Structural characterization and Hirshfeld surface analysis of a CoII complex with imidazo[1,2-a]pyridine

Synthesis, structural, multitargeted molecular docking analysis of anti-cancer, anti-tubercular, DNA interactions of benzotriazole based macrocyclic ligand

Biologically important macromolecule 1, 1', 3, 3' Bis - [2,3,5,6-Tetramethyl-p-phenylenebis(methylene)] dibenzotriazlinium dibromide hydrate (BTD) was synthesized and characterized using FT-IR, NMR and single-crystal XRD (SCXRD). SCXRD revealed that the compound was crystallized as a monoclinic system and associated through weak intermolecular interactions like H-bonding and π- π stacking interactions. These weak intermolecular interactions in BTD were studied using Crystal Explorer and Gaussian. The calculated energies for the Highest Occupied Molecular Orbital (HOMO) and the Lowest Unoccupied Molecular Orbital (LUMO) showed the stability and reactivity of the title compound. Molecular electrostatic potential (MEP) surface analysis was used to investigate the crystal's nucleophilic and electrophilic reactive sites. The molecular shape and intermolecular interactions in the crystal structure were determined using Hirshfeld surface analysis and fingerprint plots. Anticancer, anti-bacterial and DNA binding ability of BTD were investigated by experimental and theoretical techniques. The obtained results suggest that BTD possesses better anti-cancer, anti-bacterial and DNA binding abilities. The mode of action of antibiotic and anticancer approach was discussed. This provides promising therapeutic advantages for further development.

New cocrystals of heterocyclic drugs: structural, antileishmanial, larvicidal and urease inhibition studies

Many heterocycles have been developed as drugs due to their capacity to interact productively with biological systems. The present study aimed to synthesize cocrystals of the heterocyclic antitubercular agent pyrazinamide (PYZ, 1, BCS III) and the commercially available anticonvulsant drug carbamazepine (CBZ, 2, BCS class II) to study the effect of cocrystallization on the stability and biological activities of these drugs. Two new cocrystals, namely, pyrazinamide-homophthalic acid (1/1) (PYZ:HMA, 3) and carbamazepine-5-chlorosalicylic acid (1/1) (CBZ:5-SA, 4), were synthesized. The single-crystal X-ray diffraction-based structure of carbamazepine-trans-cinnamic acid (1/1) (CBZ:TCA, 5) was also studied for the first time, along with the known cocrystal carbamazepine-nicotinamide (1/1) (CBZ:NA, 6). From a combination drug perspective, these are interesting pharmaceutical cocrystals to overcome the known side effects of PYZ (1) therapy, and the poor biopharmaceutical properties of CBZ (2). The purity and homogeneity of all the synthesized cocrystals were confirmed by single-crystal X-ray diffraction, powder X-ray diffraction and FT-IR analysis, followed by thermal stability studies based on differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). Detailed intermolecular interactions and the role of hydrogen bonding towards crystal stability were evaluated quantitatively via Hirshfeld surface analysis. The solubility of CBZ at pH 6.8 and 7.4 in 0.1 N HCl and H2O were compared with the values of cocrystal CBZ:5-SA (4). The solubility of CBZ:5-SA was found to be significantly improved at pH 6.8 and 7.4 in H2O. All the synthesized cocrystals 3-6 exhibited a potent urease inhibition (IC50 values range from 17.32 ± 0.89 to 12.3 ± 0.8 µM), several times more potent than standard acetohydroxamic acid (IC50 = 20.34 ± 0.43 µM). PYZ:HMA (3) also exhibited potent larvicidal activity against Aedes aegypti. Among the synthesized cocrystals, PYZ:HMA (3) and CBZ:TCA (5) were found to possess antileishmanial activity against the miltefosine-induced resistant strain of Leishmania major, with IC50 values of 111.98 ± 0.99 and 111.90 ± 1.44 µM, respectively, in comparison with miltefosine (IC50 = 169.55 ± 0.20 µM).

