RESUMEN
In the current study, the compound 4,4-dimethoxychalcone (DMC) was structurally studied and analyzed by in silico approach against Mpro to investigate its inhibitory potential. The molecular structure of the compound was confirmed by the single crystal X-ray diffraction studies. The crystal structure packing is characterized by various hydrogen bonds, C-H…π and π…π stacking. Intermolecular interactions are quantified by Hirshfeld surface analysis and the electronic structure was optimized by DFT calculations;results are in agreement with the experimental studies. Further, DMC was virtually screened against SARS-CoV-2 main protease (PDB-ID: 6LU7) using molecular docking, and molecular dynamics (MD) simulations to identify its inhibitory potential. A significant binding affinity exists between DMC and Mpro with a-6.00 kcal/mol binding energy. A MD simulation of 30ns was carried out;the results predict DMC possessing strong binding affinity and hydrogen-bonding interactions within the active site during the simulation period. Therefore, based on the results of the current investigation, it can be inferred that a DMC molecule may be able to inhibit Mpro of COVID-19. © 2023 by the authors;licensee Growing Science, Canada.
RESUMEN
Coordination-driven self-assembly in inorganic complexes is a viable methodology to construct supramolecular coordination complexes. Crystal engineering of beta-diketone Cu(II) coordination complexes can be achieved via the host-guest complexation method. The effect of metal-ligand interactions (coordination polyhedra) on the su-pramolecular framework has been analysed by crystal structure and computational studies. A new crystal form of a Cu(II) complex with 4,4,4-trifluoro-naphthyl butanedione has been identified and characterized using various spectroscopic techniques. X-ray diffraction studies unveiled that complex 1, [Cu(TFNB)2], crystallized in the monoclinic (P21/n) space group and its solvent-induced crystal forms, complex 2, [Cu(TFNB)2DMSO] (Database Identifier: IVAKIC), and complex 3, [Cu(TFNB)2DMF] (Database Identifier: ZOCHOR), which were reported earlier, are in the triclinic (P 1) crystal system. The previously reported crystal forms (complexes 2 and 3) are examples of a single crystal coordinated solvent exchange (SCCSE) transformation. In complex 1, the beta-diketone molecules are attached to the metal ion in an equatorial form with a perfect square planar geometry, whilst complexes 2 and 3 feature a slightly distorted square pyramidal geometry with chelated donor oxygen atoms of the beta-diketone ligands in equatorial sites and the crystallizing DMSO and DMF solvents are apically coordinated to the metal centre, respectively. Interestingly, the oxygen donors of the beta-diketone ligands in complex 1 are inclined in a trans configuration, whereas in the solvent-induced pseudopolymorphic forms of complexes 2 and 3, a cis configuration is observed. The variation in the supramolecular framework with the coordination geometry in different crystal forms is analysed using the crystal structures and compared with quantum computational (Hirshfeld surface, enrichment ratio, energy framework, NCI index model and DFT) results. Molecular docking analysis was performed for all the complexes against the SARS-CoV2 main protease to explore the structur-e-property relationship.
RESUMEN
Physical and chemical property enhancement of an active pharmaceutical ingredient through a multicomponent form is an integral part of the pharmaceutical research. A novel binary compound of thymine (TY) with gallic acid (GA) has been obtained by a solid-state grinding process and preliminarily characterized by FTIR technique. The single crystals were obtained and the 3D molecular crystal structure was confirmed by X-ray diffraction studies. The novel binary compound was crystallized as a cocrystal hydrate [TY-GA-H2O] in the monoclinic P21/c space group with an 1:4:4 stoichiometry. Crystal structure analysis revealed the presence of both intra and intermolecular hydrogen bond interactions, which resulted in the formation of various supramolecular architectures. Further, the structural analysis explored the presence of lone pair–π and π…π interactions apart from the conventional hydrogen bond interactions. Furthermore, the Hirshfeld surface analysis was carried out to quantify the contribution of hydrogen bond interactions in stabilizing the crystal structure. The individual interaction energies and the total interaction energy between the molecules were computed through energy framework analysis. HOMO-LUMO plots and MEP surface were generated to understand the electronic structure and chemical reactive sites of the molecule respectively. Finally, the molecular docking analysis was carried out to examine the antiviral properties of the novel TY-GA cocrystal hydrate.
