Criegee Intermediate-Mediated Oxidation of Dimethyl Disulfide: Effect of Formic Acid and Its Atmospheric Relevance.

The oxidation-reduction reactions of disulfides are important in both chemistry and biology. Dimethyl disulfide (DMDS), the smallest reduced sulfur species with a disulfide bond, is emitted in significant quantities from natural sources and contributes to the formation of aerosols and hazardous haze. Although atmospheric removal of DMDS via the reactions with OH or NO3 radicals and photolysis is known, the reactions of DMDS with other atmospheric oxidants are yet to be explored. Herein, using quantum chemical calculations, we explored the reactions of DMDS with CH2OO (formaldehyde oxide) and other methyl-substituted Criegee intermediates. The various reaction pathways evaluated were found to have positive energy barriers. However, in the presence of formic acid, a direct oxygen-transfer pathway leading to the corresponding sulfoxide (CH3SS(O)CH3) was found to proceed through a submerged transition state below the separated reactants. Calculations for the methyl-substituted Criegee intermediates, particularly for anti-CH3CHOO, show a significant increase in the rate of the direct oxygen-transfer reaction when catalyzed by formic acid. The presence of formic acid also alters the mechanism and reduces the enthalpic barrier of a second pathway, forming thioformaldehyde and hydroperoxide without any rate enhancement. Our data indicated that, although Criegee intermediates are unlikely to be an important atmospheric sink of DMDS under normal conditions, in regions rich in DMDS and formic acid, the formic acid-catalyzed Criegee intermediate-mediated oxidation of DMDS via the direct oxygen-transfer pathway could lead to organic sulfur compounds contributing to atmospheric aerosol.

The Natural Products Withaferin A and Withanone from the Medicinal Herb Withania somnifera Are Covalent Inhibitors of the SARS-CoV-2 Main Protease.

The current COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) created a global health crisis. The ability of vaccines to protect immunocompromised individuals and from emerging new strains are major concerns. Hence antiviral drugs against SARS-CoV-2 are essential. The SARS-CoV-2 main protease Mpro is vital for replication and an important target for antivirals. Using CMap analysis and docking studies, withaferin A (wifA) and withanone (win), two natural products from the medicinal herb Withania somnifera (ashwagandha), were identified as promising candidates that can covalently inhibit the viral protease Mpro. Cell culture, enzymatic, LC-MS/MS, computational, and equilibrium dialysis based assays were performed. DFT calculations indicated that wifA and win can form stable adducts with thiols. The cytotoxicity of Mpro was significantly reduced by wifA and win. Both wifA and win were found to irreversibly inhibit 0.5 µM Mpro with IC50 values of 0.54 and 1.8 µM, respectively. LC-MS/MS analysis revealed covalent adduct formation with wifA at cysteines 145 and 300 of Mpro. The natural products wifA and win can irreversibly inhibit the SARS-CoV-2 main protease Mpro. Based on the work presented here we propose that both wifA and win have the potential to be safely used as preventative and therapeutic interventions for COVID-19.

The gas-phase structure of the asymmetric, trans-dinitrogen tetroxide (N2O4), formed by dimerization of nitrogen dioxide (NO2), from rotational spectroscopy and ab initio quantum chemistry.

We report the first experimental gas-phase observation of an asymmetric, trans-N2O4 formed by the dimerization of NO2. In additional to the dominant 14N216O4 species, rotational transitions have been observed for all species with single 15N and 18O substitutions as well as several multiply substituted isotopologues. These transitions were used to determine a complete substitution structure as well as an r0 structure from the fitted zero-point averaged rotational constants. The determined structure is found to be that of an ON-O-NO2 linkage with the shared oxygen atom closer to the NO2 than the NO (1.42 vs 1.61 Å). The structure is found to be nearly planar with a trans O-N-O-N linkage. From the spectra of the 14N15NO4 species, we were able to determine the nuclear quadrupole coupling constants for each specific nitrogen atom. The equilibrium structure determined by ab initio quantum chemistry calculations is in excellent agreement with the experimentally determined structure. No spectral evidence of the predicted asymmetric, cis-N2O4 was found in the spectra.

Microwave spectroscopic and theoretical studies on the phenylacetylene···H2O complex: C-H···O and O-H···π hydrogen bonds as equal partners.

