Influence of Endo- and Exocyclic Heteroatoms on Stabilities and 1,3-Dipolar Cycloaddition Reactivities of Mesoionic Azomethine Ylides and Imines

Bioorthogonal Delivery of Carbon Disulfide in Living Cells

Carbon disulfide (CS2) is an environmental contaminant, which is deadly hazardous to the workers under chronic or acute exposure. However, the toxicity mechanisms of CS2 are still unclear due to the scarcity of biocompatible donors, which can release CS2 in cells. Here we developed the first bioorthogonal CS2 delivery system based on the "click-and-release" reactions between mesoionic 1,3-thiazolium-5-thiolates (TATs) and strained cyclooctyne exo-BCN-OH. We successfully realized intracellular CS2 release and investigated the causes of CS2-induced hepatotoxicity, including oxidative stress, proteotoxic stress and copper-dependent cell death. It is found that CS2 can be copper vehicles bypassing copper transporters after reacting with nucleophiles in cytoplasm, and extra copper supplementation will exacerbate the loss of homeostasis of cells and ultimately cell death. These findings inspired us to explore the anticancer activity of CS2 in combination with copper by introducing a copper chelating group in our CS2 delivery system.

Pyridinium-Derived Mesoionic N-Heterocyclic Olefins (py-mNHOs)

Mesoionic polarization allows access to electron-rich olefins that have found application as organocatalysts, ligands, or nucleophiles. Herein, we report the synthesis and characterization of a series of 3-methylpyridinium-derived mesoionic olefins (py-mNHOs). We used a DFT-supported design concept, which showed that the introduction of aryl groups in the 1-, 2-, 4-, and 6-positions of the heterocyclic core allowed the kinetic stabilization of the novel mesoionic compounds. Tolman electronic parameters indicate that py-mNHOs are remarkably strong σ-donor ligands toward transition metals and main group Lewis acids. Additionally, they are among the strongest nucleophiles on the Mayr reactivity scale. In reactions of py-mNHOs with electron-poor π-systems, a gradual transition from the formation of zwitterionic adducts via stepwise to concerted 1,3-dipolar cycloadditions was observed experimentally and analyzed by quantum-chemical calculations.

Fast and Bioorthogonal Release of Isocyanates in Living Cells from Iminosydnones and Cycloalkynes

Bioorthogonal click-and-release reactions are powerful tools for chemical biology, allowing, for example, the selective release of drugs in biological media, including inside animals. Here, we developed two new families of iminosydnone mesoionic reactants that allow a bioorthogonal release of electrophilic species under physiological conditions. Their synthesis and reactivities as dipoles in cycloaddition reactions with strained alkynes have been studied in detail. Whereas the impact of the pH on the reaction kinetics was demonstrated experimentally, theoretical calculations suggest that the newly designed dipoles display reduced resonance stabilization energies compared to previously described iminosydnones, explaining their higher reactivity. These mesoionic compounds react smoothly with cycloalkynes under physiological, copper-free reaction conditions to form a click pyrazole product together with a released alkyl- or aryl-isocyanate. With rate constants up to 1000 M^-1 s^-1, this click-and-release reaction is among the fastest described to date and represents the first bioorthogonal process allowing the release of isocyanate electrophiles inside living cells, offering interesting perspectives in chemical biology.

1,3 Dipolar Cycloaddition of Münchnones: Factors behind the Regioselectivity

The 1,3 dipolar cycloaddition reactions of münchnones and alkenes provide an expedite synthetic way to substituted pyrroles, an exceedingly important structural motif in the pharmaceutical and material science fields of research. The factors governing their regioselectivity rationalization are not well understood. Using several approaches, we investigate a set of 14 reactions (featuring two münchnones, 12 different alkenes, and two alkynes). The Natural Bond Theory and the Non-Covalent Interaction Index analyses of the noncovalent interaction energies fail to predict the experimental major regioisomer. Employing global cDFT descriptors or local ones such as the Fukui function and dual descriptor yields similarly inaccurate predictions. Only the local softness pairing, within Pearson's Hard and Soft Acids and Bases principle, constitutes a reliable predictor for the major reaction product. By taking into account an estimator for the steric effects, the correct regioisomer is predicted. Steric effects play a major role in driving the regioselectivity, as was corroborated by energy decomposition analysis of the transition states.

