Ring Strain Energy in the Cyclooctyl System. The Effect of Strain Energy on [3 + 2] Cycloaddition Reactions with Azides

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.

Trans-cyclooctene-a Swiss army knife for bioorthogonal chemistry: exploring the synthesis, reactivity, and applications in biomedical breakthroughs

BACKGROUND

Trans-cyclooctenes (TCOs) are highly strained alkenes with remarkable reactivity towards tetrazines (Tzs) in inverse electron-demand Diels-Alder reactions. Since their discovery as bioorthogonal reaction partners, novel TCO derivatives have been developed to improve their reactivity, stability, and hydrophilicity, thus expanding their utility in diverse applications.

MAIN BODY

TCOs have garnered significant interest for their applications in biomedical settings. In chemical biology, TCOs serve as tools for bioconjugation, enabling the precise labeling and manipulation of biomolecules. Moreover, their role in nuclear medicine is substantial, with TCOs employed in the radiolabeling of peptides and other biomolecules. This has led to their utilization in pretargeted nuclear imaging and therapy, where they function as both bioorthogonal tags and radiotracers, facilitating targeted disease diagnosis and treatment. Beyond these applications, TCOs have been used in targeted cancer therapy through a "click-to-release" approach, in which they act as key components to selectively deliver therapeutic agents to cancer cells, thereby enhancing treatment efficacy while minimizing off-target effects. However, the search for a suitable TCO scaffold with an appropriate balance between stability and reactivity remains a challenge.

CONCLUSIONS

This review paper provides a comprehensive overview of the current state of knowledge regarding the synthesis of TCOs, and its challenges, and their development throughout the years. We describe their wide ranging applications as radiolabeled prosthetic groups for radiolabeling, as bioorthogonal tags for pretargeted imaging and therapy, and targeted drug delivery, with the aim of showcasing the versatility and potential of TCOs as valuable tools in advancing biomedical research and applications.

Angle-strained sila-cycloalkynes

Second row elements in small- and medium-rings modulate strain. Herein we report the synthesis of two novel oligosilyl-containing cycloalkynes that exhibit angle-strain, as observed by X-ray crystallography. However, the angle-strained sila-cyclooctynes are sluggish participants in cycloadditions with benzyl azide. A distortion-interaction model analysis based on density functional theory calculations was performed.

Quantifying macrocyclization-induced strain utilizing N-phenylimides as conformational reporters

Incorporating an N-phenylimide unit into macrocycles enabled measurements of macrocyclization strains by comparing the N-phenylimide's conformational changes to similar units attached to a linear-chain control. Systems of larger macrocycles displayed negligible macrocyclization strain, while smaller macrocycles demonstrated proportionate effects, emphasizing the use of N-phenylimides as conformational reporters of macrocyclization strain.

Catalyst-Free Amino-Yne Click Reaction: An Efficient Way for Immobilizing Amoxicillin onto Polymeric Surfaces

Surface modifications play a crucial role in enhancing the functionality of biomaterials. Different approaches can be followed in order to achieve the bioconjugation of drugs and biological compounds onto polymer surfaces. In this study, we focused on the immobilization of an amoxicillin antibiotic onto the surface of poly-L-lactic acid (PLLA) using a copper-free amino-yne click reaction. The utilization of this reaction allowed for a selective and efficient bioconjugation of the amoxicillin moiety onto the PLLA surface, avoiding copper-related concerns and ensuring biocompatibility. The process involved sequential steps that included surface activation via alkaline hydrolysis followed by an amidation reaction with ethylendiamine, functionalization with propiolic groups, and subsequent conjugation with amoxicillin via a click chemistry approach. Previous amoxicillin immobilization using tryptophan and fluorescent amino acid conjugation was carried out in order to determine the efficacy of the proposed methodology. Characterization techniques such as X-ray photoelectron spectroscopy (XPS), Attenuated Total Reflection (ATR)-Fourier Transform Infrared (FTIR) spectroscopy, surface imaging, water contact angle determination, and spectroscopic analysis confirmed the successful immobilization of both tryptophan and amoxicillin while maintaining the integrity of the PLLA surface. This tailored modification not only exhibited a novel method for surface functionalization but also opens avenues for developing antimicrobial biomaterials with improved drug-loading capacity.

