Synthesis of α-hydroxyalkyl dehydroazepanes via catalytic enantioselective borylative migration of an enol nonaflate

A Pd-catalyzed borylative migration methodology for cyclic enol perfluorosulfonates was applied to the synthesis of the corresponding 7-membered, azepane ring system. Throughout the optimization, it was shown that the reaction is sensitive to the nitrogen protecting group as well as the type of base and solvent. The resulting cyclic allylboronate reacts stereoselectively with aldehydes for the synthesis of novel α-hydroxyalkyl dehydroazepanes in good yield and enantioselectivity over two steps. We highlight the utility of this methodology with an efficient synthesis of the de novo 7-membered ring analogue of the piperidine alkaloid β-conhydrine.     

Protein–ligand docking using FFT based sampling: D3R case study

Fast Fourier transform (FFT) based approaches have been successful in application to modeling of relatively rigid protein–protein complexes. Recently, we have been able to adapt the FFT methodology to treatment of flexible protein–peptide interactions. Here, we report our latest attempt to expand the capabilities of the FFT approach to treatment of flexible protein–ligand interactions in application to the D3R PL-2016-1 challenge. Based on the D3R assessment, our FFT approach in conjunction with Monte Carlo minimization off-grid refinement was among the top performing methods in the challenge. The potential advantage of our method is its ability to globally sample the protein–ligand interaction landscape, which will be explored in further applications.     

Boronic Acids as Bioorthogonal Probes for Site‐Selective Labeling of Proteins

Over the past two decades, bioorthogonal chemistry has become a preferred tool to achieve site‐selective modifications of proteins. However, there are only a handful of commonly applied bioorthogonal reactions and they display some limitations, such as slow rates, use of unstable or cytotoxic reagents, and side reactions. Hence, there is significant interest in expanding the bioorthogonal chemistry toolbox. In this regard, boronic acids have recently been introduced in bioorthogonal chemistry and are exploited in three different strategies: 1) boronic ester formation between a boronic acid and a 1,2‐cis diol; 2) iminoboronate formation between 2‐acetyl/formyl‐arylboronic acids and hydrazine/hydroxylamine/semicarbazide derivatives; 3) use of boronic acids as transient groups in a Suzuki–Miyaura cross‐coupling or other reactions that leave the boronyl group off the conjugation product. In this Review, we summarize progress made in the use of boronic acids in bioorthogonal chemistry to enable site‐selective labeling of proteins and compare these methods with the most commonly utilized bioorthogonal reactions.     

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).