Switchable Cycloadditions of Mesoionic Dipoles: Refreshing up a Regioselective Approach to Two Distinctive Heterocycles

Mesoionic rings are among the most versatile 1,3-dipoles, as witnessed recently by their incorporation into bio-orthogonal strategies, and capable of affording unconventional heterocycles beyond the expected scope of Huisgen cycloadditions. Herein, we revisit in detail the reactivity of thiazol-3-ium-4-olates with alkynes, leading to thiophene and/or pyrid-2-one derivatives. A structural variation at the parent mesoionic dipole alters sufficiently the steric outcome, thereby favoring the regioselective formation of a single transient cycloadduct, which undergoes chemoselective fragmentation to either five- or six-membered heterocycles. The synthetic protocol benefits largely from microwave (MW) activation, which enhances reaction rates. The mechanism has been interrogated with the aid of density functional theory (DFT) calculations, which sheds light into the origin of the regioselectivity and points to a predictive formulation of reactivity involving competing pathways of mesoionic cycloadditions.

Mesoionic Imines (MIIs): Strong Donors and Versatile Ligands for Transition Metals and Main Group Substrates

We report the synthesis and the reactivity of 1,2,3‐triazolin‐5‐imine type mesoionic imines (MIIs). The MIIs are accessible by a base‐mediated cycloaddition between a substituted acetonitrile and an aromatic azide, methylation by established routes and subsequent deprotonation. C=O‐stretching frequencies in MII−CO₂ and −Rh(CO)₂Cl complexes were used to determine the overall donor strength. The MIIs are stronger donors than the N‐heterocyclic imines (NHIs). MIIs are excellent ligands for main group elements and transition metals in which they display substituent‐induced fluorine‐specific interactions and undergo C−H activation. DFT calculations gave insights into the frontier orbitals of the MIIs. The calculations predict a relatively small HOMO–LUMO gap compared to other related ligands. MIIs are potentially able to act as both π‐donor and π‐acceptor ligands. This report highlights the potential of MIIs to display exciting properties with a huge potential for future development.

Multicomponent formation route to a new class of oxygen-based 1,3-dipoles and the modular synthesis of furans

A new class of phosphorus-containing 1,3-dipoles can be generated by the multicomponent reaction of aldehydes, acid chlorides and the phosphonite PhP(catechyl). These 1,3-dipoles are formally cyclic tautomers of simple Wittig-type ylides, where the angle strain and moderate nucleophilicity in the catechyl-phosphonite favor their cyclization and also direct 1,3-dipolar cycloaddition to afford single regioisomers of substituted products. Coupling the generation of the dipoles with 1,3-dipolar cycloaddition offers a unique, modular route to furans from combinations of available aldehydes, acid chlorides and alkynes with independent control of all four substituents.

Heterohelicenes through 1,3-Dipolar Cycloaddition of Sydnones with Arynes: Synthesis, Origins of Selectivity, and Application to pH-Triggered Chiroptical Switch with CPL Sign Reversal

Regioselective access to heterohelicenes through the 1,3-dipolar cycloaddition of sydnones with arynes is described. Novel access to sydnones and poly(hetero)aromatic aryne precursors allowed the introduction of chemical diversity over multiple positions of the helical scaffolds. The origins of the unconventional regioselectivity during the cycloaddition steps was systematically investigated using density functional theory (DFT) calculations, unveiling the key features that control this reactivity, namely, face-to-face (π···π) or edge-to-face (C-H···π) interactions, primary orbital interactions and distortion from coplanarity in the transition structures (TSs) of the transformation. From the library of 24 derivatives synthesized, a pyridyl containing derivative displayed reversible, red-shifted, pH-triggered chiroptical switching properties, with CPL-sign reversal. It is found that protonation of the helicene causes a change of the angle between the electric and magnetic dipole moments related to the S₁ → S₀ transition, resulting in this rare case of reversible CPL sign inversion upon application of an external stimulus.

