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The melt analysis feature in most real-time polymerase chain reaction (PCR) instruments is a simple method for determining if expected or unexpected products are present. High-resolution melt (HRM) analysis seeks to improve the precision of melt temperature measurements for better PCR product sequence characterization. In the area of tuberculosis (TB) drug susceptibility screening, sequencing has shown that a single base change can be sufficient to make a first-line TB drug ineffective. In this study, a reagent-based calibration strategy based on synthetic left-handed (L)-DNA, designated LHRM, was developed to confirm validation of a PCR product with single base resolution. To test this approach, a constant amount of a double-stranded L-DNA melt comparator was added to each sample and used as a within-sample melt standard. The performance of LHRM and standard HRM was used to classify PCR products as drug-susceptible or not drug-susceptible with a test bed of nine synthetic katG variants, each containing single or multiple base mutations that are known to confer resistance to the first-line TB drug isoniazid (INH). LHRM achieved comparable classification to standard HRM relying only on within-sample melt differences between L-DNA and the unknown PCR product. Using a state-of-the-art calibrated instrument and multiple sample classification analysis, standard HRM was performed at 66.7% sensitivity and 98.8% specificity. Single sample analysis incorporating L-DNA for reagent-based calibration into every sample maintained high performance at 77.8% sensitivity and 98.7% specificity. LHRM shows promise as a high-resolution single sample method for validating PCR products in applications where the expected sequence is known.

Palladium salts and complexes were tested separately and in the presence of added ligands as potential sources of aryl radicals in ground-state coupling reactions of aryl halide with arenes under basic conditions (KO t Bu). Our recently developed assay for aryl radicals was employed to test for aryl radicals. In this assay, aryl radicals derived from the test substrate, 1-iodo-2,6-dimethylbenzene 7 , undergo base-promoted homolytic aromatic substitution (BHAS) with benzene to produce 2,6-dimethylbiphenyl 8 and biphenyl 9 in an approximately 1:4 ratio as well as m -xylene 10. The biphenyl arises from a diagnostic radical transfer reaction with the solvent benzene. Using substrate 7 with a range of Pd sources as potential initiators led to formation of 8 , 9 , and 10 in varying amounts. However, when any one of a range of diphosphinoferrocenes (e.g., dppf or dippf) or BINAP or the monophosphine, diphenylphosphinoferrocene, was added as a ligand to Pd(OAc) 2 , the ratio of [2,6-dimethylbiphenyl 8 : biphenyl 9 ] moved decisively to that expected from the BHAS (radical) pathway. Further studies were conducted with dppf. When dppf was added to each of the other Pd sources, the ratio of coupled products was also diverted to that expected for radical BHAS chemistry. Deuterium isotope studies and radical trap experiments provide strong additional support for the involvement of aryl radicals. Accordingly, under these ground-state conditions, palladium sources, in the presence of defined ligands, convert aryl iodides to aryl radicals. A rationale is proposed for these observations.

Monodentate phosphine-ligated nickel compounds, e.g. , [Ni(PPh 3 ) 4 ] are relevant as active catalysts across a broad range of reactions. This report expands upon the coordination chemistry of this family, offering the reactivity of allyl- and vinyl-substituted diphenylphosphine (PPh 2 R) with [Ni(COD) 2 ] (COD = 1,5-cyclooctadiene). These reactions provide three-coordinate dinickelacycles that are intermolecularly tethered through adjacent {Ni}-olefin interactions. The ring conformation of such cycles has been studied in the solid-state and using theoretical calculations. Here, a difference in reaction outcome is linked to the presence of an allyl vs vinyl group, where the former is observed to undergo rearrangement, bringing about challenges in clean product isolation., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Published by American Chemical Society.)

HIV develops single nucleotide polymorphisms (SNPs), some of which lead to drug resistance mutations (DRMs) that prevent therapeutic viral suppression. Genomic sequencing enables healthcare professionals to select effective combination antiretroviral therapy (ART) to achieve and maintain viral suppression. However, sequencing technologies, which are resource-intensive, are limited in their availability. This report describes the first step toward a highly specific ligation-based SNP discrimination method with endpoint PCR detection, which is more suitable for resource-limited clinics. The approach is based on magnetic bead processing to maximize reaction product transfer and minimize the carryover of incompatible buffer for three consecutive enzymatic reactions─reverse transcription (RT), oligonucleotide ligation assay (OLA), and PCR. The method improved PCR detection following RT → OLA by 8.06 cycles (∼250-fold) compared to direct pipette processing and detected between 10 3 and 10 4 RNA copies per reaction. In studies with synthesized nucleic acids based on the well-studied HIV mutation, K103N, the assay successfully differentiated between wild-type and mutant for RNA targets with high specificity. With further development, this design provides a pathway for SNP detection with more accessible PCR instrumentation and is a step toward a self-contained processing approach that incorporates the SNP specificity of the ligation reaction for more effective clinical management of DRMs in resource-constrained settings.

