Martin Michalík

Protective role of quercetin against copper(II)-induced oxidative stress: A spectroscopic, theoretical and DNA damage study

The radical scavenging and metal chelating properties of flavonoids indicate that they may play a protective role in diseases with perturbed metal homeostasis such as Alzheimers disease. In this work we investigated the effect of the coordination of quercetin to copper(II) in view of the formation of ROS in Cu-catalyzed Fenton reaction. ABTS and DPPH assays confirmed that the copper(II)-quercetin complex exhibits a stronger radical scavenging activity than does quercetin alone. EPR spin trapping experiments have shown that chelation of quercetin to copper significantly suppressed the formation of hydroxyl radicals in the Cu(II)-Fenton reaction. DNA damage experiments revealed a protective effect for quercetin, but only at higher stoichiometric ratios of quercetin relative to copper. DNA protective effect of quercetin against ROS attack was described by two mechanisms. The first mechanism lies in suppressed formation of ROS due to the decreased catalytic action of copper in the Fenton reaction, as a consequence of its chelation and direct scavenging of ROS by free quercetin. Since the Cu-quercetin complex intercalates into DNA, the second mechanism was attributed to a suppressed intercalating ability of the Cu-quercetin complex due to the mildly intercalating free quercetin into DNA, thus creating a protective wall against stronger intercalators.

The validation of quantum chemical lipophilicity prediction of alcohols

Abstract The validation of octanol-water partition coefficients (logP) quantum chemical calculations is presented for 27 alkane alcohols. The chemical accuracy of predicted logP values was estimated for six DFT functionals (B3LYP, PBE0, M06-2X, ωB97X-D, B97-D3, M11) and three implicit solvent models. Triple-zeta basis set 6-311++G(d,p) was employed. The best linear correlation with the experimental logP values was achieved for the B3LYP and B97-D3 functionals combined with the SMD model. On the other hand, no linearity was found when IEF-PCM or C-PCM implicit models were employed.

Water effect on the bond dissociation energy of O–H and N–H bonds in phenol and aniline: The testing of simple molecular dynamics model

Abstract A chemical microsolvation model for solution phase bond dissociation enthalpy (BDE) evaluation by means of molecular dynamics is presented. In this simple model, the primary solvent effect on the BDE values was estimated by placing of five water molecules nearby the studied functional groups evenly. Furthermore, the secondary solvent effect was reflected using the conductor like screening model (COSMO). From the quantum-chemical point of view, the molecular dynamics simulations based on the B3LYP functional in rather small basis set were performed. Despite of the constitutional limitations of the proposed model, the obtained O-H and N-H BDE values in phenol (363 kJ mol-1) and aniline (369 kJ mol-1) are in good agreement with the experimental solution phase data.

Theoretical study of a series of phenol derivatives: molecular properties vs. cytotoxicity

Abstract The quantum chemical calculations using DFT were performed for 2-alkyl-4X and 2,6-dialkyl-4-X substituted phenols. Based on the optimal geometries the bond dissociation enthalpies (BDEs), proton enthalpies (PAs) and the lipophilicities were computed. Additionally, simple geometry parameter was found correlating well with experimental leukemia cell toxicity of substituted phenols. Next, we have found no linear dependence between PA or BDE values and log1/C values in gas phase or in water despite the radical toxicity mechanism proposed in the literature.

Acidic and alkaline bimolecular hydrolysis of substituted formanilides. Computational analysis and modelling of substitution effects

Abstract In this article, the study of 67 compounds representing various para-, meta- and ortho- substituted formanilides is presented. These molecules and the products of their acidic and alkaline hydrolysis were studied using DFT quantum chemical methods in order to calculate the reaction enthalpies. These enthalpies are correlated with the hydrolysis rate constants, kH, published for the acid-catalysed acyl cleavage bimolecular (AAC2) mechanism and the modified base-catalysed acyl cleavage bimolecular (BAC2) mechanism. The found linear dependences can be used for the prediction of rate constants of non-synthesised formanilide derivatives.

