Bioorthogonal Ligation and Cleavage by Reactions of Chloroquinoxalines with ortho‐Dithiophenols

A bioorthogonal ligation and cleavage method via reactions of chloroquinoxalines (CQ) and ortho‐dithiophenols (DT) is presented. Double nucleophilic substitutions of ortho‐dithiophenols to chloroquinoxalines provide conjugates containing tetracyclic benzo[5,6][1,4]dithiino[2,3‐b]quinoxaline with strong built‐in fluorescence together with release of the other functional molecules. Three cleavable linkers were designed and successfully used in release of the molecules containing biotin from the protein conjugates. The CQ‐DT bioorthogonal reactions can be applied for the bioorthogonal ligations, bioorthogonal cleavages, and trans‐tagging of proteins, and show advantages of readily accessible unnatural orthogonal groups, appealing reaction kinetics (k₂≈1.3 m ^?1 s^?1), excellent biocompatibility of orthogonal groups, and high stability of conjugates. This complements previous bioorthogonal reactions and is a new route for protein‐fishing applications and in‐gel fluorescence analysis.     

A dataset of highly accurate homolytic NBr bond dissociation energies obtained by Means of W2 theory

Homolytic N? Br bond dissociation constitutes the initial step of numerous reactions involving N‐brominated species. However, little is known about the strength of N? Br bonds toward homolytic cleavage. We herein report accurate bond dissociation energies (BDEs) for a set of 18 molecules using the high‐level W2 thermochemical protocol. The BDEs (at 298 K) of the species in this set range from 162.2 kJ mol^?1 (N‐bromopyrrole) to 260.6 kJ mol^?1 ((CHO)₂NBr). In order to compute BDEs of larger systems, for which W2 theory is not applicable, we have benchmarked a wide range of more economical theoretical procedures. Of these, G3‐B3 offers the best performance (root‐mean‐square deviations = 2.9 kJ mol^?1), and using this method, we have computed N? Br BDEs for four widely used N‐brominated compounds. These include (BDEs are given in parentheses): N‐bromosuccinimide (281.6), N‐bromoglutarimide (263.2), N‐bromophthalimide (274.7), and 1,3‐dibromo‐5,5‐dimethylhydantoin (218.2 and 264.8 kJ mol^?1). © 2015 Wiley Periodicals, Inc.     

Vinylboronic Acids as Fast Reacting,Synthetically Accessible,and Stable Bioorthogonal Reactants in the Carboni–Lindsey Reaction

Bioorthogonal reactions are widely used for the chemical modification of biomolecules. The application of vinylboronic acids (VBAs) as non‐strained, synthetically accessible and water‐soluble reaction partners in a bioorthogonal inverse electron‐demand Diels–Alder (iEDDA) reaction with 3,6‐dipyridyl‐s‐tetrazines is described. Depending on the substituents, VBA derivatives give second‐order rate constants up to 27 m ^?1 s^?1 in aqueous environments at room temperature, which is suitable for biological labeling applications. The VBAs are shown to be biocompatible, non‐toxic, and highly stable in aqueous media and cell lysate. Furthermore, VBAs can be used orthogonally to the strain‐promoted alkyne–azide cycloaddition for protein modification, making them attractive complements to the bioorthogonal molecular toolbox.     

Triazinium Ligation: Bioorthogonal Reaction of N1-Alkyl 1,2,4-Triazinium Salts**

The development of reagents that can selectively react in complex biological media is an important challenge. Here we show that N1-alkylation of 1,2,4-triazines yields the corresponding triazinium salts, which are three orders of magnitude more reactive in reactions with strained alkynes than the parent 1,2,4-triazines. This powerful bioorthogonal ligation enables efficient modification of peptides and proteins. The positively charged N1-alkyl triazinium salts exhibit favorable cell permeability, which makes them superior for intracellular fluorescent labeling applications when compared to analogous 1,2,4,5-tetrazines. Due to their high reactivity, stability, synthetic accessibility and improved water solubility, the new ionic heterodienes represent a valuable addition to the repertoire of existing modern bioorthogonal reagents.     

