Biosensing with Polymerase Chain Reaction-Stable DNA-Functionalized Magnetically Susceptible Carbon-Iron Microparticles.

We demonstrate a rapid and sensitive method for DNA detection without the need for fluorescence. This is based on carbon-coated magnetic iron (Fe) microparticles with a covalent surface attachment of DNA. We show that these magnetic microparticles can capture complementary DNA. Significantly, the DNA covalent surface bonds are robust to high temperatures and can be included in a sample during polymerase chain reaction (PCR). This method is employed for the detection of targeted DNA sequences (40-50 bp). Hybridization probes on the surface of the magnetically susceptible Fe microparticle recognize the target DNA sequence-specifically. The double-stranded DNA (dsDNA) microparticles are then quickly captured with a magnet from the sample matrix. This foregoes postpurification processes, such as electrophoresis, which make our technique time- and cost-effective. Captured dsDNA can be detected with intercalating dyes such as ethidium bromide through a loss in the UV absorption signal with a limit of detection (LOD) of 24 nM within 15 min. Likewise, surface-bound DNA can act as a primer in PCR to decrease the LOD to 5 pM within 2 h. This is the first instance of a nucleotide-modified magnetically susceptible carbon substrate that is PCR-compatible. Besides DNA capture, this strategy can eventually be applied to sequence-specific nucleic acid purification and enrichment, PCR cleanup, and single-strand generation. The DNA-coated particles are stable under PCR conditions (unlike commonly used polystyrene or gold particles).

Correction: Voltammetric pH sensor based on electrochemically modified pseudo-graphite.

Correction for 'Voltammetric pH sensor based on electrochemically modified pseudo-graphite' by Haoyu Zhu et al., Analyst, 2020, 145, 7252-7259, https://doi.org/10.1039/D0AN01405B.

Engineering Escherichia coli for anaerobic alkane activation: Biosynthesis of (1-methylalkyl)succinates.

In anoxic environments, microbial activation of alkanes for subsequent metabolism occurs most commonly through the addition of fumarate to a subterminal carbon, producing an alkylsuccinate. Alkylsuccinate synthases are complex, multi-subunit enzymes that utilize a catalytic glycyl radical and require a partner, activating enzyme for hydrogen abstraction. While many genes encoding putative alkylsuccinate synthases have been identified, primarily from nitrate- and sulfate-reducing bacteria, few have been characterized and none have been reported to be functionally expressed in a heterologous host. Here, we describe the functional expression of the (1-methylalkyl)succinate synthase (Mas) system from Azoarcus sp. strain HxN1 in recombinant Escherichia coli. Mass spectrometry confirms anaerobic biosynthesis of the expected products of fumarate addition to hexane, butane, and propane. Maximum production of (1-methylpentyl)succinate is observed when masC, masD, masE, masB, and masG are all present on the expression plasmid; omitting masC reduces production by 66% while omitting any other gene eliminates production. Meanwhile, deleting iscR (encoding the repressor of the E. coli iron-sulfur cluster operon) improves product titer, as does performing the biotransformation at reduced temperature (18°C), both suggesting alkylsuccinate biosynthesis is largely limited by functional expression of this enzyme system.

Experimental and Computational Mechanistic Study of Carbonazidate-Initiated Cascade Reactions.

A variety of Huisgen cyclization or nitrene/carbene alkyne cascade reactions with different types of termination were investigated. Accessible nitrene precursors were assessed, and carbonazidates were found to be the only effective initiators. Solvents, terminal alkynyl substituents, and catalysts can all impact the reaction outcome. Study of the mechanism both computationally (by density functional theory) and experimentally revealed relevant intermediates and plausible reaction pathways.

A Comparison of Solid Electrolyte Interphase Formation and Evolution on Highly Oriented Pyrolytic and Disordered Graphite Negative Electrodes in Lithium-Ion Batteries.

