Many per- and polyfluoroalkyl substances (PFAS) have been regulated or phased-out of usage due to concerns about persistence, bioaccumulation potential, and toxicity. We investigated the atmospheric fate of a new polyfluorinated alcohol 2-(1,1,2-trifluoro-2-heptafluoropropyloxy-ethylsulfanyl)-ethanol (C3F7OCHFCF2SCH2CH2OH, abbreviated FESOH) by assessing the kinetics and products of the gas-phase reaction of FESOH with chlorine atoms and hydroxyl radicals. Experiments performed in a stainless-steel chamber interfaced to an FTIR were used to determine reaction kinetics and gas-phase products. We report reaction rate constants of k(Cl + FESOH) = (1.5 ± 0.6) × 10-11 cm3 molecule-1 s-1 and k(OH + FESOH) = (4.2 ± 2.0) × 10-12 cm3 molecule-1 s-1. This leads to a calculated FESOH gas-phase lifetime of 2.8 ± 1.3 days with respect to reaction with OH, assuming [OH] = 106 molecule1 cm-3. Gas-phase products of FESOH oxidation included at least two aldehydes, likely C3F7OCHFCF2SCH2C(O)H and C3F7OCHFCF2SC(O)H, and secondary products including COF2, SO2 and C3F7OC(O)F. Additional gas-phase experiments performed in a Teflon chamber were used to assess aqueous products by collecting gaseous samples offline into an aqueous sink prior to analysis with ultrahigh performance liquid chromatography-tandem mass spectrometry, resulting in four acidic products C3F7OCHFCF2SCH2C(O)OH, C3F7OCHFCF2S(O)(O)OH, C3F7OCHFC(O)OH, and perfluoropropanoic acid (C2F5C(O)OH).The quantum mechanical bespoke (QUBE) force-field approach has been developed to facilitate the automated derivation of potential energy function parameters for modeling protein-ligand binding. To date, the approach has been validated in the context of Monte Carlo simulations of protein-ligand complexes. We describe here the implementation of the QUBE force field in the alchemical free-energy calculation molecular dynamics simulation package SOMD. The implementation is validated by demonstrating the reproducibility of absolute hydration free energies computed with the QUBE force field across the SOMD and GROMACS software packages. We further demonstrate, by way of a case study involving two series of non-nucleoside inhibitors of HIV-1 reverse transcriptase, that the availability of QUBE in a modern simulation package that makes efficient use of graphics processing unit acceleration will facilitate high-throughput alchemical free-energy calculations.The CorA family of proteins plays a housekeeping role in the homeostasis of divalent metal ions in many bacteria and archaea as well as in mitochondria of eukaryotes, rendering it an important target to study the mechanisms of divalent transport and regulation across different life domains. Despite numerous studies, the mechanistic details of the channel gating and the transport of the metal ions are still not entirely understood. Here, we use all-atom and coarse-grained molecular dynamics simulations combined with in vitro experiments to investigate the influence of divalent cations on the function of CorA. https://www.selleckchem.com/ Simulations reveal pronounced asymmetric movements of monomers that enable the rotation of the α7 helix and the cytoplasmic subdomain with the subsequent formation of new interactions and the opening of the channel. These computational results are functionally validated using site-directed mutagenesis of the intracellular cytoplasmic domain residues and biochemical assays. The obtained results infer a complex network of interactions altering the structure of CorA to allow gating. Furthermore, we attempt to reconcile the existing gating hypotheses for CorA to conclude the mechanism of transport of divalent cations via these proteins.The development of robust analytical tools capable of probing the formation kinetics and thermodynamics of DNA nanostructures is a crucial step toward better understanding and manufacturing of diverse DNA-based materials. Herein, we introduce a real-time fluorescence anisotropy assay and rationally designed DNA reaction termination probes (DRTPs) as a set of new tools for exploring the formation mechanisms of DNA nanostructures. We deployed these tools for probing the formation of a classic tetrahedral DNA nanostructure (TDN) as a model system. Our tools revealed that the formation of TDN was dominated by simultaneous hybridization, whereas its undesired side products were caused mainly through step-wise hybridization. An optimal reaction temperature exists that favors the formation of TDN over side products. With insight into the TDN formation mechanism, we further engineered magnetic DRTPs to achieve single-step purification of TDN, enabling 10-fold improvement in the ratio between the targeted TDN and undesired side products without tedious procedures or bulky instruments. Combining the optimal reaction and purification conditions, we finally demonstrated the one-pot synthesis and purification of TDN. The analytical techniques offered in this work may hold potential to find wide applications and inspire new analytical methods for structural DNA nanotechnology.The two main strategies for enzyme engineering, directed evolution and rational design, have found widespread applications in improving the intrinsic activities of proteins. Although numerous advances have been achieved using these ground-breaking methods, the limited chemical diversity of the biopolymers, restricted to the 20 canonical amino acids, hampers creation of novel enzymes that Nature has never made thus far. To address this, much research has been devoted to expanding the protein sequence space via chemical modifications and/or incorporation of noncanonical amino acids (ncAAs). This review provides a balanced discussion and critical evaluation of the applications, recent advances, and technical breakthroughs in biocatalysis for three approaches (i) chemical modification of cAAs, (ii) incorporation of ncAAs, and (iii) chemical modification of incorporated ncAAs. Furthermore, the applications of these approaches and the result on the functional properties and mechanistic study of the enzymes are extensively reviewed. We also discuss the design of artificial enzymes and directed evolution strategies for enzymes with ncAAs incorporated. Finally, we discuss the current challenges and future perspectives for biocatalysis using the expanded amino acid alphabet.