Click and Bio-Orthogonal Reactions with Mesoionic Compounds.

Click and bio-orthogonal reactions are dominated by cycloaddition reactions in general and 1,3-dipolar cycloadditions in particular. Among the dipoles routinely used for click chemistry, azides, nitrones, isonitriles, and nitrile oxides are the most popular. This review is focused on the emerging click chemistry that uses mesoionic compounds as dipole partners. Mesoionics are a very old family of molecules, but their use as reactants for click and bio-orthogonal chemistry is quite recent. The facility to derivatize these dipoles and to tune their reactivity toward cycloaddition reactions makes mesoionics an attractive opportunity for future click chemistry development. In addition, some compounds from this family are able to undergo click-and-release reactions, finding interesting applications in cells, as well as in animals. This review covers the synthetic access to main mesoionics, their reaction with dipolarophiles, and recent applications in chemical biology and heterocycle synthesis.

Recent Advances in the Total Synthesis of Natural Products Containing Eight-Membered Carbocycles (2009-2019).

Natural products containing eight-membered carbocycles constitute a class of structurally intriguing and biologically important molecules such as the famous diterpenes taxol and vinigrol. Such natural products are being increasingly investigated because of their fascinating architectural features and potent medicinal properties. However, synthesis of natural products with cyclooctane moieties has proved to be highly challenging. This review highlights the recently completed total syntheses of natural products with eight-membered carbocycles with a focus on strategic considerations. A collection of 27 representative studies from the literature covering the decade from 2009 to 2019 is described in chronological order with relevant studies grouped together, including syntheses of the same natural product by different research groups using different strategies. Finally, a summary and outlook including a discussion of the major features of each strategy used in the syntheses are presented. This review illustrates the diversity and creativity in the elegant synthetic designs of eight-membered carbocycles. We hope this review will provide timely illumination and beneficial guidance for future synthetic efforts for organic chemists who are interested in this area.

Understanding the Liquid States of Cyclic Hydrocarbons Containing N, O, and S Atoms via the 3D-RISM-KH Molecular Solvation Theory.

The 3D-reference interaction site model (3D-RISM) molecular solvation theory in combination with the Kovalenko-Hirata (KH) closure is extended to seven heterocyclic liquids to understand their liquid states and to test the performance of the theory in solvation free energy (SFE) calculations of solutes in select solvents. The computed solvent site distribution profiles were compared with the all-atom molecular dynamics (MD) simulations, showing comparable performances. The computational results were compared against the structural parameters for liquids, whenever available, as well as against the experimental SFEs. The liquids are found to have local ordered structures held together via weak interactions in both the RISM and MD simulations. The 3D-RISM-KH computed SFEs are in good agreement with the benchmark values for the tetrahydrothiophene-S,S-dioxide, and showed comparatively larger deviations in the case of the SFEs in the tetrahydrofuran continuum.

Violations. How Nature Circumvents the Woodward-Hoffmann Rules and Promotes the Forbidden Conrotatory 4n + 2 Electron Electrocyclization of Prinzbach's Vinylogous Sesquifulvalene.

Woodward and Hoffmann, in their treatise on orbital symmetry in 1969, stated "Violations. There are none!" Prinzbach reported in 1978 that the electrocyclization of vinylogous sesquifulvalene occurs exclusively through the Woodward-Hoffmann orbital-symmetry-forbidden 14π-electron conrotatory pathway, despite the availability of a variety of orbital-symmetry-allowed processes. Prinzbach later demonstrated that an 18π-electron homologue exhibits the same forbidden behavior. And yet, the analogous vinylogous pentafulvalene and heptafulvalene both follow the orbital symmetry rules, each proceeding through its allowed conrotatory 12π and 16π process, respectively. We report the investigation of these reactions with ωB97X-D DFT. The physical origins of the flagrant Prinzbach violations of the Woodward-Hoffmann orbital symmetry selection rules have now been elucidated by these calculations in conjunction with extensive analyses and comparisons to electrocyclizations that obey the Woodward-Hoffmann rules. This remarkable reversal of the Rules (the 14π-electron-forbidden process is found to be 11 kcal/mol more energetically facile than the allowed process) occurs due to the high degree of polarization of this hydrocarbon, such that conrotatory electrocyclization of vinylogous sesquifulvalene behaves like a cyclopentadienide combining with a tropylium. These results are compared to other forbidden pericyclic processes driven by steric constraints and strain release or by diradical character of the reactants that facilitates the formation of diradical transition states for symmetry-forbidden reactions. We predict how strong donor-acceptor substitution can modify nodal properties to level the difference between allowed and forbidden electrocyclic reaction barriers, and we provide computational predictions of two such cases.

