Fast and Selective Modification of Thiol Proteins/Peptides by <Emphasis Type="Italic">N</Emphasis>-(Phenylseleno)phthalimide

We previously reported that selenamide reagents such as ebselen and N-(phenylseleno)phthalimide (NPSP) can be used to selectively derivatize thiols for mass spectrometric analysis, and the introduced selenium tags are useful as they could survive or removed with collision-induced dissociation (CID). Described herein is the further study of the reactivity of various protein/peptide thiols toward NPSP and its application to derivatize thiol peptides in protein digests. With a modified protocol (i.e., dissolving NPSP in acetonitrile instead of aqueous solvent), we found that quantitative conversion of thiols can be obtained in seconds, using NPSP in a slight excess amount (NPSP:thiol of 1.1–2:1). Further investigation shows that the thiol reactivity toward NPSP reflects its chemical environment and accessibility in proteins/peptides. For instance, adjacent basic amino acid residues increase the thiol reactivity, probably because they could stabilize the thiolate form to facilitate the nucleophilic attack of thiol on NPSP. In the case of creatine phosphokinase, the native protein predominately has one thiol reacted with NPSP while all of four thiol groups of the denatured protein can be derivatized, in accordance with the corresponding protein conformation. In addition, thiol peptides in protein/peptide enzymatic digests can be quickly and effectively tagged by NPSP following tri-n-butylphosphine (TBP) reduction. Notably, all three thiols of the peptide QCCASVCSL in the insulin peptic digest can be modified simultaneously by NPSP. These results suggest a novel and selective method for protecting thiols in the bottom-up approach for protein structure analysis.     

η3‐Allyl Coordination at Tin(II)—Reactivity towards Alkynes and Benzonitrile

We herein report the synthesis and characterization of a terphenyl‐substituted Sn^II allyl compound featuring an η³ coordination mode in solution and in the solid state. Two examples for the interesting reactivity of the allyl Sn^II molecule are presented: Reactions with terminal alkynes result in the formation of tricyclic compounds by C? C bond formation and the dimerization of two Sn moieties whereas the reaction with benzonitrile leads to a sixteen‐membered ring system through C? H activation.     

Anti-Markovnikov hydroamination and hydrothiolation of electron-deficient vinylarenes catalyzed by well-defined monomeric copper(I) amido and thiolate complexes

Monomeric Cu(I) amido and thiolate complexes that are supported by the N-heterocyclic carbene ligand 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene (IPr) catalyze the hydroamination and hydrothiolation of electron-deficient vinylarenes with reactivity patterns that are consistent with an intermolecular nucleophilic addition of the amido/thiolate ligand of (IPr)Cu(XR) (X = NH or S; R = Ph, CH2Ph) to free vinylarene.     

Divergent Biomimetic Total Syntheses of Ganocins A–C,Ganocochlearins C and D,and Cochlearol T

A divergent synthetic approach to six Ganoderma meroterpenoids, namely ganocins A–C, ganocochlearins C and D, and cochlearol T, has been developed for the first time. This synthetic route features a two‐phase strategy which includes early‐stage rapid construction of a common planar tricyclic intermediate followed by highly selective late‐stage transformations into various Ganoderma meroterpenoids. Key to the strategy are a bioinspired intramolecular hetero‐Diels–Alder reaction and Stahl‐type oxidative aromatization, allowing efficient formation of the common tricyclic phenol intermediate. A nucleophilic dearomatization of the phenol unit, combined with a regioselective 1,4‐reduction of the resulting dienone, enabled rapid access to ganocins B and C. Additionally, site‐selective Mukaiyama hydration, followed by an intramolecular oxa‐Michael addition/triflation cascade, served as a key strategic element in the chemical synthesis of ganocin A.     