Alkene–Tetrazine Ligation for Imaging Cellular DNA

5‐Vinyl‐2′‐deoxyuridine (VdU) is the first reported metabolic probe for cellular DNA synthesis that can be visualized by using an inverse electron demand Diels–Alder reaction with a fluorescent tetrazine. VdU is incorporated by endogenous enzymes into the genomes of replicating cells, where it exhibits reduced genotoxicity compared to 5‐ethynyl‐2′‐deoxyuridine (EdU). The VdU–tetrazine ligation reaction is rapid (k≈0.02 M ^?1 s^?1) and chemically orthogonal to the alkyne–azide “click” reaction of EdU‐modified DNA. Alkene–tetrazine ligation reactions provide the first alternative to azide–alkyne click reactions for the bioorthogonal chemical labeling of nucleic acids in cells and facilitate time‐resolved, multicolor labeling of DNA synthesis.     

Affinity‐Labeling‐Based Introduction of a Reactive Handle for Natural Protein Modification

A new chemical method to site‐specifically modify natural proteins without the need for genetic manipulation is described. Our strategy involves the affinity‐labeling‐based attachment of a unique reactive handle at the surface of the target protein, and the subsequent selective transformation of the reactive handle by a bioorthogonal reaction to introduce a variety of functional probes into the protein. To demonstrate this approach, we synthesized labeling reagents that contain: 1) a benzenesulfonamide ligand that directs specifically to bovine carbonic anhydrase II (bCA), 2) an electrophilic epoxide group for protein labeling, 3) an exchangeable hydrazone bond linking the ligand and the epoxide group, and 4) an iodophenyl or acetylene handle. By incubating the labeling reagent with bCA, the reactive handle was covalently attached at the surface of bCA through epoxide ring opening. Either after or before removing the ligand by a hydrazone/oxime‐exhange reaction, which restores the enzymatic activity, the reactive handle incorporated could be derivatized by Suzuki coupling or Huisgen cycloaddition reactions. This method is also applicable to the target‐specific multiple modification in a protein mixture. The availability of various (photo)affinity‐labeling reagents and bioorthogonal reactions should extend the flexibility of this strategy for the site‐selective incorporation of many functional molecules into proteins.     

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.     

Hypervalent Iodine(III)‐Mediated Benzannulation of Enamines with Alkynes: an Efficient Synthesis of Substituted Aminonaphthoic Acid Derivatives

An intermolecular two C? C bond formation procedure for the synthesis of carbocycles mediated by hypervalent iodine(III) reagents was developed. This metal free protocol provided a new approach for the synthesis of useful substituted 1‐amino‐2‐naphthoic acid derivatives via benzannulation reactions. Various N‐unsubstituted and N‐alkyl substituted aromatic enamines with terminal alkynes and non‐terminal alkynes can be converted into corresponding 1‐amino‐2‐naphthoic acid derivatives under mild reaction conditions. When meta‐substituted phenyl enamines were employed in the reaction, two cyclization paths were detected in the reaction and ortho‐cyclization products were the only or major products. Good functional group tolerance, readily available material and high atom utilization efficiency make this method a potential procedure which may find broad application in organic synthesis.     

Terminal Alkenes as Versatile Chemical Reporter Groups for Metabolic Oligosaccharide Engineering

