Molecular structure, Hirshfeld surface and density functional theoretical analysis of a NLO active chalcone derivative single crystal—A quantum chemical approach

Catalyzed syntheses of novel series of spiro thiazolidinone derivatives with nano Fe2O3: spectroscopic, X-ray, Hirshfeld surface, DFT, biological and docking evaluations

Twelve spiro thiazolidinone compounds (A-L) were synthesized via either conventional thermal or ultrasonication techniques using Fe2O3 nanoparticles. The modification of the traditional procedure by using Fe2O3 nanoparticles led to enhancement of the yield of the desired candidates to 78-93% in approximately half reaction time compared with 58-79% without catalyst. The products were fully characterized using different analytical and spectroscopic techniques. The structure of the two derivatives 4-phenyl-1-thia-4-azaspirodecan-3-one (A) and 4-(p-tolyl)-1-thia-4-azaspirodecan-3-one (B) were also determined using single crystal X-ray diffraction and Hirshfeld surface analysis. The two compounds (A and B) were crystallized in the orthorhombic system with Pbca and P212121 space groups, respectively. In addition, the crystal packing of compounds revealed the formation of supramolecular array with a net of intermolecular hydrogen bonding interactions. The energy optimized geometries of some selected derivatives were performed by density functional theory (DFT/B3LYP). The reactivity descriptors were also calculated and correlated with their biological properties. All the reported compounds were screened for antimicrobial inhibitions. The two derivatives, F and J, exhibited the highest levels of bacterial inhibition with an inhibition zone of 10-17 mm. Also, the two derivatives, F and J, displayed the most potent fungal inhibition with an inhibition zone of 15-23 mm. Molecular docking investigations of some selected derivatives were performed using a B-DNA (PDB: 1BNA) as a macromolecular target. Structure and activity relationship of the reported compounds were correlated with the data of antimicrobial activities and the computed reactivity parameters.

A drug design strategy based on molecular docking and molecular dynamics simulations applied to development of inhibitor against triple-negative breast cancer by Scutellarein derivatives

Triple-negative breast cancer (TNBC), accounting for 10-15% of all breast malignancies, is more prevalent in women under 40, particularly in those of African descent or carrying the BRCA1 mutation. TNBC is characterized by the absence of estrogen and progesterone receptors (ER, PR) and low or elevated HER2 expression. It represents a particularly aggressive form of breast cancer with limited therapeutic options and a poorer prognosis. In our study, we utilized the protein of TNBC collected from the Protein Data Bank (PDB) with the most stable configuration. We selected Scutellarein, a bioactive molecule renowned for its anti-cancer properties, and used its derivatives to design potential anti-cancer drugs employing computational tools. We applied and modified structural activity relationship methods to these derivatives and evaluated the probability of active (Pa) and inactive (Pi) outcomes using pass prediction scores. Furthermore, we employed in-silico approaches such as the assessment of absorption, distribution, metabolism, excretion, and toxicity (ADMET) parameters, and quantum calculations through density functional theory (DFT). Within the DFT calculations, we analyzed Frontier Molecular Orbitals, specifically the Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO). We then conducted molecular docking and dynamics against TNBC to ascertain binding affinity and stability. Our findings indicated that Scutellarein derivatives, specifically DM03 with a binding energy of -10.7 kcal/mol and DM04 with -11.0 kcal/mol, exhibited the maximum binding tendency against Human CK2 alpha kinase (PDB ID 7L1X). Molecular dynamic simulations were performed for 100 ns, and stability was assessed using root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF) parameters, suggesting significant stability for our chosen compounds. Furthermore, these molecules met the pharmacokinetics requirements for potential therapeutic candidates, displaying non-carcinogenicity, minimal aquatic and non-aquatic toxicity, and greater aqueous solubility. Collectively, our computational data suggest that Scutellarein derivatives may serve as potential therapeutic agents for TNBC. However, further experimental investigations are needed to validate these findings.

