Strain and stereoelectronics in cycloalkyne click chemistry

Co-delivery of antigen and adjuvant by site-specific conjugation to dendritic cell-targeted Fab fragments potentiates T cell responses

The aim of therapeutic cancer vaccines is to induce tumor-specific cellular immune responses. This requires tumor antigens to be efficiently processed and presented by antigen-presenting cells, in particular dendritic cells (DCs). In addition, DCs require maturation to upregulate the surface expression and secretion of T cell costimulatory molecules, which is achieved by co-administration of adjuvants in vaccines. Peptide-based antigen vaccination is an attractive strategy due to the established biocompatibility of peptides as well as the dosing control. To enhance the efficacy of peptide-based vaccines, antigens can be targeted to DCs. Antigen-adjuvant conjugates are known to enhance T cell activation by ensuring DC maturation upon antigen delivery. In this study, we aim to combine these two approaches in a single molecule, and present a DC-targeted antibody fragment-antigen-adjuvant (AAA)-conjugate. We generate the AAA-conjugate through a combination of site-specific sortase-mediated chemoenzymatic ligation and click chemistry. Ex vivo T cell activation assays show enhanced efficacy of the AAA-conjugate compared to non-adjuvanted control conjugates. The in vivo performance of the AAA-conjugate was suboptimal, which we hypothesize to be a consequence of the hydrophobic character of the conjugate. In vivo efficacy was rescued by co-administration of antibody fragment-antigen conjugates and antibody fragment-adjuvant conjugates, in which the antigen and adjuvant were separatedly delivered using two different DC-targeting molecules. In conclusion, this study provides a proof-of-concept for effective in vivo antigen-specific T cell activation by targeted delivery of both antigen and adjuvant to DCs in a single or separate molecule using site-specific protein engineering.

The Photoredox Paradox: Electron and Hole Upconversion as the Hidden Secrets of Photoredox Catalysis

Although photoredox catalysis is complex from a mechanistic point of view, it is also often surprisingly efficient. In fact, the quantum efficiency of a puzzlingly large portion of photoredox reactions exceeds 100% (i.e., the measured quantum yields (QYs) are >1). Hence, these photoredox reactions can be more than perfect with respect to photon utilization. In several documented cases, a single absorbed photon can lead to the formation of >100 molecules of the product, behavior known to originate from chain processes. In this Perspective, we explore the underlying reasons for this efficiency, identify the nature of common catalytic chains, and highlight the differences between HAT and SET chains. Our goal is to show why chains are especially important in photoredox catalysis and where the thermodynamic driving force that sustains the SET catalytic cycles comes from. We demonstrate how the interplay of polar and radical processes can activate hidden catalytic pathways mediated by electron and hole transfer (i.e., electron and hole catalysis). Furthermore, we illustrate how the phenomenon of redox upconversion serves as a thermodynamic precondition for electron and hole catalysis. After discussing representative mechanistic puzzles, we analyze the most common bond forming steps, where redox upconversion frequently occurs (and issometimes unavoidable). In particular, we highlight the importance of 2-center-3-electron bonds as a recurring motif that allows a rational chemical approach to the design of redox upconversion processes.

Key role of cycloalkyne nature in alkyne-dye reagents for enhanced specificity of intracellular imaging by bioorthogonal bioconjugation

Conjugates of benzothiophene-fused azacyclononyne BT9N-NH2 with fluorescent dyes were developed to visualise azidoglycans intracellularly. The significance of the cycloalkyne core was demonstrated by comparing new reagents with DBCO- and BCN-dye conjugates. To reduce non-specificity during intracellular bioconjugation using SPAAC, less reactive BT9N-dye reagents are preferred over highly reactive DBCO- and BCN-dye conjugates.