RESUMEN
To investigate the synergetic effect in the formation of crystal structure having two independent molecules in the asymmetric unit and the structure-property relationship of the molecule, we have synthesized the Schiff base compound (E)-4-(((4-chlorobenzyl)imino)methyl)benzene-1,2,3-triol. The formation of the desired compound was confirmed by the FTIR and single-crystal X-ray studies. The enriched hydroxyl group exhibits more intra and inter-strong hydrogen bonds. The chlorine-hydrogen and C6-H6‧‧‧π interaction along with other interactions form a supramolecular architecture. The Hirshfeld surface analysis and 2D fingerprint analysis provide valuable information about the intermolecular interaction present in the crystal structure. The likelihood of occurrence of intermolecular contacts present in the crystal structure was analyzed using enrichment ratio. The visualization of the interaction topology along with interaction energy between the molecules are carried out using an energy framework. QTAIM, NCI, ELF and LOL studies provide information about electron charge density distribution and the nature of intramolecular and dimeric interaction. The DFT studies provide ground state energy of the optimized structure and the HOMO-LUMO energy gap. The molecular electrostatic potential provides the reactive site and anisotropy of charge distribution of chlorine atom. The NBO studies provide stabilization energy associated with the delocalization of orbitals. The docking studies were also carried out for SARS COVID-19 and the effect of hydroxyl group substitution on binding interaction was investigated.
RESUMEN
Coordination-driven self-assembly in inorganic complexes is a viable methodology to construct supramolecular coordination complexes. Crystal engineering of β-diketone Cu(II) coordination complexes can be achieved via the host-guest complexation method. The effect of metal-ligand interactions (coordination polyhedra) on the supramolecular framework has been analysed by crystal structure and computational studies. A new crystal form of a Cu(II) complex with 4,4,4-trifluoro-naphthyl butanedione has been identified and characterized using various spectroscopic techniques. X-ray diffraction studies unveiled that complex 1, [Cu(TFNB)2], crystallized in the monoclinic (P21/n) space group and its solvent-induced crystal forms, complex 2, [Cu(TFNB)2DMSO] (Database Identifier: IVAKIC), and complex 3, [Cu(TFNB)2DMF] (Database Identifier: ZOCHOR), which were reported earlier, are in the triclinic (P 1¯) crystal system. The previously reported crystal forms (complexes 2 and 3) are examples of a single crystal coordinated solvent exchange (SCCSE) transformation. In complex 1, the β-diketone molecules are attached to the metal ion in an equatorial form with a perfect square planar geometry, whilst complexes 2 and 3 feature a slightly distorted square pyramidal geometry with chelated donor oxygen atoms of the β-diketone ligands in equatorial sites and the crystallizing DMSO and DMF solvents are apically coordinated to the metal centre, respectively. Interestingly, the oxygen donors of the β-diketone ligands in complex 1 are inclined in a trans configuration, whereas in the solvent-induced pseudopolymorphic forms of complexes 2 and 3, a cis configuration is observed. The variation in the supramolecular framework with the coordination geometry in different crystal forms is analysed using the crystal structures and compared with quantum computational (Hirshfeld surface, enrichment ratio, energy framework, NCI index model and DFT) results. Molecular docking analysis was performed for all the complexes against the SARS-CoV2 main protease to explore the structure-property relationship.
RESUMEN
Single crystal X-ray diffraction is the only experimental technique available to elucidate the complete three-dimensional structure of the samples at molecular and atomic levels. But this technique demands defect-free single crystals. Growing good quality single crystals which are suitable to collect X-ray intensity data is an art rather than science. Among the various crystal growth methods, the most effective and commonly used is the slow evaporation method. Using this method, defect-free single crystals of the ground mixture of gallic acid (GA) and butyramide (BU) taken in a 1:1 molar ratio are obtained. The compound was subjected to experimental characterizations like;PXRD, FTIR, SCXRD, and TGA. Further, these results were utilized in the computational characterizations namely, Hirshfeld surface analysis, interaction energy calculations, DFT studies, and docking studies. Structural characterization revealed that the GA-BU compound was crystallized as a cocrystal hydrate with 2:1:1 stoichiometry in a monoclinic crystal system and P21/n space group. Structural studies exposed the presence of various inter and intramolecular hydrogen bond interactions, ring synthons, DDAA environment of the water molecule, and π … π stacking interactions. The contribution of the several close contacts to the crystal structure, the influence of different interaction energies in the packing, the HOMO-LUMO energy gap, and the location of reactive sites were realized through computational studies. Further, a molecular docking study has been performed to check the antiviral activity of the title compound against COVID-19. © 2023 by the authors;licensee Growing Science, Canada.