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

Enaminonitrile pyridine derivative was used as a precursor for preparation of fourteen heterocyclic compounds using both conventional thermal and microwave techniques. Diverse organic reagents, such as chloroacetyl chloride, acetic anhydride, chloroacetic acid, carbon disulfide, p-toluene sulfonyl chloride, maleic anhydride, phthalic anhydride, were used. The chemical formulae and structures of isolated derivatives were obtained using different analytical and spectroscopic techniques such as IR, 1H-, 13C-NMR as well as mass spectrometry. The spectroscopic analyses revealed diverse structure arrangements for the products. Molecular structure optimization of certain compounds were performed by the density functional theory (DFT/B3LYP) method and the basis set 6-31 G with double zeta plus polarization (d,p). The antimicrobial inhibition and the antioxidant activity of the reported compounds were screened. Compounds 5, 6, 11 and 13 exhibited the highest antibacterial inhibition, while compound 8 gave the highest scavenging activity (IC50 43.39 µg/ml) against the DPPH radical. Structure-activity relationship of the reported compounds were correlated with the data of antibacterial and the antioxidant activity. The global reactivity descriptors were also correlated with the biological properties of compounds. The molecular docking studies of reported compounds were investigated, and the analysis showed that the docked compounds have highly negative values for the functional binding scores. The binding interaction was found to be correlated with the substituent fragments of the compounds.

Static/dynamic first and second order hyperpolarizabilities, optimized structures, IR, UV-Vis, 1H and 13C NMR spectra for effective charge transfer compounds: A DFT study

The effective charge transfer compounds, 4-N,N-dimethylamino-4'-N'-methyl-stilbazolium m-trifluoromethylbenzene-sulfonate (DSMFS) and 4-N,N-dimethylamino-4'-N'-methyl-stilbazolium p-trifluoromethylbenzene-sulfonate (DSPFS), were simulated in terms of geometric structure, IR, UV-Vis, ¹H NMR and ¹³C NMR spectra. UV-vis spectra for both molecules give two peaks at 290 and 436 nm assigned as n-π* and π-π* transitions. The HOMO-LUMO energy gap for DSMFS (2.8174 eV) was calculated as lower than that of DSPFS (4.6649 eV). The detailed frontier molecular orbital analysis also indicated that the intra- and inter-molecular charge transfers occur in DSMFS and DSPFS. The static and dynamic (ω = 532 and 1064 nm) nonlinear optical properties were also investigated by using B3LYP/6-311++G(d,p) level. Static first and second order hyperpolarizabilities (β and γ) of DSMFS were obtained 1.5726 × 10^-28 esu and 271.63 × 10^-36 esu, and those for DSPFS were obtained as 1.5528 × 10^-28 esu and 303.31 × 10^-36 esu. The dynamic β and γ were obtained as higher than the static corresponding parameters. However, the increasing wavelength in dynamic NLO calculations led to a decrease in β and γ parameters.

A DFT analysis of electronic, reactivity, and NLO responses of a reactive orange dye: the role of Hartree-Fock exchange corrections

An experimental and theoretical study based on DFT/TD-DFT approximations is presented to understand the nature of electronic excitations, reactivity, and nonlinear optical (NLO) properties of reactive orange 16 dye (RO16), an azo chromophore widely used in textile and pharmacological industries. The results show that the solvent has a considerable influence on the electronic properties of the material. According to experimental results, the absorption spectrum is formed by four intense transitions, which have been identified as [Formula: see text] states using TD-DFT calculations. However, the TD-DFT results reveal a weak [Formula: see text] in the low-lying spectral region. Continuum models of solvation indicate that these states suffer from bathochromic (ca. 15 nm) and hypsochromic shifts (ca. 4 nm), respectively. However, the expected blue shift for the absorption [Formula: see text] is only described using long-range or dispersion-corrected DFT methods. RO16 is classified as a strong electrophilic system, with electrophilicity ω > 1.5 eV. Concerning the nucleophilicity parameter (N), from vacuum to solvent, the environment is active and changes the nucleophilic status from strong to moderate nucleophile (2.0 ≤ N ≤ 3.0 eV). The results also suggest that all electrical constants are strongly dependent on long-range and Hartree-Fock exchange contributions, and the absence of these interactions gives results far from reality. In particular, the results for the NLO response show that the chromophore presents a potential application in this field with a low refractive index and first hyperpolarizability ca. 214 times bigger than the value usually reported for urea (β = 0.34 × 10^- 30 esu), which is a standard NLO material. Concerning the solvent effects, the results indicate that the polarizability increases [Formula: see text] esu from gas to solvent while the first hyperpolarizability is calculated as [Formula: see text] esu, ca. 180%, regarding the vacuum. The results suggest RO16 is a potential compound in NLO applications. Graphical Abstract The frontier molecular orbitals, and the inverse relation between the energy-gap (E_gap) and the first hyperpolarizability (β).