Theoretically Predicted and Experimentally Detected Chirality of Dibenzocyclooctynes and Their Triazole Adducts with Azides

Dibenzocyclooctynes have emerged as promising scaffolds for bioorthogonal ligation. An important structural aspect that has not been addressed so far relates to their chirality. Herein, we explore, by theoretical and experimental methods, this structural aspect that has been neglected so far. First, computational analysis is conducted, and the results are used as a guide for the experimental investigation. Next, an array of different experiments (high-performance liquid chromatography (HPLC) on chiral columns, chiroptical spectroscopy, and X-ray diffraction) for structure elucidation is scrutinized in concert. Finally, this work demonstrates the chirality and the stereodynamic behavior of dibenzocyclooctynes and their triazole derivatives with simple azides and also uncovers their conformational behavior.

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.

Radiolabelling small and biomolecules for tracking and monitoring

Radiolabelling small molecules with beta-emitters has been intensively explored in the last decades and novel concepts for the introduction of radionuclides continue to be reported regularly. New catalysts that induce carbon/hydrogen activation are able to incorporate isotopes such as deuterium or tritium into small molecules. However, these established labelling approaches have limited applicability for nucleic acid-based drugs, therapeutic antibodies, or peptides, which are typical of the molecules now being investigated as novel therapeutic modalities. These target molecules are usually larger (significantly >1 kDa), mostly multiply charged, and often poorly soluble in organic solvents. However, in preclinical research they often require radiolabelling in order to track and monitor drug candidates in metabolism, biotransformation, or pharmacokinetic studies. Currently, the most established approach to introduce a tritium atom into an oligonucleotide is based on a multistep synthesis, which leads to a low specific activity with a high level of waste and high costs. The most common way of tritiating peptides is using appropriate precursors. The conjugation of a radiolabelled prosthetic compound to a functional group within a protein sequence is a commonly applied way to introduce a radionuclide or a fluorescent tag into large molecules. This review highlights the state-of-the-art in different radiolabelling approaches for oligonucleotides, peptides, and proteins, as well as a critical assessment of the impact of the label on the properties of the modified molecules. Furthermore, applications of radiolabelled antibodies in biodistribution studies of immune complexes and imaging of brain targets are reported.

C-N Bond Forming Radical Rebound Is the Enantioselectivity-Determining Step in P411-Catalyzed Enantioselective C(sp3)-H Amination: A Combined Computational and Experimental Investigation

Engineered metalloenzymes represent promising catalysts for stereoselective C-H functionalization reactions. Recently, P450 enzymes have been evolved to allow for new-to-nature intramolecular C(sp3)-H amination reactions via a nitrene transfer mechanism, giving rise to diamine derivatives with excellent enantiocontrol. To shed light on the origin of enantioselectivity, a combined computational and experimental study was carried out. Hybrid quantum mechanics/molecular mechanics calculations were performed to investigate the activation energies and enantioselectivities of both the hydrogen atom transfer (HAT) and the subsequent C-N bond forming radical rebound steps. Contrary to previously hypothesized enantioinduction mechanisms, our calculations show that the radical rebound step is enantioselectivity-determining, whereas the preceding HAT step is only moderately stereoselective. Furthermore, the selectivity in the initial HAT is ablated by rapid conformational change of the radical intermediate prior to C-N bond formation. This finding is corroborated by our experimental study using a set of enantiomerically pure, monodeuterated substrates. Furthermore, classical and ab initio molecular dynamics simulations were carried out to investigate the conformational flexibility of the carbon-centered radical intermediate. This key radical species undergoes a facile conformational change in the enzyme active site from the pro-(R) to the pro-(S) configuration, whereas the radical rebound is slower due to the spin-state change and ring strain of the cyclization process, thereby allowing stereoablative C-N bond formation. Together, these studies revealed an underappreciated enantioinduction mechanism in biocatalytic C(sp3)-H functionalizations involving radical intermediates, opening up new avenues for the development of other challenging asymmetric C(sp3)-H functionalizations.

