Phosphorus-nitrogen compounds: part 53-synthesis, characterization, cytotoxic and antimicrobial activity, DNA interaction and molecular docking studies of new mono- and dispirocyclotriphosphazenes with pendant arm(s).

Mono-/dispirocyclotriphosphazenes with pendant arm(s) are robust, but they are less investigated inorganic ring systems. In this study, a series of mono (3 and 4)- and dispirocyclotriphosphazenes with 4-chloro-benzyl pendant arm(s) (13-16) was obtained from the Cl exchange reactions of hexachlorocyclotriphosphazene with sodium (N-benzyl)aminopropanoxides (1 and 2). When compound (3) reacted with excess pyrrolidine, morpholine, tetra-1,4-dioxa-8-azaspiro[4,5]decane (DASD) and piperidine, the fully substituted monospirocyclotriphosphazenes (7, 9, 10 and 12) occurred. But, the reactions of 4 with excess piperidine and morpholine produced the gem-piperidino (5)- and morpholino (6)-substituted monospirocyclotriphosphazenes, whereas the reactions of 4 with excess pyrrolidine and DASD gave the fully substituted monospirocyclotriphosphazenes (8) and (11). However, it should be indicated that these derivatives were obtained to be used for the investigation of their spectral, stereogenic and biological properties. The structures of 5, 7 and 14 were determined crystallographically. X-ray data of 5 and 14 displayed that both of compounds were chiral in solid state, and their absolute configurations were assigned as R and RR. Additionally, the antimicrobial activities of phosphazenes were investigated. Minimum inhibitory concentrations, minimal bacterial concentrations and minimum fungicidal concentrations of phosphazenes were determined. The interactions of phosphazenes with plasmid DNA were evaluated by agarose gel electrophoresis. The cytotoxic activities of compounds were studied against L929 fibroblast and DLD-1 colon cancer cells. In addition, density functional theory calculations of 5, 7 and 14 were reported, and their molecular docking studies with DNA, E. coli DNA gyrase and topoisomerase IV were presented.

Synthesis, crystal structure, potential drug properties for Coronavirus of Co(II) and Zn(II) 2-chlorobenzoate with 3-cyanopyridine complexes.

Two new complexes of Co(II) and Zn(II) 2-chlorobenzoate (2-ClBA) with 3-cyanopyridine (CNP) of the general formula [Co(2-ClBA)2(CNP)2(H2O)2] and [Zn(2-ClBA)2(CNP)2(H2O)2] were synthesized. The structures of the complexes were characterized by single crystal XRD and FT-IR and NMR spectroscopy and Mass Spectrometry (MALDI-TOF MS) methods. Mononuclear complexes exhibit octahedral coordination. In addition, Hirshfeld surface analysis was performed to determine non-covalent interactions in crystal packing. The geometry optimization of the molecules was carried out using the LANL2DZ level of theory of the DFT method and the obtained findings were confirmed by comparing with the data obtained from the single crystal X-ray diffraction method. The theoretical and experimental bond angles and lengths are very close to each other. The effectiveness of the complexes against SARS-CoV-2 enzymes was investigated in silico using the molecular docking method, and a binding score of -8.0 kcal/mol on NSP16 of complex 1 as an inhibitor was obtained. To investigate the drug potential of the complexes, their pharmacokinetic and toxicokinetic properties were estimated by ADMET calculations.

Acetophenone-Based 3,4-Dihydropyrimidine-2(1H)-Thione as Potential Inhibitor of Tyrosinase and Ribonucleotide Reductase: Facile Synthesis, Crystal Structure, In-Vitro and In-Silico Investigations.