This review considers phosphine and N -heterocyclic carbene complexes of gold(I) that are used as (pre)catalysts for a range of reactions in organic synthesis. These are divided according to the structure of the ligand, with the narrative focusing on studies that offer a quantitative comparison between the ligands and readily available or widely used existing systems.

The reactions of dppf-nickel(0) with alkyl halides proceed via three-coordinate nickel(0) intermediates of the form [Ni(dppf)(L)]. The effects of the identity of the added ligand (L) on catalyst speciation and the rates of reactions of [Ni(COD)(dppf)] with alkyl halides have been investigated using kinetic experiments and density functional theory calculations. A series of monodentate ligands have been investigated in attempts to identify trends in reactivity. Sterically bulky and electron-donating ligands are found to decrease the reaction rate. It was found that (i) the halide abstraction step is not always irreversible and the subsequent recombination of a nickel(I) complex with an alkyl halide can have a significant effect on the overall rate of the reaction and (ii) some ligands lead to very stable [Ni(dppf)(L) 2 ] species. The yields of prototypical (dppf)nickel-catalyzed Kumada cross-coupling reactions of alkyl halides are significantly improved by the addition of free ligands, which provides another important variable to consider when optimizing nickel-catalyzed reactions of alkyl halides., Competing Interests: The authors declare no competing financial interest., (© 2021 The Authors. Published by American Chemical Society.)

The mechanism of the reactions between dppf-Ni 0 complexes and alkyl halides has been investigated using kinetic and mechanistic experiments and DFT calculations. The active species is [Ni(κ 2 -dppf)(κ 1 -dppf)], which undergoes a halide abstraction reaction with alkyl halides and rapidly captures the alkyl radical that is formed. The rates of the reactions of [Ni(COD)(dppf)] with alkyl halides and the yields of prototypical nickel-catalyzed Kumada cross-coupling reactions of alkyl halides are shown to be significantly improved by the addition of free dppf ligand., Competing Interests: The authors declare no competing financial interest., (Copyright © 2020 American Chemical Society.)

Marine cyanobacteria are renowned for producing bioactive secondary metabolites with great structural diversity via mixed biosynthetic pathways. Lyngbya sp., a marine cyanobacterium, produces many metabolites with anti-inflammatory potentials; nevertheless, its bioactive metabolites exercising providing protection against inflammation has been deciphered inadequate. In this study, the ethanolic fraction of the Lyngbya sp. extract was purified and identified as sodium 10-amino-2-methoxyundecanoate ( SAM ) using Fourier-transform infrared spectroscopy, nuclear magnetic resonance, and electron spray ionization-mass spectroscopy. SAM showed prominent inhibition of inflammation, which was analyzed by reactive oxygen species generation and nitric oxide (NO) inhibition assay. Furthermore, the anti-inflammatory potentials of SAM were evaluated in lipopolysaccharide (LPS)-induced RAW 264.7 macrophage cell lines by fluorescence-activated cell sorting analysis, which evidenced prominent decrease in COX-2 expression (∼90%) with SAM -treated cells than the control. Subsequently, a semiquantitative real-time polymerase chain reaction analysis also revealed the downregulation of COX -2, iNOS , TNF -α, NF -κß, IL -1α, IL -1ß, IL -4, and IL -6 gene expression in SAM -treated LPS-induced RAW 264.7 cells. To further enhance the delivery of SAM into the cells, it was combined with N-doped graphene quantum dots (N-GQDs) for the anti-inflammatory potentials. It resulted in improved downregulation of COX -2, iNOS , TNF -α, NF -κß, IL -1α, IL -1ß, IL -4, and IL -6 than cells treated with SAM alone. Conclusively, N-GQDs combined with SAM have the effective therapeutic potential as an inhibitor of inflammation by modulating the expression of different cytokine genes., Competing Interests: The authors declare no competing financial interest.