QMugs, quantum mechanical properties of drug-like molecules

Machine learning approaches in drug discovery, as well as in other areas of the chemical sciences, benefit from curated datasets of physical molecular properties. However, there currently is a lack of data collections featuring large bioactive molecules alongside first-principle quantum chemical information. The open-access QMugs (Quantum-Mechanical Properties of Drug-like Molecules) dataset fills this void. The QMugs collection comprises quantum mechanical properties of more than 665 k biologically and pharmacologically relevant molecules extracted from the ChEMBL database, totaling ~2 M conformers. QMugs contains optimized molecular geometries and thermodynamic data obtained via the semi-empirical method GFN2-xTB. Atomic and molecular properties are provided on both the GFN2-xTB and on the density-functional levels of theory (DFT, ωB97X-D/def2-SVP). QMugs features molecules of significantly larger size than previously-reported collections and comprises their respective quantum mechanical wave functions, including DFT density and orbital matrices. This dataset is intended to facilitate the development of models that learn from molecular data on different levels of theory while also providing insight into the corresponding relationships between molecular structure and biological activity.

Accurate Ring Strain Energies of Unsaturated Three-Membered Heterocycles with One Group 13-16 Element

High-quality ring strain energy (RSE) data for 1H-unsaturated (CH)₂X parent rings, where X is a group 13–16 element, are reported in addition to the 2H-isomers of the pnictogenirene rings. RSE data are obtained from appropriate homosdesmotic reactions and calculated at the DLPNO-CCSD(T)/def2-TZVPP//B3LYP-D3/def2-TZVP(ecp) level. 1H-Tallirene and 1H-plumbirene have unique donor–acceptor structures between an acetylene π(CC) orbital and an empty p orbital of a metallylene subunit (a Dewar–Chatt–Duncanson description) and therefore cannot be described as proper rings but as pseudocyclic structures. Also, 1H-indirene and 1H-oxirene lack ring critical points and constitute borderline cases of pseudorings. 1H-Unsaturated rings exhibit enhanced RSE compared to their saturated homologues. The mechanism of ring strain relaxation by increasing the s character in the lone pair (LP) of group 15–16 elements is remarkable and increases on descending the groups. Furthermore, RSE is affected by the aromatic character of group 13 rings and certain aromatic or antiaromatic character in group 14 or 15–16 rings, respectively, which tend to vanish on descending the group as shown by NICS(1) values. 2H-Unsaturated rings were found only for group 15 elements (although only 2H-azirine shows a proper cyclic structure) and displayed lower RSE (higher stability) than the corresponding 1H-isomers.

Accurate ring strain energies (RSE) are calculated for three-membered 1H-unsaturated rings containing a 13−16 group element and group 15 2H-isomers. The presence or absence of lone pairs at the heteroatom and the existence of intrinsic or residual (anti)aromaticity were shown to affect the RSE.

SPAAC iClick: progress towards a bioorthogonal reaction in-corporating metal ions

Combining strain-promoted azide-alkyne cycloaddition (SPAAC) and inorganic click (iClick) reactivity provides access to metal 1,2,3-triazolates. Experimental and computational insights demonstrate that iClick reactivity of the tested metal azides (LM-N₃, M = Au, W, Re, Ru and Pt) depends on the accessibility of the azide functionality rather than electronic effects imparted by the metal. SPAAC iClick reactivity with cyclooctyne is observed when the azide functionality is sterically unencumbered, e.g. [Au(N₃)(PPh₃)] (Au-N3), [W(η³-allyl)(N₃)(bpy)(CO)₂] (W-N3), and [Re(N₃)(bpy)(CO)₃] [bpy = 2,2'-bipyridine] (Re-N3). Increased steric bulk and/or preequilibria with high activation barriers prevent SPAAC iClick reactivity for the complexes [Ru(N₃)(Tp)(PPh₃)₂] [Tp = tris(pyrazolyl)borate] (Ru-N3), [Pt(N₃)(CH₃)(PⁱPr₃)₂] [ⁱPr = isopropyl] (Pt(II)-N3), and [Pt(N₃)(CH₃)₃]₄ ((PtN3)4). Based on these computational insights, the SPAAC iClick reactivity of [Pt(N₃)(CH₃)₃(P(CH₃)₃)₂] (Pt(IV)-N3) was successfully predicted.

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.

Design and Synthesis of Metabolic Chemical Reporters for the Visualization and Identification of Glycoproteins

Glycosylation events play an invaluable role in regulating cellular processes including enzymatic activity, immune recognition, protein stability, and cell-cell interactions. However, researchers have yet to realize the full range of glycan mediated biological functions due to a lack of appropriate chemical tools. Fortunately, the past 25 years has seen the emergence of modified sugar analogs, termed metabolic chemical reporters (MCRs), which are metabolized by endogenous enzymes to label complex glycan structures. Here, we review the major reporters for each class of glycosylation and highlight recent applications that have made a tremendous impact on the field of glycobiology.