The presence and stability of solid electrolyte interphase (SEI) on graphitic electrodes is vital to the performance of lithium-ion batteries (LIBs). However, the formation and evolution of SEI remain the least understood area in LIBs due to its dynamic nature, complexity in chemical composition, heterogeneity in morphology, as well as lack of reliable in situ/operando techniques for accurate characterization. In addition, chemical composition and morphology of SEI are not only affected by the choice of electrolyte, but also by the nature of the electrode surface. While introduction of defects into graphitic electrodes has promoted their electrochemical properties, how such structural defects influence SEI formation and evolution remains an open question. Here, utilizing nondestructive operando electrochemical atomic force microscopy (EChem-AFM) the dynamic SEI formation and evolution on a pair of representative graphitic materials with and without defects, namely, highly oriented pyrolytic and disordered graphite electrodes, are systematically monitored and compared. Complementary to the characterization of SEI topographical and mechanical changes during electrochemical cycling by EChem-AFM, chemical analysis and theoretical calculations are conducted to provide mechanistic insights underlying SEI formation and evolution. The results provide guidance to engineer functional SEIs through design of carbon materials with defects for LIBs and beyond.

Rate Dependence on Inductive and Resonance Effects for the Organocatalyzed Enantioselective Conjugate Addition of Alkenyl and Alkynyl Boronic Acids to ß-Indolyl Enones and ß-Pyrrolyl Enones.

Two key factors bear on reaction rates for the conjugate addition of alkenyl boronic acids to heteroaryl-appended enones: the proximity of inductively electron-withdrawing heteroatoms to the site of bond formation and the resonance contribution of available heteroatom lone pairs to stabilize the developing positive charge at the enone ß-position. For the former, the closer the heteroatom is to the enone ß-carbon, the faster the reaction. For the latter, greater resonance stabilization of the benzylic cationic charge accelerates the reaction. Thus, reaction rates are increased by the closer proximity of inductive electron-withdrawing elements, but if resonance effects are involved, then increased rates are observed with electron-donating ability. Evidence for these trends in isomeric substrates is presented, and the application of these insights has allowed for reaction conditions that provide improved reactivity with previously problematic substrates.

Voltammetric pH sensor based on electrochemically modified pseudo-graphite.

A nanocrystalline graphite-like amorphous carbon (graphite from the University of Idaho thermolyzed asphalt reaction, GUITAR) shares morphological features with classical graphites, including basal and edge planes (BP, EP). However, unlike graphites and other sp2-hybridized carbons, GUITAR has fast heterogenous electron transfer (HET) across its basal planes, and resistance to corrosion similar to sp3-C and boron-doped diamond electrodes. In this contribution, quinoid modified BP-GUITAR (q-GUITAR) is examined as a sensor for pH determination. This modification is performed by applying 2.0 V (vs. Ag/AgCl) for 150 seconds followed by 15 cyclic voltammetric scans from -0.7 to 1.0 V at 50 mV s-1 in 1.0 M H2SO4. The quinoid surface coverage of q-GUITAR is 1.35 × 10-9 mol cm-2, as measured by cyclic voltammetry. X-ray photoelectron spectroscopy analysis also confirms the high surface coverage. The quinoid surface concentration ranks highest in literature when compared with other basal plane graphitic materials. This yields a sensor that responds through a square wave voltammetric reduction peak shift of 63.3 mV per pH over a pH range from 0 to 11. The response on q-GUITAR is stable for >20 measurements and no surface re-activation is required between the measurements. The common interferents, Na+, K+ and dissolved oxygen, have no effect on the response of the q-GUITAR-based pH sensor.

Chiral Diol-Based Organocatalysts in Enantioselective Reactions.

Organocatalysis has emerged as a powerful synthetic tool in organic chemistry in the last few decades. Among various classes of organocatalysis, chiral diol-based scaffolds, such as BINOLs, VANOLs, and tartaric acid derivatives, have been widely used to induce enantioselectivity due to the ability of the hydroxyls to coordinate with the Lewis acidic sites of reagents or substrates and create a chiral environment for the transformation. In this review, we will discuss the applications of these diol-based catalysts in different types of reactions, including the scopes of reactions and the modes of catalyst activation. In general, the axially chiral aryl diol BINOL and VANOL derivatives serve as the most competent catalyst for most examples, but examples of exclusive success using other scaffolds, herein, suggests that they should not be overlooked. Lastly, the examples, to date, are mainly from tartrate and biaryl diol catalysts, suggesting that innovation may be available from new diol scaffolds.

