hirshfeld and curvedness surface analysis. Chains of hydrogen-bonded nucleobases extend parallel to the b direction and are linked to equivalent chains by hydrogen bonds involving the sugar moieties to form a sheet. A comparison of the solid-state structures of the anomeric 2'-deoxyadenosines revealed significant differences of their conformational parameters.

Synthesis, spectroscopic, topological, hirshfeld surface analysis, and anti-covid-19 molecular docking investigation of isopropyl 1-benzoyl-4-(benzoyloxy)-2,6-diphenyl-1,2,5,6-tetrahydropyridine-3-carboxylate

Two co-crystals of 2,3-dimethylquinoxaline (DMQ) and dimethylglyoxime (DMG) have been synthesized and characterized by single crystallographic X-ray, IR and thermal studies. Co-crystal I is colorless while co-crystal II is orange in color. In the co-crystals, both hydrogen-bonding and π··· interactions assemble both DMQ and DMG within the crystal structure. For co-crystal I, 2D supramolecular sheet structure is formed by utilizing both hydrogen bonding and π··· interactions, while for co-crystal II supramolecular 1D chain motifs are formed by O–H···N hydrogen bonding interactions which are held together by C–H···O interactions to form 2D supramolecular network. These 2D supramolecular networks are further stacked by π···π and C–H···π interactions of aromatic rings of DMQ leading to the formation of 3D supramolecular structure. Examination of the intermolecular interactions and crystal packing via Hirshfeld surface analysis reveals that most of the close contacts are associated with weak interactions. The fingerprint plots indicate that these weak interactions have significant role in crystal packing. Thermogravimetric analyses of the co-crystals have been carried out. Two concomitant co-crystals of active pharmaceutical ingredients (API) 2,3-dimethylquinaxoline (DMQ) and co-crystallizing agent dimethylglyoxime (DMG) have been synthesized and characterized by X-ray crystal structure, IR analysis along with their detailed Hirshfeld surfaces analyses.

Solvent effect on neutral Co (II) complexes of paeonol derivative –qualitative and quantitative studies from energy frame work and Hirshfeld surface analysis

The indoline portion of the title molecule, C16H13NO2, is planar. In the crystal, a layer structure is generated by C—H...O hydrogen bonds and C—H...π(ring), π-stacking and C=O...π(ring) interactions. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H...H (43.0%), H...C/C...H (25.0%) and H...O/O...H (22.8%) interactions. Hydrogen bonding and van der Waals interactions are the dominant interactions in the crystal packing. The volume of the crystal voids and the percentage of free space were calculated to be 120.52 Å3 and 9.64%, respectively, showing that there is no large cavity in the crystal packing. Evaluation of the electrostatic, dispersion and total energy frameworks indicate that the stabilization is dominated by the dispersion energy contributions in the title compound. Moreover, the DFT-optimized structure at the B3LYP/6-311G(d,p) level is compared with the experimentally determined molecular structure in the solid state.

In the title mol-ecule, C20H21N3O3, the allyl substituent is rotated out of the plane of its attached phenyl ring [torsion angle 100.66 (15)°]. In the crystal, C-HMthphn⋯OMthphn (Mthphn = meth-oxy-phen-yl) hydrogen bonds lead to the formation of (100) layers that are connected into a three-dimensional network by C-H⋯π(ring) inter-actions, together with π-π stacking inter-actions [centroid-to-centroid distance = 3.7318 (10) Å] between parallel phenyl rings. Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯H (48.7%) and H⋯C/C⋯H (23.3%) inter-actions. Computational chemistry reveals that the C-HMthphn⋯OMthphn hydrogen bond energy is 47.1 kJ mol-1. The theoretical structure, optimized by density functional theory (DFT) at the B3LYP/ 6-311 G(d,p) level, is compared with the experimentally determined mol-ecular structure. The HOMO-LUMO behaviour was elucidated to determine the energy gap.