The acetophenone-based 3,4-dihydropyrimidine-2(1H)-thione was synthesized by the reaction of 4-methylpent-3-en-2-one (1), 4-acetyl aniline (2) and potassium thiocyanate. The spectroscopic analysis including: FTIR, 1H-NMR, and single crystal analysis proved the structure of synthesized compound (4), with the six-membered nonplanar ring in envelope conformation. In crystal structure, the intermolecular N-H ⋯ S and C-H ⋯ O hydrogen bonds link the molecule in a two-dimensional manner which is parallel to (010) the plane enclosing R22 (8) and R22 (10) ring motifs. After that, the Hirshfeld surfaces and their related two-dimensional fingerprint plots were used for thorough investigation of intermolecular interactions. According to Hirshfeld surface analysis, the most substantial contributions to the crystal packing are from H ⋯ H (59.5%), H ⋯ S/S ⋯ H (16.1%), and H ⋯ C/C ⋯ H (13.1%) interactions. The electronic properties and stability of the compound were investigated through density functional theory (DFT) studies using B3LYP functional and 6-31G* as a basis set. The compound 4 displayed the high chemical reactivity with chemical softness of 2.48. In comparison to the already reported known tyrosinase inhibitor, the newly synthesized derivatives exhibited almost seven-fold better inhibition of tyrosinase (IC50 = 1.97 µM), which was further supported by molecular docking studies. The compound 4 inside the active pocket of ribonucleotide reductase (RNR) exhibited a binding energy of -19.68 kJ/mol, and with mammalian deoxy ribonucleic acid (DNA) it acts as an effective DNA groove binder with a binding energy of -21.32 kJ/mol. The results suggested further exploration of this compound at molecular level to synthesize more potential leads for the treatment of cancer.

Synthesis, X-ray, Hirshfeld surface analysis, exploration of DNA binding, urease enzyme inhibition and anticancer activities of novel adamantane-naphthyl thiourea conjugate.

1-(adamantane-1-carbonyl-3-(1-naphthyl)) thiourea (C22H24N2OS (4), was synthesized by the reaction of freshly prepared adamantane-1-carbonyl chloride from corresponding acid (3) with ammonium thiocyanate in 1:1 M ratio in dry acetone to afford the adamantane-1-carbonyl isothiocyanate (2) in situ followed by treatment with 1-naphthyl amine (3). The structure was established by elemental analyses, FTIR, 1H, 13C NMR and mass spectroscopy. The molecular and crystal structure were determined by single crystal X-ray analysis. It belongs to triclinic system P - 1 space group with a = 6.7832(5) Å, b = 11.1810(8) Å, c = 13.6660(10) Å, α = 105.941(6)°, ß = 103.730(6)°, γ = 104.562(6)°, Z = 2, V = 910.82(11) Å3. The naphthyl group is almost planar. In the crystal structure, intermolecular CH···O hydrogen bonds link the molecules into centrosymmetric dimers, enclosing R22(14) ring motifs, while the intramolecular NH···O hydrogen bonds enclose S(6) ring motifs, in which they may be effective in the stabilization of the structure. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H … H (59.3%), H … C/C … H (19.8%) and H … S/S … H (10.1%) interactions. Hydrogen bonding and van der Waals interactions are the dominant interactions in the crystal packing. DFT, molecular docking and urease inhibition studies revealed stability and electron withdrawing nature of 4 as compared to DNA base pairs and residues of urease. The DNA binding results from docking, UV- visible spectroscopy, and viscosity studies indicated significant binding of 4 with the DNA via intercalation and groove binding. Further investigation of the compound was done on hepatocellular carcinoma; Huh-7 cell line as well as normal human embryonic kidney; Hek-293 cell line. The compound showed significant cytotoxic activity against Huh-7 cells in comparison to normal Hek-293 cells indicating selective cytotoxicity towards cancer cells.

Synthesis and Crystallographic, Absorption and Emission Studies of 4-Pyridine Carboxamide of Zn(II) 4-Chlorophenylacetate.