Snapshot of cyclooctyne ring-opening to a tethered alkylidene cyclic polymer catalyst

Cyclooctyne reacts with the trianionic pincer ligand supported alkylidyne [ t BuOCO]WCC(CH3)3(THF)2 (1) to yield tungstacyclopropene (3) and tungstacyclopentadiene (4) complexes. The ratio of 3 and 4 in the reaction mixture depends on the stoichiometry of the reaction. The maximum concentration of 3 occurs with one equiv. of cyclooctyne and 4 is the exclusive product of the reaction above three equivalents. Both complexes 3 and 4 convert to the cyclooctyne ring-opened product 5 upon heating. While the conversion of 4 to 5 is accompanied by formation of polycyclooctyne as a white precipitate during the reaction, conversion of 3 to 5 is homogeneous. Exhibiting Ring Expansion Polymerization (REP), complexes 4 and 5 initiate the polymerization of phenylacetylene to generate cyclic poly(phenylacetylene) (c-PPA).

Beyond Strain Release: Delocalization-Enabled Organic Reactivity

The release of strain energy is a fundamental driving force for organic reactions. However, absolute strain energy alone is an insufficient predictor of reactivity, evidenced by the similar ring strain but disparate reactivity of cyclopropanes and cyclobutanes. In this work, we demonstrate that electronic delocalization is a key factor that operates alongside strain release to boost, or even dominate, reactivity. This delocalization principle extends across a wide range of molecules containing three-membered rings such as epoxides, aziridines, and propellanes and also applies to strain-driven cycloaddition reactions. Our findings lead to a "rule of thumb" for the accurate prediction of activation barriers in such systems, which can be easily applied to reactions involving many of the strained building blocks commonly encountered in organic synthesis, medicinal chemistry, polymer science, and bioconjugation. Given the significance of electronic delocalization in organic chemistry, for example in aromatic π-systems and hyperconjugation, we anticipate that this concept will serve as a versatile tool to understand and predict organic reactivity.

Computational Organic Chemistry: The Frontier for Understanding and Designing Bioorthogonal Cycloadditions

Computational organic chemistry has become a valuable tool in the field of bioorthogonal chemistry, offering insights and aiding in the progression of this branch of chemistry. In this review, I present an overview of computational work in this field, including an exploration of both the primary computational analysis methods used and their application in the main areas of bioorthogonal chemistry: (3 + 2) and [4 + 2] cycloadditions. In the context of (3 + 2) cycloadditions, detailed studies of electronic effects have informed the evolution of cycloalkyne/1,3-dipole cycloadditions. Through computational techniques, researchers have found ways to adjust the electronic structure via hyperconjugation to enhance reactions without compromising stability. For [4 + 2] cycloadditions, methods such as distortion/interaction analysis and energy decomposition analysis have been beneficial, leading to the development of bioorthogonal reactants with improved reactivity and the creation of orthogonal reaction pairs. To conclude, I touch upon the emerging fields of cheminformatics and machine learning, which promise to play a role in future reaction discovery and optimization.

Clicking in harmony: exploring the bio-orthogonal overlap in click chemistry

In the quest to scrutinize and modify biological systems, the global research community has continued to explore bio-orthogonal click reactions, a set of reactions exclusively targeting non-native molecules within biological systems. These methodologies have brought about a paradigm shift, demonstrating the feasibility of artificial chemical reactions occurring on cellular surfaces, in the cell cytosol, or within the body - an accomplishment challenging to achieve with the majority of conventional chemical reactions. This review delves into the principles of bio-orthogonal click chemistry, contrasting metal-catalyzed and metal-free reactions of bio-orthogonal nature. It comprehensively explores mechanistic details and applications, highlighting the versatility and potential of this methodology in diverse scientific contexts, from cell labelling to biosensing and polymer synthesis. Researchers globally continue to advance this powerful tool for precise and selective manipulation of biomolecules in complex biological systems.

