An open-source approach to automation in organic synthesis: The flow chemical formation of benzamides using an inline liquid-liquid extraction system and a homemade 3-axis autosampling/product-collection device

Several open-source hardware and software technologies (RAMPS, Python, PySerial, OpenCV) were used to control an automated flow chemical synthesis system. The system was used to effect the synthesis of a series of benzamides. An inexpensive Raspberry Pi single board computer provided an electronic interface between the control computer and the RAMPS motor driver boards.     

Modeling the active sites in metalloenzymes. 3. Density functional calculations on models for [Fe]-hydrogenase: structures and vibrational frequencies of the observed redox forms and the reaction mechanism at the Diiron Active Center.

Optimized structures for the redox species of the diiron active site in [Fe]-hydrogenase as observed by FTIR and for species in the catalytic cycle for the reversible H(2) oxidation have been determined by density-functional calculations on the active site model, [(L)(CO)(CN)Fe(mu-PDT)(mu-CO)Fe(CO)(CN)(L')](q)(L = H(2)O, CO, H(2), H(-); PDT = SCH(2)CH(2)CH(2)S, L' = CH(3)S(-), CH(3)SH; q = 0, 1-, 2-, 3-). Analytical DFT frequencies on model complexes (mu-PDT)Fe(2)(CO)(6) and [(mu-PDT)Fe(2)(CO)(4)(CN)(2)](2)(-) are used to calibrate the calculated CN(-) and CO frequencies against the measured FTIR bands in these model compounds. By comparing the predicted CN(-) and CO frequencies from DFT frequency calculations on the active site model with the observed bands of D. vulgaris [Fe]-hydrogenase under various conditions, the oxidation states and structures for the diiron active site are proposed. The fully oxidized, EPR-silent form is an Fe(II)-Fe(II) species. Coordination of H(2)O to the empty site in the enzyme's diiron active center results in an oxidized inactive form (H(2)O)Fe(II)-Fe(II). The calculations show that reduction of this inactive form releases the H(2)O to provide an open coordination site for H(2). The partially oxidized active state, which has an S = (1)/(2) EPR signal, is an Fe(I)-Fe(II) species. Fe(I)-Fe(I) species with and without bridging CO account for the fully reduced, EPR-silent state. For this fully reduced state, the species without the bridging CO is slightly more stable than the structure with the bridging CO. The correlation coefficient between the predicted CN(-) and CO frequencies for the proposed model species and the measured CN(-) and CO frequencies in the enzyme is 0.964. The proposed species are also consistent with the EPR, ENDOR, and M?ssbauer spectroscopies for the enzyme states. Our results preclude the presence of Fe(III)-Fe(II) or Fe(III)-Fe(III) states among those observed by FTIR. A proposed reaction mechanism (catalytic cycle) based on the DFT calculations shows that heterolytic cleavage of H(2) can occur from (eta(2)-H(2))Fe(II)-Fe(II) via a proton transfer to "spectator" ligands. Proton transfer to a CN(-) ligand is thermodynamically favored but kinetically unfavorable over proton transfer to the bridging S of the PDT. Proton migration from a metal hydride to a base (S, CN, or basic protein site) results in a two-electron reduction at the metals and explains in part the active site's dimetal requirement and ligand framework which supports low-oxidation-state metals. The calculations also suggest that species with a protonated Fe-Fe bond could be involved if the protein could accommodate such species.     

Quantitative studies on the peroxidation of human low-density lipoprotein initiated by superoxide and by charged and neutral alkylperoxyl radicals.

