Journal of Chemical Crystallography最新文献

The ionic compound N-(2-hydroxyethyl)piperazinium chloride (HEPH)Cl, containing a piperazinium cation with a + 1 charge, was crystallized in the orthorhombic space group P2₁2₁2₁. The unit cell parameters were determined to be a = 8.6083(3) Å, b = 8.8523(3) Å, and c = 10.7405(4) Å. The volume of the unit cell was found to be 818.46(5) ų, with a Z value of 4. Refinement yielded R[F² > 2σ(F²)] = 0.018, wR(F²) = 0.028, and a goodness-of-fit parameter of S = 1.77. The crystal structure reveals the presence of three hydrogen bonds: O1–H1o1···Cl1, N1–H1n1···N2, and N1–H2n1···Cl1, which contribute to the specific molecular arrangements within the crystal lattice.Electrochemical properties of (HEPH)Cl were examined by cyclic voltammetry (CV). Molecular docking experiments were conducted to assess the interactions of (HEPH)Cl with Mycobacterium tuberculosis DNA gyrase, coronavirus main protease, Plasmodium falciparum protein, and human serum albumin.

Graphical Abstract

N-(2-hydroxyethyl)piperazinium chloride cation uniquely adopts a chair conformation carrying a +1 charge, stabilized by crucial hydrogen bonding interactions that enhance molecular recognition and binding affinity observed in docking study.

Crystals of mono- and dibromo as well as two isomeric tribromocymantrenes [Mn(C₅H_5-nBr_n)(CO)₂(PPh₃)] (n = 1–3) were obtained and examined by X-ray diffraction. The degree of substitution has only minor influence on bond lengths and angles. However, the relative orientations of bromo substituents and PPh₃ ligand as well as relative orientation of the cyclopentadienyl ring and the MnC₂P tripod are sensitive to the number and position of bromines. All compounds show weak Br…O interactions, mostly combined with hydrogen bonds, while Br…Br interactions are unimportant. These interactions lead to sometimes complicated chain structures.

Graphical Abstract

In the crystal structures of the bromocymantrenes [Mn(C₅H_5-nBr_n)(CO)₂(PPh₃₎] (n = 1–3) a combination of H bonds and Br…O/Br…Br interactions leads to one-dimensional molecular chains or double-chains, which are not further connected in the other dimensions.

4-(2-amino-2-oxoethyl) phenyl 4-methylbenzenesulfonate (APMBS), a novel compound, has been synthesized and characterized by spectro-analytical techniques. X-ray diffraction data reveals it crystallizes in the triclinic crystal system with space group (Poverline{1}). The structure is stabilized through strong N–H⋯O, weak C–H⋯O and C–H⋯π hydrogen bond interactions yielding a supramolecular structure. The N1A–H1AA⋯O4A, C4–H4⋯O3, and C14–H14⋯Cg1 (Ring: C8–C13) interactions link the molecules into dimers, while the interaction C9-H9–O2 results in the formation of a molecular chain along the a-axis. The optimized structural geometry, by and large, as calculated using DFT and HF techniques is in conformity with the corresponding X-ray data. The DFT computation further aid in the follow up investigations including frontier molecular orbitals (FMOs), density of states (DOS), atomic charges, and molecular electrostatic potential surface (MEP). For a comprehensive description of various molecular intersections, Hirsheld surface and fingerprint plots analysis has been reported, besides the combined atoms-in-molecules (QTAIM) and reduced density gradient (RDG) analysis. Docking studies have been performed against the target protein Tubulin-Colchicine: Stathmin-Like Domain Complex.

Graphical Abstract

A new coordination polymer, namely, {[Zn(DTPP)(H₂O)₂]·H₂O}_n (H₂DTPP = 3-(3,5-di(2H-tetrazol-5-yl)phenoxy)pyridine, compound 1), was successfully assembled by using a new semirigid tripodal nitrogen-containing heterotopic ligand and characterized by single-crystal X-ray diffraction, elemental analysis, infrared spectroscopy, TG, and luminescence. X-ray single-crystal diffraction analysis revealed that compound 1 crystallizes in an orthorhombic crystal system with space groups of Ibca. It is a 2D coordination network with (4·8²) topology, and the 2D networks are further connected by hydrogen bonds between coordinated water molecules and tetrazole N atoms to form a 3D supramolecular framework. Moreover, compound 1 exhibits intense blue emission centered at 345 nm upon excitation at 276 nm and has the ability to sense Fe³⁺ via photoluminescence quenching.

