Effects of the Hydrophobicity of the Reactants on Diels−Alder Reactions in Water

Genetic code expansion, click chemistry, and light-activated PI3K reveal details of membrane protein trafficking downstream of receptor tyrosine kinases

Ligands such as insulin, epidermal growth factor, platelet-derived growth factor, and nerve growth factor (NGF) initiate signals at the cell membrane by binding to receptor tyrosine kinases (RTKs). Along with G-protein-coupled receptors, RTKs are the main platforms for transducing extracellular signals into intracellular signals. Studying RTK signaling has been a challenge, however, due to the multiple signaling pathways to which RTKs typically are coupled, including MAP/ERK, PLCγ, and Class 1A phosphoinositide 3-kinases (PI3K). The multi-pronged RTK signaling has been a barrier to isolating the effects of any one downstream pathway. Here, we used optogenetic activation of PI3K to decouple its activation from other RTK signaling pathways. In this context, we used genetic code expansion to introduce a click chemistry noncanonical amino acid into the extracellular side of membrane proteins. Applying a cell-impermeant click chemistry fluorophore allowed us to visualize delivery of membrane proteins to the plasma membrane in real time. Using these approaches, we demonstrate that activation of PI3K, without activating other pathways downstream of RTK signaling, is sufficient to traffic the TRPV1 ion channels and insulin receptors to the plasma membrane.

Modelling chemical processes in explicit solvents with machine learning potentials

Solvent effects influence all stages of the chemical processes, modulating the stability of intermediates and transition states, as well as altering reaction rates and product ratios. However, accurately modelling these effects remains challenging. Here, we present a general strategy for generating reactive machine learning potentials to model chemical processes in solution. Our approach combines active learning with descriptor-based selectors and automation, enabling the construction of data-efficient training sets that span the relevant chemical and conformational space. We apply this strategy to investigate a Diels-Alder reaction in water and methanol. The generated machine learning potentials enable us to obtain reaction rates that are in agreement with experimental data and analyse the influence of these solvents on the reaction mechanism. Our strategy offers an efficient approach to the routine modelling of chemical reactions in solution, opening up avenues for studying complex chemical processes in an efficient manner.

An Electrochemical Perspective on Reaction Acceleration in Microdroplets

Analytical techniques operating at the nanoscale introduce confinement as a tool at our disposal. This review delves into the phenomenon of accelerated reactivity within micro- and nanodroplets. A decade of accelerated reactivity observations was succeeded by several years of fundamental studies aimed at mechanistic enlightenment. Herein, we provide a brief historical context for rate enhancement in and around micro- and nanodroplets and summarize the mechanisms that have been proposed to contribute to such extraordinary reactivity. We highlight recent electrochemical reports that make use of restricted mass transfer to enhance electrochemical reactions and/or quantitatively measure reaction rates within droplet-confined electrochemical cells. A comprehensive approach to nanodroplet reactivity is paramount to understanding how nature takes advantage of these systems to provide life on Earth and, in turn, how to harness the full potential of such systems.

Genetic code expansion, click chemistry, and light-activated PI3K reveal details of membrane protein trafficking downstream of receptor tyrosine kinases

Ligands such as insulin, epidermal growth factor, platelet derived growth factor, and nerve growth factor (NGF) initiate signals at the cell membrane by binding to receptor tyrosine kinases (RTKs). Along with G-protein coupled receptors, RTKs are the main platforms for transducing extracellular signals into intracellular signals. Studying RTK signaling has been a challenge, however, due to the multiple signaling pathways to which RTKs typically are coupled, including MAP/ERK, PLCγ, and Class 1A phosphoinositide 3-kinases (PI3K). The multi-pronged RTK signaling has been a barrier to isolating the effects of any one downstream pathway. Here, we used optogenetic activation of PI3K to decouple its activation from other RTK signaling pathways. In this context, we used genetic code expansion to introduce a click chemistry noncanonical amino acid into the extracellular side of membrane proteins. Applying a cell-impermeant click chemistry fluorophore allowed us to visualize delivery of membrane proteins to the plasma membrane in real time. Using these approaches, we demonstrate that activation of PI3K, without activating other pathways downstream of RTK signaling, is sufficient to traffic the TRPV1 ion channels and insulin receptors to the plasma membrane.

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.