Rotational spectra of five isotopologues of the title complex, C(6)H(5)CCH···H(2)O, C(6)H(5)CCH···HOD, C(6)H(5)CCH···D(2)O, C(6)H(5)CCH···H(2)(18)O and C(6)H(5)CCD···H(2)O, were measured and analyzed. The parent isotopologue is an asymmetric top with κ = -0.73. The complex is effectively planar (ab inertial plane) and both 'a' and 'b' dipole transitions have been observed but no c dipole transition could be seen. All the transitions of the parent complex are split into two resulting from an internal motion interchanging the two H atoms in H(2)O. This is confirmed by the absence of such doubling for the C(6)H(5)CCH···HOD complex and a significant reduction in the splitting for the D(2)O analog. The rotational spectra, unambiguously, reveal a structure in which H(2)O has both O-H···π (π cloud of acetylene moiety) and C-H···O (ortho C-H group of phenylacetylene) interactions. This is in agreement with the structure deduced by IR-UV double resonance studies (Singh et al., J. Phys. Chem. A, 2008, 112, 3360) and also with the global minimum predicted by advanced electronic structure theory calculations (Sedlack et al., J. Phys. Chem. A, 2009, 113, 6620). Atoms in Molecule (AIM) theoretical analysis of the complex reveals the presence of both O-H···π and C-H···O hydrogen bonds. More interestingly, based on the electron densities at the bond critical points, this analysis suggests that both these interactions are equally strong. Moreover, the presence of both these interactions leads to significant deviation from linearity of both hydrogen bonds.

DNA damage by Withanone as a potential cause of liver toxicity observed for herbal products of Withania somnifera (Ashwagandha).

Withania somnifera, commonly known as Ashwagandha, is a medicinal plant used for thousands of years for various remedies. Extracts of Ashwagandha contain more than 200 metabolites, with withanone (win) being one of the major ones responsible for many of its medicinal properties. Recently, several cases of liver toxicity resulting from commercially available Ashwagandha products have been reported. The first report of Ashwagandha-related liver damage was from Japan, which was quickly resolved after drug-withdrawal. Later, similar cases of liver toxicity due to Ashwagandha consumption were reported from the USA and Iceland. Towards understanding the liver toxicity of Ashwagandha extracts, we studied win, a representative withanolide having toxicophores or structural alerts that are commonly associated with adverse drug reactions. We found that win can form non-labile adducts with the nucleosides dG, dA, and dC. Using various biochemical assays, we showed that win forms adducts in DNA and interfere with its biological property. Win also forms adducts with amines and this process is reversible. Based on the data presented here we concluded that win is detoxified by GSH but under limiting GSH levels it can cause DNA damage. The work presented here provides a potential mechanism for the reported Ashwagandha-mediated liver damage.

The hydrogen bond: a molecular beam microwave spectroscopist's view with a universal appeal.

In this manuscript, we propose a criterion for a weakly bound complex formed in a supersonic beam to be characterized as a 'hydrogen bonded complex'. For a 'hydrogen bonded complex', the zero point energy along any large amplitude vibrational coordinate that destroys the orientational preference for the hydrogen bond should be significantly below the barrier along that coordinate so that there is at least one bound level. These are vibrational modes that do not lead to the breakdown of the complex as a whole. If the zero point level is higher than the barrier, the 'hydrogen bond' would not be able to stabilize the orientation which favors it and it is no longer sensible to characterize a complex as hydrogen bonded. Four complexes, Ar2-H2O, Ar2-H2S, C2H4-H2O and C2H4-H2S, were chosen for investigations. Zero point energies and barriers for large amplitude motions were calculated at a reasonable level of calculation, MP2(full)/aug-cc-pVTZ, for all these complexes. Atoms in molecules (AIM) theoretical analyses of these complexes were carried out as well. All these complexes would be considered hydrogen bonded according to the AIM theoretical criteria suggested by Koch and Popelier for C-H...O hydrogen bonds (U. Koch and P. L. A. Popelier, J. Phys. Chem., 1995, 99, 9747), which has been widely and, at times, incorrectly used for all types of contacts involving H. It is shown that, according to the criterion proposed here, the Ar2-H2O/H2S complexes are not hydrogen bonded even at zero kelvin and C2H4-H2O/H2S complexes are. This analysis can naturally be extended to all temperatures. It can explain the recent experimental observations on crystal structures of H2S at various conditions and the crossed beam scattering studies on rare gases with H2O and H2S.

Au nanoparticles and polyaniline coated resin beads for simultaneous catalytic oxidation of glucose and colorimetric detection of the product.

In this letter, we report the synthesis of Au nanoparticles (NPs) and polyaniline (PANI) on the same cation-exchange resin beads and demonstrate their use in catalyzing the oxidation of glucose to gluconic acid by Au NPs and simultaneously in detecting the formation of the acid by the color change of PANI. The synthesis was carried out by exchanging the cations of the resins with HAuCl4 and anilinuium chloride and then reducing the metal ions by NaBH4 to produce Au NPs followed by polymerization of aniline using H2O2. The green emeraldine salt form of PANI thus obtained was treated with NaOH to be converted to blue emeraldine base before use. The deposition of Au NPs was confirmed by a change in color of the bead, visible spectroscopy, X-ray diffraction, and scanning electron microscopic measurements. On the other hand, the presence of PANI was confirmed by Fourier transform infrared (FTIR) and ultraviolet-visible (UV-vis) spectroscopy. The formation of gluconic acid from glucose was confirmed by FTIR spectroscopy. We could detect the presence of glucose of a minimum 1.0 mM concentration in water, using the present method. Our experimental observations demonstrate the possibility of the incorporation of multifunctional components on the surfaces of resins for carrying out a chemical reaction as well as detection of the product.