A new zinc(II) complex, [Zn(CB)2(INA)2] (where CB is 4-chlorophenylacetate and INA is 4-pyridine carboxamide) was synthesized. The structure of the complex was characterized by elemental analysis, FT-IR spectroscopy and single-crystal X-ray diffraction technique. Besides, the thermal stability of the complex was investigated by TGA/DTA analysis method. Moreover, the optical absorption and the emission features of the complex were examined by using UV-Vis and fluorescence spectrophotometers, respectively. Furthermore, Density Functional Theory (DFT) calculations were carried out to support the experimental results. Accordingly, it was determined that the complex crystallized in a monoclinic system with space group Pc, a = 8.3329 (2) Å, b = 25.6530 (4) Å, c = 13.5048 (3) Å, α = 90°, ß = 91.703 (3)° and γ = 90°. The complex consists two crystallographically independent molecules. In each molecule, the ZnII ion adopts a distorted trigonal pyramidal coordination formed by two O atoms from the two 4 chlorophenylacetate ligand and two N atoms of the two 4-pyridine carboxamide ligands. It was observed that the linear absorption spectra of the complex were similar to linear absorption spectra of the semiconductors. In addition, two emission peaks were observed in the fluorescence spectra which could be due to the formation of excimer and the interactions of the benzene and pyridine rings. The energy gap (ΔEgap = ELUMO - EHOMO) of the complex has been calculated as 3.712 eV and this value is very close to the experimentally measured value (3.86 eV). Therefore, because of higher fluorescence intensity of emission peak that was observed between 309 and 556 nm wavelength besides other traits, the complex could potentially be used in the blue light OLED application by filtering of the emission peak around 710 nm wavelength. Graphical Abstract It was reported synthesis and spectroscopic, structural and optical characterization of a new complex that is Zn(II) of 4-Chlorophenylacetate with isonicotinamide. The complex characterized by elemental analysis, Single crystal X-ray diffraction and FT-IR Spectroscopy. Thermal stabilities of the complex have also been investigated. The studying of the optical absorption and fluorescence spectra of the prepared complex is very important for the determination of the optical application areas. The fluorescence measurements showed that these materials are much suitable for application area of the detection of nitroaromatic explosives. In addition to the Density Functional Theory (DFT) calculations were carried out to support the experimental results. It was reported synthesis and spectroscopic, structural and optical characterization of a new complex that is Zn(II) of 4-Chlorophenylacetate with isonicotinamide. The complex characterized by elemental analysis, Single crystal X-ray diffraction and FT-IR Spectroscopy. Thermal stabilities of the complex have also been investigated. The studying of the optical absorption and fluorescence spectra of the prepared complex is very important for the determination of the optical application areas. In addition to the Density Functional Theory (DFT) calculations were carried out to support the experimental results.

Phosphorus-nitrogen compounds: part 30. Syntheses and structural investigations, antimicrobial and cytotoxic activities and DNA interactions of vanillinato-substituted NN or NO spirocyclic monoferrocenyl cyclotriphosphazenes.

The gradual Cl replacement reactions of NN (1-3) or NO spirocyclic monoferrocenyl cyclotriphosphazenes (4 and 5) with the potassium salt of 4-hydroxy-3-methoxybenzaldehyde (potassium vanillinate) resulted in the mono (1a-5a), geminal (gem-1b-5b), non-geminal (cis-5b and trans -1b-4b), tri (1c, 3c-5c) and tetra-vanillinato-substituted phosphazenes (1d-5d). All the phosphazene derivatives have stereogenic P-center(s), except tetra-substituted ones. The vanillinatophosphazenes have reversible voltammograms with one-electron anodic and cathodic peaks which are attributed to ferrocenyl redox probe. The structures of the new phosphazene compounds were determined by FTIR, MS, (1)H, (13)C{(1)H} and (31)P{(1)H} NMR spectral data. The solid-state structure of cis -5b was examined by single-crystal X-ray diffraction techniques. In addition, the compounds were tested in HeLa cancer cell lines using MTT assay. The 12 phosphazene derivatives were screened for antimicrobial activity, and 3c was very effective against S. aureus even at 4.88 µM concentration, taking into account the MIC values. Besides, interactions between the phosphazenes and pBR322 plasmid DNA were also investigated.

Methyl 6-O-trityl-α-d-gluco-pyran-oside methanol disolvate.

The asymmetric unit of the title compound, C26H28O6·2CH3OH, contains two independent methyl 6-O-trityl-α-d-gluco-pyran-oside mol-ecules and four methanol solvent mol-ecules. The rings of two methyl α-d-gluco-pyran-oside adopt chair conformations. In the crystal, extensive intra- and inter-molecular O-H⋯O and C-H⋯O hydrogen bonds link the mol-ecules into a three-dimensional supra-molecular architecture.