Increasing the versatility of the biphenyl-fused-dioxacyclodecyne class of strained alkynes

Biphenyl-fused-dioxacyclodecynes are a promising class of strained alkyne for use in Cu-free 'click' reactions. In this paper, a series of functionalised derivatives of this class of reagent, containing fluorescent groups, are described. Studies aimed at understanding and increasing the reactivity of the alkynes are also presented, together with an investigation of the bioconjugation of the reagents with an azide-labelled protein.

Oxa-azabenzobenzocyclooctynes (O-ABCs): heterobiarylcyclooctynes bearing an endocyclic heteroatom

We report the synthesis of heterobiarylcyclooctynes bearing an endocyclic heteroatom, oxa-azabenzobenzocyclooctynes (O-ABCs). The integration of design strategies for accelerating strain-promoted azide-alkyne cycloadditions results in reactivity with organic azides that surpasses all cyclooctyne reagents reported to date. O-ABCs and related compounds provide insights into the effects of structural modifications on reactivity that can aid in the design of new reagents for click and bioorthogonal chemistry.

Development of Fluorescent Isocoumarin-Fused Oxacyclononyne - 1,2,3-Triazole Pairs

Fluorescent isocoumarin-fused cycloalkynes, which are reactive in SPAAC and give fluorescent triazoles regardless of the azide nature, have been developed. The key structural feature that converts the non-fluorescent cycloalkyne/triazole pair to its fluorescent counterpart is the pi-acceptor group (COOMe, CN) at the C6 position of the isocoumarin ring. The design of the fluorescent cycloalkyne/triazole pairs is based on the theoretical study of the S1 state deactivation mechanism of the non-fluorescent isocoumarin-fused cycloalkyne IC9O using multi-configurational ab initio and DFT methodologies. The calculations revealed that deactivation proceeds through the electrocyclic ring opening of the α-pyrone cycle and is accompanied by a redistribution of electron density in the fused benzene ring. We proposed that the S1 excited state deactivation barrier could be increased by introducing a pi-acceptor group into a position that is in direct conjugation with the formed C=O group and has a reduced electron density in the transition state. As a proof of concept, we designed and synthesized two fluorescent isocoumarin-fused cycloalkynes IC9O-COOMe and IC9O-CN bearing pi-acceptors at the C6 position. The importance of the nature of a pi-acceptor group was shown by the example of much less fluorescent CF3 -substituted cycloalkyne IC9O-CF3 .

Formation of 3-Oxa- and 3-Thiacyclohexyne from Ring Expansion of Heterocyclic Alkylidene Carbenes: A Mechanistic Study

The rearrangement pathways of two alkylidene carbenes appended to an oxa or thiacyclopentane into the corresponding heterocyclohexynes were elucidated using 13C-labeling experiments. Both carbenes exhibited a preference for migration of the allylic carbon bound to the heteroatom. Anomeric interactions involving a heteroatom lone pair and antibonding orbital of the migrating bond and inductive destabilization of the minor migratory pathway are discussed as plausible reasons for the observed trends.

Remote Strain Activation in a Sulfate-Linked Dibenzocycloalkyne

Cycloalkynes and their utilization in cycloaddition reactions enable modular strategies spanning the molecular sciences. Strain─imparted by deviation from linearity─enables sufficient alkyne reactivity without the need for a catalyst (e.g., copper); however, the design and synthesis of stable reagents with suitable reactivity remains an ongoing challenge. We report the incorporation of an endocyclic sulfate within a dibenzocyclononyne scaffold to generate a cyclononyne displaying remarkable reactivity and stability. Through computational analyses, we revealed that the endocyclic sulfate group shares nearly half the total strain energy, providing an activation strategy that reduces alkyne bending. Rehybridization of alkyne carbons in the formation of the heterocyclic product relieves strain both at the reactive site and in the transannular sulfate group. This mode of remote activation enables rapid reactivity while minimizing distortion─and strain─at the reactive site (the alkyne). The result: a design strategy for a new class of cycloalkynes with increased stability and reactivity.