Click and Bio-Orthogonal Reactions with Mesoionic Compounds

Click and bio-orthogonal reactions are dominated by cycloaddition reactions in general and 1,3-dipolar cycloadditions in particular. Among the dipoles routinely used for click chemistry, azides, nitrones, isonitriles, and nitrile oxides are the most popular. This review is focused on the emerging click chemistry that uses mesoionic compounds as dipole partners. Mesoionics are a very old family of molecules, but their use as reactants for click and bio-orthogonal chemistry is quite recent. The facility to derivatize these dipoles and to tune their reactivity toward cycloaddition reactions makes mesoionics an attractive opportunity for future click chemistry development. In addition, some compounds from this family are able to undergo click-and-release reactions, finding interesting applications in cells, as well as in animals. This review covers the synthetic access to main mesoionics, their reaction with dipolarophiles, and recent applications in chemical biology and heterocycle synthesis.

Diradicalar Character and Ring Stability of Mesoionic Heterocyclic Oxazoles and Thiazoles by Ab Initio Mono and Multi-Reference Methods

Mesoionics are neutral compounds that cannot be represented by a fully covalent or purely ionic structure. Among the possible mesomeric structures of these compounds are the diradical electronic configurations. Theoretical and experimental studies indicate that some mesoionic rings are unstable, which may be related to a significant diradical character, that until then is not quantified. In this work, we investigated the diradical character of four heterocycles: 1,3-oxazol-5-one, 1,3-oxazol-5-thione, 1,3-thiazole-5-one, and 1,3-thiazole-5-thione. The oxazoles are known to be significatively less stable than thiazoles. DFT and ab initio single (B3LYP, MP2, CCSD, and QCISD) and ab initio multi-reference (MR-CISD) methods with three basis sets (6-311+G(d), aug-cc-pVDZ, and aug-cc-pVTZ) were employed to assess the diradical character of the investigated systems, in gas phase and DMSO solvent, from three criteria: (i) HOMO-LUMO energy gap, (ii) determination of energy difference between singlet and triplet wave functions, and (iii) quantification of the most significant diradical character (y₀, determined in the unrestricted formalism). All of the results showed that the diradical character of the investigated systems is very small. However, the calculated electronic structures made it possible to identify the possible origin of the oxazoles instability, which can help the design of mesoionic systems with the desired properties.

Understanding chemical reactivity using the activation strain model

Understanding chemical reactivity through the use of state-of-the-art computational techniques enables chemists to both predict reactivity and rationally design novel reactions. This protocol aims to provide chemists with the tools to implement a powerful and robust method for analyzing and understanding any chemical reaction using PyFrag 2019. The approach is based on the so-called activation strain model (ASM) of reactivity, which relates the relative energy of a molecular system to the sum of the energies required to distort the reactants into the geometries required to react plus the strength of their mutual interactions. Other available methods analyze only a stationary point on the potential energy surface, but our methodology analyzes the change in energy along a reaction coordinate. The use of this methodology has been proven to be critical to the understanding of reactions, spanning the realms of the inorganic and organic, as well as the supramolecular and biochemical, fields. This protocol provides step-by-step instructions-starting from the optimization of the stationary points and extending through calculation of the potential energy surface and analysis of the trend-decisive energy terms-that can serve as a guide for carrying out the analysis of any given reaction of interest within hours to days, depending on the size of the molecular system.