4-Methyl-N-(4-methyl-phenyl-sulfon-yl)-N-phenyl-benzene-sulfonamide.

The whole mol-ecule of the title compound, C20H19NO4S2, is generated by twofold rotational symmetry. The N atom is located on the twofold rotation axis and has a trigonal-planar geometry. It is bonded by two S atoms of two symmetry-related 4-methyl-phenyl-sulfonyl groups and by the C atom of the phenyl ring, which is bis-ected by the twofold rotation axis. The benzene and phenyl rings are oriented at a dihedral angle of 51.48 (5)° while the pendant benzene rings are inclined to one another by 87.76 (9)°. In the crystal, weak C-H⋯O hydrogen bonds link the mol-ecules, forming a three-dimensional network.

(4,9-Dimethyl-9H-carbazol-3-yl)meth-anol.

In the title compound, C15H15NO, the carbazole skeleton includes a methanol group at the 3-position. The indole ring system is almost planar [maximum deviation = 0.045 (2) Å]. In the crystal, O-H⋯O hydrogen bonds link the mol-ecules into zigzag chains along the b-axis direction. There are weak C-H⋯π inter-actions within the chains and linking neighbouring chains forming sheets lying parallel to (001).

4-{[4-(Di-methyl-amino)-benzyl-idene]amino}-benzene-sulfonamide.

The title Schiff base compound, C15H17N3O2S, is non-planar with a dihedral angle of 69.88 (4)° between the planes of the benzene rings. In the crystal, pairs of N-H⋯N hydrogen bonds, between the sulfonamide nitro-gen-H atom and the azomethine N atom, link the mol-ecules into inversion dimers, forming R 2 (2)(16) ring motifs. These dimers are linked by N-H⋯O hydrogen bonds, between the sulfonamide nitro-gen-H atom and one sulfonamide O atom, forming sheets lying parallel to (100). Within the sheets there are weak parallel slipped π-π inter-actions involving inversion-related benzene-sulfonamide rings [centroid-centroid distance = 3.8800 (9) Å; normal distance = 3.4796 (6) Å; slippage = 1.717 Å].

Methyl 2-[(3RS,4RS)-3-phenyl-4-(phenyl-sulfon-yl)isoxazolidin-2-yl]acetate.

In the title compound, C18H19NO5S, the five-membered isoxazolidine ring is in a half-chair conformation, and the phenyl rings are oriented at a dihedral angle of 66.53 (3)°. In the crystal, C-H⋯O hydrogen bonds link the mol-ecules into a three-dimensional supra-molecular structure. A weak C-H⋯π inter-action is also observed between adjacent mol-ecules.

catena-Poly[[di-aqua-bis-(4-formyl-benzoato-κO (1))copper(II)]-µ-pyrazine-κ(2) N:N'].

In the title polymeric compound, [Cu(C8H5O3)2(C4H4N2)(H2O)2] n , the Cu(II) atom is located on a twofold rotation axis and has a slightly distorted octa-hedral coordination sphere. In the equatorial plane, it is coordinated by two carboxyl-ate O atoms of two symmetry-related monodentate formyl-benzoate anions and by two N atoms of the bridging pyrazine ligand, which is bis-ected by the twofold rotation axis. The axial positions are occupied by two O atoms of the coordinating water mol-ecules. In the formyl-benzoate anion, the carboxyl-ate group is twisted away from the attached benzene ring by 6.2 (2)°, while the benzene and pyrazine rings are oriented at a dihedral angle of 68.91 (8)°. The pyrazine ligands bridge the Cu(II) cations, forming polymeric chains running along the b-axis direction. Strong intra-molecular O-H⋯O hydrogen bonds link the water mol-ecules to the carboxyl-ate O atoms. In the crystal, O-Hwater⋯Owater hydrogen bonds link adjacent chains into layers parallel to the bc plane. The layers are linked via C-Hpyrazine⋯Oform-yl hydrogen bonds, forming a three-dimensional network. There are also weak C-H⋯π inter-actions present.