Synthesis of push-pull-activated ynol ethers and their evaluation in the bioorthogonal hydroamination reaction

A new class of push-pull-activated alkynes featuring di- and trifluorinated ynol ethers was synthesized. The difluorinated ynol ether exhibited an optimal balance of stability and reactivity, displaying a substantially improved half-life in the presence of aqueous thiols over the previously reported 1-haloalkyne analogs while reacting just as fast in the hydroamination reaction with N,N-diethylhydroxylamine. The trifluorinated ynol ether reacted significantly faster, exhibiting a second order rate constant of 0.56 M-1 s-1 in methanol, but it proved too unstable toward thiols. These fluorinated ynol ethers further demonstrate the importance of the hyperconjugation-rehybridization effect in activating alkynes and demonstrate how substituent effects can both activate and stabilize alkynes for bioorthogonal reactivity.

M, Zarrintaj P, Formela K, Saeb MR, Bencherif SA. Clickable Polysaccharides for Biomedical Applications: A Comprehensive Review

Recent advances in materials science and engineering highlight the importance of designing sophisticated biomaterials with well-defined architectures and tunable properties for emerging biomedical applications. Click chemistry, a powerful method allowing specific and controllable bioorthogonal reactions, has revolutionized our ability to make complex molecular structures with a high level of specificity, selectivity, and yield under mild conditions. These features combined with minimal byproduct formation have enabled the design of a wide range of macromolecular architectures from quick and versatile click reactions. Furthermore, copper-free click chemistry has resulted in a change of paradigm, allowing researchers to perform highly selective chemical reactions in biological environments to further understand the structure and function of cells. In living systems, introducing clickable groups into biomolecules such as polysaccharides (PSA) has been explored as a general approach to conduct medicinal chemistry and potentially help solve healthcare needs. De novo biosynthetic pathways for chemical synthesis have also been exploited and optimized to perform PSA-based bioconjugation inside living cells without interfering with their native processes or functions. This strategy obviates the need for laborious and costly chemical reactions which normally require extensive and time-consuming purification steps. Using these approaches, various PSA-based macromolecules have been manufactured as building blocks for the design of novel biomaterials. Clickable PSA provides a powerful and versatile toolbox for biomaterials scientists and will increasingly play a crucial role in the biomedical field. Specifically, bioclick reactions with PSA have been leveraged for the design of advanced drug delivery systems and minimally invasive injectable hydrogels. In this review article, we have outlined the key aspects and breadth of PSA-derived bioclick reactions as a powerful and versatile toolbox to design advanced polymeric biomaterials for biomedical applications such as molecular imaging, drug delivery, and tissue engineering. Additionally, we have also discussed the past achievements, present developments, and recent trends of clickable PSA-based biomaterials such as 3D printing, as well as their challenges, clinical translatability, and future perspectives.

Synthesis, Characterization and Reactivity of a σ-Donating Ni0 -Stabilized Silyliumylidene Ion

The synthesis of a silyliumylidene cation complex 2 stabilized by a Ni0 -based donating ligand is reported. Experimental and theoretical studies demonstrate that the highly electrophilic SiII center is stabilized by a dative Ni→Si σ-interaction and π-donations from the amino- and Ni-moieties. Due to the energetically close frontier orbitals localized on the Si and Ni atoms, complex 2 presents a competitive reactivity at Si and Ni sites.

A Swiss Army knife for surface chemistry

Voltage pulses offer a way to control single-molecule reactions on a surface

Synthesis of Endocyclic Cycloalkyne Amino Acids

"Click-ligation" is a widely adopted and valuable means to ligate biomolecules whereby two appended biologically inert moieties, such as alkynes and azides, link by cycloaddition. For terminal alkynes, Cu⁺¹ catalysis is required which degrades oligonucleotides by catalyzing their hydrolysis but is also physiologically incompatible. The smallest activated alkynes that do not require Cu⁺¹ catalysis are cyclooctynes or dibenzo-cyclooctynes. For this purpose, there are commercially available nucleosides and amino acids that are appended to these moieties. However, these structures are bulky, dissimilar to native amino acids, and when incorporated within biological molecules could likely perturb native structural configuration. Presented are the syntheses of structural analogues of proline with an inserted propargyl moiety within a series of ring sizes. Moreover, a synthetic pathway to medium-size ring heterocycloalkynes mediated by using mild Mitsunobu conditions in tandem with a Nicholas-related strategy for cyclization is introduced. Avoiding the usual harsh acidic conditions for the Nicholas reaction allows improved functional group compatibility.