Controlled Cyclopolymerization of 1,5-Hexadiynes to Give Narrow Band Gap Conjugated Polyacetylenes Containing Highly Strained Cyclobutenes

For decades, cyclopolymerization of α,ω-diyne derivatives has been an effective method to synthesize various soluble polyacetylenes containing five- to seven-membered rings in the backbone. However, cyclopolymerization to form four-membered carbocycles was considered impossible due to their exceptionally high ring strain (∼30 kcal/mol). Herein, we demonstrate the successful cyclopolymerization of rationally designed 1,5-hexadiyne derivatives to afford various polyacetylenes containing highly strained cyclobutenes in each repeat unit. After screening, Ru catalysts containing bulky diisopropylphenyl groups promoted challenging four-membered ring cyclization efficiently from various monomers, enabling the synthesis of high molecular weight (up to 40 kDa) polyacetylenes in a controlled manner. Furthermore, living polymerization allowed for block copolymer synthesis by combining with ring-opening metathesis polymerization as well as block copolymerization of two different 1,5-hexadiyne monomers to give a fully conjugated polyacetylene. These new polymers unexpectedly showed much narrower band gaps than conventional substituted polyacetylenes by >0.2 eV. Interestingly, computational studies showed much smaller bond length alternation in the conjugated backbone containing cyclobutenes, resulting in highly delocalized π electrons along the polymer chain and lower band gaps.

Molecular mechanism of Hetero Diels-Alder reactions between (E)-1,1,1-trifluoro-3-nitrobut-2-enes and enamine systems in the light of Molecular Electron Density Theory

The molecular mechanism of the reaction of (E)-1,1,1-trifluoro-3-nitrobut-2-ene 1 with 3,3-dimethyl-2-morpholinobutene 2 has been studied within the Molecular Electron Density Theory (MEDT). This theoretical study confirm the possibility of the formation of zwitterionic structures in the first reaction stage. Interestingly, that localized zwitterions are however not common intermediates for identified in the postreaction mixture products. The further Bonding Evolution Theory (BET) study show, that the key, HDA reaction takes place in one-step but in a non-concerted manner since three stages are clearly identified. First the C5-C6 double bond breaks, then the C1-C2 bond breaks, and in the last phase we observed the formation of the C1-C6 single bond and V(C2) and V' (C2) pseudoradical centers in Z1 molecule. In turn, the molecular mechanism of the conversion of zwitterion Z1 to product 3 can be divided also in three groups in which we observed the disappearance of the two pseudoradical centers and formation O4-C5 single and C3-N3 double bonds, respectively.

Developing bioorthogonal probes to span a spectrum of reactivities

Bioorthogonal chemistries enable researchers to interrogate biomolecules in living systems. These reactions are highly selective and biocompatible and can be performed in many complex environments. However, like any organic transformation, there is no perfect bioorthogonal reaction. Choosing the "best fit" for a desired application is critical. Correspondingly, there must be a variety of chemistries-spanning a spectrum of rates and other features-to choose from. Over the past few years, significant strides have been made towards not only expanding the number of bioorthogonal chemistries, but also fine-tuning existing reactions for particular applications. In this Review, we highlight recent advances in bioorthogonal reaction development, focusing on how physical organic chemistry principles have guided probe design. The continued expansion of this toolset will provide more precisely tuned reagents for manipulating bonds in distinct environments.

Strain visualization for strained macrocycles

Strain has a unique and sometimes unpredictable impact on the properties and reactivity of molecules. To thoroughly describe strain in molecules, a computational tool that relates strain energy to reactivity by localizing and quantifying strain was developed. Strain energy is calculated local to every coordinate in the molecule and areas of higher strain are shown experimentally to be more reactive. Not only does this tool directly compare strain energy in parts of the same molecule, but it also computes total strain to give a full picture of molecular strain energy. It is freely available to the public on GitHub under the name StrainViz and much of the workflow is automated to simplify use for non-experts. Unique insight into the reactivity of curved aromatic molecules and strained alkyne bioorthogonal reagents is described within.

