Synthesis, crystallographic structure, DFT calculations and Hirshfeld surface analysis of a fumarate bridged Co(II) coordination polymer

Water soluble palladium complexes bearing NNN-pincer ligands: synthesis, DFT modeling, cT-DNA interactions and in vitro cytotoxicity studies against breast cancer cell lines

In the pursuit of designing new anticancer pharmaceuticals and enhancing the therapeutic effectiveness of metal-containing compounds, two new Pd(II) pincer complexes, [Pd(o-LMe)Cl](OTf) (5) and [Pd(o-L'Me)Cl](OTf) (6), where o-LMe is (N2Z,N6Z)-N2,N6-bis(1-methylpyridin-2(1H)-ylidene)pyridine-2,6-dicarboxamide and o-L'Me is (N2Z,N6Z)-N2,N6-bis(1,4-dimethylpyridin-2(1H)-ylidene)pyridine-2,6-dicarboxamide, commonly known as pyridylidene amide (PYA) ligands, were successfully synthesized and subjected to characterization through various spectroscopic methodologies. The PYA ligands were generated from proligands, o-H2LMe(OTf)2 (3) and o-H2L'Me(OTf)2 (4), during the complexation reaction. The precursors, 1 (o-H2L) and 2 (o-H2L'), were synthesized by treatment of dipicolinic acid with 2-aminopicoline and 2-amino-4-methylpicoline, respectively, in the presence of triphenyl phosphite followed by methylation to obtain o-H2LMe(OTf)2 (3) and o-H2L'Me(OTf)2 (4). The molecular structure of the palladium complex (5) has been thoroughly analyzed through SC-XRD, revealing a distorted square planar configuration encompassing two five-membered metallacyclic rings. The DFT approach was adopted to meticulously investigate the electronic features, molecular electrostatic potential, and frontier molecular orbitals of the complexes. The nature of the compound's interaction with cT-DNA and the implications of pincer-PYA coordination on the binding affinity of Pd(II) complexes were probed through UV-visible spectrophotometry and viscometry. The results elucidated the intercalative mode of interaction alongside elevated binding parameters for 5 (105 dm3 mol-1) and 6 (104 dm3 mol-1). Molecular docking of complex 5 was performed, which exhibited a strong interaction with DNA and supported the experimental findings. The in vitro cytotoxic effects of the samples were systematically assessed using the MTT protocol on breast cancer (MCF-7 and T47D) and normal (Vero) cell lines. According to the determined IC50 values, Pd(II) complexes demonstrated a prominent influence in augmenting cytotoxicity. The cytotoxicity values associated with these compounds follow a hierarchy of 5 > cisplatin > 6 > 4 > 3 within neoplastic cells. The apoptotic effects of 5 and 6 on the MCF-7 cancer cell line were examined to elucidate the mechanistic pathway responsible for its maximal cytotoxic efficacy.

Exploring structural and spectroscopic aspects, solvent effect (polar and non-polar) on electronic properties, topological insights, ADME and molecular docking study of thiocolchicoside: A promising candidate for antiviral and antitumor pharmacotherapy

Thiocolchicoside (TCS), a colchicine derivative, was analyzed using experimental and theoretical spectroscopic methods. The bond angle C24-C30-C32 showed a simulated value of 136.0° and an observed value of 132.9°, higher than the standard value of 120°, due to the electronic or steric effects of the oxygen atom (O10). The vibrational spectra identified the stretching and deformation modes of several functional groups, including O-H, N-H, C-H, CH2, CH3, CO, C-O, C-C, and C-S. In polar solvents like water, DMSO, and acetone, the HOMO and LUMO energies were more stabilized compared to non-polar solvents like toluene, indicating stronger solvent-solute interactions. The FMO energy gap was largest in water and DMSO (3.53 eV) and smallest in toluene (3.51 eV), suggesting greater reactivity in non-polar solvents. Electron donation by nitrogen (N12) and oxygen (O10) lone pairs to the electron acceptors O11-C34 and N12-C34 resulted in the highest stabilization in NBO analysis, with energies of 44.62 and 25.34 kJ/mol, respectively, due to L(2)-π* and L(2)-σ* transitions. Topological analysis showed hydrogen atoms H54 and H43 in the sugar moiety, methoxy (O-CH3), and acetyl (CO-CH3) marked in red, indicating electron localization, while blue around C13, C15, and C32 indicated delocalized electron regions. ADME prediction shows that TCS has low GI absorption and no permeability across the BBB, with five hydrogen bond donors and ten acceptors. Molecular docking analysis confirmed TCS's biological activity, demonstrating binding affinities for COVID-19 main proteases 6LU7, spike protein 6VXX, and SMAD proteins 1U7V (SMAD4) and 1U7F (SMAD3) with binding energies of -9.52, -3.59, -5.18, and -5.85 kcal/mol, indicating its potential antiviral and antitumor effects.