SuFExable NH-Pyrazoles via 1,3-Dipolar Cycloadditions of Diazo Compounds with Bromoethenylsulfonyl Fluoride

"Click" reactions have transformed the molecular sciences. Augmenting cycloaddition reactions, sulfur(VI) fluoride exchange (SuFEx) chemistry has diversified the landscape of molecular assembly. Herein, we report a facile strategy to access SuFExable NH-pyrazoles via strain and catalyst-free 1,3-dipolar cycloadditions of stabilized diazo compounds under mild conditions. Subsequent SuFEx proceeds efficiently with various N- and O-nucleophiles. Access to SuFExable NH-pyrazoles─a class of compounds containing two common pharmacophores─enables future opportunities within drug discovery, chemical biology, materials chemistry, and related fields.

Detection of Ylide Formation between an Alkylidenecarbene and Acetonitrile by Femtosecond Transient Absorption Spectroscopy

Femtosecond laser flash photolysis of 3-(1a,9b-dihydro-1H-cyclopropa[l]phenanthren-1-ylidene)tetrahydrofuran produces singlet 3-oxacyclopentylidenecarbene which reacts with acetonitrile solvent to form an ylide. This is the first direct detection of ylide formation by an alkylidenecarbene. This new type of ylide was observed to have a broad absorption band in the visible region with λ_max ∼450 nm and a lifetime of ∼13.5 ps. As with other "conventional" carbenes (the divalent carbon atom is separately bound to two substituents), this ylide formation method could be also useful for detecting alkylidenecarbenes, especially those that do not absorb at wavelengths suitable for direct observation. Furthermore, the mechanisms by which 3-oxacyclopentylidenecarbene forms the ylide and the overall favorability of ylide formation, vis-à-vis ring expansion of the carbene to strained 3-oxacyclohexyne, were supported by results from density functional theory calculations.

Heterocycloalkynes Fused to a Heterocyclic Core: Searching for an Island with Optimal Stability-Reactivity Balance

In the search for fundamentally new, active, stable, and readily synthetically accessible cycloalkynes as strain-promoted azide-alkyne cycloaddition (SPAAC) reagents for bioorthogonal bioconjugation, we integrated two common approaches: the reagent destabilization by the increase of a ring strain and the transition state stabilization through electronic effects. As a result new SPAAC reagents, heterocyclononynes fused to a heterocyclic core, were created. These compounds can be obtained through a general synthetic route based on four crucial steps: the electrophile-promoted cyclization, Sonogashira coupling, Nicholas reaction, and final deprotection of Co-complexes of cycloalkynes from cobalt. Varying the natures of the heterocycle and heteroatom allows for reaching the optimal stability-reactivity balance for new strained systems. Computational and experimental studies revealed similar SPAAC reactivities for stable 9-membered isocoumarin- and benzothiophene-fused heterocycloalkynes and their unstable 8-membered homologues. We discovered that close reactivity is a result of the interplay of two electronic effects, which stabilize SPAAC transition states (πin* → σ* and π* → πin*) with structural effects such as conformational changes from eclipsed to staggered conformations in the cycloalkyne scaffold, that noticeably impact alkyne bending and reactivity. The concerted influence of a heterocycle and a heteroatom on the polarization of a triple bond in highly strained cycles along with a low HOMO-LUMO gap was assumed to be the reason for the unpredictable kinetic instability of all the cyclooctynes and the benzothiophene-fused oxacyclononyne. The applicability of stable isocoumarin-fused azacyclononyne IC9N-BDP-FL for in vitro bioconjugation was exemplified by labeling and visualization of HEK293 cells carrying azido-DNA and azido-glycans.