Push-pull nitronates in the [3+2] cycloaddition with nitroethylene: Molecular Electron Density Theory study

The structure and the participation of the N-methoxy-N-[bis(methoxycarbonyl)methylene]amine N-oxide as model push-pull nitronate 1 with nitroethylene 2 in [3 + 2] cycloaddition (32CA) reaction have been analyzed within the Molecular Electron Density Theory (MEDT) using Density Functional Theory (DFT) calculations at the B3LYP(PCM)/6-31G(d) level. Topological analysis of the Electron Localization Function (ELF) of nitronate 1 reveals that this compound has pseudoradical center, while the conceptual DFT reactivity indices characterizes this three-atom-component (TAC) as a strong electrophile. The analyzed 32CA reaction takes place through a one-step mechanism. A Bonding Evolution Theory (BET) study of the more favorable reaction path associated with the 32CA reaction of nitronate 1 with nitroethylene 2 indicates that it is associated with a non-concerted two-stage one-step mechanism, in which the activation energy is mainly related with to the initial formation of the O3-C4 single bond. In the case of this reaction, an additional mechanism with formation of intermediate 7 is also found.

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.

Reactions of Thiiranium and Sulfonium Ions with Alkenes in the Gas Phase

Ion-molecule reactions between thiiranium ion 11 (m/z 213) and cyclohexene and cis-cyclooctene resulted in the formation of addition products 17a and 17b (m/z 295 and m/z 323, respectively) via an electrophilic addition pathway. Associative π-ligand exchange involving direct transfer of the PhS⁺ moiety, which has been observed for analogous seleniranium ions in the gas phase, did not occur despite previous solution experiments suggesting it as a valid pathway. DFT calculations at the M06-2X/def2-TZVP level of theory showed high barriers for the exchange reaction, while the addition pathway was more plausible. Further support for this pathway was provided with Hammett plots showing the rate of reaction to increase as the benzylic position of thiiranium ion derivatives became more electrophilic (ρ = +1.69; R² = 0.974). The more reactive isomeric sulfonium ion 22 was discounted as being responsible for the observed reactivity with infrared spectroscopy and DFT calculations suggesting little possibility for isomerization. To further explore the differences in reactivity, thiiranium ion 25 and sulfonium ion 27 were formed independently, with the latter ion reacting over 260 times faster toward cis-cyclooctene than the thiiranium ion rationalized by calculations suggesting a barrierless pathway for sulfonium ion 27 to react with the cycloalkene.

Design and Synthesis of Aza-Bicyclononene Dienophiles for Rapid Fluorogenic Ligations

Fluorogenic bioorthogonal reactions enable visualization of biomolecules under native conditions with excellent signal-to-noise ratio. Here, we present the design and synthesis of conformationally-strained aziridine-fused trans-cyclooctene (aza-TCO) dienophiles, which lead to the formation of fluorescent products in tetrazine ligations without the need for attachment of an extra fluorophore moiety. The presented aza-TCOs adopt the highly strained "half-chair" conformation, which was predicted computationally and confirmed by NMR measurements and X-ray crystallography. Kinetic studies revealed that the aza-TCOs belong to the most reactive dienophiles known to date. The potential of the newly developed aza-TCO probes for bioimaging applications is demonstrated by protein labeling experiments, imaging of cellular glycoconjugates and peptidoglycan imaging of live bacteria.

18 F-Labeling of Sensitive Biomolecules for Positron Emission Tomography

Positron emission tomography (PET) imaging study of fluorine-18 labeled biomolecules is an emerging and rapidly growing area for preclinical and clinical research. The present review focuses on recent advances in radiochemical methods for incorporating fluorine-18 into biomolecules via "direct" or "indirect" bioconjugation. Recently developed prosthetic groups and pre-targeting strategies, as well as representative examples in 18 F-labeling of biomolecules in PET imaging research studies are highlighted.

Mechanistic applications of click chemistry for pharmaceutical drug discovery and drug delivery

The concept of click chemistry (CC), first introduced by K.B. Sharpless, has been widely adopted for use in drug discovery, novel drug delivery systems (DDS), polymer chemistry, and material sciences. In this review, we outline novel aspects of CC related to drug discovery and drug delivery, with a brief overview of molecular mechanisms underlying each click reaction commonly used by researchers, and the main patents that paved the way for further diverse medicinal applications. We also describe recent progress in drug discovery and polymeric and carbon material-based drug delivery for potential pharmaceutical applications and advancements based on the CC approach, and discuss some intrinsic limitations of this popular conjugation reaction. The use of CC is likely to significantly advance drug discovery and bioconjugation development.