In vitro-in silico pharmacology and chemistry of Stercularin, isolated from Sterculia diversifolia

Stercularin is a coumarin, isolated from the ethyl acetate fraction of stem bark and leaves of S. diversifolia. Pharmacologically it is active against cancer, diabetes, and inflammation etc. The molecule is further screened for in vitro pharmacological activities. In addition, a detailed description on its drug likeness and pharmacokinetic profile has been established to further explore its fate as a drug candidate. Stercularin exhibited antiglycation, immunomodulatory, and leishmanicidal activity in three different in vitro models. The IC50 values obtained in these three assays were 80.22 ± 0.46 mg/ml, 12.8 ± 1.6 μg/ml, and 8.32 ± 0.42 μg/ml, respectively. In case of drug likeness evaluation, Stercularin has acceptable physicochemical properties and compliant with major drug likeness descriptors i.e., Lipinski rule, Pfizer rule, GSK rule, and "golden triangle". Accepting Lipinski rule implies the oral drug development of Stercularin. Pharmacokinetically, Stercularin is permeable to Caco-2 and MDCK cell lines. 'Boiled-egg' plot suggest intestinal route of absorption, blood brain barrier nonpermeating, and not affected by p-glycoprotein. Stercularin has high plasma protein binding with low free fraction circulating in the plasma. Stercularin proved to be the substrate and/or inhibitor of CYP 450 system with a moderate half-life and clearance rate to allow flexible dosing regimen. Finally, slight risk of toxicity exists for Stercularin, but not being limiting factors of drug knock out. A nature isolated Stercularin possess pharmacological activities and is predicted to have acceptable pharmacokinetic profile. Further drug development and in vivo studies are desirable for optimization.

Mechanism of arsenic release process from arsenopyrite chemical oxidation

Oxidation of arsenopyrite is one of the main causes of arsenic pollution in the environment. This study, examind changes in the surface properties of arsenopyrite in the presence of oxygen. Furthermore, X-ray photoelectron spectroscopy, in situ Raman analysis, high-resolution transmission electron microscopy, and ab initio molecular dynamics were carried out on arsenopyrite, and the oxidation properties and processes of the arsenopyrite surface, along with the Fe/As/S oxidation processes, were analysed In situ-Raman spectroscopy data clearly showed that in the presence of oxygen, Fe2+ ions were transformed into Fe3+ ions on the surface of arsenopyrite at 207 cm-1, and the content of iron oxides on the surface of arsenopyrite increased significantly over time. The presence of iron promoted the oxidation of As(III), and the oxidation process was found to affect the oxidation of As atoms on the surface of arsenopyrite due to the presence of FeS bonds. The presence of As3+ intensified the oxidation of arsenopyrite surface (139 cm-1).The main reason was the presence of O2·-/HO2· on the surface of arsenopyrite, the change of Fe2+ → FeOH2+ → Fe3+ on the surface of arsenopyrite, and the change of As3+ → As4+ → As5+, which strengthened the overflow of As, leading to reconstruction and changes on the surface of arsenopyrite.