Acceleration of 1,3-Dipolar Cycloadditions by Integration of Strain and Electronic Tuning

The 1,3-dipolar cycloaddition between azides and alkynes provides new means to probe and control biological processes. A major challenge is to achieve high reaction rates with stable reagents. The optimization of alkynyl reagents has relied on two strategies: increasing strain and tuning electronics. We report on the integration of these strategies. A computational analysis suggested that a CH → N aryl substitution in dibenzocyclooctyne (DIBO) could be beneficial. In transition states, the nitrogen of 2-azabenzo-benzocyclooctyne (ABC) engages in an n→π* interaction with the C=O of α-azidoacetamides and forms a hydrogen bond with the N-H of α-diazoacetamides. These dipole-specific interactions act cooperatively with electronic activation of the strained π-bond to increase reactivity. We found that ABC does indeed react more quickly with α-azidoacetamides and α-diazoacetamides than its constitutional isomer, dibenzoazacyclooctyne (DIBAC). ABC and DIBAC have comparable chemical stability in a biomimetic solution. Both ABC and DIBO are accessible in three steps by the alkylidene carbene-mediated ring expansion of commercial cycloheptanones. Our findings enhance the accessibility and utility of 1,3-dipolar cycloadditions and encourage further innovation.

Click Chemistry with Cyclopentadiene

Cyclopentadiene is one of the most reactive dienes in normal electron-demand Diels-Alder reactions. The high reactivities and yields of cyclopentadiene cycloadditions make them ideal as click reactions. In this review, we discuss the history of the cyclopentadiene cycloaddition as well as applications of cyclopentadiene click reactions. Our emphasis is on experimental and theoretical studies on the reactivity and stability of cyclopentadiene and cyclopentadiene derivatives.

Sterically hindering the trajectory of nucleophilic attack towards p-benzynes by a properly oriented hydrogen atom: an approach to achieve regioselectivity

Nucleophilic addition to p-benzynes derived via Bergman cyclization has become a topic of keen interest. Studying the regioselectivity in such addition can reveal important information regarding the parameters controlling such addition. Recently, high regioselectivity has been achieved in nucleophilic addition to a p-benzyne derived from an ortho substituted benzo fused cyclic azaenediyne. Rather than having a freely rotating substitution, a rigid hydrogen atom coming from a suitable naptho fused enediyne and residing in the plane of the p-benzyne ring can offer hindrance to the trajectory of the nucleophile. This can lead to regioselectivity provided the other side remains relatively free of such hindrance. Based on that approach, halide addition to p-benzynes derived from naphtho fused cyclic azaenediynes was studied and a high level of regioselectivity was observed. Steric hindrance to the trajectory of nucleophile by the bay hydrogen was found to be the main cause of such regioselectivity; however, differential electrostatic potential as well as distortions at reactive centres have a minor role in controlling the regioselectivity. The products of such high yielding addition are the halo naphtho tetrahydroisoquinolines.

Nitrone and Alkyne Cascade Reactions for Regio- and Diastereoselective 1-Pyrroline Synthesis

The synthesis of 1-pyrrolines from N-alkenylnitrones and alkynes has been explored as a retrosynthetic alternative to traditional approaches. These cascade reactions are formal [4+1] cycloadditions that proceed through a proposed dipolar cycloaddition and N-alkenylisoxazoline [3,3']-sigmatropic rearrangement. A variety of cyclic alkynes and terminal alkynes have been shown to undergo the transformation with N-alkenylnitrones under mild conditions to provide the corresponding spirocyclic and densely substituted 1-pyrrolines with high regio- and diastereoselectivity. Mechanistic studies provide insight into the balance of steric and electronic effects that promote the cascade process and control the diastereo- and regioisomeric preferences of the 1-pyrroline products. Diastereoselective derivatization of the 1-pyrrolines prepared by the cascade reaction demonstrate the divergent synthetic utility of the new method.