A General, Multimetallic Cross-Ullmann Biheteroaryl Synthesis from Heteroaryl Halides and Heteroaryl Triflates.

Despite their importance to medicine and materials science, the synthesis of biheteroaryls by cross-coupling remains challenging. We describe here a new, general approach to biheteroaryls: the Ni- and Pd-catalyzed multimetallic cross-Ullmann coupling of heteroaryl halides with triflates. An array of 5-membered, 6-membered, and fused heteroaryl bromides and chlorides, as well as aryl triflates derived from heterocyclic phenols, proved to be viable substrates in this reaction (62 examples, 63 ± 17% average yield). The generality of this approach to biheteroaryls was further demonstrated in 96-well plate format at 10 µmol scale. An array of 96 possible products provided >90% hit rate under a single set of conditions. Further, low-yielding combinations could be rapidly optimized with a single "Toolbox Plate" of ligands, additives, and reductants.

Desorption Temperature, Solid-Phase Microextraction (SPME), and Natural Product Analyses, how Low Can we Go?

Solid phase microextraction (SPME) has become a common technique for volatile sampling due to its ease of use and limited technical requirements. The solvent-free nature of SPME is also exceptionally attractive for gas chromatography mass spectrometry (GC/MS) analysis. To ensure efficient transfer of the sample to the GC, the manufacturer recommend injector desorption temperatures in the range of 200 to 320 °C. A high desorption temperature can, however, have unwanted effects on analyses of plant and insect produced semiochemicals. By investigating the quantitative and qualitative chromatographic responses at varying inlet temperatures for a component blend of seven plant produced volatile compounds, we found the thermally labile plant-nematode signaling compound, pregeijerene to degrade to geijerene at all tested temperatures within the recommended range (200, 240, and 280 °C), but that it did not break down with an inlet temperature below 200 °C (100 °C and 150 °C). Degradation was also detected for the sesquiterpene germacrene D, but only at the highest inlet temperature tested (280 °C). Surprisingly, an inlet temperature of 200 °C gave the highest sample recovery, measured as total peak area while an inlet temperature of 100 °C as well as 280 °C gave the lowest total area values. An increase in desorption time from 3 to 5 min. Resulted in a recovery at 100 °C close to that obtained at 200 °C. Peak broadening was minimal, and only observed at the 100 °C inlet temperature. Based on these results, we highly recommend that SPME users include desorption temperature as one variable when developing sampling procedures for novel biological systems to ensure that potentially present thermally labile compounds are not degraded.

Smokeless tobacco analysis: Simultaneous extraction and purification of alkaloids, volatile N-nitrosamines, and polycyclic hydrocarbons for GC-MS/MS.

