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

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.

How cycloalkane fusion enhances the cycloaddition reactivity of dibenzocyclooctynes

Dibenzoannulated cyclooctynes have emerged as valuable compounds for bioorthogonal reactions. They are commonly used in combination with azides in strain-promoted 1,3-dipolar cycloadditions. They are typically, however, unreactive towards 3,6-disubstituted tetrazines in inverse electron-demand Diels-Alder cycloadditions. Recently a dibenzoannulated bicyclo[6.1.0]nonyne derivative (DMBO) with a cyclopropane fused to the cyclooctyne core was described, which showed surprising reactivity towards tetrazines. To elucidate the unusual reactivity of DMBO, we performed density functional theory calculations and revealed that a tub-like structure in the transition state results in a much lower activation barrier than in the absence of cyclopropane fusion. The same transition state geometry is found for different cycloalkanes fused to the cyclooctyne core albeit higher activation barriers are observed for increased ring sizes. This conformation is energetically unfavored for previously known dibenzoannulated cyclooctynes and allows tetrazines and azides to approach DMBO from the face rather than the edge, a trajectory that was hitherto not observed for this class of activated dieno- and dipolarophiles.

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.

Introducing Azomethine Imines to Chemical Biology: Bioorthogonal Reaction with Isonitriles

Azomethine imines are valuable substrates for chemical synthesis in organic solvents that often require anhydrous conditions. Here, we introduce C,N-cyclic-N'-acyl azomethine imines (AMIs) to bioorthogonal reactions in an aqueous environment. These AMIs are stable under physiological conditions and react rapidly (k2 = 0.1-250 M-1 s-1, depending on pH) and chemoselectively with isonitriles in the presence of biological nucleophiles, including thiols. Live-cell imaging of cell-surface-bound isonitriles underlines the biocompatibility of the AMI-isonitrile ligation, and simultaneous one-pot triple-protein labeling demonstrates its orthogonality to commonly used bioorthogonal reactions, such as the SPAAC and iEDDA ligations.

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 .

Synthesis of Functionalized Dibenzoazacyclooctynes by a Decomplexation Method for Dibenzo-Fused Cyclooctyne-Cobalt Complexes

A concise route for dibenzoazacyclooctynes (DIBACs) synthesis was developed based on Pictet-Spengler reaction and a novel cobalt decomplexation method established for dibenzo-fused cyclooctyne-cobalt complexes. The method allowed for the facile preparation of functionalized DIBACs, including bisDIBAC, which served as an efficient bisreactive linker for protein modification via the double-click reaction.

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.

The 1,3-Dipolar Cycloaddition From Conception to Quantum Chemical Design

The 1,3‐dipolar cycloaddition (1,3‐DCA) reaction, conceptualized by Rolf Huisgen in 1960, has proven immensely useful in organic, material, and biological chemistry. The uncatalyzed, thermal transformation is generally sluggish and unselective, but the reactivity can be enhanced by means of metal catalysis or by the introduction of either predistortion or electronic tuning of the dipolarophile. These promoted reactions generally go with a much higher reactivity, selectivity, and yields, often at ambient temperatures. The rapid orthogonal reactivity and compatibility with aqueous and physiological conditions positions the 1,3‐DCA as an excellent bioorthogonal reaction. Quantum chemical calculations have been critical for providing an understanding of the physical factors that control the reactivity and selectivity of 1,3‐DCAs. In silico derived design principles have proven invaluable for the design of new dipolarophiles with tailored reactivity. This review discusses everything from the conception of the 1,3‐DCA all the way to the state‐of‐the‐art methods and models used for the quantum chemical design of novel (bioorthogonal) reagents.

Photoactivatable Fluorogenic Azide-Alkyne Click Reaction: A Dual-Activation Fluorescent Probe

Aryl azide and diaryl tetrazole are both photoactive molecules, which can form nitrene and nitrile imine intermediates respectively by photolysis. Depending on the new finding that the azide can suppress the photolysis of tetrazole in the azide-tetrazole conjugated system, we developed aryl azide-tetrazole probes for the photoactivatable fluorogenic azide alkyne click (PFAAC) reaction, in which the aryl azide-tetrazole probes were not phoroactivatable fluorogenic itself, but the triazole products after click reaction were prefluorophore that can be activated by light. Therefore, in PFAAC chemistry, the fluorescent probes can be activated by two orthogonal events: azide-alkyne click reaction and light, which leads to spatiotemporal resolution and high signal-to-noise ratio. This PFAAC process was proved in vitro by copper catalyzed or strain-promoted azide-alkyne reactions and in live cells by spatiotemporally controlled organelle imaging. By incorporation a linker to the azide-tetrazole conjugate, this PFAAC chemistry could covalently label extra probes to the biomolecules and spatiotemporally detecting this process by photoinduced fluorescence.

Uncovering the Key Role of Distortion in Bioorthogonal Tetrazine Tools That Defy the Reactivity/Stability Trade-Off

The tetrazine/trans-cyclooctene ligation stands out from the bioorthogonal toolbox due to its exceptional reaction kinetics, enabling multiple molecular technologies in vitro and in living systems. Highly reactive 2-pyridyl-substituted tetrazines have become state of the art for time-critical processes and selective reactions at very low concentrations. It is widely accepted that the enhanced reactivity of these chemical tools is attributed to the electron-withdrawing effect of the heteroaryl substituent. In contrast, we show that the observed reaction rates are way too high to be explained on this basis. Computational investigation of this phenomenon revealed that distortion of the tetrazine caused by intramolecular repulsive N–N interaction plays a key role in accelerating the cycloaddition step. We show that the limited stability of tetrazines in biological media strongly correlates with the electron-withdrawing effect of the substituent, while intramolecular repulsion increases the reactivity without reducing the stability. These fundamental insights reveal thus far overlooked mechanistic aspects that govern the reactivity/stability trade-off for tetrazines in physiologically relevant environments, thereby providing a new strategy that may facilitate the rational design of these bioorthogonal tools.

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.

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 (π_in* → σ* and π* → π_in*) 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.

Taming the reactivity of alkyl azides by intramolecular hydrogen bonding: site-selective conjugation of unhindered diazides

The intramolecular hydrogen bonding in the α-azido secondary acetamides (α-AzSAs) enabled site-selective integration onto the diazide modular hubs even without steric hindrance.