Marriage of Peroxides and Nitrogen Heterocycles: Selective Three-Component Assembly, Peroxide-Preserving Rearrangement, and Stereoelectronic Source of Unusual Stability of Bridged Azaozonides

Stable bridged azaozonides can be selectively assembled via a catalyst-free three-component condensation of 1,5-diketones, hydrogen peroxide, and an NH-group source such as aqueous ammonia or ammonium salts. This procedure is scalable and can produce gram quantities of bicyclic stereochemically rich heterocycles. The new azaozonides are thermally stable and can be stored at room temperature for several months without decomposition and for at least 1 year at -10 °C. The chemical stability of azaozonides was explored for their subsequent selective transformations including the first example of an aminoperoxide rearrangement that preserves the peroxide group. The amino group in aminoperoxides has remarkably low nucleophilicity and does not participate in the usual amine alkylation and acylation reactions. These observations and the 15 pK_a units decrease in basicity in comparison with a typical dialkyl amine are attributed to the strong hyperconjugative n_N→σ*_C-O interaction with the two antiperiplanar C-O bonds. Due to the weakness of the complementary n_O→σ*_C-N donation from the peroxide oxygens (a consequence of "inverse α-effect"), this interaction depletes electron density from the NH moiety, protects it from oxidation, and makes it similar in properties to an amide.

Cycloaddition of Strained Cyclic Alkenes and Ortho-Quinones: A Distortion/Interaction Analysis

The chemistry of strained unsaturated cyclic compounds has experienced remarkable growth in recent years via the development of metal–free click reactions. Among these reactions, the cycloaddition of cyclopropenes and their analogues to ortho-quinones has been established as a highly promising click reaction. The present work investigates the mechanism involved in the cycloaddition of strained dienes to ortho-quinones and structural factors that would influence this reaction. For this purpose, we use B97D density functional theory calculations throughout, and for relevant cases, we use spin component–scaled MP2 calculations and single–point domain-based local pair natural orbital coupled cluster (DLPNO-CCSD(T)) calculations. The outcomes are analyzed in detail using the distortion/interaction model, and suggestions for future experimental work are made.

Recent developments in bioorthogonal chemistry and the orthogonality within

The emergence of bioorthogonal reactions has greatly advanced research in the fields of biology and medicine. They are not only valuable for labeling, tracking, and understanding biomolecules within living organisms, but also important for constructing advanced bioengineering and drug delivery systems. As the systems studied are increasingly complex, the simultaneous use of multiple bioorthogonal reactions is equally desirable. In this review, we take a look at the different bioorthogonal reactions that have recently been developed, the methods of cellular incorporation and the strategies to create orthogonality within the bioorthogonal landscape.

The effect of solvation in torquoselectivity: ring opening of monosubstituted cyclobutenes

The paradigmatic electrocyclic ring opening of monosubstituted cyclobutenes has been used to diagnose possible solvation effects tuning the torquoselectivity observed in these reactions. This kind of selectivity in electrocyclic reactions is mostly due to strong orbital interactions, particularly when they involve powerful electron donors and acceptors, which also combine with usually milder steric effects. Orbital interactions are established between the cleaving C-C bond and the HOMO/LUMO of the EDG/EWG substituent. This implies that the larger torquoselectivity-featuring substrates may also suffer stronger solvation effects due to the higher polarity imposed by the substituent. This premise is tested and the source of solvation effects as a consequence of substitution analyzed.