The synthesis of functionalized bridged polycycles via C-H bond insertion.

This review presents examples from the chemical literature of syntheses of bridged-polycyclic products via C-H bond insertion by carbenes and nitrenes. Applications to natural product synthesis, a description of the essential elements in substrate-controlled reactions, and mechanistic details of transformations are presented. Overall, these transformations allow the construction of important ring systems rapidly and efficiently, though additional catalyst development is needed.

Hydrazone-initiated carbene/alkyne cascades to form polycyclic products: ring-fused cyclopropenes as mechanistic intermediates.

A hydrazone-based carbene/alkyne cascade produced a variety of bridged and fused polycyclic products. NaOSiMe3 is a superior base for conversion of hydrazones to diazoalkanes. A key mechanistic intermediate, a ring-fused cyclopropene, has been isolated and characterized.

Evolution of a unified, stereodivergent approach to the synthesis of communesin F and perophoramidine.

Expedient synthetic approaches to the highly functionalized polycyclic alkaloids communesin F and perophoramidine are described using a unified approach featuring a key decarboxylative allylic alkylation to access a crucial and highly congested 3,3-disubstituted oxindole. Described are two distinct, stereoselective alkylations that produce structures in divergent diastereomeric series possessing the critical vicinal all-carbon quaternary centers needed for each synthesis. Synthetic studies toward these challenging core structures have revealed a number of unanticipated modes of reactivity inherent to these complex alkaloid scaffolds. Additionally, several novel and interesting intermediates en route to the target natural products, such as an intriguing propellane hexacyclic oxindole encountered in the communesin F sequence, are disclosed. Indeed, such unanticipated structures may prove to be convenient strategic intermediates in future syntheses.

Biomimetic synthesis and studies toward enantioselective synthesis of flindersial alkaloids.

A strategy allowing both stereocontrol and control over structural isomer formation has been defined for the antimalarial flindersial alkaloids. The recently reported flinderoles were demonstrated to be derived from the natural product borrerine. The structural isomers of flinderoles, the borreverines, were also produced in vitro along with the flinderoles through the dimerization of borrerine in acidic conditions. This result is thought to replicate the biosynthesis of these compounds. Flinderoles A, B, and C, desmethylflinderole C, isoborreverine, and dimethylisoborreverine can each be synthesized in three steps from tryptamine. Furthermore, progress toward a concise enantioselective synthesis of flinderoles A, B, and C is described. This work includes enantioselective conjugate addition to an unprotected indole-appended enone.

Organocatalyzed Asymmetric Conjugate Addition of Heteroaryl and Aryl Trifluoroborates: a Synthetic Strategy for Discoipyrrole†D.

Bis-heteroaryl or bis-aryl stereocenters were formed by an organocatalytic enantioselective conjugate addition using the respective trifluoroborate salts as nucleophiles. Control studies suggested that fluoride dissociation is necessary in the anhydrous conditions. This strategy is applicable to the synthesis of discoipyrrole D, an inhibitor of BR5 fibroblast migration.

Toward a symphony of reactivity: cascades involving catalysis and sigmatropic rearrangements.

Catalysis and synthesis are intimately linked in modern organic chemistry. The synthesis of complex molecules is an ever evolving area of science. In many regards, the inherent beauty associated with a synthetic sequence can be linked to a certain combination of the creativity with which a sequence is designed and the overall efficiency with which the ultimate process is performed. In synthesis, as in other endeavors, beauty is very much in the eyes of the beholder. It is with this in mind that we will attempt to review an area of synthesis that has fascinated us and that we find extraordinarily beautiful, namely the combination of catalysis and sigmatropic rearrangements in consecutive and cascade sequences.

Regio- and enantioselective synthesis of acyclic quaternary carbons via organocatalytic addition of organoborates to (Z)-Enediketones.