One-pot synthesis, X-ray crystal structure, and identification of potential molecules against COVID-19 main protease through structure-guided modeling and simulation approach

Although antimicrobial resistance before the Covid-19 pandemic is a top priority for global public health, research is already ongoing on novel organic compounds with antimicrobial and antiviral properties in changing medical environments in connection with Covid 19. Thanks to the Biginelli reaction, which allows the synthesis of pyrimidine compounds, blockers of calcium channels, antibodies, antiviral, antimicrobial, anti-inflammatory, or antioxidant therapeutic compounds were investigated. In this paper, we aim to present Biginelli's synthesis, its therapeutic properties, and the structural-functional relationship in the test compounds that allows the synthesis of antimicrobial compounds. Both the DFT and TD-DFT computations of spectral data, molecular orbitals (HOMO, LUMO) analysis, and electrostatic potential (MEP) surfaces are carried out as an add-on to synthetic research. Hirshfeld surface analysis was also used to segregate the different intermolecular hydrogen bonds involved in the molecular packing strength. Natural Bond Orbital (NBO) investigation endorses the existence of intermolecular interactions mediated by lone pair, bonding, and anti-bonding orbitals. The dipole moment, linear polarizability, and first hyperpolarizabilities have been explored as molecular parameters. All findings based on DFT exhibit the best consistency with experimental findings, implying that synthesized molecules are highly stable. To better understand the binding mechanism of the SARS-CoV-2 Mpro, we performed molecular docking, molecular dynamics (MD) simulations, and binding free energy calculations.

Novel Pb(II) Complexes: X-Ray Structures, Hirshfeld Surface Analysis and DFT Calculations

Herein we report the synthesis and detailed structural characterization of two new centrosymmetric dinuclear coordination compounds of Pb(II) [Pb2L2(NCS)4] (1) and [Pb2L2(NO3)4]∙2MeOH (2), using the organic ligand 1,2-diphenyl-1,2-bis((methyl(pyridin-2-yl)methylene)hydrazono)ethane (L). In both complexes, each subunit [PbLX2 (X = NO3 or NCS)] adopts a quasi-aromatic Möbius metal chelate structure. Each ligand L is coordinated in a tetradentate coordination mode to Pb(II), yielding the 12π electron chelate ring via two pyridyl-imine units. In compound (1), the coordination sphere is completed by one disordered N,S-coordinated thiocyanate anion and two μ1,1-bridging N-coordinated thiocyanate anions. In compound (2), the coordination sphere of Pb(II) is completed by two monodentate and two bidentate nitrato ligands (two of them acting as bridging ligands). Crystal packing of both compounds is stabilized by intermolecular hydrogen bonds, intra- and intermolecular C–H∙∙∙π interactions. The Hirshfeld molecular surfaces of (1) and (2) demonstrate that their packing is dominated by C–H∙∙∙O/N/S interactions as well as by far less favored H∙∙∙H contacts.

Efficient Synthesis, SC-XRD, and Theoretical Studies of O-Benzenesulfonylated Pyrimidines: Role of Noncovalent Interaction Influence in Their Supramolecular Network

Crystalline organic compounds, 2-amino-6-methylpyrimidin-4-yl benzenesulfonate (AMPBS) and 2,6-diaminopyrimidin-4-yl benzenesulfonate (DAPBS), were prepared via O-benzenesulfonylation of 2-amino-6-methylpyrimidin-4-ol 1 and 2,6-diaminopyrimidin-4-ol 2, respectively. The structural interpretations were achieved unambiguously by single-crystal X-ray diffraction (SC-XRD) analysis. The Hirshfeld surface study showed that C-H···O, N-H···N, and especially C-H···C hydrogen bond interactions are the key contributors to the intermolecular stabilization in the crystal. Density functional theory (DFT) studies were used to obtain a better understanding of natural bond orbitals (NBOs) and nonlinear optical (NLO) analysis for AMPBS and DAPBS at the B3LYP/6-311G(d,p) level. The time-dependent density functional theory (TD-DFT)/CAM-B3LYP/6-311G(d,p) level was employed for frontier molecular orbital analysis of both compounds. DFT-based vibrations for C-H, C=N, N-H, and stretching for C-C were found to be in good agreement with the experimental data. Overall, the theoretical findings were acquired in correspondence to the SC-XRD-based parameters. Intracharge transfer occurred in AMPBS and DAPBS compounds, which was evaluated through FMO activity. Global reactivity indices had been acquired utilizing energies of HOMO-LUMO orbitals. Overall, the theoretical findings related to AMPBS and DAPBS consist of promising correspondence to experimental findings. The theoretical-based study also exhibited that both AMPBS and DAPBS compounds contain promising NLO features.