Rates of peroxidation of human LDL and rates of consumption of the LDL's alpha-tocopherol (TocH) have been measured at 37 degrees C. Peroxidation was initiated by radicals generated in the aerated aqueous phase at known rates by thermal decomposition of appropriate precursors: superoxide (O2(*-)/HOO(*)) from a hyponitrite and alkylperoxyls (ROO(*), two positively charged, one negatively charged and one neutral) from azo compounds. The efficiencies of escape from the solvent cage of the geminate pair of neutral carbon-centered radicals was found to be 0.1, but it was 0.5 for the three charged radicals, a result attributed to radical/radical Coulombic repulsion within the cage. All four alkylperoxyls initiated and terminated tocopherol-mediated peroxidation (TMP) with about equal efficiency and essentially all of these radicals that were generated were consumed in these two reactions. TMP is a radical chain process, and when initiated by the alkylperoxyls, the rate of LDL peroxidation was faster in the early stages while TocH was present than later, after all of this "antioxidant" had been consumed. In contrast, only about 3-4% of the generated superoxide radicals reacted in any measurable fashion with TocH-containing LDL at pH's from 7.6 to 6.5 and peroxidation was much slower than with a similar rate of generation of alkylperoxyls. After all the TocH had been consumed, LDL peroxidation was negligible at pH 7.6 and 7.4, but at pH 6.8 and 6.5, the peroxidation rates showed a large increase over the rates while the TocH had been present. That is, endogenous TocH behaves as an antioxidant in LDL subjected to attack by the physiologically relevant superoxide radical, whereas TocH behaves as a prooxidant in LDL subjected to attack by the probably far less physiologically important alkylperoxyls. Rates of LDL peroxidation initiated by superoxide increased as the pH was decreased, and the results are consistent with the initiation of peroxidation of fresh LDL occurring via H-atom abstraction from TocH by HOO(*) to form the Toc(*) radical and termination by reaction of O2(*-) with Toc(*), a process that occurs partly by addition leading to TocH consumption and partly by electron plus proton transfer leading to the regeneration of TocH.     

Synthesis and photochemistry of pH-sensitive GFP chromophore analogs

GFP chromophore analogs (7a-e, 8, and 10a,b) containing 2-thienyl-, 5-methyl-2-furyl-, 2-pyrryl, and 6-methyl-2-pyridyl-groups were synthesized and their fluorescence spectra recorded in the pH range 1-7. NMR studies showed that protonation of 8 (2-thienyl system) inhibited photoisomerization (Z-E) about the exocyclic double bond but that protonation of 7c (E + Z) (2-pyrryl system) gave only 7cE. Fluorescence studies revealed enhancement of fluorescence intensity of 7c and 7b,e (furyl system) below pH 2.5 and gave a similar result for 10a (pyridyl system) below pH 6. Quantum yields at pH 1 were low, probably due to excited state proton transfer (ESPT).     

LSPR Biosensor Signal Enhancement Using Nanoparticle-Antibody Conjugates

A method to amplify the wavelength shift observed from localized surface plasmon resonance (LSPR) bioassays is developed using gold nanoparticle-labeled antibodies. The technique, which involves detecting surface-bound analytes using gold nanoparticle conjugated antibodies, provides a way to enhance LSPR shifts for more sensitive detection of low-concentration analytes. Using the biotin and antibiotin binding pair as a model, we demonstrate up to a 400% amplification of the shift upon antibody binding to analyte. In addition, the antibody-nanoparticle conjugate improves the observed binding constant by 2 orders of magnitude, and the limit of detection by nearly 3 orders of magnitude. This amplification strategy provides a way to improve the sensitivity of plasmon-based bioassays, paving the way for single molecule-based detection and clinically relevant diagnostics.     

Synthesis and characterization of BaZrO3-doped YBa2Cu3O7−δ microtapes with improved critical current densities

We have recently demonstrated that through a sol–gel route, superconductor crystallization in the presence of simple biopolymers results in a drastic alteration of morphology, producing technologically useful nanowires and porous architectures. Morphological control is of the utmost importance to bulk high-temperature superconductors, as grain boundaries act as weak links in limiting the achievable critical current density (J_c). Here we show that, as expected, the incorporation of nanoparticulate barium zirconate (BaZrO₃) species into a biopolymer-mediated synthetic protocol for YBa₂Cu₃O_7?δ (Y123) leads to a significantly improved in-field J_c compared to that observed in a sample without BaZrO₃ additions. To ameliorate degradation of the BaZrO₃ species in this protocol, we demonstrate that by drawing the precursor sol into fibers, a microtape architecture is able to be formed, leading to lengthy, anisotropic structures having enhanced J_c through the retention of the BaZrO₃ species.     

Scandium-catalyzed allylboration of aldehydes as a practical method for highly diastereo- and enantioselective construction of homoallylic alcohols

A general approach for the allylation of aldehydes using stable, air-tolerant camphor-based chiral allylboronates under Sc(OTf)3 catalysis is described. This practical methodology provides both syn and anti propionate units and other homoallylic alcohols with very high levels of diastereo- and enantioselectivity for several substrates, including functionalized aliphatic aldehydes useful toward the elaboration of complex natural products.