Synthesis, theoretical analysis, and biological properties of a novel tridentate Schiff base palladium (II) complex.

Schiff base complexes play a crucial role in bioinorganic chemistry. A novel curcumin/phenylalanine tridentate Schiff base ligand and its palladium (II) complex were synthesized so that they were stable in aqueous buffer. The structure of the complex was investigated using a variety of methods, including DFT, NBO analysis, FMOs, and MESP. The interaction of the complex with a plasmid (pUC19) and CT-DNA was studied. The anticancer, antibacterial, and antioxidant activities of the complex were examined. The statistical analysis of the MTT assay was compared using the 1-way ANOVA and Tukey test. Results showed that the complexes were stable in aqueous buffer, pH 8. The extrinsic fluorescence emission of the plasmid and CT-DNA was quenched while interacting with the complex. The complex had an IC50 of 72.47 µM against MCF-7 cells. The ANOVA and Tukey analysis of MTT data demonstrated a statistically significant difference between groups (P < 0.0001). The minimum inhibitory concentrations (MIC) of the complex for E. coli and S. aureus were 300 and 200 µg/mL, with 96.3 and 95.2% biofilm growth inhibition at 250 µg/mL, respectively. The sample concentrations contributing to 50% radical inhibition in the 1,1-diphenyl-2-picrylhydrazyl (DPPH) test for curcumin, ligand, and palladium (II) complex were 33.62, 21.27, and 51.26 µM, respectively. The results suggest that the complex interaction with DNA is one of the potential mechanisms for eliminating cancer cells and bacteria in the planktonic and biofilm. On the other hand, while stability in an aqueous buffer at pH 8 increases, the modified curcumin antioxidant effect decreases.

Effect of the Intramolecular Hydrogen Bond on the Active Metabolite Analogs of Leflunomide for Blocking the Plasmodium falciparum Dihydroorotate Dehydrogenase Enzyme: QTAIM, NBO, and Docking Study.

BACKGROUND: Leflunomide (LFM) and its active metabolite, teriflunomide (TFM), have drawn a lot of attention for their anticancer activities, treatment of rheumatoid arthritis and malaria due to their capability to inhibit dihydroorotate dehydrogenase (DHODH) and Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) enzyme. In this investigation, the strength of intramolecular hydrogen bond (IHB) in five analogs of TFM (ATFM) was analyzed employing density functional theory (DFT) using B3LYP/6-311++G (d, p) level and molecular orbital analysis in the gas phase and water solution. A detailed electronic structure study was performed using the quantum theory of atoms in molecules (QTAIM) and the hydrogen bond energies (EHB) of stable conformer obtained in the range of 76-97 kJ/mol, as a medium hydrogen bond. The effect of substitution on the IHB nature was studied by natural bond orbital analysis (NBO). 1H NMR calculations showed an upward trend in the proton chemical shift of the enolic proton in the chelated ring (14.5 to 15.7ppm) by increasing the IHB strength. All the calculations confirmed the strongest IHB in 5-F-ATFM and the weakest IHB in 2-FATFM. Molecular orbital analysis, including the HOMO-LUMO gap and chemical hardness, was performed to compare the reactivity of inhibitors. Finally, molecular docking analysis was carried out to identify the potency of inhibition of these compounds against PfDHODH enzyme. TFM acts as an inhibitor of dihydroorotate dehydrogenase (DHODH) and Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) enzyme. Leflunomide and its active metabolite teriflunomide have been identified as drugs for treatment of some diseases, such as multiple sclerosis (MS), rheumatoid arthritis (RA), malaria, and cancer. Hydrogen bonds play a key role in the interaction between drugs and enzymes. OBJECTIVES: The aim of the present work is to investigate the effect of the strength of intramolecular hydrogen bonds (IHBs) in the active metabolite analogs of leflunomide or analogs of teriflunomide (ATFMs) and study the interaction of these inhibitors against the PfDHODH enzyme using quantum mechanical methods. METHODS: At first, intramolecular hydrogen bonds in five ATFMs were evaluated by the DFT method, quantum theory of atoms in molecules (QTAIM), nuclear magnetic resonance (NMR), natural bond orbital (NBO), and molecular orbital (MO) analyses. Then, the interaction of these inhibitors against the PfDHODH enzyme were compared using molecular docking study. RESULTS: All the computed results confirm the following trend in the intramolecular hydrogen bond strength in five mono-halo-substituted 2-cyano-3-hydroxy-N-phenylbut-2-enamide (ATFM): 5-FATFM> 4-Br-ATFM ≈ 3-Br-ATFM>3-Cl-ATFM>TFM-Z>2-F-ATFM which is in agreement with QTAIM, NMR, and NBO results. Docking results show that 5-F-ATFM (EHB=97kJ/mol) has the minimum MolDock score due to its considerable IHB strength. CONCLUSION: For strong IHBs (EHB>100kJ/mol), C=O and O-H group are involved in the intramolecular interactions and do not contribute to the external interactions. Also, the docking study revealed maximum binding energy between TFM-Z and PfDHODH enzyme.