External electric field control: driving the reactivity of metal-free azide–alkyne click reactions

An external electric field is demonstrated as an efficient catalyst to accelerate click reactions.

Competing fragmentation processes of β-substituted propanoate ions upon collision-induced dissociation

RATIONALE

When subjected to collisional activation, gas-phase carboxylate ions typically undergo decarboxylation. However, alternative fragmentation processes dominate when the carboxylate group is located within certain structural motifs. In this work, the fragmentation processes of β-substituted carboxylate ions are characterized to improve correlations between reactivity and structure.

METHODS

Mass spectra were collected using both ion trap and triple quadrupole mass spectrometers operating in the negative ion mode; collision-induced dissociation (CID) of ions was used to study the relationship between product ions and the structures of their precursor ions. Quantum mechanical computations were performed on a full range of reaction geometries at the MP2/6-311++G(2d,p)//B3LYP/6-31++G(2d,p) level of theory.

RESULTS

For a series of β-substituted carboxylate ions, a product ion corresponding to the anion of the β-substituent was obtained upon CID. Detailed computations indicated that decarboxylative elimination and at least one other fragmentation mechanism had feasible energetics for the formation of substituent anions differing in their gas-phase basicities. Predicted energetics for anti- and synperiplanar alignments in the transition structures for decarboxylative elimination correlated with the positions of crossover points in breakdown curves acquired for conformationally constrained ions.

CONCLUSIONS

The feasibility of more than one mechanism was established for the fragmentation of β-substituted propanoates. The contribution of each mechanistic pathway to the formation of the substituent anion was influenced by structural variations and conformational constraints, but mostly depended on the nature of the substituent. Copyright © 2016 John Wiley & Sons, Ltd.

Decreasing Distortion Energies without Strain: Diazo-Selective 1,3-Dipolar Cycloadditions

The diazo group has attributes that complement those of the azido group for applications in chemical biology. Here, we use computational analyses to provide insights into the chemoselectivity of the diazo group in 1,3-dipolar cycloadditions. Dipole distortion energies are responsible for ∼80% of the overall energetic barrier for these reactions. Here, we show that diazo compounds, unlike azides, provide an opportunity to decrease that barrier substantially without introducing strain into the dipolarophile. The ensuing rate enhancement is due to the greater nucleophilic character of a diazo group compared to that of an azido group, which can accommodate decreased distortion energies without predistortion. The tuning of distortion energies with substituents in a diazo compound or dipolarophile can enhance reactivity and selectivity in a predictable manner. Notably, these advantages of diazo groups are amplified in water. Our findings provide a theoretical framework that can guide the design and application of both diazo compounds and azides in "orthogonal" contexts, especially for biological investigations.

Rapid cycloaddition of a diazo group with an unstrained dipolarophile

The cycloaddition of a diazoacetamide with ethyl 4,4,4-trifluorocrotonate proceeds with k = 0.1 M-1s-1. This second-order rate constant rivals those of optimized strain-promoted azide- alkyne cycloadditions, even though the reaction does not release strain. The regioselectivity and a computational distortion/interaction analysis of the reaction energetics are consistent with the formation of an N-H…F-C hydrogen bond in the transition state and the electronic character of the trifluorocrotonate. Analogous reactions with an azidoacetamide dipole or with an acrylate or crotonate dipolarophile were much slower. These findings suggest a new strategy for the design of diazo-selective reagents for chemical biology.

Strain-Promoted 1,3-Dipolar Cycloaddition of Cycloalkynes and Organic Azides

A nearly forgotten reaction discovered more than 60 years ago-the cycloaddition of a cyclic alkyne and an organic azide, leading to an aromatic triazole-enjoys a remarkable popularity. Originally discovered out of pure chemical curiosity, and dusted off early this century as an efficient and clean bioconjugation tool, the usefulness of cyclooctyne-azide cycloaddition is now adopted in a wide range of fields of chemical science and beyond. Its ease of operation, broad solvent compatibility, 100 % atom efficiency, and the high stability of the resulting triazole product, just to name a few aspects, have catapulted this so-called strain-promoted azide-alkyne cycloaddition (SPAAC) right into the top-shelf of the toolbox of chemical biologists, material scientists, biotechnologists, medicinal chemists, and more. In this chapter, a brief historic overview of cycloalkynes is provided first, along with the main synthetic strategies to prepare cycloalkynes and their chemical reactivities. Core aspects of the strain-promoted reaction of cycloalkynes with azides are covered, as well as tools to achieve further reaction acceleration by means of modulation of cycloalkyne structure, nature of azide, and choice of solvent.