The Diels–Alder reaction with inverse electron demand (DAinv reaction) of 1,2,4,5‐tetrazines with electron rich or strained alkenes was proven to be a bioorthogonal ligation reaction that proceeds fast and with high yields. An important application of the DAinv reaction is metabolic oligosaccharide engineering (MOE) which allows the visualization of glycoconjugates in living cells. In this approach, a sugar derivative bearing a chemical reporter group is metabolically incorporated into cellular glycoconjugates and subsequently derivatized with a probe by means of a bioorthogonal ligation reaction. Here, we investigated a series of new mannosamine and glucosamine derivatives with carbamate‐linked side chains of varying length terminated by alkene groups and their suitability for labeling cell‐surface glycans. Kinetic investigations showed that the reactivity of the alkenes in DAinv reactions increases with growing chain length. When applied to MOE, one of the compounds, peracetylated N‐butenyloxycarbonylmannosamine, was especially well suited for labeling cell‐surface glycans. Obviously, the length of its side chain represents the optimal balance between incorporation efficiency and speed of the labeling reaction. Sialidase treatment of the cells before the bioorthogonal labeling reaction showed that this sugar derivative is attached to the glycans in form of the corresponding sialic acid derivative and not epimerized to another hexosamine derivative to a considerable extent.     

Reaction of Aromatic Peroxyl Radicals with Alkynes: A Mass Spectrometric and Computational Study Using the Distonic Radical Ion Approach

The reaction of the aromatic distonic peroxyl radical cations N‐methyl pyridinium‐4‐peroxyl (PyrOO^.+) and 4‐(N,N,N‐trimethyl ammonium)‐phenyl peroxyl (AnOO^.+), with symmetrical dialkyl alkynes 10a – c was studied in the gas phase by mass spectrometry. PyrOO^.+ and AnOO^.+ were produced through reaction of the respective distonic aryl radical cations Pyr^.+ and An^.+ with oxygen, O₂. For the reaction of Pyr^.+ with O₂ an absolute rate coefficient of k₁=7.1×10^?12 cm³ molecule^?1 s^?1 and a collision efficiency of 1.2 % was determined at 298 K. The strongly electrophilic PyrOO^.+ reacts with 3‐hexyne and 4‐octyne with absolute rate coefficients of k_hexyne=1.5×10^?10 cm³ molecule^?1 s^?1 and k_octyne=2.8×10^?10 cm³ molecule^?1 s^?1, respectively, at 298 K. The reaction of both PyrOO^.+ and AnOO^.+ proceeds by radical addition to the alkyne, whereas propargylic hydrogen abstraction was observed as a very minor pathway only in the reactions involving PyrOO^.+. A major reaction pathway of the vinyl radicals 11 formed upon PyrOO^.+ addition to the alkynes involves γ‐fragmentation of the peroxy O? O bond and formation of PyrO^.+. The PyrO^.+ is rapidly trapped by intermolecular hydrogen abstraction, presumably from a propargylic methylene group in the alkyne. The reaction of the less electrophilic AnOO^.+ with alkynes is considerably slower and resulted in formation of AnO^.+ as the only charged product. These findings suggest that electrophilic aromatic peroxyl radicals act as oxygen atom donors, which can be used to generate α‐oxo carbenes 13 (or isomeric species) from alkynes in a single step. Besides γ‐fragmentation, a number of competing unimolecular dissociative reactions also occur in vinyl radicals 11 . The potential energy diagrams of these reactions were explored with density functional theory and ab initio methods, which enabled identification of the chemical structures of the most important products.     

Highly Selective Addition of a Broad Spectrum of Trimethylsilane Pro‐nucleophiles to N‐tert‐Butanesulfinyl Imines

Addition of organotrimethylsilane reagents to chiral N‐tert‐butanesulfinyl imines can be achieved in good yields and with excellent diastereoselectivities by employing TMSO^?/Bu₄N⁺ as a Lewis base activator in THF. A variety of aliphatic, aromatic, heteroaromatic and organometallic chiral imines were utilised as electrophiles for the synthesis of enantioenriched N‐tert‐butanesulfinyl amides. Remarkably, the same sets of reaction conditions could be used with a highly diverse range of bench‐stable organotrimethylsilane reagents, which highlights the generality and robustness of this methodology.     