The chemical synthesis of molecules with closely packed atoms having their bond coordination saturated is a challenge to synthetic chemists, especially when three-dimensional control is required. The organocatalyzed asymmetric synthesis of acyclic alkenylated, alkynylated and heteroarylated quaternary carbon stereocenters via 1,4-conjugate addition is here catalyzed by 3,3´-bisperfluorotoluyl-BINOL. The highly useful products (31 examples) are produced in up to 99% yield and 97:3 er using enediketone substrates and potassium trifluoroorganoborate nucleophiles. In addition, mechanistic experiments show that the (Z)-isomer is the reactive form, ketone rotation at the site of bond formation is needed for enantioselectivity, and quaternary carbon formation is favored over tertiary. Density functional theory-based calculations show that reactivity and selectivity depend on a key n→π* donation by the unbound ketone's oxygen lone pair to the boronate-coordinated ketone in a 5-exo-trig cyclic ouroboros transition state. Transformations of the conjugate addition products to key quaternary carbon-bearing synthetic building blocks proceed in good yield.

Can Twisted Double Bonds Facilitate Stepwise [2 + 2] Cycloadditions?

Computational studies for a series of low to high strain anti-Bredt alkenes suggest that those with highly twisted bridgehead double bonds and a small singlet-triplet energy gap may undergo facile stepwise [2 + 2] cycloadditions to furnish four membered rings. A selection of reaction substrates, including ethylene, acetylene, perfluoroethylene, and cyclooctyne are considered.

Photoactivation of Hydrazones for the Synthesis of Diarylalkanes and Trialkylmethylboronates: The Key Role Played by Soluble Base.

The synthesis of diaryl alkanes and tertiary organoboronates via Barluenga coupling at room temperature occurred via photoactivated conversion of aryl sulfonyl hydrazones to diazo compounds in the presence of soluble bases. The combination of arylsulfonyl hydrazone and a soluble base is necessary to provide a near-UV chromophore. Using aromatic hydrazones and aromatic boronic acids resulted in rapid deboronation because of the instability of dibenzylic boron intermediates. Alkyl hydrazones allowed the isolation of derivatives of the tertiary boronate.

Enantioseparation of flinderoles and borreverines by HPLC on Chirobiotic V and V2 stationary phases and by CE using cyclodextrin selectors.

Racemic mixtures of the promising anti-malarial bisindole alkoids, flinderole A-C, desmethyl flinderole C, borreverine and isoborreverine, are baseline-separated for the first time by HPLC using vancomycin-based stationary phases and partially separated by capillary electrophoresis (CE) using cyclodextrin selectors. The HPLC results compare the performance of Chirobiotic V and V2 in the polar organic and reversed phase modes and their complementary selectivity is discussed. The performance of the cyclodextrin selectors in CE, while less effective, are discussed in terms of their selectivity in normal and reversed polarity modes.

Enantioselective Total Synthesis of Cannabinoids via a Tandem Conjugate Addition/Enolate Alkylation Annulation with Ambiphilic Organoboronates.

Cannabinoid research depends on synthesizing derivatives for structure-activity relationship studies. (-)-Δ9-Tetrahydrocannabinol and cannabidiol were synthesized via a tandem enantioselective conjugate addition/enolate alkylation annulation with a novel ambiphilic trifluoroborate in seven steps. A new class of alkenyl and aryl ambiphilic trifluoroborates were synthesized and showed great compatibility with various functional groups, high yields, and excellent enantio- and diastereoselectivity. A novel benzo-fused cannabinoid analogue and tandem quaternary stereocenter-containing reaction products were synthesized with good to excellent enantioselectivity.

Plant traits poorly predict winner and loser shrub species in a warming tundra biome.

Climate change is leading to species redistributions. In the tundra biome, shrubs are generally expanding, but not all tundra shrub species will benefit from warming. Winner and loser species, and the characteristics that may determine success or failure, have not yet been fully identified. Here, we investigate whether past abundance changes, current range sizes and projected range shifts derived from species distribution models are related to plant trait values and intraspecific trait variation. We combined 17,921 trait records with observed past and modelled future distributions from 62 tundra shrub species across three continents. We found that species with greater variation in seed mass and specific leaf area had larger projected range shifts, and projected winner species had greater seed mass values. However, trait values and variation were not consistently related to current and projected ranges, nor to past abundance change. Overall, our findings indicate that abundance change and range shifts will not lead to directional modifications in shrub trait composition, since winner and loser species share relatively similar trait spaces.