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Design, synthesis, docking, Hirshfeld surface analysis and DFT calculations of 2-methylxanthen-9-with the FtsZ protein from Staphylococcus aureus.

ABSTRACT: It is of interest to document the design, synthesis, docking, Hirshfeld surface analysis and DFT calculations of 2-methylxanthen-9-with the FtsZ protein (PDB ID: 3VOB) from Staphylococcus aureus for antimicrobial applications. We report the quantitative structure function data in this context.

SUBMITTER: Ranganatha VL

PROVIDER: S-EPMC8131576 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Synthesis, X-Ray Structure, Hirshfeld Surface Analysis, DFT Calculations, and Molecular Docking Studies of Nickel(II) Complex with Thiosemicarbazone Derivative.

Project description:This article presents both experimental and computational study of a new Ni(II) complex, namely, bis{2-(2-trifluoromethylbenzylidene)hydrazine-1-carbothioamido-κ 2N2, S}nickel(II) (abbreviate as NiL2). The complex was synthesized and well characterized using various spectroscopic methods. The single X-ray crystallographic study revealed a distorted square planar geometry around Ni(II) metal ion centre in which the angles deviated from ideal 90° with a maximum value of 6.57° occupied by nitrogen and sulphur donor atoms. The theoretical bond lengths and angles for the NiL2 complex were obtained by using the B3LYP level of density function theory (DFT) with LANL2DZ/6-311G (d, p) basis sets. These results showed very good agreement with the experimental X-ray values. The electrophilicity index (ω = 50.233 eV) shows that the NiL2 complex is a very strong electrophile. In addition, strong F⋯H/H⋯F interactions with 28.5% of the total Hirshfeld surface analyses in NiL2 were obtained indicating that the complex could bind with protein effectively. Furthermore, the new NiL2 complex was docked with plasma retinol-binding protein 4 (RBP4) (PDB id: 5NU7), which implied that the NiL2 complex bound to Tyrosine 133 and Aspartate 102 amino acids via N-H intermolecular hydrogen bonds.

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Synthesis, crystal structure, DFT calculations and Hirshfeld surface analysis of 2-(1-decyl-2-oxo-indolin-3-yl-idene)propanedi-nitrile.

Project description:In the title mol-ecule, C21H25N3O, the 1-decyl substituents are in an extended conformation and inter-calate in the crystal packing to form hydro-phobic bands. The packing is further organized by ?-?-stacking inter-actions between pyrrole and phenyl rings [centroid-centroid distance = 3.6178?(11)?Å] and a C=O??(pyrrole) inter-action [3.447?(2)?Å]. Hirshfeld surface analysis indicates that the H?N/N?H inter-actions make the highest contribution (17.4%) to the crystal packing.

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New 1,2,3-Triazole-Containing Hybrids as Antitumor Candidates: Design, Click Reaction Synthesis, DFT Calculations, and Molecular Docking Study.

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Synthesis, crystal structure, DFT calculations and Hirshfeld surface analysis of 3-butyl-2,6-bis-(4-fluoro-phen-yl)piperidin-4-one.

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Crystal structure, DFT calculations and Hirshfeld surface analysis of 3-(4-methyl-phen-yl)-6-nitro-1H-indazole.

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Novel Fluorescent Benzothiazolyl-Coumarin Hybrids as Anti-SARS-COVID-2 Agents Supported by Molecular Docking Studies: Design, Synthesis, X-ray Crystal Structures, DFT, and TD-DFT/PCM Calculations.

Project description:This study revealed the design and preparation of new 3-(benzo[d]thiazol-2-yl)-2H-chromen-2-one derivatives 9a-h. The structures of the synthesized products were elucidated by their spectroscopic data and X-ray crystallography for compounds 9a and 9d. The prepared new compounds were measured for their fluorescence, and a good result indicated that the emission efficiency was decreased by increasing the electron-withdrawing groups from the unsubstituted compound 9a to the highly substituted derivative 9h (2 Br heavy atoms). On the other hand, the B3LYP/6-311G** theoretical level of theory was used to optimize the quantum mechanical calculations of the geometrical characteristics and energy of the novel compounds 9a-h under study. The electronic transition was investigated using the TD-DFT/PCM B3LYP approach, which uses time-dependent density functional calculations. Moreover, the compounds exhibited nonlinear optical properties (NLO) and a small HOMO-LUMO energy gap, which makes them easy to polarize. Furthermore, the acquired infrared spectra were compared with the expected harmonic vibrations of the substances 9a-h. On the other hand, binding energy analyses of compounds 9a-h with human corona virus nucleocapsid protein Nl63 (PDB ID: 5epw) were predicted using molecular docking and virtual screening tools. The results showed a promising binding and how these potent compounds were inhibiting the COVID-19 virus. Compound 9h was the most active anti-COVID-19 agent among all the synthesized benzothiazolyl-coumarin derivatives, as it forms five bonds. The presence of the two bromine atoms in its structure was responsible for the potent activity.

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Chitosan Catalyzed Novel Piperidinium Dicoumarol: Green Synthesis, X-ray Diffraction, Hirshfeld Surface and DFT Studies.

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Synthesis, spectroscopic, DFT calculations, biological activity, SAR, and molecular docking studies of novel bioactive pyridine derivatives.

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| S-EPMC10511440 | biostudies-literature

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