Intermolecular interactions in antipyrine-like derivatives 2-halo-N-(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)benzamides: X-ray structure, Hirshfeld surface analysis and DFT calculations

Based on experimental and computational data, a complex network of intermolecular interactions has been rationalized for antipyrine compounds.

Solvent induced mononuclear and dinuclear mixed ligand Cu(ii) complex: structural diversity, supramolecular packing polymorphism and molecular docking studies

Phenolate bridged dinuclear and solvent induced mononuclear supramolecular isomers of Cu(ii) complex have been reported to explore the structural diversity and their antibacterial activity supported by molecular docking studies.

Supramolecular Assemblies in Pb(II) Complexes with Hydrazido-Based Ligands

Herein, we describe the synthesis and single crystal X-ray diffraction characterization of several Pb(II) complexes using Schiff base hydrazido-based ligands and different counterions (NO3−, I– and ClO4). In the three complexes reported in this work, the lead(II) metal exhibits a high coordination number (n > 8) and thus it is apparently not involved in tetrel bonding interactions. Moreover, the aromatic ligands participate in noncovalent interactions that play an important role in the formation of several supramolecular assemblies in the solid state of the three Pb(II) complexes. These assemblies have been analyzed by means of Hirshfeld surface analysis and DFT calculations.

The Importance of CH···X (X = O, π) Interaction of a New Mixed Ligand Cu(II) Coordination Polymer: Structure, Hirshfeld Surface and Theoretical Studies

In this study, a new equimolar (1:1:1) mixed ligand Cu(II) polymer, [Cu(IDA)(ImP)]n (1) with iminodiacetato (IDA) and imidazo[1,2-a]-pyridine (ImP) was synthesized and characterized by single crystal X-ray diffraction analysis. X-ray crystallography reveals that compound (1) consists of polymeric zigzag chain along [010] the carboxylate carbonyl oxygen atom by two-fold symmetry screw axis. The solid-state structure is stabilized through C–H···O hydrogen bonds and C–H···π interactions that lead the molecules to generate two-dimensional supramolecular assemblies. The intricate combinations of hydrogen bonds and C–H···π interactions are fully described along with computational studies. A thorough analysis of Hirshfeld surface and fingerprint plots elegantly quantify the interactions involved within the structure. The binding energies associated with the noncovalent interactions observed in the crystal structure and the interplay between them were calculated using theoretical DFT calculations. Weak noncovalent interactions were analyzed and characterized using Bader’s theory of ‘‘atoms-in-molecules’’ (AIM). Finally, the solid-state supramolecular assembly was characterized by the “Noncovalent Interaction” (NCI) plot index.

Weak inter-actions in crystals: old concepts, new developments

Andrei Batsanov presents a general review of weak interactions in crystals, which highlights the history, state-of-the art and future developments of this field.

On the importance of Pb⋯X (X = O, N, S, Br) tetrel bonding interactions in a series of tetra- and hexa-coordinated Pb(ii) compounds

We study Pb⋯X (X = N, S, Br) tetrel bonding interactions in a series of tetra- and hexa-coordinated Pb(ii) compounds that exhibit hemidirectional coordination.