Synthesis, spectroscopic, chemical reactivity, topology analysis and molecular docking study of ethyl 5-hydroxy-2-thioxo-4-(p-tolyl)-6-(trifluoromethyl)hexahydropyrimidine-5-carboxylate

The organofluorine hexahydropyrimidine derivatives are used in the drug discovery due to its steric nature to hydrogen and its extreme electronegativity. The Ethyl 5-hydroxy-2-thioxo-4-(p-tolyl)-6-(trifluoromethyl)hexahydropyrimidine-5-carboxylate (ETP5C) compound was synthesized and characterized by NMR (13C and 1H), FT-IR and UV-Vis spectroscopic techniques for experimentally and theoretically and elemental analyses, mass spectra also investigated. The most stable structure of synthesized molecule was studied by PES analysis in gas and liquid medium. The structural parameters such as bond length and bond angle of the title molecule have been obtained by DFT/B3LYP/6-311++G (d,p) set and compared with the structurally related experimental data of the compounds. The π-to-π* transition of the ETP5C molecule is identified using UV-Vis absorption spectral analysis. In addition, the chemical stability and reactivity are investigated using HOMO-LUMO analysis. The minimal HOMO-LUMO energy gap (4.6255 eV) clearly explains that the ETP5C molecule is more reactive for receptors. The nucleophilic and electrophilic regions such as active sites have been shown by MEP, ELF, LOL and Fukui functions. The second order optical effect has been explained by NLO analysis. The docking was performed with antineoplastic proteins that exhibit against the development of tumor cells.

Synthesis, characterization, Hirshfeld surface analysis, antioxidant and selective β-glucuronidase inhibitory studies of transition metal complexes of hydrazide based Schiff base ligand

The synthesis of N'-[(4-hydroxy-3-methoxyphenyl)methylidene] 2-aminobenzohydrazide (H-AHMB) was performed by condensing O-vanillin with 2-aminobenzohydrazide and was characterized by FTIR, high resolution ESI(+) mass spectral analysis, 1H and 13C-NMR. The compound H-AHMB was crystallized in orthorhombic Pbca space group and studied for single crystal diffraction analysis. Hirshfeld surface analysis was also carried out for identifying short interatomic interactions. The major interactions H…H, O…H and C…H cover the Hirshfeld surface of H-AHMB. The metal complexes [M(AHMB)n] where M = Co(II), Ni(II), Cu(II) and Zn(II) were prepared from metal chlorides and H-AHMB ligand. The bonding was unambigously assigned using FTIR and UV/vis analysis. The synthesized ligand H-AHMB and its metal complexes were studied for β-glucuronidase enzyme inhibition. Surprisingly the metal complexes were found more active than the parent ligand and even the standard drug. Zn-AHMB shown IC50 = 17.3 ± 0.68 µM compared to IC50 = 45.75 ± 2.16 µM shown by D-saccharic acid-1,4-lactone used as standard. The better activity by Zn-AHMB implying zinc based metallodrug for the treatment of diseases associated with β-glucuronidase enzyme. The DPPH radical scavenging activities were also studied for all the synthesized compounds. The Co-AHMB complex with IC50 = 98.2 ± 1.78 µM was the only candidate to scavenge the DPPH free radicals.

Spectroscopic properties (FT-IR, NMR and UV) and DFT studies of amodiaquine

Amodiaquine (AQ) was synthesized by a condensation reaction and characterized by experimental FT-IR, 1H and 13C nuclear magnetic resonance (NMR) and UV spectroscopies. In the present work, Density Functional Theory (DFT) calculations. The structural and spectroscopic (FT-IR, 1H and 13C NMR and UV) data of amodiaquine molecule in ground state have been investigated by using Density Functional Theory (DFT). The calculations have been performed at the using B3LYP method with 6-311++G(d,p) and 6-311++G(2d, p) basis sets theory level were performed, first, to confirm its structure, then to explain its reactive nature through its molecular properties such as natural charges, local and global reactivity descriptors or natural bond orbital (NBO). Afterwards, the calculated properties were compared with experimental results. The 1H and 13C NMR chemical shifts were calculated by using the gauge-independent atomic orbital (GIAO) method, while the electronic UV-Vis spectrum is predicted using the time-dependent density functional theory (TD-DFT). Globally, the computerized results showed good agreement close similarity with the experimental values. The molecular properties such as natural charges, local and global reactivity descriptors, molecular electrostatic potential (MEP), natural bond orbital (NBO) of title molecule were calculated insights into the stability, reactivity and reactive sites on the molecule. The calculated energy band gap (ELUMO-EHOMO) value of AQ was found to be 4.09 eV suggesting that it could be considered as a hard molecule with high stability, supported by global reactivity descriptors. Molecular electrostatic potential (MEP) analysis revealed heteroatoms (oxygen and nitrogen) as the most putative nucleophilic sites when hydrogen atoms to which they are linked appear as electrophilic sites. The potential use of amodiaquine as non-linear optical (NLO) material and its thermodynamic indicators have also been assessed.