2-{N-[(2,3,4,9-Tetra-hydro-1H-carbazol-3-yl)meth-yl]methyl-sulfonamido}-ethyl methane-sulfonate.

In the title compound, C17H24N2O5S2, the indole ring system is nearly planar [maximum deviation = 0.032 (1) Å] and the cyclo-hexene ring has a half-chair conformation. In the crystal, N-H⋯O hydrogen bonds link the mol-ecules into a chain running along the b-axis direction. Weak C-H⋯O hydrogen bonds and weak C-H⋯π inter-actions are observed between the chains.

catena-Poly[[aqua-bis-(4-formyl-benzoato-κ(2) O (1),O (1'))cadmium]-µ-pyrazine-κ(2) N:N'].

The polymeric title compound, [Cd(C8H5O3)2(C4H4N2)(H2O)] n , contains two 4-formyl-benzoate (FB) anions, one pyrazine mol-ecule and one coordinating water mol-ecule; the FB anions act as bidentate ligands. The O atom, the aldehyde H atom and the benzene ring of one of the FB anions are disordered over two positions. The O atoms were freely refined [refined occupancy ratio 0.79 (2):0.21 (2)], while the aldehyde H atoms and the benzene ring atoms were refined with fixed occupancy ratios of 0.8:0.2 and 0.5:0.5, respectively. In the ordered FB anion, the carboxyl-ate group is twisted away from the attached benzene ring (A) by 22.7 (8)°. In the disordered FB anion, the corresponding angles are 15.6 (10) and 11.4 (11)° for rings B and B', respectively. Benzene rings A and B are oriented at a dihedral angle of 24.2 (7), A and B' at 43.0 (8)°. The pyrazine ring makes dihedral angles of 67.5 (4), 89.6 (7) and 86.2 (7)°, respectively, with benzene rings A, B and B'. The pyrazine ligands bridge the Cd(II) cations, forming polymeric chains running along the b-axis direction. In the crystal, O-Hwater ⋯ Ocarboxyl-ate hydrogen bonds link adjacent chains into layers parallel to the bc plane. These layers are linked via C-Hpyrazine ⋯ Oform-yl hydrogen bonds, forming a three-dimensional network. π-π interactions [centroid-centroid distances = 3.870 (11)-3.951 (5) Å] further stabilize the crystal structure. There is also a weak C-H⋯π inter-action present.

catena-Poly[[di-aqua-bis-(4-formyl-benzo-ato-κO (1))nickel(II)]-µ-pyrazine-κ(2) N:N'].

In the title polymeric compound, [Ni(C8H5O3)2(C4H4N2)(H2O)2] n , the Ni(II) atom is located on a twofold rotation axis and has a slightly distorted octa-hedral coordination sphere. In the equatorial plane, it is coordinated by two carboxyl-ate O atoms of two symmetry-related monodentate formyl-benzoate anions and by two N atoms of the bridging pyrazine ligand, which is bis-ected by the twofold rotation axis. The axial positions are occupied by two O atoms of the coordinating water mol-ecules. In the formyl-benzoate anion, the carboxyl-ate group is twisted away from the attached benzene ring by 7.0 (6)°, while the benzene and pyrazine rings are oriented at a dihedral angle of 66.2 (3)°. The pyrazine ligands bridge the Ni(II) cations, forming polymeric chains running along the b-axis direction. Intra-molecular O-H⋯O hydrogen bonds link the water ligands to the carboxyl-ate O atoms. In the crystal, water-water O-H⋯O hydrogen bonds link adjacent chains into layers parallel to the bc plane. Pyrazine-formyl C-H⋯O hydrogen bonds link the layers, forming a three-dimensional network. There are also weak C-H⋯π inter-actions present. The title compound is isotypic with the copper(II) complex [Çelik et al. (2014a). Acta Cryst. E70, m4-m5].

Ethyl 4,9-dimethyl-9H-carbazole-3-carboxyl-ate.