Globally stabilized bent carbon-carbon triple bond by hydrogen-free inorganic-metallic scaffolding Al4F6

For over 100 years, known bent C[triple bond, length as m-dash]C compounds have been limited to those with organic (I) and all-carbon (II) scaffoldings. Here, we computationally report a novel type (III) of bent C[triple bond, length as m-dash]C compound, i.e., C2Al4F6-01, which is the energetically global minimum isomer and bears an inorganic-metallic scaffolding and unexpected click reactivity.

Intramolecular Nicholas Reactions in the Synthesis of Heteroenediynes Fused to Indole, Triazole, and Isocoumarin

The applicability of an intramolecular Nicholas reaction for the preparation of 10-membered O- and N-enediynes fused to indole, 1,2,3-triazole, and isocoumarin was investigated. The general approach to acyclic enediyne precursors fused to heterocycles includes inter- and intramolecular buta-1,3-diyne cyclizations with the formation of iodoethynylheterocycles, followed by Sonogashira coupling. The nature of both a heterocycle and a nucleophilic group affects the possibility of a 10-membered ring closure by the Nicholas reaction. Among oxacycles, an isocoumarin-fused enediyne was obtained. In the case of O-enediyne annulated with indole, instead of the formation of a 10-membered cycle, BF₃-promoted addition of an OH-group to the proximal triple bond at the C3 position afforded dihydrofuryl-substituted indole. For 1,2,3-triazole-fused analogues, using NH-Ts as a nucleophilic functional group allowed obtaining 10-membered azaenediyne, while the substrate with a hydroxyl group gave only traces of the desired 10-membered oxacycle. An improved method for the deprotection of Co-complexes of cyclic enediynes using tetrabutylammonium fluoride in an acetone/water mixture and the investigation of the 10-membered enediynes' reactivity in the Bergman cyclization are also reported. In the solid state, all synthesized iodoethynylheterocycles were found to be involved in halogen bond (XB) formation with either O or N atoms as XB acceptors.

Unravelling the strain-promoted [3+2] cycloaddition reactions of phenyl azide with cycloalkynes from the molecular electron density theory perspective

The increase of the strain not only increases the reaction rate and the exothermic character of these reactions, but also changes the mechanism for the small cycloalkynes from a non-polar to a polar reaction.

A.E.Favorskii’s scientific legacy in modern organic chemistry: prototropic acetylene – allene isomerization and the acetylene zipper reaction

Alexei Evgrafovich Favorskii was an outstanding organic chemist who left a great scientific legacy as a result of long time and fruitful work. Most of the theoretically and practically important discoveries of A.E.Favorskii were made in the chemistry of acetylene and its derivatives. Nowadays, the reactions discovered by him, which include acetylene – allene isomerization, the Favorskii and retro-Favorskii reactions, the Favorskii rearrangement and the vinylation reaction, are widely used in industry and in laboratory synthesis. This review summarizes the main scientific achievements of A.E.Favorskii, as well as their development in modern organic chemistry. Much consideration is given to acetylene – allene isomerization as a convenient method for the synthesis of methyl-substituted acetylenes and to the acetylene zipper reaction as a synthetic tool for obtaining terminal acetylenes. The review presents examples of the application of these reactions in modern organic synthesis of complex molecules, including natural compounds and their analogues.

The bibliography includes 266 references.

A strained alkyne-containing bipyridine reagent; synthesis, reactivity and fluorescence properties

We report the synthesis of a bipyridyl reagent containing a strained alkyne, which significantly restricts its flexibility. Upon strain-promoted alkyne-azide cycloaddition (SPAAC) with an azide, which does not require a Cu catalyst, the structure becomes significantly more flexible and an increase in fluorescence is observed. Upon addition of Zn(ii), the fluorescence is enhanced further. The reagent has the potential to act as a fluorescent labelling agent with azide-containing substrates, including biological molecules.

A bipyridyl reagent containing a strained alkyne 7, reacts with benzyl azide to give a significantly more flexible product 10 and an increase in fluorescence is observed. Upon addition of Zn(ii), the fluorescence is enhanced further.