PyFrag 2019-Automating the exploration and analysis of reaction mechanisms

We present a substantial update to the PyFrag 2008 program, which was originally designed to perform a fragment-based activation strain analysis along a provided potential energy surface. The original PyFrag 2008 workflow facilitated the characterization of reaction mechanisms in terms of the intrinsic properties, such as strain and interaction, of the reactants. The new PyFrag 2019 program has automated and reduced the time-consuming and laborious task of setting up, running, analyzing, and visualizing computational data from reaction mechanism studies to a single job. PyFrag 2019 resolves three main challenges associated with the automated computational exploration of reaction mechanisms: it (1) computes the reaction path by carrying out multiple parallel calculations using initial coordinates provided by the user; (2) monitors the entire workflow process; and (3) tabulates and visualizes the final data in a clear way. The activation strain and canonical energy decomposition results that are generated relate the characteristics of the reaction profile in terms of intrinsic properties (strain, interaction, orbital overlaps, orbital energies, populations) of the reactant species. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.

Factors Controlling the Diels-Alder Reactivity of Hetero-1,3-Butadienes

We have quantum chemically explored the Diels-Alder reactivities of a systematic series of hetero-1,3-butadienes with ethylene by using density functional theory at the BP86/TZ2P level. Activation strain analyses provided physical insight into the factors controlling the relative cycloaddition reactivity of aza- and oxa-1,3-butadienes. We find that dienes with a terminal heteroatom, such as 2-propen-1-imine (NCCC) or acrolein (OCCC), are less reactive than the archetypal 1,3-butadiene (CCCC), primarily owing to weaker orbital interactions between the more electronegative heteroatoms with ethylene. Thus, the addition of a second heteroatom at the other terminal position (NCCN and OCCO) further reduces the reactivity. However, the introduction of a nitrogen atom in the backbone (CNCC) leads to enhanced reactivity, owing to less Pauli repulsion resulting from polarization of the diene HOMO in CNCC towards the nitrogen atom and away from the terminal carbon atom. The Diels-Alder reactions of ethenyl-diazene (NNCC) and 1,3-diaza-butadiene (NCNC), which contain heteroatoms at both the terminal and backbone positions, are much more reactive due to less activation strain compared to CCCC.

Origins of halogen effects in bioorthogonal sydnone cycloadditions

Halogen substituents increase sydnone cycloaddition reactivities substantially. Fluoro-sydnones are superior to bromo- and chloro-sydnones, and can achieve extremely high second-order rate constants with strained alkynes. Computational studies have revealed the fluorine substituent increases the reactivity of sydnone mainly by lowering its distortion energy.

Computational Screening of New Orthogonal Metal-Free Dipolar Cycloadditions of Mesomeric Betaines

Computational strategies have gained increasing impact in the de novo design of large molecular sets targeted to a desired application. Herein, DFT-assisted theoretical analyses of cycloadditions, involving mesoionic dipoles and strained cycloalkynes, unveil a series of unexplored mesomeric betaines as vastly superior candidates for orthogonal applications. Thus, isosydnones; thiosydnones; and a six-membered homolog, 6-oxo-1,3-oxazinium-4-olate, exhibit enhanced reactivity with respect to sydnone, which is the archetypal mesoionic ring employed so far in orthogonal chemistry. These compounds were found by assessing energy barriers and transition structures, which are largely governed by electron fluxes from dipolarophile to dipole and noncovalent interactions. Charge-transfer analysis also accounts for previous experimental and theoretical results gathered in the literature, and provides a rationale for further substitution variations. The above naked dipoles release only CO₂ as a byproduct through retro-Diels-Alder of the resulting cycloadducts. These results should invite practitioners to look at such underestimated dipoles and could also help to minimize the number of experiments.

On the dual reactivity of a Janus-type mesoionic dipole: experiments and theoretical validation

A mesoionic bicycle, easily synthesized from a proteinogenic amino acid, l-leucine, behaves as both thiazolium-olate and diazolium-olate dipoles, as unveiled by its dipolar cycloadditions.