Metal Free Azide-Alkyne Click Reaction: Role of Substituents and Heavy Atom Tunneling

Metal free click reactions provide an excellent noninvasive tool to modify and understand the processes in biological systems. Release of ring strain in cyclooctynes on reaction with azides on the formation of triazoles results in small activation energies for various intermolecular Huisgen reactions (1-9). Substitution of difluoro groups at the α, α' position of the cyclooctyne ring enhances the rates of cycloadditions by 10 and 20 times for methyl azide and benzyl azide respectively at room temperature. The computed rate enhancement on difluoro substitution using direct dynamical calculations using the canonical variational transition state theory (CVT/CAG) with small curvature tunneling (SCT) corrections are in excellent agreement with the experimental results. For the intramolecular click reaction (10) notwithstanding its much higher activation energy, quantum mechanical tunneling (QMT) enhances the rate of cycloaddition significantly and increases the N(14)/N(15) primary kinetic isotope effect at 298 K. QMT is shown to be rather efficient in 10 due to a thin barrier of ∼2.4 Å. The present study shows that tunneling effects can be significant for intramolecular click reactions.

AlCl₃-Catalyzed Ring Expansion Cascades of Bicyclic Cyclobutenamides Involving Highly Strained Cis,Trans-Cycloheptadienone Intermediates

We report the first experimental evidence for the generation of highly strained cis,trans-cycloheptadienones by electrocyclic ring opening of 4,5-fused cyclobutenamides. In the presence of AlCl3, the cyclobutenamides rearrange to [2.2.1]-bicyclic ketones; DFT calculations provide evidence for a mechanism involving torquoselective 4π-electrocyclic ring opening to a cis,trans-cycloheptadienone followed by a Nazarov-like recyclization and a 1,2-alkyl shift. Similarly, 4,6-fused cyclobutenamides undergo AlCl3-catalyzed rearrangements to [3.2.1]-bicyclic ketones through cis,trans-cyclooctadienone intermediates. The products can be further elaborated via facile cascade reactions to give complex tri- and tetracyclic molecules.

Cardanol benzoxazines – interplay of oxazine functionality (mono to tetra) and properties

Cardanol, an agrowaste – solventless synthesis and processability of benzoxazine monomers. Tailoring the polymer properties as a function of oxazine functionality in the monomers.

Theoretical elucidation of the origins of substituent and strain effects on the rates of Diels-Alder reactions of 1,2,4,5-tetrazines

The Diels-Alder reactions of seven 1,2,4,5-tetrazines with unstrained and strained alkenes and alkynes were studied with quantum mechanical calculations (M06-2X density functional theory) and analyzed with the distortion/interaction model. The higher reactivities of alkenes compared to alkynes in the Diels-Alder reactions with tetrazines arise from the differences in both interaction and distortion energies. Alkenes have HOMO energies higher than those of alkynes and therefore stronger interaction energies in inverse-electron-demand Diels-Alder reactions with tetrazines. We have also found that the energies to distort alkenes into the Diels-Alder transition-state geometries are smaller than for alkynes in these reactions. The strained dienophiles, trans-cyclooctene and cyclooctyne, are much more reactive than unstrained trans-2-butene and 2-butyne, because they are predistorted toward the Diels-Alder transition structures. The reactivities of substituted tetrazines correlate with the electron-withdrawing abilities of the substituents. Electron-withdrawing groups lower the LUMO+1 of tetrazines, resulting in stronger interactions with the HOMO of dienophiles. Moreover, electron-withdrawing substituents destabilize the tetrazines, and this leads to smaller distortion energies in the Diels-Alder transition states.

Finding the right (bioorthogonal) chemistry

Bioorthogonal chemistries can be used to tag diverse classes of biomolecules in cells and other complex environments. With over 20 unique transformations now available, though, selecting an appropriate reaction for a given experiment is challenging. In this article, we compare and contrast the most common classes of bioorthogonal chemistries and provide a framework for matching the reactions with downstream applications. We also discuss ongoing efforts to identify novel biocompatible reactions and methods to control their reactivity. The continued expansion of the bioorthogonal toolkit will provide new insights into biomolecule networks and functions and thus refine our understanding of living systems.