Ligand metathesis of Pd(II) complexes is mechanistically essential for cross-coupling. We present a study of halide→OH anion metathesis of (Ar)Pd II complexes using vinylBPin as a bifunctional chemical probe with Pd(II)-dependent cross-coupling pathways. We identify the variables that profoundly impact this event and allow control to be leveraged. This then allows control of cross-coupling pathways via promotion or inhibition of organoboron transmetalation, leading to either Suzuki-Miyaura or Mizoroki-Heck products. We show how this transmetalation switch can be used to synthetic gain in a cascade cross-coupling/Diels-Alder reaction, delivering borylated or non-borylated carbocycles, including steroid-like scaffolds.

We describe the hybridization of our previously reported acyclic and cyclic CC chemokine receptor 2 (CCR2) antagonists to lead to a new series of dual antagonists of CCR2 and CCR5. Installation of a γ-lactam as the spacer group and a quinazoline as a benzamide mimetic improved oral bioavailability markedly. These efforts led to the identification of 13d, a potent and orally bioavailable dual antagonist suitable for use in both murine and monkey models of inflammation.

New complexes of the type trans-[IrCl(η(2)-COE)(NHC)2] (COE = cis-cyclooctene; NHC = N-heterocyclic carbene) have been prepared in one step from the reaction of ca. 4 equiv of NHC or [AgCl(NHC)] with [IrCl(η(2)-COE)2]2 in benzene. These new complexes have been characterized by techniques including NMR and IR spectroscopy, X-ray crystallography, and elemental analysis. Exposing trans-[IrCl(COE)(I(i)Pr(Me))2] to CO yielded trans-[IrCl(CO)(I(i)Pr(Me))2], which is the only bis(NHC) analogue of Vaska's complex trans-[IrCl(CO)(PPh3)2] known to date. The synthesis of trans-[Ir(CO)(I(i)Pr(Me))2(R)] (R = MeO, PhCC, OSiPh3, O2CPh) complexes has been achieved via deprotonation reactions involving the new hydroxide species trans-[Ir(OH)(CO)(I(i)Pr(Me))2].

Unambiguous evidence for covalent sidewall functionalization of single-walled carbon nanotubes (SWCNTs) has been a difficult task, especially for nanomaterials in which slight differences in functionality structure produce significant changes in molecular characteristics. Nuclear magnetic resonance (NMR) spectroscopy provides clear information about the structural skeleton of molecules attached to SWCNTs. In order to establish the generality of proton NMR as an analytical technique for characterizing covalently functionalized SWCNTs, we have obtained and analyzed proton NMR data of SWCNT-substituted benzenes across a variety of para substituents. Trends obtained for differences in proton NMR chemical shifts and the impact of o -, p -, and m -directing effects of electrophilic aromatic substituents on phenyl groups covalently bonded to SWCNTs are discussed.

A published model for revealing solvent effects on the ring-closing metathesis (RCM) reaction of diethyl diallylmalonate 7 has been evaluated over a wider range of conditions, to assess its suitability for new applications. Unfortunately, the model is too flexible and the published rate constants do not agree with experimental studies in the literature. However, by fixing the values of important rate constants and restricting the concentration ranges studied, useful conclusions can be drawn about the relative rates of RCM of different substrates, precatalyst concentration can be simulated accurately and the effect of precatalyst loading can be anticipated. Progress has also been made toward applying the model to precatalyst evaluation, but further modifications to the model are necessary to achieve much broader aims.

This report is important to achieving SWCNT solvation, understanding adsorption of molecules on SWCNT surfaces, and SWCNT characterization by NMR. Complexation of 1-methyl-2-pyrrolidone (NMP) and other selected organonitrogens with single-walled carbon nanotubes (SWCNTs) was studied by proton nuclear magnetic resonance (NMR). The magnitude of (1)H NMR chemical shift change upon SWCNT:organonitrogen complex formation represents the strength of the association. Magnitudes of changes in NMR signals of different protons in the organonitrogen reveal which protons are in close proximity to SWCNTs. Results reveal that (1) in amides and aminoketones, SWCNT association with carbonyls is stronger than with nitrogen, (2) in aminoalcohols, SWCNT association with nitrogen is stronger than with oxygen, and (3) protons bonded to heteroatoms have greater changes in their chemical shifts than those bonded to carbons. Changes (broadening and downfield shifts) in (1)H NMR signals of the organonitrogen compounds, which accompany SWCNT:organonitrogen association, are dependent upon (1) type of proton within R (α, β, etc.), (2) proximity to the carbonyl (R-CO versus NR(2)), (3) steric effects of alkyls, (4) electronic effects of alkyls, and (5) effects of tethering two ends of a molecule.