Hydrogen bond strength and vibrational assignment of the enol form of 3-(ortho-methoxyphenylthio) and 3-(para-methoxyphenylthio)pentane-2,4-dione.

The molecular structure of 3-(ortho-methoxyphenylthio) pentane-2,4-dione (o-MPTPD) and 3-(para-methoxyphenylthio) pentane-2,4-dione (p-MPTPD) has been investigated by means of Density Functional Theory (DFT) calculations. The results were compared with 3-(phenylthio) pentane-2,4-dione (PTPD), 3-(methylthio) pentane-2,4-dione (MTPD), and their parent, pentane-2,4-dione (known as acetylacetone, AA). The full optimized geometry, the IR and Raman frequencies and their intensities has been calculated at the B3LYP/6-311++G(∗∗) level of theory. The calculated frequencies were compared with the experimental results. The IR and Raman spectra of o-MPTPD and p-MPTPD and their deuterated analogs are recorded in the 3200-200 cm(-1) range. The quantum theory of atoms in molecules (QTAIM) was applied to calculate the topological parameters of electron density distributions and charge transfer energy associated with the intramolecular hydrogen bond (IHB). Natural bond orbital analysis (NBO) was performed for investigation of electron delocalization in these compounds. According to the theoretical and experimental data, the hydrogen bond strength in the 3-thio-pentane-2,4-dione derivatives is much stronger than that in AA. The results of theoretical calculations are in excellent agreement with the vibrational and NMR spectroscopy data.

Spectra and structure of binary azeotropes V-acetone-cyclopentane.

Acetone and cyclopentane make a minimum boiling homogeneous binary azeotrope with mole ratio 2:3. Some characteristic vibrational modes, as well as (1)H NMR signals change due to the azeotrope formation. The extend of interaction of these molecules causes significant changes on some vibrational modes involved and (1)H NMR signals show some changes on their position. In this work the FTIR and (1)H NMR spectra of pure acetone, pure cyclopentane and corresponding azeotrope were recorded, mutual influences resulting from azeotrope formation have been analyzed, and spectral changes has been discussed. The unit-structure of cluster have been deduced, based on mole ratio, boiling point depression of constituents, and comparison between the spectra obtained by FTIR and (1)H NMR techniques.

The most stable tautomer of 3-amino-1,2,4-triazin-5-one and its structural geometry.

With the purpose of finding predominant tautomer among five possible isomers of 3-amino-1,2,4-triazin-5-one and to refine some unreasonable structural parameters previously reported from X-ray diffraction measurements, a series of ab initio calculations were carried out. In agreement with previous results, our calculations show that 3-amino-1,2,4-triazin-5(2H)-one tautomer is the most stable one. Concerning the predominant tautomer, comparisons were made between structural parameters calculated and those obtained by X-ray crystallographic analysis. The structural geometry of the main skeleton of the molecule calculated by the B3LYP/6-311++G** density functional method are generally in good agreement with the experimental values, and those predicted by Pauling's method. Bond distance values calculated are in excellent agreement with the conventionally accepted bond lengths in similar molecules. All bond distances, bond angles, dihedral angles, dipole moments and rotational constants are presented.

Structure and vibrational assignment of the enol form of 1,1,1-trifluoro-2,4-pentanedione.

Molecular structure of 1,1,1-trifluoro-pentane-2,4-dione, known as trifluoro-acetylacetone (TFAA), has been investigated by means of Density Functional Theory (DFT) calculations and the results were compared with those of acetylacetone (AA) and hexafluoro-acetylacetone (HFAA). The harmonic vibrational frequencies of both stable cis-enol forms were calculated at B3LYP level of theory using 6-31G** and 6-311++G** basis sets. We also calculated the anharmonic frequencies at B3LYP/6-31G** level of theory for both stable cis-enol isomers. The calculated frequencies, Raman and IR intensities, and depolarization ratios were compared with the experimental results. The energy difference between the two stable cis-enol forms, calculated at B3LYP/6-311++G**, is only 5.89 kJ/mol. The observed vibrational frequencies and Raman and IR intensities are in excellent agreement with the corresponding values calculated for the most stable conformation, 2TFAA. According to the theoretical calculations, the hydrogen bond strength for the most stable conformer is 57 kJ/mol, about 9.5kJ/mol less than that of AA and about 14.5 kJ/mol more than that of HFAA. These hydrogen bond strengths are consistent with the frequency shifts for OH/OD stretching and OH/OD out-of-plane bending modes upon substitution of CH(3) groups with CF(3) groups. By comparing the vibrational spectra of both theoretical and experimental data, it was concluded that 2TFAA is the dominant isomer.