Graphical Abstract

A new coordination polymer synthesized from a new semirigid tripodal nitrogen-containing heterotopic ligand, {[Zn(DTPP)(H₂O)₂]·H₂O}_n, was characterized.

New polymorphs of (2-(chloro(pyrrol-2-ylidene)methyl)pyrrole)-difluoro-borane (1) and (2-(chloro(4-ethyl-3,5-dimethyl-2H-pyrrol-2-ylidene)methyl)pyrrole)-4-ethyl-3,5-dimethyl-1H-pyrrolato)-difluoro-borane (2) were identified using single crystal X-ray diffraction. The new polymorph of 1 crystallises in the triclinic, P-1 space group with an asymmetric unit comprising two crystallographically-independent molecules (Z′ = 2). The differences between this structure and that of the known polymorph of 1 are attributed to the formation of two distinct dimer motifs in each polymorph and the packing between these dimer units. The new polymorph structure of 2, exhibits a similar asymmetric unit to the known form, comprising 3 molecules (Zʹ = 3). The two structures differ in the orientation of the molecules within the trimeric asymmetric unit and the manner in which these trimers pack along the crystallographic [010] direction.

Graphical Abstract

The triclinic polymorph of 8-chloro BODIPY exhibits an asymmetric unit with two crystallographically-independent molecules.

In this study, we have synthesized a novel organic–inorganic hybrid crystal 4-nitrobenzyl-4-aminopyridinium tetrachlorocuprate(II) [4NO₂Bz-4NH₂Py]₂[CuCl₄](1). The single-crystal X-ray diffraction analysis revealed that the crystal belongs to the triclinic space group P–1, and consists of four [4NO₂Bz-4NH₂Py]⁺ cations and two [CuCl₄]²⁻ anions. O⋯π, C–H⋯π, π⋯π, N–H⋯Cl, C–H⋯Cl, C–H⋯O, and C–H⋯N weak interactions in the crystals play an important role in facilitating the stacking and stabilization of the crystals. The different types of contribution have been quantified by the calculation of Hirshfeld surface percentage and depicted by fingerprint plots. The bulk phase purity, homogeneity, and morphology of the desired compound were checked using powder XRD, and SEM–EDX analysis. Vibrational, optical, and thermal properties were investigated by FT-IR, UV–Vis spectrum, and TG–DTA measurements of [4NO₂Bz-4NH₂Py]₂[CuCl₄](1), respectively. The low energy gap (2.41 eV) suggested that the crystal was a suitable semiconductor material for optical applications. In addition, the compound presented good bactericidal activity against E. coli and S. aureus.

Graphical Abstract

A novel organic–inorganic hybrid material, 4-nitrobenzyl-4-aminopyridinium tetrachlorocuprate(II), has been synthesised and characterized with a study of its crystal structure, vibrational spectra, weak interaction, Hirshfield surface, thermal stability and antibacterial activity.

A new polymorph of tert-butyl (2-aminophenyl)carbamate was identified using single crystal X-ray diffraction. The compound crystallised in the centrosymmetric, monoclinic space group P2₁/n with an asymmetric unit comprising two crystallographically-independent molecules (Zʹ = 2). This new structure was compared to that of the known polymorph with the differences between the two being attributed to a combination of space group symmetry, conformational variation, hydrogen bonding network dimensionality and crystal packing.

