An Assessment of Computational Methods for Calculating Accurate Structures and Energies of Bio-Relevant Polysulfur/Selenium-Containing Compounds

Describing the Disulfide Bond: From the Density Functional Theory and Back through the "Lego Brick" Approach

Selected molecular species containing the disulfide bond, RSSR, have been considered, these ranging from hydrogen disulfide, H2S2 (R = H), to diphenyl disulfide with R = C6H5. The aim of this work is two-fold: (i) to investigate different computational approaches in order to derive accurate equilibrium structures at an affordable cost, (ii) to employ the results from the first goal in order to benchmark cheaper methodologies rooted in the density functional theory. Among the strategies used for the accurate geometrical determinations, the semiexperimental approach has been exploited in combination with a reduced-dimensionality VPT2 model, without however obtaining satisfactory results. Instead, the so-called "Lego brick" approach turned out to be very effective despite the flexibility of the systems investigated. Concerning the second target of this work, the focus was mainly on the S-S bond and the structural parameters related to it. Among those tested, PBE0(-D3BJ), M06-2X(-D3) and DSD-PBEP86-D3BJ have been found to be the best-performing functionals.

Origin of Optoelectronic Contradictions in 3,4-Cycloalkyl[c]-chalcogenophenes: A Computational Study

The planar morphology of the backbone significantly contributes to the subtle optoelectronic features of π-conjugated polymers. On the other hand, the atomistic tuning of an otherwise identical π-backbone could also impact optoelectronic properties systematically. In this manuscript, we compare a series of 3,4-cycloalkylchalcogenophenes by tuning them atomistically using group-16 elements. Additionally, the effect of systematically extending these building blocks in the form of oligomers and polymers is studied. The size of the 3,4-substitution affected the morphology of the oligomers. In addition, the heteroatoms contributed to a further alteration in their geometry and resultant optoelectronic properties. The chalcogenophenes, containing smaller 3,4-cycloalkanes, resulted in lower bandgap oligomers or polymers compared to those with larger 3,4-cycloalkanes. Natural bonding orbital (NBO) calculations were performed to understand the disparity alongside the contour maps of frontier molecular orbitals (FMO).

The redox riddle of selenium sulfide

Selenium sulfide, in analogy with selenium dioxide, is often considered as SeS2. At closer inspection, however, selenium sulfide represents a large family of rather complicated molecules which differ depending on the mode of preparation. Together, these compounds share extraordinarily low solubility in virtually any solvent with a biological activity rather impressive for such simple molecules. The surface reactivity of such microscopic and nanoscopic materials, prepared chemically or by fermentation, may provide an answer to this riddle and explain activities by a combination of physical, redox, metal binding, covalent, and non-covalent interactions with biomolecules and cells.

The Se-S Bond Formation in the Covalent Inhibition Mechanism of SARS-CoV-2 Main Protease by Ebselen-like Inhibitors: A Computational Study

The inhibition mechanism of the main protease (Mpro) of SARS-CoV-2 by ebselen (EBS) and its analog with a hydroxyl group at position 2 of the benzisoselenazol-3(2H)-one ring (EBS-OH) was studied by using a density functional level of theory. Preliminary molecular dynamics simulations on the apo form of Mpro were performed taking into account both the hydrogen donor and acceptor natures of the Nδ and Nε of His41, a member of the catalytic dyad. The potential energy surfaces for the formation of the Se-S covalent bond mediated by EBS and EBS-OH on Mpro are discussed in detail. The EBS-OH shows a distinctive behavior with respect to EBS in the formation of the noncovalent complex. Due to the presence of canonical H-bonds and noncanonical ones involving less electronegative atoms, such as sulfur and selenium, the influence on the energy barriers and reaction energy of the Minnesota hybrid meta-GGA functionals M06, M06-2X and M08HX, and the more recent range-separated hybrid functional wB97X were also considered. The knowledge of the inhibition mechanism of Mpro by the small protease inhibitors EBS or EBS-OH can enlarge the possibilities for designing more potent and selective inhibitor-based drugs to be used in combination with other antiviral therapies.

Chemistry and Chemical Biology of Selenenyl Sulfides and Thioseleninic Acids

Significance: Selenenyl sulfides (RSeSRs) and thioseleninic acids (RSeSHs) are the monoselenium (Se) analogs of disulfides and persulfides that contain Se-S bonds. These bonds are found in several antioxidant-regenerating enzymes as derivatives of selenocysteine, making them an important player in redox biology as it pertains to sulfur redox regulation. Recent Advances: Mechanistic studies of redox-regulating selenoenzymes such as thioredoxin reductase and glutathione peroxidase suggest crucial Se-S bonds in the active sites. Peptide models and small-molecule mimics of these active sites have been prepared to study their fundamental chemistry. These advances help pave the road to better understand the functions of the Se-S bond in the body. Critical Issues: The Se-S bond is unstable at atmospheric temperatures and pressures. Therefore, studying their properties proposes a major challenge. Currently, there are no trapping reagents specific to RSeSRs or RSeSHs, making their presence, identity, and fates in biological environments difficult to track. Future Directions: Further understanding of the fundamental chemistry/biochemistry of RSeSRs and RSeSHs is needed to understand what their intracellular targets are and to what extent they impact signaling. Besides antioxidant regeneration and peroxide radical reduction, the roles of RSeSR and RSeSHs in other systems need to be further explored.

Sulfur Species, Bonding Environment, and Metal Mobilization in Mining-Impacted Lake Sediments: Column Experiments Replicating Seasonal Anoxia and Deposition of Algal Detritus

The oxidation state of sulfur [S] is a primary control on mobility of metals in sediments impacted by legacy mining practices. Coeur d’Alene Lake of northern Idaho, USA, has been impacted by upstream legacy mining practices that deposited an estimated 75 Mt of metal(loid)- and S-rich sediments into the lake. Future lake conditions are expected to include algal blooms, which may alter S and metal remobilization during the seasonal euxinic environment. Cores of the lake sediments were exposed to anoxic and anoxic + algal detritus conditions for eight weeks at 4.5 °C through introduction of a N2 atmosphere and addition of algal detritus. At a location 2.5 cm below the sediment-water interface, anoxic conditions promoted a shift in S species to continually larger concentrations of reduced species and an associated shift in the bonding environment reflective of increased S–metal bonds. Anoxic + algal detritus conditions suppressed the increasing trend of reduced S species and induced greater release of Mn compared to the anoxic-only conditions but did not appear to enhance the release of As, Cd, or Fe. The addition of algal detritus to the sediment-water interface of these Fe- and S-rich sediments enhanced mobilization of Mn likely because of dissimilatory metal reduction where the anaerobic oxidation of the algal detritus stimulated Mn reduction. Results of the study indicate that future metal release from the lake sediments will be altered with the likely deposition of algal detritus, but the effect may not enhance the release of acutely toxic metals, such as As or Cd, or substantially impact Fe cycling in the sediments.