Efavirenz, an antiviral medication for HIV, is known for its significant binding to inhibit HIV-1 reverse transcriptase. In this study, we highlighted the structural and electronic properties of both the monomer and dimer through computational evaluations using DFT at the B3LYP/6 − 311 + + G(d, p) theoretical approach. The dimer was created from the monomer by intermolecular hydrogen bonding N–H…O, and it’s electronic, structural, and reactivity properties were compared to those of the monomer. The quantification of intermolecular interactions and mechanical strength has been obtained from the Hirshfeld surface analysis. The red spots seen at the hydrogen of the NH group and the oxygen of the C=O group in the Hirshfeld surface justified the intermolecular hydrogen bonding in crystal packing. The red spots seen at the hydrogen of the NH group and the oxygen of the C=O group in the Hirshfeld surface justified the intermolecular hydrogen bonding in crystal packing. The intermolecular hydrogen bonding interaction in the dimer is illustrated by the quantum theory of atoms in molecule analysis and interaction energy evaluated to be − 16.27 kcal/mol. The maximum positive potential of 51.51 kcal/mol is associated with H28, while the lowest potential of − 40.52 kcal/mol is related to O30 in the monomer, as revealed from the molecular electrostatic potential surface analysis. This result suggests that the (NH) and (C = O) groups in efavirenz are ideal sites for intermolecular interactions, contributing to its biological activity. Significant interaction energy between the monomers revealed from computational evaluation leads to a stable dimer. High packing efficiency observed from void calculations confirmed the mechanical stability of the crystal. Smaller frontier molecular orbitals energy gap in dimer compared to monomer shows increase in its chemical reactivity.

Phenytoin from antiepileptic to covid-19: Synthesis, crystal structure, DFT, HSA, MEP and green biological study of phenytoin derivative as potential covid-19 drug candidates

We presented two new ABX3 postperovskite coordination polymers, (C5H13NCl)[M(dca)3] (dca = N(CN)2–, M = Mn2+ for 1 and Cd2+ for 2), as well as their phase transition behaviors disclosed by using differential scanning calorimetry measurements, variable-temperature single-crystal X-ray analyses, dielectric measurements, and Hirshfeld surface analyses. Both 1 and 2 have same structure (Cmcm) at room temperature, in which their A-site organic cations are fourfold disordered about two mirror planes and undergo order–disorder phase transition mainly caused by the freezing of A-site cations upon cooling. The different metal ions endow them distinct structural flexibility, resulting in different phase transition behaviors and dielectric responses; that is, the smaller and coordinatively rigid Mn2+ ion results in two-step Cmcm (Z = 4) ↔ Pbcm (Z = 4) ↔ Pbca (Z = 8) transitions accompanied with obvious dielectric relaxation, whereas the larger and coordinatively flexible Cd2+ ion results in one-step Cmcm (Z = 4) ↔ Pbca (Z = 16) transition accompanied with a sharp dielectric switching. This study well demonstrates the tunability of postperovskite, as a new kind of host–guest model, for modulating the phase transition and relevant switching physical properties.

The title salt (systematic name: 2-methyl-4-oxo-3,4-dihydroquinazolin-1-ium chloride), C9H9N2O+·Cl-, has ortho-rhom-bic (Pbcm) symmetry. Except for two methyl H atoms, all atoms of the mol-ecular cation are located about a mirror plane, making the quinazolinium moiety exactly planar. Individual mol-ecules are arranged in (001) layers in the crystal. Supra-molecular features include N-H⋯Cl hydrogen-bonding inter-actions, leading to zigzag chains along [010] with D 1 1(2) and C 1 2(6) graph-set motifs. Additionally, weak π-π stacking inter-actions occur between benzene rings in adjacent layers. Hirshfeld surface analysis revealed that the most important contributions to the surface contacts are from H⋯H (36.1%), H⋯C/C⋯H (25.8%), and H⋯O/O⋯H (17.7%) inter-actions.