Validation of crystal structure of 2-acetamidophenyl acetate: an experimental and theoretical study

In this present study, we have determined the crystal structure of 2-acetamidophenyl acetate (2-AAPA) commonly used as influenza neuraminidase inhibitor, to analyze the polymorphism. Molecular docking and molecular dynamics have been performed for the 2-AAPA-neuraminidase complex as the ester-derived benzoic group shows several biological properties. The X-ray diffraction studies confirmed that the 2-AAPA crystals are stabilized by N-H···O type of intermolecular interactions. Possible conformers of 2-AAPA crystal structures were computationally predicted by ab initio methods and the stable crystal structure was identified. Hirshfeld surface analysis of both experimental and predicted crystal structure exhibits the intermolecular interactions associated with 2D fingerprint plots. The lowest docking score and intermolecular interactions of 2-AAPA molecule against influenza neuraminidase confirm the binding affinity of the 2-AAPA crystals. The quantum theory of atoms in molecules analysis of these intermolecular interactions was implemented to understand the charge density redistribution of the molecule in the active site of influenza neuraminidase to validate the strength of the interactions.Communicated by Ramaswamy H. Sarma.

The Role of the Bridge in Single-Ion Magnet Behaviour: Reinvestigation of Cobalt(II) Succinate and Fumarate Coordination Polymers with Nicotinamide

Two previously synthesized cobalt(II) coordination polymers; {[Co(μ2-suc)(nia)2(H2O)2]·2H2O}n (suc = succinate(2−), nia = nicotinamide) and [Co(μ2-fum)(nia)2(H2O)2]n (fum = fumarate(2−)) were prepared and thoroughly characterized. Both complexes form 1D coordination chains by bonding of Co(nia)2(H2O)2 units through succinate or fumarate ligands while these chains are further linked through hydrogen bonds to 3D supramolecular networks. The intermolecular interactions of both complexes are quantified using Hirshfeld surface analysis and their infrared spectra, electronic spectra and static magnetic properties are confronted with DFT and state-of-the-art ab-initio calculations. Dynamic magnetic measurements show that both complexes exhibit single-ion magnet behaviour induced by a magnetic field. Since they possess very similar chemical structure, differing only in the rigidity of the bridge between the magnetic centres, this chemical feature is put into context with changes in their magnetic relaxation.

Crystal structure, Hirshfeld surface analysis and DFT studies of (E)-4-methyl-2-{[(4-methyl-phen-yl)imino]-meth-yl}phenol

In the title compound, C15H15NO, the configuration of the C=N bond of the Schiff base is E, and an intra-molecular O-H⋯N hydrogen bond is observed, forming an intra-molecular S(6) ring motif. The phenol ring is inclined by 45.73 (2)° from the plane of the aniline ring. In the crystal, mol-ecules are linked along the b axis by O-H⋯N and C-H⋯O hydrogen bonds, forming polymeric chains. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the packing arrangement are from H⋯H (56.9%) and H⋯C/C⋯H (31.2%) inter-actions. The density functional theory (DFT) optimized structure at the B3LYP/ 6-311 G(d,p) level is compared with the experimentally determined mol-ecular structure, and the HOMO-LUMO energy gap is provided. The crystal studied was refined as an inversion twin.

Synthesis, crystal structure, spectroscopic features and Hirshfeld surfaces of 2-methyl-3-[(2-methyl-phen-yl)carbamo-yl]phenyl acetate

The title compound, C17H17NO3, was synthesized, characterized by IR spectroscopy and its crystal structure was determined from single-crystal diffraction data. The asymmetric unit contains two mol-ecules, which adopt different conformations. In one mol-ecule, the acet-oxy and the terminal 2-methyl-phenyl groups are positioned on opposite sides of the plane formed by the central benzene ring, whereas in the other mol-ecule they lie on the same side of this plane. In the crystal, the mol-ecules are linked through strong N-H⋯O hydrogen bonds into chains along [010]. Hirshfeld surface analysis and fingerprint plots were used to investigate the inter-molecular inter-actions in the solid state.