Several smokeless tobacco products are available in the market and comprise complex chemical matrices. Sample preparation for analysis of the multiple classes of harmful compounds in smokeless tobacco products is highly cumbersome. In this study, a simultaneous extraction scheme was developed for three toxic analyte classes in smokeless tobacco products using a two-phase solution consisting of 5% aqueous NaOH and dichloromethane in a 1:4 ratio. The dichloromethane extract was used to analyze four alkaloids directly at levels greater than parts per million; however, passing the layer through a silica cartridge for further purification and concentration was necessary for determining 18 polycyclic aromatic hydrocarbons and four volatile N-nitrosoamines at the ppt level. The multitargets were determined by using gas chromatography with tandem mass spectrometry. The limits of detection for the 18 polycyclic aromatic hydrocarbons, four volatile N-nitrosoamines, three minor alkaloids, and nicotine were 0.2-1.2, 0.2-0.4, 0.6-1.0, and 10.2 µg/g, respectively. Four different smokeless tobacco substrates were fortified with three levels of mixed standards, and the recoveries ranged between 83 and 110%. The method was highly efficient, reduced the sample amounts, solvents, and the time required by approximately 60%. The method was used to assay 18 smokeless tobacco products, and showed potentials in assaying drugs and other plant-based substrates.

Lipophilic Toxins in Wild Bivalves from the Southern Gulf of California, Mexico.

Most of the shellfish fisheries of Mexico occur in the Gulf of California. In this region, known for its high primary productivity, blooms of diatoms and dinoflagellates are common, occurring mainly during upwelling events. Dinoflagellates that produce lipophilic toxins are present, where some outbreaks related to okadaic acid and dinophisystoxins have been recorded. From January 2015 to November 2017 samples of three species of wild bivalve mollusks were collected monthly in five sites in the southern region of Bahía de La Paz. Pooled tissue extracts were analyzed using LC-MS/MS to detect lipophilic toxins. Eighteen analogs of seven toxin groups, including cyclic imines were identified, fortunately individual toxins did not exceed regulatory levels and also the total toxin concentration for each bivalve species was lower than the maximum permitted level for human consumption. Interspecific differences in toxin number and concentration were observed in three species of bivalves even when the samples were collected at the same site. Okadaic acid was detected in low concentrations, while yessotoxins and gymnodimines had the highest concentrations in bivalve tissues. Although in low quantities, the presence of cyclic imines and other lipophilic toxins in bivalves from the southern Gulf of California was constant.

Levels of PAHs, PCBs, and toxic metals in Ruditapes philippinarum and Donax trunculus in Marmara Sea, Turkey.

BACKGROUND: The manila clam Ruditapes philippinarum and the wedge clam Donax trunculus are economic bivalve species which constitute an important part of the natural bivalve beds in the Marmara Sea, Turkey. Toxic chemicals such as, dioxins, dioxin-like polychlorinated biphenyls (PCBs), polycyclic hydrocarbons (PAHs), and toxic metals are recognized as important health risk factors that threaten public health via food or directly in the environment. In the present study, we aimed to determine and monitor levels of these toxic chemicals in both clam species, R. philippinarum and D. trunculus, between 2013 and 2017. RESULTS: According to the results, maximum levels of dioxins, PAHs, and toxic metals (lead, cadmium, mercury) during the period were determined as 0.18 pg g-1 , 2.43 mg kg-1 , and 0.44-0.53-0.1 mg kg-1 , respectively. The level of contaminants in both clam species were determined to be below the threshold or tolerable daily intake values established by the European Commission, European Food Safety Authority (EFSA), and Food and Agriculture Organization/World Health Organization (FAO/WHO). Seasonal fluctuations were observed to be similar in both species and also in seasons, but elevated levels of PCBs and PAHs were detected in warmer months during the period. CONCLUSION: As a consequence, toxic chemicals in both clam species were found at low concentrations in this study from the point of view of public health concerns; however, the contaminants should be closely monitored in the future due to their elevated levels in samples. © 2020 Society of Chemical Industry.

Synthesis, antiproliferative activity in cancer cells and DNA interaction studies of [Pt(cis-1,3-diaminocycloalkane)Cl2] analogs.