Theoretical and experimental study of donor-bridge-acceptor system: model 2-[5-(9H-fluoren-9-ylidenemethyl)thiophen-2-yl]-1,3,4-oxadiazole derivatives

The theoretical study of the titled model acceptor-bridge-donor molecular series based on 9H-fluoren-9-ylidenemethyl and 1,3,4-oxadiazole heterocycles is presented. The subunits are linked through a thienyl moiety, and the second α-site of oxadiazole was modified. The quantum chemical model indicated that the electron-donating properties of 9H-fluoren-9-ylidenemethyl were significantly supported or suppressed by the terminal substitution of 1,3,4-oxadiazole which affected the possible semiconductivity. Finally, the possible synthesis of selected molecules is described, and the prepared derivatives were fully characterized by 1H NMR, 13C NMR, IR, and elemental analysis together with optical and electrochemical measurements.Graphical abstract

Theoretical study of substituent effects on the geometry and strain enthalpy in [2,2]paracyclophanes

Abstract The substituent effect on the geometry and strain enthalpy of [2,2]paracyclophane is theoretically investigated by density functional theory. Gas-phase calculations were performed for twenty distinct electron donating and electron withdrawing substituents. The largest out-of-plane distortion of phenyl rings is exhibited by —SCN and —CF3 groups. On the other hand, —OH, —CH3 and —F groups show the minimal deformation. The strain enthalpy for unsubstituted [2,2]paracyclophane associated with repulsive forces between phenyl units reached up to 118.5 kJ mol−1. Any substitution causes increase of the strain enthalpy value proportionally to the absolute values of Hammett para-substituent constants. Two separate linear dependences with similar slopes were obtained for monosubstituted as well as double symmetrically substituted derivatives.

Water liquid-vapor equilibrium by molecular dynamics: Alternative equilibrium pressure estimation

Abstract The molecular dynamics simulations of the liquid-vapor equilibrium of water including both water phases — liquid and vapor — in one simulation are presented. Such approach is preferred if equilibrium curve data are to be collected instead of the two distinct simulations for each phase separately. Then the liquid phase is not restricted, e.g. by insufficient volume resulting in too high pressures, and can spread into its natural volume ruled by chosen force field and by the contact with vapor phase as vaporized molecules are colliding with phase interface. Averaged strongly fluctuating virial pressure values gave untrustworthy or even unreal results, so need for an alternative method arisen. The idea was inspired with the presence of vapor phase and by previous experiences in gaseous phase simulations with small fluctuations of pressure, almost matching the ideal gas value. In presented simulations, the first idea how to calculate pressure only from the vapor phase part of simulation box were applied. This resulted into very simple method based only on averaging molecules count in the vapor phase subspace of known volume. Such simple approach provided more reliable pressure estimation than statistical output of the simulation program. Contrary, also drawbacks are present in longer initial thermostatization time or more laborious estimation of the vaporization heat. What more, such heat of vaporization suffers with border effect inaccuracy slowly decreasing with the thickness of liquid phase. For more efficient and more accurate vaporization heat estimation the two distinct simulations for each phase separately should be preferred.

Gallic acid: thermodynamics of the homolytic and heterolytic phenolic O—H bonds splitting-off

Abstract The DFT study of primary antioxidant action of gallic acid and its carboxylic anion is presented in the gas-phase, benzene and water. Corresponding reaction enthalpies for three possible mechanisms was calculated using B3LYP/6-311++G** method. Bond dissociation enthalpy (BDE) and proton dissociation enthalpy (PDE) of 4-OH group was found to be the lowest in gas-phase as well as in both solvents approximated by IEF-PCM model. Ionization potentials (IPs) were higher than BDEs in all cases. Deprotonation of carboxylic group result in increased antioxidant potency as drop in BDE, proton affinities (PAs) and IPs was indicated in all environments.

Theoretical study of the first step of SPLET mechanism: O–H bond cleavage in the mono-substituted benzoic acids

Abstract The first step of SPLET mechanism in solution phase for 15 benzoic acid derivatives was studied from the thermodynamic point of view. For this purpose, proton affinities (PAs) of corresponding carboxylate or phenoxide anions were computed by means of DFT method employing B3LYP and M062X functionals with 6-311++G** basis set and SMD or IEF-PCM solvent model. The substituent effect on PAs was analyzed in terms of Hammett constants, σp. Found dependences exhibit satisfactory linearity and enable quick estimation of solution phase PAs from the Hammett constants.