Balancing the Rate of Cluster Growth and Etching for Gram‐Scale Synthesis of Thiolate‐Protected Au25 Nanoclusters with Atomic Precision

We report a NaOH‐mediated NaBH₄ reduction method for the synthesis of mono‐, bi‐, and tri‐thiolate‐protected Au₂₅ nanoclusters (NCs) with precise control of both the Au core and thiolate ligand surface. The key strategy is to use NaOH to tune the formation kinetics of Au NCs, i.e., reduce the reduction ability of NaBH₄ and accelerate the etching ability of free thiolate ligands, leading to a well‐balanced reversible reaction for rapid formation of thermodynamically favorable Au₂₅ NCs. This protocol is facile, rapid (≤3 h), versatile (applicable for various thiolate ligands), and highly scalable (>1 g Au NCs). In addition, bi‐ and tri‐thiolate‐protected Au₂₅ NCs with adjustable ratios of hetero‐thiolate ligands were easily obtained. Such ligand precision in molecular ratios, spatial distribution and uniformity resulted in richly diverse surface landscapes on the Au NCs consisting of multiple functional groups such as carboxyl, amine, and hydroxy. Analysis based on NMR spectroscopy revealed that the hetero‐ligands on the NCs are well distributed with no ligand segregation. The unprecedented synthesis of multi‐thiolate‐protected Au₂₅ NCs may further promote the practical applications of functional metal NCs.     

Chemical cross‐linking with NHS esters: a systematic study on amino acid reactivities

Structure elucidation of tertiary or quaternary protein structures by chemical cross‐linking and mass spectrometry (MS) has recently gained importance. To locate the cross‐linker modification, dedicated software is applied to analyze the mass or tandem mass spectra (MS/MS). Such software requires information on target amino acids to limit the data analysis time. The most commonly used homobifunctional N‐hydroxy succinimide (NHS) esters are often described as reactive exclusively towards primary amines, although side reactions with tyrosine and serine have been reported. Our goal was to systematically study the reactivity of NHS esters and derive some general rules for their attack of nucleophilic amino acid side chains in peptides. We therefore studied the cross‐linking reactions of synthesized and commercial model peptides with disuccinimidyl suberate (DSS). The first reaction site in all cases was expectedly the α‐NH₂‐group of the N‐terminus or the ε‐NH₂‐group of lysine. As soon as additional cross‐linkers were attached or loops were formed, other amino acids were also involved in the reaction. In addition to the primary amino groups, serine, threonine and tyrosine showed significant reactivity due to the effect of neighboring amino acids by intermediate or permanent Type‐1 cross‐link formation. The reactivity is highly dependent on the pH and on adjacent amino acids. Copyright © 2009 John Wiley & Sons, Ltd.     

Synthesis of thioether derivatives of brominated poly(isobutylene‐co‐isoprene): Direct coupling chemistry for silica reinforcement

Thioether derivatives of brominated poly(isobutylene‐co‐isoprene) (BIIR) were prepared through base‐mediated nucleophilic substitution reactions of the elastomer with thiolate ions formed in situ from thiols. The characterization of the reaction products was accomplished with studies of a model compound, brominated 2,2,4,8,8‐pentamethyl‐4‐nonene, the reactivity of which was shown to be consistent with that of the polymer. The reaction of aliphatic thiols with the allylic bromide functionality of BIIR required a strong base, and base‐catalyzed air oxidation of the thiol to disulfide operated concurrently to reduce the yield of the desired substitution products. An efficient and direct method of coupling BIIR to silica with (3‐mercaptopropyl)trimethoxysilane improved filler dispersion, thereby overcoming problematic agglomeration of reinforcing siliceous fillers in these compounds. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 2937–2944, 2002     

Hydrogen‐bonding interactions in the active site of a low molecular weight protein‐tyrosine phosphatase