The search for more effective platinum anticancer drugs has led to the design, synthesis, and preclinical testing of hundreds of new platinum complexes. This search resulted in the recognition and subsequent FDA approval of the third-generation Pt(II) anticancer drug, [Pt(1,2-diaminocyclohexane)(oxalate)], oxaliplatin, as an effective agent in treating colorectal and gastrointestinal cancers. Another promising example of the class of anticancer platinum(II) complexes incorporating the Pt(1,n-diaminocycloalkane) moiety is kiteplatin ([Pt(cis-1,4-DACH)Cl2], DACH = diaminocyclohexane). We report here our progress in evaluating the role of the cycloalkyl moiety in these complexes focusing on the synthesis, characterization, evaluation of the antiproliferative activity in tumor cells and studies of the mechanism of action of new [Pt(cis-1,3-diaminocycloalkane)Cl2] complexes wherein the cis-1,3-diaminocycloalkane group contains the cyclobutyl, cyclopentyl, and cyclohexyl moieties. We demonstrate that [Pt(cis-1,3-DACH)Cl2] destroys cancer cells with greater efficacy than the other two investigated 1,3-diamminocycloalkane derivatives, or cisplatin. Moreover, the investigated [Pt(cis-1,3-diaminocycloalkane)Cl2] complexes show selectivity toward tumor cells relative to non-tumorigenic normal cells. We also performed several mechanistic studies in cell-free media focused on understanding some early steps in the mechanism of antitumor activity of bifunctional platinum(II) complexes. Our data indicate that reactivities of the investigated [Pt(cis-1,3-diaminocycloalkane)Cl2] complexes and cisplatin with glutathione and DNA binding do not correlate with antiproliferative activity of these platinum(II) complexes in cancer cells. In contrast, we show that the higher antiproliferative activity in cancer cells of [Pt(cis-1,3-DACH)Cl2] originates from its highest hydrophobicity and most efficient cellular uptake.

Annulation reaction enables the identification of an exocyclic amide tricyclic chemotype as retinoic acid Receptor-Related orphan receptor gamma (RORγ/RORc) inverse agonists.

RORγt is the master regulator of the IL-23/IL-17 axis, a pathway that is clinically validated for the treatment of various immunological disorders. Over the last few years, our group has reported different chemotypes that potently act as inverse agonists of RORγt. One of them, the tricyclic pyrrolidine chemotype, has demonstrated biologic-like preclinical efficacy and has led to our clinical candidate BMS-986251. In this letter, we discuss the invention of an annulation reaction which enabled the synthesis of a tricyclic exocyclic amide chemotype and the identification of compounds with RORγt inverse agonist activity. Preliminary structure activity relationships are disclosed.

A Case for Bond-Network Analysis in the Synthesis of Bridged Polycyclic Complex Molecules: Hetidine and Hetisine Diterpenoid Alkaloids.

A key challenge in the synthesis of diterpenoid alkaloids lies in identifying strategies that rapidly construct their multiply bridged polycyclic skeletons. Existing approaches to these structurally intricate secondary metabolites are discussed in the context of a "bond-network analysis" of molecular frameworks, which was originally devised by Corey some 40 years ago. The retrosynthesis plans that emerge from a topological analysis of the highly bridged frameworks of the diterpenoid alkaloids are discussed in the context of eight recent syntheses of hetidine and hetisine natural products and their derivatives. This Minireview highlights the extent to which network analyses of the type described here sufficed for designing synthesis plans, as well as areas where they had to be amalgamated with functional group oriented synthetic planning considerations.

Enabling Two-Electron Pathways with Iron and Cobalt: From Ligand Design to Catalytic Applications.