We describe the design, synthesis, and evaluation of novel disubstituted cyclohexanes as potent CCR2 antagonists. Exploratory SAR studies led to the cis-disubstituted derivative 22, which displayed excellent binding affinity for CCR2 (binding IC50 = 5.1 nM) and potent functional antagonism (calcium flux IC50 = 18 nM and chemotaxis IC 50 = 1 nM). Site-directed mutagenesis studies with 22 suggest the compound is binding near the key receptor residue Glu291, however, 22 is not reliant on Glu291 for its binding affinity.

Plots of the logarithms of relative rates of homogeneous catalytic hydrogenation of alkenes (log k(rel) values) by using Wilkinson's catalyst versus their ionization potentials (IPs) and versus their lowest unoccupied molecular orbital energy levels (LUMOs) display good-to-excellent correlations. The correlations indicate that the rate-determining step of this reaction is a nucleophilic addition to the alkene double bond, which is dependent upon both electronic effects and steric effects. This conclusion is in agreement with only two of three previously proposed mechanisms for the reaction, effectively ruling out one in which the rate-determining step involves electrophilic addition to the alkene. Characteristics of the analysis using these correlations are compared and contrasted with other additions to alkenes, such as the Wacker oxidation, to probe patterns in transition state characteristics.

The absence of Gln-tRNA synthetase in certain bacteria necessitates an alternate pathway for the production of Gln-tRNA(Gln): misacylated Glu-tRNA(Gln) is transamidated by a Gln-dependent amidotransferase (Glu-AdT) via catalysis of Gln hydrolysis, ATP hydrolysis, activation of Glu-tRNA(Gln), and aminolysis of activated tRNA by Gln-derived NH(3). As observed for other Gln-coupled amidotransferases, substrate binding, Gln hydrolysis, and transamidation by Glu-AdT are tightly coordinated [Horiuchi, K. Y., Harpel, M. R., Shen, L., Luo, Y., Rogers, K. C., and Copeland, R. A. (2001) Biochemistry 40, 6450-6457]. However, Glu-AdT does not employ an active-site Cys nucleophile for Gln hydrolysis, as is common in all other glutaminases: some Glu-AdT lack Cys, but all contain a conserved Ser (Ser176 in the A subunit of Streptococcus pyogenes Glu-AdT) within a sequence signature motif of Ser-based amidases. Our current results with S. pyogenes Glu-AdT support this characterization of Glu-AdT as a Ser-based glutaminase. Slow-onset (approximately 50 M(-1) s(-1)), tight-binding (t(1/2) > 2.5 h for complex dissociation), Gln-competitive inhibition of the Glu-tRNA(Gln)/ATP-independent glutaminase activity of Glu-AdT by gamma-Glu boronic acid is consistent with engagement of a Ser nucleophile in the glutaminase active site. Conversion to rapidly reversible, yet still potent (K(i) = 73 nM) and Gln-competitive, inhibition under full transamidation conditions mirrors the coupling between Gln hydrolysis and aminolysis reactions during productive transamidation. Site-directed replacement of Ser176 by Ala abolishes glutaminase and Gln-dependent transamidase activities of Glu-AdT (>300-fold), but retains a wild-type level of NH(3)-dependent transamidation activity. These results demonstrate the essentiality of Ser176 for Gln hydrolysis, provide additional support for coordinated coupling of Gln hydrolysis and transamidase transition states during catalysis, and validate glutaminase-directed inhibition of Glu-AdT as a route for antimicrobial chemotherapy.

