Quantum chemical hydrogenolysis strategy for elimination of heteroatoms in biomass homologous organic compounds based on oxolane and thiolane.

Bio-oils obtained from biomass contain heteroatoms compounds, like oxolane and thiolane. It is quite difficult for industrialist to purify such refractory bio-oils. One of the efficient strategies for the elimination of heteroatoms is hydrogenolysis process, which results in the formation of H2O and H2S residues as by-products. In this work, quantum chemical studies have been used to analyse the reaction mechanism for the removal of hetero atoms (S and O) as H2O and H2S. We selected B3LYP functional of DFT with Pople's basis set 6-311G(d,p) for computing the hydrogenolysis steps without catalyst. LANL2DZ basis set, is used for studying hydrogenolysis steps involving AlCl3 and WS3H3+ as catalysts. All the reactions are analysed at the temperature of 600 K and pressure of 40 bars. Structural, thermodynamic, kinetic properties have been employed to study this process. The analysis of variations parameters during the hydrogenolysis process reveals that these two organic biomass compounds undergo sequential ring opening at C-X (X = O, S) bonds. Butanol and Butanethiol are obtained as a result of first hydrogenolysis process, and these compounds are converted to butane during second catalytic process while eliminating heteroatoms.

In silico investigations of some Cyperus rotundus compounds as potential anti-inflammatory inhibitors of 5-LO and LTA4H enzymes.

The present study aimed to experimentally identify the essential oil of Algerian Cyperus rotundus L. and to model the interaction of some known anti-inflammatory molecules with two key enzymes involved in inflammation, 5-Lypoxygenase (5-LO) and leukotriene A4 hydrolase (LTA4H). Gas chromatography/gas chromatography-mass spectrometry (GC/GC-MS) revealed that 92.7% of the essential oil contains 35 compounds, including oxygenated sesquiterpenes (44.2%), oxygenated monoterpenes (30.2%), monoterpene hydrocarbons (11.8%) and sesquiterpene hydrocarbons (6.5%). The major identified oxygenated terpenes are humulene oxide II, caryophyllene oxide, khusinol, agarospirol, spathulinol and trans-pinocarveol Myrtenol and α-terpineol are known to exhibit anti-inflammatory activities. Several complexes obtained after docking the natural terpenes with 5-LO and LTA4H have shown strong hydrogen bonding interactions. The best docking energies were found with α-terpineol, Myrtenol and khusinol. The interaction between the natural products and amino-acid residues HIS367, ILE673 and GLN363 appears to be critical for 5-LO inhibition, while the interaction with residues GLU271, HIS295, TYR383, TYR378, GLU318, GLU296 and ASP375 is critical for LTA4H inhibition. Molecular dynamics (MD) trajectories of the selected docked complexes showed stable backbone root mean square deviation (RMSD), supporting the stability of the natural product-enzyme interaction.Communicated by Ramaswamy H. Sarma.

Effect of the main constituents of Pistacia lentiscus leaves against the DPPH radical and xanthine oxidase: experimental and theoretical study.