Homogeneous catalysis with Earth-abundant, first-row transition metals, including iron and cobalt, has gained considerable recent attention as a potentially cost-effective and sustainable alternative to more commonly and historically used precious metals. Because fundamental organometallic transformations, such as oxidative addition and reductive elimination, are two-electron processes and essential steps in many important catalytic cycles, controlling redox chemistry-in particular overcoming one-electron chemistry-has been as a central challenge with Earth-abundant metals. This Perspective focuses on approaches to impart sufficiently strong ligand fields to generate electron-rich metal complexes able to promote oxidative addition reactions where the redox changes are exclusively metal-based. Emphasis is placed on how ligand design and exploration of fundamental organometallic chemistry coupled with mechanistic understanding have been used to discover iron catalysts for the hydrogen isotope exchange in pharmaceuticals and cobalt catalysts for C(sp2)-H borylation reactions. A pervasive theme is that first-row metal complexes often promote unique chemistry from their precious-metal counterparts, demonstrating that these elements offer a host of new opportunities for reaction discovery and for more sustainable catalysis.

Nonconjugated Hydrocarbons as Rigid-Linear Motifs: Isosteres for Material Sciences and Bioorganic and Medicinal Chemistry.

Nonconjugated hydrocarbons, like bicyclo[1.1.1]pentane, bicyclo[2.2.2]octane, triptycene, and cubane are a unique class of rigid linkers. Due to their similarity in size and shape they are useful mimics of classic benzene moieties in drugs, so-called bioisosteres. Moreover, they also fulfill an important role in material sciences as linear linkers, in order to arrange various functionalities in a defined spatial manner. In this Review article, recent developments and usages of these special, rectilinear systems are discussed. Furthermore, we focus on covalently linked, nonconjugated linear arrangements and discuss the physical and chemical properties and differences of individual linkers, as well as their application in material and medicinal sciences.

Dibenzocyclooctynes: Effect of Aryl Substitution on Their Reactivity toward Strain-Promoted Alkyne-Azide Cycloaddition.

Five new dibenzocyclooctynes bearing different substituents on their aryl moieties were synthesized and evaluated for their reactivity toward strain-promoted alkyne-azide cycloaddition (SPAAC). The dinaphthylcyclooctynes proved to be poorly reactive with azides, and the formation of triazole required many days compared to a few hours for the other cyclooctynes. Fluoride atoms and methoxy groups were also introduced to the aryl rings, leading to more active compounds. Oxidation of the alcohol on the cyclooctyne ring also increased the reaction rates by 3.5- to 6-fold. 3,9-Difluoro-4,8-dimethoxy-dibenzocyclooctyne-1-one thus displayed a SPAAC kinetic rate of 3.5 M-1 s-1, which is one of the highest rates ever described. Furthermore, the dibenzocyclooctyn-1-one displayed fluorescence properties that have allowed their detection in the protozoan parasites Plasmodium falciparum and Trypanosoma brucei by microscopy imaging, proving that they can cross cell membranes and that they are stable enough in biological media.

Sarcomililate A, an Unusual Diterpenoid with Tricyclo[11.3.0.02,16]hexadecane Carbon Skeleton, and Its Potential Biogenetic Precursors from the Hainan Soft Coral Sarcophyton mililatensis.

A novel diterpenoid, sarcomililate A (1), possessing a previously undescribed tricyclo[11.3.0.02,16]hexadecane scaffold, along with two new cembranoids, sarcomililatols A and B (2 and 3), and two known related diterpenoids (4 and 5), was isolated from the Hainan soft coral Sarcophyton mililatensis. The complete chemical structure including absolute configuration (AC) of 1 was unambiguously determined by a combination of residual dipolar coupling (RDC)-based NMR analysis, TDDFT-ECD (ECD = electronic circular dichroism) calculation, and Snatzke's method. The AC of 1 was further confirmed by a comparison with 2, whose AC was determined by anomalous X-ray diffraction. A plausible biogenetic relationship of 1-3 was further proposed. All the reported compounds exhibited interesting inhibitory effects on the ConA-induced T lymphocytes and/or lipopolysaccharide (LPS)-induced B lymphocytes proliferation.

N-containing compounds from Periplaneta americana and their activities against wound healing.

