Atmospheric oxidation of furanones by •OH and •Cl radicals: In situ FTIR rate coefficient determinations, SAR and theoretical studies.

Gas-phase kinetics of the overall reactions of •OH and •Cl radicals with dihydrofuran-3(2H)-one (oxolan-3-one) and dihydro-2-methyl-3(2H)-furanone (2MTHF-3-one) were studied at 298 K and atmospheric pressure. The rate coefficients were determined using the relative method in a 480 L multipass glass reactor coupled to an FT-IR detection system. The rate coefficients found for oxolan 3-one and 2MTHF-one with •OH radicals (k1 and k2) and with •Cl atoms (k3 and k4) at 298 K and atmospheric pressure (in cm3 molecule-1 s-1) were: k1 = (1.86 ± 0.29) × 10-11, k2 = (2.64 ± 0.47) × 10-11, k3= (1.15 ± 0.28) × 10 -10, and k4 = (1.33 ± 0.32) × 10-10, respectively. Reactivity trends were developed by comparison with other similar structures and Fukui indices employed to determine the reactivity of different sites on the ring. The singularity of the reaction with •OH was assessed by computational studies which showed the formation of several stable hydrogen bonded complexes, explaining the difference with the reaction with the •Cl atom. SAR estimations of the rate coefficients were calculated and compared to the experimental values.

Correcting the Experimental Enthalpies of Formation of Some Members of the Biologically Significant Sulfenic Acids Family.

Sulfenic acids are important intermediates in the oxidation of cysteine thiol groups in proteins by reactive oxygen species. The mechanism is influenced heavily by the presence of polar groups, other thiol groups, and solvent, all of which determines the need to compute precisely the energies involved in the process. Surprisingly, very scarce experimental information exists about a very basic property of sulfenic acids, the enthalpies of formation. In this Article, we use high level quantum chemical methods to derive the enthalpy of formation at 298.15 K of methane-, ethene-, ethyne-, and benzenesulfenic acids, the only ones for which some experimental information exists. The methods employed were tested against well-known experimental data of related species and extensive CCSD(T) calculations. Our best results consistently point out to a much lower enthalpy of formation of methanesulfenic acid, CH3SOH (ΔfH0(298.15K) = -35.1 ± 0.4 kcal mol-1), than the one reported in the NIST thermochemical data tables. The enthalpies of formation derived for ethynesulfenic acid, HC≡CSOH, +32.9 ± 1.0 kcal/mol, and benzenesulfenic acid, C6H5SOH, -2.6 ± 0.6 kcal mol-1, also differ markedly from the experimental values, while the enthalpy of formation of ethenesulfenic acid CH2CHSOH, not available experimentally, was calculated as -11.2 ± 0.7 kcal mol-1.

Dipolar 1,3-cycloaddition of thioformaldehyde S-methylide (CH2 SCH2 ) to ethylene and acetylene. A comparison with (valence) isoelectronic O3 , SO2 , CH2 OO and CH2 SO.

Methods rooted in the density functional theory and in the coupled cluster ansatz were employed to investigate the cycloaddition reactions to ethylene and acetylene of 1,3-dipolar species including ozone and the derivatives issued from replacement of the central oxygen atom by the valence-isoelectronic sulfur atom, and/or of one or both terminal oxygen atoms by the isoelectronic CH2 group. This gives rise to five different 1,3-dipolar compounds, namely ozone itself (O3 ), sulfur dioxide (SO2 ), the simplest Criegee intermediate (CH2 OO), sulfine (CH2 SO), and thioformaldehyde S-methylide (CH2 SCH2 , TSM). The experimental and accurate theoretical data available for some of those molecules were employed to assess the accuracy of two last-generation composite methods employing conventional or explicitly correlated post-Hartree-Fock contributions (jun-Cheap and SVECV-f12, respectively), which were then applied to investigate the reactivity of TSM. The energy barriers provided by both composite methods are very close (the average values for the two composite methods are 7.1 and 8.3 kcal mol-1 for the addition to ethylene and acetylene, respectively) and comparable to those ruling the corresponding additions of ozone (4.0 and 7.7 kcal mol-1 , respectively). These and other evidences strongly suggest that, at least in the case of cycloadditions, the reactivity of TSM is similar to that of O3 and very different from that of SO2 .

Purification, structural elucidation, antioxidant capacity and neuroprotective potential of the main polyphenolic compounds contained in Achyrocline satureioides (Lam) D.C. (Compositae).

Achyrocline satureioides (Lam) D.C (Compositae) is a native medicinal plant of South America traditionally utilized for its anti-inflammatory, sedative and anti-atherosclerotic properties among others. Neuroprotective effects have been reported in vivo and could be associated to its elevated content of flavonoid aglycones. In the present study we performed the isolation and structure elucidation of the major individual flavonoids of A. satureioides along with the in vitro characterization of their individual antioxidant and neuroprotective properties in order to see their putative relevance for treating neurodegeneration. Exact mass, HPLC-MS/MS and 1H NMR identified dicaffeoyl quinic acid isomers, quercetin, luteolin, isoquercitrin, and 3-O-methylquercetin as the mayor polyphenols. Flavonoids intrinsic redox properties were evaluated in the presence of the endogenous antioxidants GSH and Ascorbate. Density Functional Theory (DFT) molecular modeling and electron density studies showed a theoretical basis for their different redox properties. Finally, in vitro neuroprotective effect of each isolated flavonoid was evaluated against hydrogen peroxide-induced toxicity in a primary neuronal culture paradigm. Our results showed that quercetin was more efficacious than luteolin and isoquercitrin, while 3-O-methylquercetin was unable to afford neuroprotection significantly. This was in accordance with the susceptibility of each flavonoid to be oxidized and to react with GSH. Overall our results shed light on chemical and molecular mechanisms underlying bioactive actions of A. satureioides main flavonoids that could contribute to its neuroprotective effects and support the positive association between the consumption of A. satureioides as a natural dietary source of polyphenols, and beneficial health effect.