Thermal Behavior of N,N＇Bis[N-（2,2,2-trinitroethyl）-N-nitro]ethylenediamine

The thermal behavior and kinetic parameters of the exothermic decomposition reaction of N‐N‐bis[N‐(2,2,2‐tri‐nitroethyl)‐N‐nitro]ethylenediamine in a temperature‐programmed mode have been investigated by means of differential scanning calorimetry (DSC). The results show that kinetic model function in differential form, apparent activation energy E_a and pre‐exponential factor A of this reaction are 3(1 ‐α)^2/3, 203.67 kJ·mol^?1 and 10^20.61s^?1, respectively. The critical temperature of thermal explosion of the compound is 182.2 °C. The values of ΔS^≠ ΔH^≠ and ΔG^≠ of this reaction are 143.3 J·mol^?1·K^?1, 199.5 kJ·mol^?1 and 135.5 kJ·mol^?1, respectively.     

Super‐Resolution Imaging of Plasma Membrane Glycans

Much of the physiology of cells is controlled by the spatial organization of the plasma membrane and the glycosylation patterns of its components, however, studying the distribution, size, and composition of these components remains challenging. A bioorthogonal chemical reporter strategy was used for the efficient and specific labeling of membrane‐associated glycoconjugates with modified monosaccharide precursors and organic fluorophores. Super‐resolution fluorescence imaging was used to visualize plasma membrane glycans with single‐molecule sensitivity. Our results demonstrate a homogeneous distribution of N‐acetylmannosamine (ManNAc)‐, N‐acetylgalactosamine (GalNAc)‐, and O‐linked N‐acetylglucosamine (O‐GlcNAc)‐modified plasma membrane proteins in different cell lines with densities of several million glycans on each cell surface.     

Activated Anilide in Heterocyclic Synthesis: Synthesis of New Dihydropyridines,Dihydropyridazines and Thiourea Derivatives

A series of new dihydropyridines, butanamide, dihydropyridazines and thiourea derivatives have been prepared through the reactions of 3‐aminopyridine ( 1 ) and N‐(pyridin‐3‐yl)‐3‐(pyridin‐3‐ylimino)butanamide 3 with some electrophilic reagents, aryl diazonium salts and isothiocyanates. Elementary analysis, MS, IR, and ¹H NMR spectra confirmed the identity of the products.     

Iminoboronate Formation Leads to Fast and Reversible Conjugation Chemistry of α‐Nucleophiles at Neutral pH

Bioorthogonal reactions that are fast and reversible under physiological conditions are in high demand for biological applications. Herein, it is shown that an ortho boronic acid substituent makes aryl ketones rapidly conjugate with α‐nucleophiles at neutral pH. Specifically, 2‐acetylphenylboronic acid and derivatives were found to conjugate with phenylhydrazine with rate constants of 10² to 10³ M ^?1 s^?1, comparable to the fastest bioorthogonal conjugations known to date. ¹¹B NMR analysis revealed the varied extent of iminoboronate formation of the conjugates, in which the imine nitrogen forms a dative bond with boron. The iminoboronate formation activates the imines for hydrolysis and exchange, rendering these oxime/hydrazone conjugations reversible and dynamic under physiological conditions. The fast and dynamic nature of the iminoboronate chemistry should find wide applications in biology.     

Vinylboronic Acids as Fast Reacting,Synthetically Accessible,and Stable Bioorthogonal Reactants in the Carboni–Lindsey Reaction

Bioorthogonal reactions are widely used for the chemical modification of biomolecules. The application of vinylboronic acids (VBAs) as non‐strained, synthetically accessible and water‐soluble reaction partners in a bioorthogonal inverse electron‐demand Diels–Alder (iEDDA) reaction with 3,6‐dipyridyl‐s‐tetrazines is described. Depending on the substituents, VBA derivatives give second‐order rate constants up to 27 m ⁻¹ s⁻¹ in aqueous environments at room temperature, which is suitable for biological labeling applications. The VBAs are shown to be biocompatible, non‐toxic, and highly stable in aqueous media and cell lysate. Furthermore, VBAs can be used orthogonally to the strain‐promoted alkyne–azide cycloaddition for protein modification, making them attractive complements to the bioorthogonal molecular toolbox.     