RESUMEN
We synthesized the halogenated Schiff base compound to understand the influence of halogen and hydrogen bonding interactions. The Schiff base compound is characterized by FTIR, SEM-EDAX and single-crystal X-ray diffraction studies. The structural studies reveal that the 4-chloro-2-(((4-chlorobenzyl) imino) methyl) phenol crystallizes in the monoclinic, P 2 1 / n space group. The O1-H1 center dot center dot center dot N1 strong hydrogen bond forms the intramolecular pseudo chelating ring motif and acts as a coordinating site for metal complexes. The intra, intermolecular and 7r center dot center dot center dot 7r interactions were involved in the construction of supramolecular architecture. The interesting type-I halogen bonds having trans geometry are exhibited. Hirshfeld surface analysis supports the interactions observed in the crystal structure, and the energy framework analysis provides the stabilization interaction energy among the molecular pairs. The enrichment ratio provides favored contacts between the atomic pair and gives strong validation to the halogen center dot center dot center dot halogen and halogen center dot center dot center dot hydrogen bonds. The DFT studies give more insight into electronic structure and provide a global and local parameter of the molecule. NBO studies provide stabilization energy and charge transfer within the molecule. The QTAIM studies were used to calculate the strength of the halogen, hydrogen and stacking intermolecular interaction. Further, docking studies were carried out for COVID-19 proteins to reveal the structural-function properties of halogen and hydrogen bonds present in the synthesized compound.
RESUMEN
Detailed structural and non-covalent interactions in thioxotriaza-spiroderivative (DZ2) are investigated by single crystal structure anslysis and computational approaches. Its results were compared with the previously reported spiroderivative (DZ1). The crystal structure analysis revealed various C-H O, N-H O, C-H N and N-H S hydrogen bonds involved in constructing several dimeric motifs to stabilize the crystal packing. The differences and similarities in the relative contribution of non-covalent interactions in DZ1 and DZ2 compounds are compared using the Hirshfeld surface analysis and 2D fingerprint plots. The binding energies of specific molecular pairs and homodimers have been obtained using molecule-molecule interaction energy calculation. The hierarchy and topology of pair-wise intermolecular interactions are visualized through energy frameworks. The nature and strength of intra and intermolecular interactions were characterized using non-covalent interaction index analysis and the quantum theory of atoms in molecule approach. Further, molecular docking of compounds (DZ1 and DZ2) with SARS-CoV-2 main protease for COVID-19 is performed. And the superposition of these ligands and inhibitor N3, which is docked into the binding pocket of 7BQY, is presented. The binding affinity of -6.7 kcal/mol is observed, attributed to hydrogen bonding and hydrophobic interactions between the ligand and the amino acid residues of the receptor.
RESUMEN
In December 2019, a new type of SARS corona virus emerged from China and caused a globally pandemic corona virus disease (COVID-19). This highly infectious virus has been named as SARS-CoV-2 by the International Committee of the Taxonomy of Viruses. It has severely affected a large population and economy worldwide. Globally various scientific communities have been involved in studying this newly emerged virus and is lifecycle. Multiple diverse studies are in progress to design novel therapeutic agents, in which understanding of interactions between the target and drug ligand is a significant key for this challenge. Structures of proteins involved in the life cycle of the virus have been revealed in RCSB PDB by researchers. In this study, we employed molecular docking study of 4-Acetamido-3-nitrobenzoic acid (ANBA) with corona virus proteins (spike protein, spike binding domain with ACE2 receptor and Main protease, RNA-dependent RNA polymerase). Single crystal X-ray analysis and density functional theory calculations were carried out for ANBA to explore the structural and chemical-reactive parameters. Intermolecular interactions which are involved in the ligand-protein binding process are validated by Hirshfeld surface analysis. To study the behaviour of ANBA in a living organism and to calculate the physicochemical parameters, ADMET analysis was done using SwissADME and Osiris data warrior tools. Further, Toxicity of ANBA was predicted using pkCSM online software. Based on the molecular docking analysis, we introduce here a potent drug molecule that binds to the COVID-19 proteins.Communicated by Ramaswamy H. Sarma.