Effect of bromine atom on the different tautomeric forms of microhydrated 5-bromouracil, in the DNA:RNA microhelix and in the interaction with human proteins

Base pairs with 5-chloroorotic acid and comparison with the natural nucleobase. Structural and spectroscopic study, and three suggested antiviral modified nucleosides

A structural and spectroscopic study of 5-chloroorotic acid (5-ClOA) biomolecule was carried out by IR and FT-Raman and the results obtained were compared to those achieved in 5-fluoroorotic acid and 5-aminoorotic acid compounds. The structures of all possible tautomeric forms were determined using DFT and MP2 methods. To know the tautomer form present in the solid state, the crystal unit cell was optimized through dimer and tetramer forms in several tautomeric forms. The keto form was confirmed through an accurate assignment of all the bands. For this purpose, an additional improvement in the theoretical spectra was carried out using linear scaling equations (LSE) and polynomic equations (PSE) deduced from uracil molecule. Base pairs with uracil, thymine and cytosine nucleobases were optimized and compared to the natural Watson-Crick (WC) pairs. The counterpoise (CP) corrected interaction energies of the base pairs were also calculated. Three nucleosides were optimized based on 5-ClOA as nucleobase, and their corresponding WC pairs with adenosine. These modified nucleosides were inserted in DNA:DNA and RNA:RNA microhelices, which were optimized. The position of the -COOH group in the uracil ring of these microhelices interrupts the DNA/RNA helix formation. Because of the special characteristic of these molecules they can be used as antiviral drugs.Communicated by Ramaswamy H. Sarma.

Synthesis, spectroscopic characterization, molecular docking and in vitro cytotoxicity investigations on 8-Amino-6-Methoxy Quinolinium Picrate: a novel breast cancer drug

Density Functional Theory (DFT) studies of the 8-Amino-6-Methoxy Quinolinium Picrate (8A6MQP) molecule have been carried out with extensive and accurate investigations of detailed vibrational and spectroscopic investigations as well as validated experimentally. The 8A6MQP sample was synthesized and characterized using FT-IR, FT-Raman, FT-NMR and UV-Vis spectroscopic techniques. Subsequently, the optimized molecular structure and harmonic resonance frequencies of the molecule were computed based on DFT/B3LYP method with a 6-311G++(d,p) basis set using the Gaussian 09 program. The experimental and calculated vibrational wavenumbers were assigned. The absorption spectrum of the molecule was computed in the liquid phase (ethanol), which exhibits n to л* electronic transition and compared with the observed UV-Vis spectrum. Frontier molecular orbital analysis shows the molecular reactivity and kinetic stability of the molecule. The Mulliken atomic charge distribution and molecular electrostatic potential surface analysis of the molecule validate the reactive site of the molecule. The natural bond orbital analysis proves the bioactivity of the molecule. Molecular docking analysis indicates that the 8A6MQP molecule inhibits the action of DNA topoisomerase 2-alpha protein, which is associated with breast cancer. In addition, the in vitro cytotoxicity analysis of the 8A6MQP molecule against human cervical cancer cell lines (ME180) and human breast cancer cell lines (MDA MB 231) were determined by MTT assay, which evidences that the title molecule exhibits higher inhibition against the breast cancer cell lines compared to that of cervical cancer cell lines. Hence, the present study paves the way for the development of novel drugs in the treatment of breast cancer.Communicated by Ramaswamy H. Sarma.

Spectroscopic, quantum chemical, molecular docking and molecular dynamics investigations of hydroxylic indole-3-pyruvic acid: a potent candidate for nonlinear optical applications and Alzheimer's drug

In this paper, a complete theoretical investigation of hydroxylic indole-3-pyruvic acid (HIPyA) molecule was performed using the DFT quantum chemical, molecular docking and molecular dynamics calculations. The conformational analysis of HIPyA molecule was carried out using density functional theory quantum chemical calculations. The most stable structure of the studied molecule was predicted by means of DFT/B3LYP method with cc-pVTZ basis set. The simulated vibrational frequencies were assigned and proved to be in agreement with the available experimental FT-IR data. The effects of gas phase and solvents on UV-visible spectra of HIPyA molecule were simulated using TD-DFT/B3LYP method with cc-pVTZ basis set. The analysis of the density of states spectrum validates the frontier molecular orbitals results, which reveals the charge transfer interaction in HIPyA molecule. The molecular electrostatic potential surface confirms the electrophilic and nucleophilic reactive sites of the studied molecule. The natural bond orbital analysis evidences the bioactivity of the studied molecule. The obtained first order hyperpolarizability value is 33.596 times greater than urea, which confirms the nonlinear optical activity of HIPyA molecule. The molecular docking analysis reveals that the studied molecule under interest can act as a potent inhibitor against the amyloid β-protein (Aβ) enzyme, which causes the Alzheimer's disease. The molecular dynamics analysis confirms the reliability of the docking results.Communicated by Ramaswamy H. Sarma.

Comparative investigation of Cu(II) complexes with dithiocarbazate: Structural design, theoretical calculation, and in vitro antitumor activity

The present work reports the synthesis and investigation by semi-empirical Density Functional Theory (DFT), physical chemistry, and spectroscopic methods of two dithiocarbazates, 2-acetylpyridine-S-p-bromobenzyl-dithiocarbazate (HL¹) and 2-acetylpyridine-S-p-nitrobenzyl-dithiocarbazate (HL²) and their Cu(II) complexes, [Cu(L¹)Cl] (1), [Cu(L¹)Br] (2), [Cu(L²)Cl] (3) and [Cu(L²)Br] (4). Single crystal X-ray analyzes showed distorted square planar geometry to the metal centers, which tridentate ligands coordinated by the NNS system and an additional halogen (Cl^- or Br^-) to complete the coordination sphere. Mass spectrometry data indicated the presence of [Cu(L¹)(DMF)]⁺ and [Cu(L²)(DMF)]⁺, due to the exchanging of chloride/bromide ions and characteristic fragmentations of the compounds. The DFT composite method B97-3c was employed to optimize the geometries of ligands and complexes and IR spectra were calculated revealing good agreement with experimental data. Hydrogen bonds and π⋅⋅⋅π stacking interactions upon the molecular packing were investigated by Hirshfeld surface and fingerprint plots with the main interactions attributed to the H⋅⋅⋅H contacts. The biological activity of the dithiocarbazates and their Cu(II) complexes were evaluated in vitro against the human glioma U251 cells. Results revealed that the free dithiocarbazates present great in vitro antitumor activity that is increased after the complexation with copper. The measurement of cytotoxicity of the compounds showed biological activity in a low range of concentration, which indicates high efficiency as potential drugs.