Synthesis, Structural Characterizations, and Quantum Chemical Investigations on 1-(3-Methoxy-phenyl)-3-naphthalen-1-yl-propenone

In the present study, 1-(3-methoxy-phenyl)-3-naphthalen-1-yl-propenone (MPNP) is synthesized and characterized by several experimental techniques such as Fourier transform-infrared spectroscopy (FT-IR), FT-Raman, NMR and UV-vis spectral methods. The similar techniques are also investigated by the computational method using Gaussian software. The density functional theory (DFT) method is used to obtain the optimized structure using the B3LYP/6-311++G(d,p) basis set. This optimization procedure of the molecule gives the minimum energy confirmation of the structure. The computed geometrical parameters are compared with experimental data. The experimental FT-IR and FT-Raman spectra of MPNP are obtained in the regions 4000-400 and 4000-50 cm-1 respectively. The detailed vibrational assignments of the molecule are obtained with the support of potential energy distribution. The theoretical NMR (1H and 13C) analysis is conducted by the GIAO method for its structural characterization and compared with experimental chemical shifts. The experimental UV-vis spectrum is obtained in the dimethyl sulfoxide solvent and compared with the theoretically computed spectrum by the time-dependent DFT method. In addition to these studies, other analyses such as nonlinear optical, natural bonds orbital, frontier molecular orbital, molecular electrostatic potential, and NCI have been conducted to understand the nature of the molecule. The title molecule is docked and also the drug-likeness, ADMET studies were carried out. The RBD domain bound to the ACE2 receptor during the fusion makes spike glycoprotein an elusive therapeutic target in SARS-CoV-2 infection.

Structural, vibrational, electronic properties, hirshfeld surface analysis topological and molecular docking studies of N-[2-(diethylamino)ethyl]-2-methoxy-5-methylsulfonylbenzamide

The theoretical (Freebase, Cationic species) and experimental investigations on the molecular structural, spectroscopic characterization, and electronic properties of N2M5MB are reported. The most stable structure of the N2M5MB was analysed by employing Density Functional Theory (DFT) at different functional such as B3LYP, PBEPBE, TPSSTPSS and IEF-PCM (Freebase) and Cationic (B3LYP, IEF-PCM)/ 6-311++G (d,p) basis set level. The Potential Energy Scan (PES) analysis has been employed to investigate the conformational preference of the title molecule. The optimized molecular geometry, vibrational assignments (FT-IR, FT-Raman) of wavenumbers have been performed for freebase, cationic species (Gas, PCM) for the individual modes of vibration. The experimental UV-Vis absorption spectrum was obtained and compared with the simulated (Freebase, Cationic species) Time-Dependent (TD-DFT-M062X) method. The FMO's, electron-hole distributions, HOMA, FLU, Hirshfeld surface analysis, Electrostatic potential surface (ESP), Fukui functions, and topological parameters were discussed. Molecular docking studies were performed for the N2M5MB (ligand) into the active site of targeted proteins (1H22, 4DTL, 5OV9) which belong to AChE inhibitors with the minimum binding energy was detected.