The aim of this work is to study the content of phenolic compounds in P lentiscus leaves and their antioxidant effect. After extracting the phenolic compounds, fractionation by liquid/liquid partition with increasing polarity gives five extracts. Three of them (ButF, AqF and ButA) were found to have good antioxidant activity. Their IC50s for the inhibition of the free radical formation of DPPH are 1.76 µg/mL, 1.307 µg/ml, and 1.77 µg/mL, respectively. These values are very interesting, considering the effect of the powerful flavonoid quercetin, whose IC50 against DPPH is 1.53 µg/mL. These extracts are also active against xanthine oxidase (XO). The IC50s measured are 0.14 mg/mL, 0.186 mg/mL and 0.33 mg/mL for ButF, Aq F and ButAq F extract respectively, in comparison with allopurinol (0.44 mg/mL). A phytochemical analysis by LC/ESI-MS-MS was performed to explain the observed activities. The results show 22 peaks representing: flavanols, namely catechin, d-Gallocatechin, and gallocatechin gallate. The only flavone detected in the studied extracts was luteolin glucuronide and was found to be in higher amounts in butanolic extract (2,71mg/mL). The phenolic acids and derivatives were also identified in the extracts. A theoretical study was performed to deduce the specificity of the binding between the major compounds identified in the P. lentiscus extract and the xanthine oxidase enzyme using Schrödinger software. The docking procedure was validated using the extraction of ligands from the binding site. Their re-anchoring to the xanthine oxidase structure using quercetin and allopurinol was considered reference molecules. After docking, post-docking minimization was performed to achieve the best scoring poses with the MM-GBSA approach. The dGBind energy of MM-GBSA representing the binding energy of the receptor and the ligand was calculated based on molecular mechanics. Results reveal that ß-Glucogallin compounds such as Digalloylquinic acid, Gallocatechin, and Myricetin-3-O rhamnoside are more active than allopurinol, with stronger Docking score (Gscore) and MM-GBSA dGBind.Communicated by Ramaswamy H. Sarma.

Nucleic Acids under Stress: Understanding and Simulating Nucleobase Fragmentation Pathways.

The effects of radiations on nucleic acids and their constituents is widely studied across several research fields using different experimental and theoretical protocols. While a large number of studies were performed in this context, many fundamental physical and chemical effects are still being investigated, particularly involving the effect of the biological environment. As an example, the interpretation of experimental nucleic acid bases mass spectra, and hence inferring their reactivity in complex environment still poses great challenge. This Minireview summarizes recent theoretical advancements aiming to predict and interpret the reactivity of nucleic acid bases. We focus not only on the understanding of the inherent fragmentation pathways of isolated nucleobases but also on the modeling of a realistic nano-environments highlighting the importance of molecular dynamics simulations and the non-innocent role of the environment and also the possibility to open novel fragmentation pathways.

Adsorption of Toluene and Water over Cationic-Exchanged Y Zeolites: A DFT Exploration.

In this study, density functional theory (DFT) calculations have been performed to investigate the adsorption mechanisms of toluene and water onto various cationic forms of Y zeolite (LiY, NaY, KY, CsY, CuY and AgY). Our computational investigation revealed that toluene is mainly adsorbed via π-interactions on alkalis exchanged Y zeolites, where the adsorbed toluene moiety interacts with a single cation for all cases with the exception of CsY, where two cations can simultaneously contribute to the adsorption of the toluene, hence leading to the highest interaction observed among the series. Furthermore, we find that the interaction energies of toluene increase while moving down in the alkaline series where interaction energies are 87.8, 105.5, 97.8, and 114.4 kJ/mol for LiY, NaY, KY and CsY, respectively. For zeolites based on transition metals (CuY and AgY), our calculations reveal a different adsorption mode where only one cation interacts with toluene through two carbon atoms of the aromatic ring with interaction energies of 147.0 and 131.5 kJ/mol for CuY and AgY, respectively. More importantly, we show that water presents no inhibitory effect on the adsorption of toluene, where interaction energies of this latter were 10 kJ/mol (LiY) to 47 kJ/mol (CsY) higher than those of water. Our results point out that LiY would be less efficient for the toluene/water separation while CuY, AgY and CsY would be the ideal candidates for this application.

Investigation of tautomerism of 1,3,5-triazine derivative, stability, and acidity of its tautomers from density functional theory.

Recent studies have identified N2,N4-bis(4-fluorophenethyl)-N6-(3-(dimethylamino)propyl)-1,3,5-triazine-2,4,6-triamine (1TZ(7,8,9)) as a potent, pure antagonist that inhibits thermosensory transient receptor potential vanilloid 1 channel (TRPV1) channel activity. This study provides theoretical data on the stability and acidity of the tautomers of this molecule. We show that this triazine can exist as three predominant tautomers (2TZ(5,7,8), 4TZ(3,7,9), 7TZ(1,8,9)). In the aqueous phase, equilibrium constants calculations show that only the tautomeric equilibria between 1TZ(7,8,9) and the three most stable triazines can be present which suggests that these three tautomeric equilibria would be the basis of 1TZ(7,8,9)'s biological activity.