Crystal structure and Hirshfeld surface analysis of (E)-2,4-di-tert-butyl-6-[(3-chloro-4-methyl-phenyl-imino)-meth-yl]phenol

The title Schiff base compound, C22H28ClNO, shows mirror symmetry with all its non-H atoms, except the tert-butyl groups, located on the mirror plane. There is an intra-molecular O-H⋯N hydrogen bond present forming an S(6) ring motif. In the crystal, the mol-ecules are connected by C-H⋯π inter-actions, generating a three-dimensional supra-molecular structure. Hirshfeld surface analysis and two dimensional fingerprint plots were used to analyse the inter-molecular inter-actions present in the crystal, indicating that the most important contributions for the crystal packing are from H⋯H (68.9%) and C⋯H/H⋯C (11.7%) inter-actions.

Crystal structure and Hirshfeld surface analysis of tetra-aqua-bis-(isonicotinamide-κN 1)nickel(II) fumarate

The reaction of NiCl2 with fumaric acid and isonicotinamide in a basic solution produces the title complex, [Ni(C6H6N2O)2(H2O)4](C4H2O4). The nickel(II) ion of the complex cation and the fumarate anion are each located on an inversion centre. The NiII ion is coordinated octa-hedrally by four water O atoms and two N atoms of isonicotinamide mol-ecules. The fumarate anion is linked to neighbouring complex cations via Owater-H⋯Ofumarate hydrogen bonds. In the crystal, the complex cations are further linked by O-H⋯O, N-H⋯O and C-H⋯O hydrogen bonds, forming a three-dimensional supra-molecular architecture. Hirshfeld surface analysis and two-dimensional fingerprint plots were used to analyse the inter-molecular inter-actions present in the crystal and indicate that the most important contributions for the crystal packing are from H⋯O/O⋯H (41.8%), H⋯H (35.3%) and H⋯C/C⋯H (10.2%) inter-actions.

Synthesis, crystallographic analysis and Hirshfeld surface analysis of 4-bromo-2-{[2-(5-bromo-2-nitro-phen-yl)hydrazin-1-yl-idene]meth-yl}-5-fluoro-phenol

The title compound, C13H8Br2FN3O3, is nearly planar with a dihedral angle of 10.6 (4)° between the two benzene rings. Intra-molecular N-H⋯O and O-H⋯N hydrogen bonds occur. In the crystal, the mol-ecules are linked by weak C-H⋯O and C-H⋯Br hydrogen bonds. The roles of the inter-molecular inter-actions in the crystal packing were clarified using Hirshfeld surface analysis.

Crystal structure and Hirshfeld surface analysis and of 2-ammoniumylmeth-yl-1H-benzimidazol-3-ium chloride monohydrate

The asymmetric unit of the title compound, C8H11N3 2+·2Cl-·H2O, contains three organic cations, six chloride anions and three water mol-ecules of crystallization, which are connected by extensive hydrogen-bonding inter-actions into a three-dimensional supra-molecular architecture. Hirshfeld surface analysis and two-dimensional fingerprint plots indicate that the most important contributions to the crystal packing are from H⋯H (37.4%), Cl⋯H/H⋯Cl (35.5%), C⋯H/H⋯C (9.5%) and C⋯C (6.9%) inter-actions.

Crystal structure and Hirshfeld surface analysis of N,N'-bis-(3-tert-butyl-2-hy-droxy-5-methyl-benzyl-idene)ethane-1,2-di-amine

The title compound, C26H36N2O2, crystallizes in the phenol-imine form. In the mol-ecule, there are intra-molecular O-H⋯N hydrogen bonds forming S(6) ring motifs, and the two aromatic rings are inclined to each other by 37.9 (7)°. In the crystal, mol-ecules are linked by pairs of weak C-H⋯O hydrogen bonds, forming inversion dimers. Hirshfeld surface analysis and two-dimensional fingerprint plots indicate that the most important contributions to the crystal packing are from H⋯H (77.5%), H⋯C/C⋯H (16%), H⋯O/O⋯H (3.1%) and H⋯N/N⋯H (1.7%) inter-actions.