The crystal and molecular structure of 7-dimethylamino-4-hydroxycoumarin as its hydrate (1, C₁₁H₁₁NO₃ • H₂O) has been determined. Crystals are monoclinic, space group P2(1)/n with a = 7.1435(4) Å, b = 20.1763(6) Å, c = 7.8590(3) Å, β = 110.018(5)^o and V = 1064.28(8)ų for 4 formula units per cell. Both coumarin enol ester hydroxy and carboxy groups engage in hydrogen-bonding with the water of crystallization. Several 3-substituted derivatives were prepared from this material including 7-dimethylamino-3-benzyl-4-hydroxycoumarin (2) and 7-dimethylaminowarfarin (4). Compound 2 (C₁₈H₁₆NO₃) crystallizes in the triclinic system, space group P-1, with a = 7.0180(7) Å, b = 7.8143(7) Å, c = 14.3158(10) Å, α = 90.586(6)^o, β = 94.738(5)^o, γ = 104.639(7)^o, and V = 756.57(9) ų for 2 molecules in the cell. For compound 2, the crystal structure shows infinite hydrogen-bonded translational β-chains linking well aligned hydroxy and ester carboxy groups with a repeat distance of 7.018 Å. The dipolar nature of the substituted 4-hydroxycoumarin strengthens the β-chains compared to unsubstituted systems in which the repeat is longer and weaker at 7.17 Å. Computations (DFT) support the bond length changes due to a dipolar influence of the 7-dimethylamino group (compared to the unsubstituted compounds), and a more negative carboxy oxygen hydrogen-bond acceptor. For compound 4 (C₂₁H₂₁NO₄), a stereoselective synthesis allowed preparation of the (S)-isomer which crystallized in the orthorhombic system, space group P2(1)2(1)2(1), with a = 6.7857(3) Å, b = 14.7140(5) Å, c = 17.4652(7) Å and V = 1743.81(12) ų for 4 molecules in the cell. Compound 4 forms the trans cyclic hemiketal from methanol in the crystal. In CDCl₃ solution (298 K), 4 exists as an equilibrium mixture of three tautomers: 12.8% open form, 45.5% cis hemiketal and 41.7% trans hemiketal (coumarin forms).

Graphical Abstract

Elisei Cosovan, Victor Cosovan, Daniel A. Osborne, David H. Magers, Edward J. Valente-3-Benzyl-4-hydroxy-7-dimethylaminocoumarin forms enhanced translational β-chain hydrogen-bonded arrays in the crystal

Synthesis, characterization and structural relevance of four new copper carboxylate complexes (1–4) has been presented here. The complexes have been synthesized by direct treatment of the substituted phenyl acetate and pyridine ligands in aqueous medium. The complexes were stable indefinitely with excellent yields and were characterized using spectroscopic and single crystal XRD techniques. FTIR spectroscopy revealed the bridging bidentate coordination mode for the carboxylate moiety in accordance to the actual structure revealed by XRD. Moreover, UV-Visible spectroscopic and cyclic voltammetric studies helped in their characterization and yielded signals which were typical of the copper(II) complexes. Successfully solved single crystal XRD data showed binuclear paddlewheel structures for all the complexes with both copper ions linked through four OCO bridges of ortho-methoxy phenyl acetate (1–3) and ortho-methyl-meta-nitrophenyl acetate (4). The geometry around each copper was distorted square pyramidal where the apical positions are occupied by meta-bromopyridine (1), meta-methylpyridine (2) and DMSO (3 and 4) molecules. The complexes exhibited excellent DNA-binding activity majorly via intercalation as revealed by four experimental techniques. This preliminary study showed that the synthesized complexes add to the existing treasury on the paddlewheel complexes.

The Index Abstract

Air stable newly synthesized and purified crystalline complexes with their preliminary structural relevance.

The presented study describe the crystal structure of 2-(Ethoxymethylene)malononitrile (1), C₆H₆N₂O, in the monoclinic space group P2₁/m with Z = 2, a = 6.798(3), b = 6.172(3), c = 8.844(5) Å. The unit cell of a single crystal of 1 contains two antiparallel oriented molecules. Ethyl fragment demonstrates a disorder with equal occupancy values of 0.5 and a total site-occupation factor (s.o.f.) of 1.0. The molecules of 1 are linked into infinite chains of co-oriented molecules parallel to the a axis via N-H···N ≡ C close contacts with the distance of 2.494(3) Å. There are also weak hydrogen bonds > O···H- between the oxygen atom and the ethyl moiety. The estimation of the energy of non-covalent interactions was conducted by DFT method with different functionals. The best reproducibility of the geometric parameters of those interactions was obtained by using M06-2X functional. The estimated energy value was found to be − 1.20 kcal/mol.

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