Three new compounds, periplanamides A (1) and B (2), periplanpyrazine A (3), a new naturally occurring compound salicyluric acid methyl ester (6), and seventeen known compounds were isolated from the medicinal insect Periplaneta americana. The structures of the new compounds were elucidated on the basis of spectroscopic methods. The absolute configurations of 2 were assigned by computational methods. Biological activities of these isolates except 1, 9, 11, and 13 toward nitric oxide (NO) production, cell proliferation in HDFs, cell migration and angiogenesis in HUVECs were evaluated.

Quantitative Analysis of Organic Liquid Three-Component Systems: Near-Infrared Transmission versus Raman Spectroscopy, Partial Least Squares versus Classical Least Squares Regression Evaluation and Volume versus Weight Percent Concentration Units.

The band shapes and band positions of near-infrared (NIR) and Raman spectra change depending on the concentrations of specific chemical functionalities in a multicomponent system. To elucidate these effects in more detail and clarify their impact on the analytical measurement techniques and evaluation procedures, NIR transmission spectra and Raman spectra of two organic liquid three-component systems with variable compositions were analyzed by two different multivariate calibration procedures, partial least squares (PLS) and classical least-squares (CLS) regression. Furthermore, the effect of applying different concentration units (volume percent (%V) and weight percent (%W) on the performance of the two calibration procedures have been tested. While the mixtures of benzene/cyclohexane/ethylbenzene (system 1) can be regarded as a blended system with comparatively low molecular interactions, hydrogen bonding plays a dominant role in the blends of ethyl acetate/1-heptanol/1,4-dioxane (system 2). Whereas system 1 yielded equally good calibrations by PLS and CLS regression, for system 2 acceptable results were only obtained by PLS regression. Additionally, for both sample systems, Raman spectra generally led to lower calibration performance than NIR spectra. Finally, volume and weight percent concentration units yielded comparable results for both chemometric evaluation procedures.

A Metallaphotoredox Strategy for the Cross-Electrophile Coupling of α-Chloro Carbonyls with Aryl Halides.

Here, we demonstrate that a metallaphotoredox-catalyzed cross-electrophile coupling mechanism provides a unified method for the α-arylation of diverse activated alkyl chlorides, including α-chloroketones, α-chloroesters, α-chloroamides, α-chlorocarboxylic acids, and benzylic chlorides. This strategy, which is effective for a wide variety of aryl bromide coupling partners, is predicated upon a halogen atom abstraction/nickel radical-capture mechanism that is generically successful across an extensive range of carbonyl substrates. The construction and use of arylacetic acid products have further enabled two-step protocols for the delivery of valuable building blocks for medicinal chemistry, such as aryldifluoromethyl and diarylmethane motifs.

Diastereodivergent Reductive Cross Coupling of Alkynes through Tandem Catalysis: Z- and E-Selective Hydroarylation of Terminal Alkynes.

A diastereodivergent hydroarylation of terminal alkynes is accomplished using tandem catalysis. The hydroarylation allows highly selective synthesis of both E and Z diastereoisomers of aryl alkenes, from the same set of starting materials, using the same combination of palladium and copper catalysts. The selectivity is controlled by simple changes in the stoichiometry of the alcohol additive. The hydroarylation has excellent substrate scope and can be accomplished in the presence of various classes of compounds, including esters, nitriles, alkyl halides, epoxides, carbamates, acetals, ethers, silyl ethers, and thioethers. The Z-selective hydroarylation is accomplished using a new approach based on tandem Sonogashira coupling and catalytic semireduction. The E-selective hydroarylation involves an additional catalytic isomerization of the Z-alkene. Our explorations of the reaction mechanism explain the role of individual reaction components and how the subtle changes in the reaction conditions influence the rates of specific steps of the hydroarylation. Our studies also show that, although the Z- and E-selective hydroarylation reactions are mechanistically closely related, the roles of the palladium and copper catalysts in the two reactions are different.