Examining the reaction between antioxidant compounds and 2,2-diphenyl-1-picrylhydrazyl (DPPH) through a computational investigation

In this work, we present a computational investigation on the reactions between two well-known antioxidants (quercetin and morin) and 2,2-diphenyl-1-picrylhydrazyl (DPPH). A density functional theory (DFT) approach with the B3LYP functional and the 6-31G(d,p) basis set was used for the simulations. The structural and energetic parameters (Gibbs free-energy, ΔG, and Gibbs free-energy of activation, ΔG⁺⁺) were determined to provide information on the antioxidant activity as well as to evaluate the contributions of each hydroxyl group to the referred property. According to the results obtained, quercetin presented three hydroxyls as being thermodynamically spontaneous in the reaction with DPPH (4\(^{\prime }\)-ArOH, 3\(^{\prime }\)-ArOH, and 3-ArOH, with ΔG = -4.93 kcal/mol, -2.89 kcal/mol, and -1.87 kcal/mol, respectively) against only two in the case of morin (2\(^{\prime }\)-ArOH and 3-ArOH, with ΔG = -7.56 kcal/mol and -4.57 kcal/mol, respectively). Hence, quercetin was found to be a more efficient antioxidant, which is in agreement with different experimental and computational investigations of bond dissociation enthalpies (BDEs). However, the order of contribution of the OH groups of each compound to the antioxidant potential present some differences when compared to what was seen in the previous investigations, especially for morin. These findings are in contrast to what was observed in studies based on the determinations of BDEs. Therefore, experimental investigations on the hydrogen-atom transfer mechanism (HAT) for both compounds are encouraged in order to clarify these observations.     

Light and Electron Microscope Studies on Synergistic Interaction between Gibbereffic Acid and 4-Ethoxy-1-(p-tolyl)-s-triazine-2,6 (1H, 3H)-dione in Growth of Rice Leaf Sheaths

4-Ethoxy-1-(p-tolyl)-s-triazine-2,6(1H,3H)-dione (TA) dramaticallyand synergistically promoted gibberellic acid-induced elongationof rice second leaf sheaths. The elongation from 84 to 132 hafter sowing occurred only at the region 0–2 mm from thebase in control samples, at the 0–4 mm region in TA- orGA-treated samples, and at the 0–12 mm region in TA plusGA-treated samples. The increase in elongation rate inducedby TA and/or GA was greatest in the 0–2 mm region anddecreased gradually toward the ligule. The longitudinal growthinduced by TA and/or GA was due to the increase in cell numbersby cell division, as well as to increase in length of cells.Electron microscopic examinations revealed that TA and/or GAsuppressed the development of plastids which caused the leafcolour to be pale. Irrespective of TA and/or GA treatment(s),microtubules were observed to be exclusively oriented perpendicularto the longitudinal axis of the cell in actively elongatingzones, and in fully elongated zones they were randomly oriented.     

1H NMR study of an ethidium dimer poly(dA-dT) complex: evidence of a transition between bis and monointercalation

Comparative 1H NMR and optical studies of the interaction between poly(dA-dT), ethidium bromide (Et) and ethidium dimer (Et2) in 0.7 M NaCl are reported as a function of the temperature. Denaturation of the complexes followed at both polynucleotide and drug levels leads to a biphasic melting process for poly(dA-dT) complexed with ethidium dimer (t1/2 = 75 degrees C; 93 degrees C) but a monophasic one in poly(dA-dT): ethidium bromide complex (t1/2 = 74 degrees C). In both cases drug signals exhibit monophasic thermal dependence (Et = 81 degrees C; Et2 = 95 degrees C). Evidence is presented showing that the ethidium dimer bisintercalates into poly(dA-dT) in high salt, based on the observation that i) dimer and monomer ring protons exhibit similar upfield shifts upon DNA binding, ii) upfield shifts of DNA sugar protons are twice as large with the dimer than with ethidium bromide. Comparison between native DNA fraction and bound drug fraction indicates that ethidium covers, n = 2.5-3 base pairs. The dimer bisintercalates and covers, n = 5.7 base pairs when the helix fraction is high but as the number of available sites decreases the binding mode changes and the drug monointercalates (n = 2.9).     