The α‐effect exhibited in gas‐phase SN2@N and SN2@C reactions

In order to explore the existence of α‐effect in gas‐phase S_N2@N reactions, and to compare its similarity and difference with its counterpart in S_N2@C reactions, we have carried out a theoretical study on the reactivity of six α‐oxy‐Nus (FO^?, ClO^?, BrO^?, HOO^?, HSO^?, H₂NO^?) in the S_N2 reactions toward NR₂Cl (R = H, Me) and RCl (R = Me, i‐Pr) using the G2(+)_M theory. An enhanced reactivity induced by the α‐atom is found in all examined systems. The magnitude of the α‐effect in the reactions of NR₂Cl (R = H, Me) is generally smaller than that in the corresponding S_N2 reaction, but their variation trend with the identity of α‐atom is very similar. The origin of the α‐effect of the S_N2@N reactions is discussed in terms of activation strain analysis and thermodynamic analysis, indicating that the α‐effect in the S_N2@N reactions largely arises from transition state stabilization, and the “hyper‐reactivity” of these α‐Nus is also accompanied by an enhanced thermodynamic stability of products from the n_(N) → σ*_(O?Y) negative hyperconjugation. Meanwhile, it is found that the reactivity of oxy‐Nus in the S_N2 reactions toward NMe₂Cl is lower than toward i‐PrCl, which is different from previous experiments, that is, the S_N2 reactions of NH₂Cl is more facile than MeCl. © 2013 Wiley Periodicals, Inc.     

The preparation of covalent triazine‐based framework via Friedel‐Crafts reaction of 2,4,6‐trichloro‐1,3,5‐triazine with N,N′‐diphenyl‐N,N′‐di(m‐tolyl)benzidine for capturing and sensing to iodine

The covalent triazine‐based framework (TDPDB) has been prepared by Friedel‐Crafts polymerization reaction of N,N′‐diphenyl‐N,N′‐di(m‐tolyl)benzidine (DPDB) with 2,4,6‐trichloro‐1,3,5‐triazine (TCT) catalyzed by methanesulfonic acid. The yield of the reaction (94.85%) is very high. TDPDB was provided with Brunauer‐Emmett‐Teller specific surface area of 592.18 m² g^?1 and pore volume of 0.5241 cm³ g^?1. TDPDB demonstrated an excellent capacity for capturing iodine (3.93 g g^?1) and an outstanding ability to fluorescent sensing to iodine with Ksv of 5.83 × 10⁴ L mol^?1. It also showed high fluorescent sensing sensitivity to picric acid.     

Ultrafluorogenic Coumarin–Tetrazine Probes for Real‐Time Biological Imaging

We have developed a series of new ultrafluorogenic probes in the blue‐green region of the visible‐light spectrum that display fluorescence enhancement exceeding 11 000‐fold. These fluorogenic dyes integrate a coumarin fluorochrome with the bioorthogonal trans‐cyclooctene(TCO)–tetrazine chemistry platform. By exploiting highly efficient through‐bond energy transfer (TBET), these probes exhibit the highest brightness enhancements reported for any bioorthogonal fluorogenic dyes. No‐wash, fluorogenic imaging of diverse targets including cell‐surface receptors in cancer cells, mitochondria, and the actin cytoskeleton is possible within seconds, with minimal background signal and no appreciable nonspecific binding, opening the possibility for in vivo sensing.     

An Acid‐Catalyzed Fragmentation Reaction of a Triamine‐Linked Acridine Dimer

An acid‐catalyzed cleavage of the C‐N^? bond from N^?‐(2,3,4,5‐tetrahydroxyvaleryl) substituted side chain and/or its acetonide form of a triamine‐linked acridine dimer is de scribed. An envisaged multi‐neighboring group‐assisted solvolysis reaction mechanism is proposed.