DNA Nucleobase under Ionizing Radiation: Unexpected Proton Transfer by Thymine Cation in Water Nanodroplets.

The effect of ionizing radiation on DNA constituents is a widely studied fundamental process using experimental and computational techniques. In particular, radiation effects on nucleobases are usually tackled by mass spectrometry in which the nucleobase is embedded in a water nanodroplet. Here, we present a multiscale theoretical study revealing the effects and the dynamics of water droplets towards neutral and ionized thymine. In particular, by using both hybrid quantum mechanics/molecular mechanics and full ab initio molecular dynamics, we reveal an unexpected proton transfer from thymine cation to a nearby water molecule. This leads to the formation of a neutral radical thymine and a Zundel structure, while the hydrated proton localizes at the interface between the deprotonated thymine and the water droplet. This observation opens entirely novel perspectives concerning the reactivity and further fragmentation of ionized nucleobases.

Ab Initio Study of the Stepwise versus Concerted Fragmentation Pathways in Microhydrated Thymine Radical Cations.

Thymine radiation-induced fragmentation is characterised by ring opening and the loss of HNCO/NCO. These pathways have been investigated using DFT calculations in the presence of zero, one and two water molecules. In addition to the already characterised stepwise fragmentation mechanism, we propose a novel concerted pathway reported here for the first time. We show that both the stepwise and concerted mechanisms are competitive with activation energies of 2.05 eV and 2.00 eV, respectively, in the gas phase. The effect of microhydration on these mechanisms are examined based on the most stable conformations found by an exploration of the potential energy surface performed by using DFT-based ab initio molecular dynamics. Microhydration is also accompanied by an increase in the activation energies, with respect to gas phase, amounting to 0.47 eV-an increase that is associated to a stabilising effect of water in agreement with recent experimental studies. However, we also point out that this effect is greatly dependent on the specific water arrangement around thymine and could be limited to only 0.13 eV for some configurations.

Electronic structure and optical properties of isolated and TiO2 -grafted free base porphyrins for water oxidation: A challenging test case for DFT and TD-DFT.

Seven free base porphyrins employed in dye-sensitized photoelectrosynthetic cells are investigated with the aim of benchmarking the ability of different density functional theory (DFT) and time-dependent DFT approaches in reproducing their structure, vertical, and E0-0 excitation energies and the energy levels alignment (red-ox properties) at the interface with the TiO2 . We find that both vertical and E0-0 excitation energies are accurately reproduced by range-separated functionals, among which the ωB97X-D delivers the lowest absolute deviations from experiments. When the dye/TiO2 interface is modeled, the physical interfacial energetics is only obtained when the B3LYP functional is employed; on the other hand, M06-2X (54% of exchange) and the two long-range corrected approaches tested (CAM-B3LYP and ωB97X-D) excessively destabilize the semiconductor conduction band levels with respect to the dye's lowest unoccupied molecular orbitals (LUMOs), predicting no pathway for electron injection. © 2019 Wiley Periodicals, Inc.

Ionization and fragmentation of uracil upon microhydration.

We study at the DFT level the ionization and the fragmentation of uracil in the presence of zero, one and two water molecules, to unravel the effect of microhydration on the reactivity of this nucleobase. We show that the microhydration lowers the adiabatic and vertical ionization potentials by 0.41 eV and 0.22 eV, respectively. Furthermore, microhydration increases the activation energies of the different dissociation channels up to 0.5 eV and restricts the formation of some fragments, in particular those corresponding to the C5-C6 fragmentation pathway. For the first time, our theoretical study shows new transition states and minima not found for the gas phase, hence indicating a change in the fragmentation mechanisms, as well as a stabilizing effect of microhydration, confirming previous experimental studies.