Molecular dynamics simulation of the Michaelis complex, phospho‐enzyme intermediate, and the wild‐type and C12S mutant have been carried out to examine hydrogen‐bonding interactions in the active site of the bovine low molecular weight protein‐tyrosine phosphatase (BPTP). It was found that the S_γ atom of the nucleophilic residue Cys‐12 is ideally located at a position opposite from the phenylphosphate dianion for an inline nucleophilic substitution reaction. In addition, electrostatic and hydrogen‐bonding interactions from the backbone amide groups of the phosphate‐binding loop strongly stabilize the thiolate anion, making Cys‐12 ionized in the active site. In the phospho‐enzyme intermediate, three water molecules are found to form strong hydrogen bonds with the phosphate group. In addition, another water molecule can be identified to form bridging hydrogen bonds between the phosphate group and Asp‐129, which may act as the nucleophile in the subsequent phosphate hydrolysis reaction, with Asp‐129 serving as a general base. The structural difference at the active site between the wild‐type and C12S mutant has been examined. It was found that the alkoxide anion is significantly shifted toward one side of the phosphate binding loop, away from the optimal position enjoyed by the thiolate anion of the wild‐type enzyme in an S_N2 process. This, coupled with the high pK_a value of an alcoholic residue, makes the C12S mutant catalytically inactive. These molecular dynamics simulations provided details of hydrogen bonding interactions in the active site of BPTP, and a structural basis for further studies using combined quantum mechanical and molecular mechanical potential to model the entire dephosphorylation reaction by BPTP. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1192–1203, 2000     

Spectroscopic and Mechanistic Studies on Oxidation Reactions Catalyzed by the Functional Model SR Complex for Cytochrome P450: Influence of Oxidant,Substrate, and Solvent

Kinetic and mechanistic studies on the formation of an oxoiron(IV) porphyrin cation radical bearing a thiolate group as proximal ligand are reported. The SR complex, a functional enzyme mimic of P450, was oxidized in peroxo‐shunt reactions under different experimental conditions with variation of solvent, temperature, and identity and excess of oxidant in the presence of different organic substrates. Through the application of a low‐temperature rapid‐scan stopped‐flow technique, the reactive intermediates in the SR catalytic cycle, such as the initially formed SR acylperoxoiron(III) complex and the SR high‐valent iron(IV) porphyrin cation radical complex [( SR ^.+)Fe^IV?O], were successfully identified and kinetically characterized. The oxidation of the SR complex under catalytic conditions provided direct spectroscopic information on the reactivity of [( SR ^.+)Fe^IV?O] towards the oxidation of selected organic substrates. Because the catalytically active species is a synthetic oxoiron(IV) porphyrin cation radical bearing a thiolate proximal group, the effect of the strong electron donor ligand on the formation and reactivity/stability of the SR high‐valent iron species is addressed and discussed in the light of the reactivity pattern observed in substrate oxygenation reactions catalyzed by native P450 enzyme systems.     

General and Facile Route to Isomerically Pure Tricyclic Peptides Based on Templated Tandem CLIPS/CuAAC Cyclizations

We report a one‐pot ligation/cyclization technology for the rapid and clean conversion of linear peptides into tricyclic peptides that is based on using tetravalent scaffolds containing two benzyl bromide and two alkyne moieties. These react via CLIPS/CuAAC reactions with cysteines and azides in the peptide. Flexibility in the scaffolds is key to the formation of isomerically pure products as the flexible scaffolds T4 ₁ and T4 ₂ mostly promote the formation of single isomeric tricycles while the rigid scaffolds T4 ₃ and T4 ₄ do not yield clean products. There seems to be no limitation to the number and types of amino acids present as 18 canonical amino acids were successfully implemented. We also observed that azides at the peptide termini and cysteine residues in the center gave better results than compounds with the functional groups placed the other way round.     

Solid‐Phase Parallel Synthesis of Functionalised Medium‐to‐Large Cyclic Peptidomimetics through Three‐Component Coupling Driven by Aziridine Aldehyde Dimers

The first solid‐phase parallel synthesis of macrocyclic peptides using three‐component coupling driven by aziridine aldehyde dimers is described. The method supports the synthesis of 9‐ to 18‐membered aziridine‐containing macrocycles, which are then functionalized by nucleophilic opening of the aziridine ring. This constitutes a robust approach for the rapid parallel synthesis of macrocyclic peptides.     