In the title compound, C17H17NO2, the carbazole skeleton includes an eth-oxy-carbonyl group at the 3-position. The indole three-ring system is almost planar [maximum deviation = 0.065 (2) Å], and the ethyl ester group is inclined to its mean plane by 15.48 (2)°. In the crystal, there are π-π stacking inter-actions between parallel benzene rings and between parallel benzene and pyrrole rings of adjacent mol-ecules [centroid-centroid distances = 3.9473 (8) and 3.7758 (8) Å, respectively]. Weak C-H⋯π inter-actions are also present.

2-[2-(2,6-Di-chloro-benz-yloxy)-2-phenyl-eth-yl]-2H-indazole.

In the title compound, C22H18Cl2N2O, the indazole ring system is approximately planar [maximum deviation = 0.031 (2) Å], its mean plane is oriented at 3.17 (4) and 19.34 (4)° with respect to the phenyl and benzene rings. In the crystal, weak C-H⋯π inter-actions link the mol-ecules into supra-molecular chains running along the b-axis direction.

1-(Furan-2-yl)-2-(2H-indazol-2-yl)ethanone.

The asymmetric unit of the title compound, C13H10N2O2, contains two crystallographically independent mol-ecules (A and B). The indazole ring systems are approximately planar [maximum deviations = 0.0037 (15) and -0.0198 (15) Å], and their mean planes are oriented at 80.10 (5) and 65.97 (4)° with respect to the furan rings in mol-ecules A and B, respectively. In the crystal, pairs of C-H⋯N hydrogen bonds link the B mol-ecules, forming inversion dimers. These dimers are bridged by the A mol-ecules via C-H⋯O hydrogen bonds, forming sheets parallel to (011). There are also C-H⋯π inter-actions present, and π-π inter-actions between neighbouring furan and the indazole rings [centroid-centroid distance = 3.8708 (9) Å] of inversion-related mol-ecules, forming a three-dimensional structure.

Crystal structure, Hirshfeld surface analysis, calculations of inter-molecular inter-action energies and energy frameworks and the DFT-optimized mol-ecular structure of 1-[(1-butyl-1H-1,2,3-triazol-4-yl)meth-yl]-3-(prop-1-en-2-yl)-1H-benzimidazol-2-one.

The benzimidazole entity of the title mol-ecule, C17H21N5O, is almost planar (r.m.s. deviation = 0.0262 Å). In the crystal, bifurcated C-H⋯O hydrogen bonds link individual mol-ecules into layers extending parallel to the ac plane. Two weak C-H⋯π(ring) inter-actions may also be effective in the stabilization of the crystal structure. Hirshfeld surface analysis of the crystal structure reveals that the most important contributions for the crystal packing are from H⋯H (57.9%), H⋯C/C⋯H (18.1%) and H⋯O/O⋯H (14.9%) inter-actions. Hydrogen bonding and van der Waals inter-actions are the most dominant forces in the crystal packing. Evaluation of the electrostatic, dispersion and total energy frameworks indicate that the stabilization of the title compound is dominated via dispersion energy contributions. The mol-ecular 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 in the solid state.

Crystal structure determination and analyses of Hirshfeld surface, crystal voids, inter-molecular inter-action energies and energy frameworks of 1-benzyl-4-(methyl-sulfan-yl)-3a,7a-di-hydro-1H-pyrazolo-[3,4-d]pyrimidine.

The pyrazolo-pyrimidine moiety in the title mol-ecule, C13H12N4S, is planar with the methyl-sulfanyl substituent lying essentially in the same plane. The benzyl group is rotated well out of this plane by 73.64 (6)°, giving the mol-ecule an approximate L shape. In the crystal, C-H⋯π(ring) inter-actions and C-H⋯S hydrogen bonds form tubes extending along the a axis. Furthermore, there are π-π inter-actions between parallel phenyl rings with centroid-to-centroid distances of 3.8418 (12) Å. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions to the crystal packing are from H⋯H (47.0%), H⋯N/N⋯H (17.6%) and H⋯C/C⋯H (17.0%) inter-actions. The volume of the crystal voids and the percentage of free space were calculated to be 76.45 Å3 and 6.39%, showing that there is no large cavity in the crystal packing. Evaluation of the electrostatic, dispersion and total energy frameworks indicate that the cohesion of the crystal structure is dominated by the dispersion energy contributions.