To search for TNF-alpha (tumor necrosis factor alpha) converting enzyme (TACE) inhibitors, we designed a new class of macrocyclic hydroxamic acids by linking the P1 and P2' residues of acyclic anti-succinate-based hydroxamic acids. A variety of residues including amide, carbamate, alkyl, sulfonamido, Boc-amino, and amino were found to be suitable P1-P2' linkers. With an N-methylamide at P3', the 13-16-membered macrocycles prepared exhibited low micromolar activities in the inhibition of TNF-alpha release from LPS-stimulated human whole blood. Further elaboration in the P3'-P4' area using the cyclophane and cyclic carbamate templates led to the identification of a number of potent analogues with IC(50) values of

Plots of log k(rel) versus IP or versus HOMO for the title reactions are presented; similarities and differences among the reactions are discussed. The Cl2 and Br2 data each show a single line of correlation with positive slope for all alkenes regardless of the steric requirements; increasing substitution at the double bond increases the reaction rate, indicating an electrophilic reaction. Each plot of the I2 data calculated for adsorption exhibits a natural separation into groups of similarly substituted alkenes, in which increased substitution reduces the rate. Within each group, a good-to-excellent correlation is observed, with a lower IP generally corresponding to a higher relative rate. The results indicate that the relative magnitude of the steric requirements about the double bond is similar to that of the electronic effects in iodination. Plot shapes for iodination are compared to those of other reactions, such as hydroboration, oxymercuration, complexation with Ag+, and complexation with MeHg+.

Investigations of the title reaction, carried out by plotting logs of the relative reaction rates vs IPs, vs HOMOs, and vs LUMOs, reveal multiple nearly parallel lines of correlation with small negative slopes in each. Overall, the natural grouping into monosubstituted and disubstituted alkenes gives better correlations than that obtained by using all alkenes. Comparison with analogous plots for other reactions indicates that the mechanism for this reaction has similarities to that for hydroboration, the major difference being that the lines in the plots for hydroboration have positive slopes, indicating an electrophilic rate-determining step involving the pi electrons, while those for the title reaction have small negative slopes, indicating a nucleophilic rate-determining step. Of the two reaction mechanisms proposed for the title reaction, only one has a nucleophilic attack at the complexed alkene as the rate-determining step, and therefore, this work supports that reaction mechanism.

Synthetic methodology was developed for the preparation of chondrotin-4-sulfate reagents that could be specifically attached to the surface of diaspirin cross-linked hemoglobin (DCLHb), a chemically stabilized human hemoglobin. The surface-modified hemoglobin solutions had a significantly higher colloidal osmotic pressures (COP) than DCLHb. The P(50) of the modified DCLHb was dependent upon the reactive end group of the chondrotin-4-sulfate reagents that was used for the protein modification. Modification of DCLHb with the chondroitin-4-sulfate derivatives containing the maleimide end group 23 provided a hemoglobin with a P(50) value of 23 mmHg, while the P(50) of hemoglobins prepared from chondroitin-4-sulfate derivatives containing the aldehyde end group 13 and 18 remained unchanged from that of DCLHb.

Diaspirin cross-linked hemoglobin (DCLHb), a human hemoglobin that is intramolecularly cross-linked between the alpha chains (lysine 99(alpha)(1)-lysine 99(alpha)(2)), was polymerized with a number of water-soluble, nonimmunogenic polyamide cross-linking agents. The degree of polymerization and the oxygen-carrying capacity depended upon the polyamide reagent, the starting concentration of DCLHb, the molar ratio of the polyamide reagent to DCLHb used, the reaction pH, and whether oxy- or deoxy-DCLHb was used in the polymerization reaction.

Novel polyamides were developed that can be used as cross-linking agents for proteins such as hemoglobin. Water-soluble, nonimmunogenic polyamides containing oxygen and sulfur atoms in the backbone were prepared by the polycondensation of the diacids bis(carboxymethyloxyacetyl)-1,4-diaminobutane (1a) or 3, 3'-thiodipropionic acid (1b) with diethylene glycol bis(3-aminopropyl) ether (2). The resulting alpha,omega-diacids were converted to the corresponding activated esters using any of a variety of carboxylic acid activating reagents including the novel reagent diphenyl(1-methylimidazol-2-thiyl)phosphonate (9). The resulting polyamides could be activated with a broad spectrum of groups that allow for the cross-linking and surface modification of proteins.

13C nuclear magnetic resonance is used to detect the Ca2+ ion controlled conformational transition in muscle calcium binding parvalbumin and to study its intramolecular motions. Nuclear relaxation parameters are used to evaluate the reorientation rates of the protein and some of the amino acid side chains. While peripheral residues exhibit greater motional freedom than the protein interior, an interesting finding is that significant rapid internal motion is present in the phenylalanine rings comprising the hydrophobic core of the protein.