Intramolecular Long‐Distance Nucleophilic Reactions as a Rapid Fluorogenic Switch Applicable to the Detection of Enzymatic Activity

Long‐distance intramolecular nucleophilic reactions are promising strategies for the design of fluorogenic probes to detect enzymatic activity involved in lysine modifications. However, such reactions have been challenging and hence have not been established. In this study, we have prepared fluorogenic peptides that induce intramolecular reactions between lysine nucleophiles and electrophiles in distal positions. These peptides contain a lysine and fluorescence‐quenched fluorophore with a carbonate ester, which triggers nucleophilic transesterification resulting in fluorogenic response. Transesterification occurred under mild aqueous conditions despite the presence of a long nine‐amino‐acid spacer between the lysine and fluorophore. In addition, one of the peptides showed the fastest reaction kinetics with a half‐life time of 3.7 min. Furthermore, the incorporation of this fluorogenic switch into the probes allowed rapid fluorogenic detection of histone deacetylase (HDAC) activity. These results indicate that the transesterification reaction has great potential for use as a general fluorogenic switch to monitor the activity of lysine‐targeting enzymes.     

Oxygen anion (O−) and hydroxide anion (HO−) reactivity with a series of old and new refrigerants

The reactivity of a series of commonly used halogenated compounds (trihalomethanes, chlorofluorocarbon, hydrochlorofluorocarbon, fluorocarbons, and hydrofluoroolefin) with hydroxide and oxygen anion is studied in a compact Fourier transform ion cyclotron resonance. O⁻ is formed by dissociative electron attachment to N₂O and HO⁻ by a further ion‐molecule reaction with ammonia. Kinetic experiments are performed by increasing duration of introduction of the studied molecule at a constant pressure. Hydroxide anion reactions mainly proceed by proton transfer for all the acidic compounds. However, nucleophilic substitution is observed for chlorinated and brominated compounds. For fluorinated compounds, a specific elimination of a neutral fluorinated alkene is observed in our results in parallel with the proton transfer reaction. Oxygen anion reacts rapidly and extensively with all compounds. Main reaction channels result from nucleophilic substitution, proton transfer, and formal H₂⁺ transfer. We highlight the importance of transfer processes (atom or ion) in the intermediate ion‐neutral complex, explaining part of the observed reactivity and formed ions. In this paper, we present the first reactivity study of anions with HFO 1234yf. Finally, the potential of O⁻ and HO⁻ as chemical ionization reagents for trace analysis is discussed.     

Rhodium(III)‐Catalyzed N‐Nitroso‐Directed CH Addition to Ethyl 2‐Oxoacetate for Cycloaddition/Fragmentation Synthesis of Indazoles

Rh^III‐catalyzed N‐nitroso‐directed C?H addition to ethyl 2‐oxoacetate allows subsequent construction of indazoles, a privileged heterocycle scaffold in synthetic chemistry, through the exploitation of reactivity between the directing group and installed group. The formal [2+2] cycloaddition/fragmentation reaction pathway identified herein, a unique reactivity pattern hitherto elusive for the N‐nitroso group, emphasizes the importance of forward reactivity analysis in the development of useful C?H functionalization‐based synthetic tools. The synthetic utility of the protocol is demonstrated with the synthesis of a tricyclic‐fused ring system. The diversity of covalent linkages available for the nitroso group should enable the extension of the genre of reactivity reported herein to the synthesis of other types of heterocycles.     

Heterobimetallic Catalysis: Platinum‐Gold‐Catalyzed Tandem Cyclization/C−X Coupling Reaction of (Hetero)Arylallenes with Nucleophiles

Heterobimetallic catalysis offers new opportunities for reactivity and selectivity but still presents challenges, and only a few metal combinations have been explored so far. Reported here is a Pt‐Au heterobimetallic catalyst system for the synthesis of a family of multi‐heteroaromatic structures through tandem cyclization/C?X coupling reaction. Au‐catalyzed 6‐endo‐cyclization takes place as the first fast step. Pt‐Au clusters are proposed to be responsible for the increased reactivity in the second step, that is, the intermolecular nucleophilic addition which occurs through an outer‐sphere mechanism by hybrid homogeneous‐heterogeneous catalysis.     