An in silico study of the citrus dioxygenases CCD4 family substrates.

The coloration of Citrus fruits is related with the concentration of carotenoids, isoprenoid pigments of 40 carbon atoms (C40). Rodrigo et al. and Ma et al. reported a CCD4-type citrus dioxygenase responsible for the generation of C30 apocarotenoids providing a reddish-orange pigmentation to the peel of many mandarins and oranges. Among them, CCD4b was the first case described of a dioxygenase that cleaves carotenoids C40 in the double bond 7', 8' or 7, 8, generating ß-citraurin or 8-ß-apocarotenal. Here we report the three-dimensional structures of CCD4a and CCD4b, modeled by sequence homology (2BIW) and validated by molecular dynamics (MD). Docking calculations were performed in CCD4a and CCD4b structures with thousands of rotated initial carotenoid conformations and all the possible poses in the active site were found. The interaction energy was measured by means of ASE scoring, Amber99 refinement and London ΔG rescoring. For the case of CCD4a model, the results showed London ΔG score of -19, -17 and -15 kcal/mol for zeaxanthin, ß-cryptoxanthin and ß-carotene, respectively. The same sequence in the estimated interaction strength for the three ligands was obtained using MD. The interaction energy of CCD4b indicated that, in agreement with experimental data, zeaxanthin and ß-cryptoxanthin could be cleaved by the enzyme, ß- and α-carotene have chances to be oxidized and lycopene has not good interaction energy to be predicted as substrate. These findings will be discussed considering the potential in vivo substrates and products, and the physiological role in Citrus fruits. Communicated by Ramaswamy H. Sarma.

Theoretical study of the reactions of the hydroselenyl radical (HSe●) with the selenenic radical (HSeO●).

The formation of selenium species in some biological processes involves the generation of ionic and radical intermediates such as RSe●, RSe-, RSeO●, and RSeO-, among others. We performed a theoretical study of the possible mechanisms for the reaction of the two simplest Se radicals-the hydroselenyl (HSe●) and selenenic (HSeO●) radicals, in which the possible products, intermediates, and transition-state structures were investigated. Density functional theory (DFT) was applied at the B3LYP/6-311++G(3df,3pd) level and the Ahlrichs Coulomb fitting basis sets were employed with an effective core potential (ECP) for both Se atoms. The same procedure was used to calculate the electronic density. All calculations were also performed using the M06-2X functional, which describes weaker bonds better than B3LYP does. In the reaction of interest, the so-called CR complex (HSe····SeOH) is formed initially. After passing through the transition state TS1, cis-HSeSeOH is obtained as a product. If a low barrier is then overcome (passing through the transition state TS32), the trans-HSeSeOH species is obtained. The CR complex can also rearrange into the intermediate INT after overcoming the barrier presented by the transition state TS2. Additionally, the decomposition of INT to H2O and 1Se2 is possible through another transition state. This reaction is not included in this study. We also observed a second possible route for the conversion of INT to one of the HSeSeOH species; this route occurs through two pathways (with transition states TS31 and TS32). A comparison of some of the results with those obtained for sulfur analogs along the same pathways is also presented in this work. Graphical abstract Electronic envelopes for HSeO● and HSe● radicals.

Theoretical insight into the mechanism for the inhibition of the cysteine protease cathepsin B by 1,2,4-thiadiazole derivatives.

Several cellular disorders have been related to the overexpression of the cysteine protease cathepsin B (CatB), such as rheumatic arthritis, muscular dystrophy, osteoporosis, Alzheimer's disease, and tumor metastasis. Therefore, inhibiting CatB may be a way to control unregulated cellular functions and prevent tissue malformations. The inhibitory action of 1,2,4-thiadiazole (TDZ) derivatives has been associated in the literature with their ability to form disulfide bridges with the catalytic cysteine of CatB. In this work, we present molecular modeling and docking studies of a series of eight 1,2,4-thiadiazole compounds. Substitutions at two positions (3 and 5) on the 1,2,4-thiadiazole ring were analyzed, and the docking scores were correlated to experimental data. A correlation was found with the sequence of scores of four related compounds with different substituents at position 5. No correlation was observed for changes at position 3. In addition, quantum chemistry calculations were performed on smaller molecular models to study the mechanism of inhibition of TDZ at the active site of CatB. All possible protonation states of the ligand and the active site residues were assessed. The tautomeric form in which the proton is located on N2 was identified as the species that has the structural and energetic characteristics that would allow the ring opening of 1,2,4-thiadiazole.

Conformational analyses and docking studies of a series of 5-nitrofuran- and 5-nitrothiophen-semicarbazone derivatives in three possible binding sites of trypanothione and glutathione reductases.

To explore three possible binding sites of trypanothione and glutathione reductase, namely, the active, the dimer interface and the coenzyme NADPH binding site, a series of eight compounds, nitrofurans and nitrothiophenes derivatives, were docked, using their crystallographic and modeled conformations. Docking results showed that, for both families and both enzymes, compounds are more likely to bind in the interface site, even though there is some probability of binding in the active site. These studies are in agreement with experimental data, which suggest that these class of compounds can act either as uncompetitive or mixed type inhibitors, and also with the finding that there is an alpha-helix which connects the active with the interface site, thus allowing charge transference between them.