Molecular recognition between oligopeptides and nucleic acids. Sequence specific binding of (4S)-(+)- and (4R)-(-)-dihydrokikumycin B to DNA deduced from 1H NMR, footprinting studies and thermodynamic data

The sequence specific binding of the antibiotic (4S)-(+)-dihydrokikumycin B and its (4R)-(-) enantiomer, [(S)-1 and (R)-1, respectively] to DNA were characterized by DNase I and MPE footprinting, calorimetry, UV spectroscopy, circular dichroism, and 1H NMR studies. Footprinting analyses showed that both enantiomers [(S)-1 and (R)-1] bind to AT-rich regions of DNA. 1H NMR studies (ligand induced chemical shift changes and NOE differences) of the dihydrkikumycins with d-[CGCAATTGCG]2 show unambiguously that the N to C termini of the ligands are bound to 5'-A5T6T7-3' reading from left to right. From quantitative 1D-NOE studies, the AH2(5)-ligand H7 distance of complex A [(S)-1 plus decamer (which is bound more strongly)] and complex B [(R)-1 and decamer] are estimated to be 3.8 +/- 0.3 A and 4.9 +/- 0.4 A, respectively. This difference in binding properties is reflected in the thermodynamic profiles of the two enantiomeric ligands determined by a combination of spectroscopic and calorimetric techniques. The binding free energies (delta G degrees) of (S)-1 and (R)-1 to poly d(AT).poly d(AT) at 25 degrees C are -31.8 and -29.3 kJ mol-1, respectively while the corresponding binding enthalpies (delta H degrees) are -11.3 and -0.8 kJ mol-1. These data permit the construction of models for the binding of the enantiomeric dihydrokikumycins to DNA and account for the more efficient binding of the natural (S) isomer to DNA.     

The angles between the C(1)-, C(5)-, and C(9)-methyl bonds of the retinylidene chromophore and the membrane normal increase in the M intermediate of bacteriorhodopsin: direct determination with solid-state (2)H NMR.

The orientations of three methyl bonds of the retinylidene chromophore of bacteriorhodopsin were investigated in the M photointermediate using deuterium solid-state NMR ((2)H NMR). In this key intermediate, the chromophore has a 13-cis, 15-anti conformation and a deprotonated Schiff base. Purple membranes containing wild-type or mutant D96A bacteriorhodopsin were regenerated with retinals specifically deuterated in the methyl groups of either carbon C(1) or C(5) of the beta-ionone ring or carbon C(9) of the polyene chain. Oriented hydrated films were formed by drying concentrated suspensions on glass plates at 86% relative humidity. The lifetime of the M state was increased in the wild-type samples by applying a guanidine hydrochloride solution at pH 9.5 and in the D96A sample by raising the pH. (2)H NMR experiments were performed on the dark-adapted ground state (a 2:1 mixture of 13-cis, 15-syn and all-trans, 15-anti chromophores), the cryotrapped light-adapted state (all-trans, 15-anti), and the cryotrapped M intermediate (13-cis, 15-anti) at -50 degrees C. Bacteriorhodopsin was first completely converted to M under steady illumination of the hydrated films at +5 degrees C and then rapidly cooled to -50 degrees C in the dark. From a tilt series of the oriented sample in the magnetic field and an analysis of the (2)H NMR line shapes, the angles between the individual C-CD(3) bonds and the membrane normal could be determined even in the presence of a substantial degree of orientational disorder. While only minor differences were detected between dark- and light-adapted states, all three angles increase in the M state. This is consistent with an upward movement of the C(5)-C(13) part of the polyene chain toward the cytoplasmic surface or with increased torsional strain. The C(9)-CD(3) bond shows the largest orientational change of 7 degrees in M. This reorientation of the chromophore in the binding pocket provides direct structural support for previous suggestions (based on spectroscopic evidence) for a steric interaction in M between the C(9)-methyl group and Trp 182 in helix F.