Understanding local electrophilicity/nucleophilicity activation through a single reactivity difference index

A local reactivity difference index R(k) is shown to be able to predict the local electrophilic and/or nucleophilic activation within an organic molecule. Together with the electrophilic and/or nucleophilic behavior of the center k given by the sign, the magnitude of the R(k) index accounts for the extent of the electronic activation, a behavior that allows for the use of the R(k) index as a measure of the molecular reactivity especially in polar processes.     

Competition between vinylic substitution and conjugate addition in the reactions of vinyl selenoxides and vinyl selenones with nucleophiles in DMF

Vinyl selenoxides and vinyl selenones present a different reactivity towards thiolate or alkoxide anions in DMF. In the case of selenoxides the addition of the nucleophiles regioselectively occurs at the α-carbon leading to the formation of the vinylic substitution products with complete retention of configuration. These reactions occur under very mild conditions indicating that the seleninyl group markedly enhances nucleophilic vinylic substitution rates. The results obtained with vinyl selenones are consistent with competitive nucleophilic attack at the α- and at the β-carbon. The former yields irreversibly the vinylic substitution products, whereas attack at the β-carbon leads to the reversible formation of selenonyl stabilized carbanions. The fate of these intermediates depends upon the nucleophilic reagent employed. With thiolate anions the vinyl selenones are rapidly subtracted from the equilibrium and the carbanion does not give any other product. With methoxide anions, on the contrary, the vinylic substitution is a slow process and the carbanion can give rise to conjugate addition products also. Malonate anions react only at the β-carbon of vinyl selenones and the resulting carbanions suffer proton transfer and intramolecular displacement of the selenonyl group to afford cyclopropane derivatives.     

Stereo‐ and Regioselective Synthesis of Tricyclic Spirolactones by Diastereoisomeric Differentiation of a Collective Key Precursor

A general, parallel, and collective synthesis of 5/5/5‐ and 5/5/6‐ring fusion topologies of tricyclic spiranoid lactones through the controlled cyclizations of easily accessible, common key precursors is described. The rapid composition of key cycloalkyl methylene precursors yielded an assembly of bicyclic diastereoisomeric iodolactones, which were individually converted into a wide range of tricyclic, angularly fused spiranoid lactones in a regioselective and stereodirected fashion through the diastereoisomeric differentiation of a collective key precursor. The critical stereochemical assignment of the bicyclic starting materials, as well as the tricyclic targets, was confirmed by X‐ray crystal structure determination.     

Mechanism of the N-protecting group dependent annulations of 3-aryloxy alkynyl indoles under gold catalysis: a computational study

The mechanism of the gold-catalyzed annulations of 3-aryloxy alkynyl indoles developed by Tu et al. was studied by DFT calculations. It was found that both indole derivatives of electron-donating and electron-withdrawing protective groups would first undergo the 5-exo-dig cyclization simultaneously upon activation by cationic [PR(3)Au(+)] species. However, divergent reactivity of the resulting spirocyclic intermediate in competitive 1,2-alkenyl migration and nucleophilic water addition reactions towards C3 was predicted. When protected by electron-donating group, the 1,2-alkenyl migration occurs to generate a tricyclic intermediate, from which an aromatic Claisen rearrangement/nucleophilic addition sequence results in the observed 1,2-phenoxy migration. In case of electron-withdrawing group, the 1,2-alkenyl migration would be unfavorable. Instead, the nucleophilic addition of water oxygen to C3 is more facile, and leads to the hemiketal intermediate. The possible roles of water-cluster and OTf anion as proton shuttles in both reactions were also evaluated.