Co-crystal of the N,N´-(((3,6-dichloro-9H-carbazole-1,8-diyl)bis(azanediyl))bis(carbonothioyl))bis(2,2-dimethylpropanamide) as a carbazole-based thiourea derivative (CBT) with acetic acid (AcOH) was prepared and its molecular structure examined using the single crystal X-ray diffraction study and the Hirshfeld surface analysis. This co-crystal was designed to explore the supramolecular synthons and intermolecular interactions diversity between the components of co-crystal. The analysis of the crystal structure and packing revealed that the CBT:AcOH co-crystal are formed by a strong O–H⋯S and C-H···O hydrogen bonding interactions between components of co-crystal. In addition, its’ structure is further stabilized by strong C-H···π stacking interactions and N-H···O and N-H···S homosynthons between CBT molecules. The Hirshfeld surfaces and associated two-dimensional fingerprint plots of the co-crystal were also analyzed to clarify the nature of the hydrogen bond interactions and close intermolecular interactions in the crystal structure. The Hirshfeld surfaces and the associated two-dimensional fingerprint plots analysis revealed that the majority of close contacts forming supramolecular structure were associated with relatively weak interactions such as H···H, C···H and N···H. So, it can be said that these interactions play a major role in molecular crystal packing.

Two new copper (II) carboxylate complexes based on N,N,N',N'-tetramethylethyleneamine: Synthesis, crystal structures, spectral properties, dft studies and hirshfeld surface analysis

Investigation of intermolecular interactions in finasteride drug crystals in view of X-ray and Hirshfeld surface analysis

Two tetramethylguanidinium halostannate inorganic-organic hybrid compounds was isolated and structurally investigated by single crystal X-ray crystallography and Hirshfeld surface analysis. The compound [(C6H14N3)2SnCl6] (1), crystallizes in the orthorhombic space group Fddd with Z = 8 / Z’ = 0.25, a = 7.3474(3) Å, b = 22.3678(8) Å, c = 28.4908(10) Å and V = 4682.3(3) Å3. The compound [(C6H14N3)2SnBr6] (2), crystallizes in the orthorhombic space group Fddd with Z = 8 / Z’ = 0.25, a = 7.5767(5) Å, b = 23.0591(17) Å, c = 29.008(2) Å and V = 5068.0(6) Å3. The isolation of 1 undergoes a redox process from Sn(II) to Sn(IV) in solution and in a non-controlled atmosphere. Both compounds 1 and 2 describe TMG+ ions with a central carbon atom in a trigonal–planar fashion. With respect to this CN3 plane, the pairs of di­methyl­ammonium groups are twisted by 13.70 (8) and 32.21 (8)° for 1, 14.88 (13) and 31.95(13)° for 2. The SnX6 dianions evidence a slightly distorted octahedron (Oh) about Sn centre for hybrids 1 and 2. Within the structures of the hybrid materials 1 and 2, N-H···Cl inter-species hydrogen bonding patterns between the inorganic stannate and the organic entities give rise a one-dimensional chain, wherein inorganic and organic species alternate. The propagation of the chain generates rings. The weak C-H···X hydrogen bonds formed from the methyl groups to adjacent tetramethylguanidinium-stannate chains result in a supramolecular three-dimensional hydrogen-bonded network. The Hirshfeld surface analysis shows existence of both strong and weak hydrogen bonding interactions. Inspection of 1 and 2 by the Hirshfeld surface analysis, show isostructural behavior. Hybrids 1 and 2 are the first crystal reports of a tetramethylguanidinium tetra- or hexa-halostannate.

A novel centrosymmetric hybrid organic-inorganic material (1,4-dimethylpiperazine tetrachlorocuprate (II)) has been prepared and analyzed using single crystal X-ray diffraction, spectroscopic studies, photoluminescence properties, DFT studies and Hirshfeld surface analyses. The single crystal X-ray analysis indicates that the compound crystallizes in the P21/c monoclinic space group. The N–H···Cl hydrogen bonds are alternately connected by organic cations [C6H16N2]2+ and inorganic moieties [CuCl4]2-. The Hirshfeld surfaces investigated the nature and quantity of different interactions and their role in crystal packing. Infrared and Hirshfeld measurements were performed to confirm the results obtained by X-ray diffraction. In addition, optical measurements were used to investigate the IR and photoluminescence properties. The di-electrical investigations show interesting electrical behavior of the compound. In addition, an insilico investigation using molecular docking of the compound against SARS-CoV-2 variation (B.1.1.529) was also conducted to better understand the non-covalent interaction of cuprate(II) complexes with active amino acids in the SARS-CoV-2 spike proteins. These studies were supported by drug-likeness and absorption, distribution, metabolism, and excretion (ADME) analyses.