Collective Effects of Multiple Fluorine Atoms Causing π-philic Characteristic within a Caged Polyoxometalate Framework

Perfluorination brings about distinctive properties arising from the unusual nature of the F element, which have been extensively developed in materials science and chemistry. Herein we report that the construction of F-rich inner space within a hollowed Mo132 O372 cage ([Mo132 O372 (OCOR)30 (H2 O)72 ]42- ) leads to the emergence of unique guest binding activities in encapsulation. Prominently, the trifluoroacetate-modified cage (R=CF3 , 2) having as many as 90 F groups inside favors trapping cyclopentadiene (Cp), which is hardly trapped by the non-fluorinated counterpart (R=CH3 , 1). Systematic studies using related hydrocarbons show that the amount of the encapsulated guest is correlated with the unsaturation degree of the guests, implying the involvement of the attractive interaction of the CF3 -modified interior wall with the guest π-electron clouds. Control experiments using the semi-fluorinated analogues (R=CF2 H, CFH2 ) reveal that the perfluorination is a critical factor to facilitate the Cp encapsulation by 2, indicating that collective effects of polar C-F bonds spreading over the interior surface, rather than the polarity of the individual C-F bonds, are responsible. We also provide a successful example of the physical molecular confinement within the cage through the "ship-in-a-bottle" Diels-Alder reaction between trapped diene and dienophile.

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

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

Enhancing the Activity of Surface Immobilized Antimicrobial Peptides Using Thiol-Mediated Tethering to Poly(ethylene glycol)

Considering the need for versatile surface coatings that can display multiple bioactive signals and chemistries, the use of more novel surface modification methods is starting to emerge. Thiol-mediated conjugation of biomolecules is shown to be quite advantageous for such purposes due to the reactivity and chemoselectivity of thiol functional groups. Herein, the immobilization of poly(ethylene glycol) (PEG) and antimicrobial peptides (AMPs) to silica colloidal particles based on thiol-mediated conjugation techniques, along with an assessment of the antimicrobial potential of the functionalized particles against Pseudomonas aeruginosa and Staphylococcus aureus is investigated. Immobilization of PEG to thiolated Si particles is performed by either a two-step thiol-ene "photo-click" reaction or a "one-pot" thiol-maleimide type conjugation using terminal acrylate or maleimide functional groups, respectively. It is demonstrated that both immobilization methods result in a significant reduction in the number of viable bacterial cells compared to unmodified samples after the designated incubation periods with the PEG-AMP-modified colloidal suspensions. These findings provide a promising outlook for the fabrication of multifunctional surfaces based upon the tethering of PEG and AMPs to colloidal particles through thiol-mediated biocompatible chemistry, which has potential for use as implant coatings or as antibacterial formulations that can be incorporated into wound dressings to prevent or control bacterial infections.

Redox-Responsive Comparison of Diselenide and Disulfide Core-Cross-Linked Micelles for Drug Delivery Application

In this study, diselenide (Se–Se) and disulfide (S–S) redox-responsive core-cross-linked (CCL) micelles were synthesized using poly(ethylene oxide)2k-b-poly(furfuryl methacrylate)1.5k (PEO2k-b-PFMA1.5k), and their redox sensitivity was compared. A single electron transfer-living radical polymerization technique was used to prepare PEO2k-b-PFMA1.5k from FMA monomers and PEO2k-Br initiators. An anti-cancer drug, doxorubicin (DOX), was incorporated into PFMA hydrophobic parts of the polymeric micelles, which were then cross-linked with maleimide cross-linkers, 1,6-bis(maleimide) hexane, dithiobis(maleimido) ethane and diselenobis(maleimido) ethane via Diels–Alder reaction. Under physiological conditions, the structural stability of both S–S and Se–Se CCL micelles was maintained; however, treatments with 10 mM GSH induced redox-responsive de-cross-linking of S–S and Se–Se bonds. In contrast, the S–S bond was intact in the presence of 100 mM H2O2, while the Se–Se bond underwent de-crosslinking upon the treatment. DLS studies revealed that the size and PDI of (PEO2k-b-PFMA1.5k-Se)2 micelles varied more significantly in response to changes in the redox environment than (PEO2k-b-PFMA1.5k-S)2 micelles. In vitro release studies showed that the developed micelles had a lower drug release rate at pH 7.4, whereas a higher release was observed at pH 5.0 (tumor environment). The micelles were non-toxic against HEK-293 normal cells, which revealed that they could be safe for use. Nevertheless, DOX-loaded S–S/Se–Se CCL micelles exhibited potent cytotoxicity against BT-20 cancer cells. Based on these results, the (PEO2k-b-PFMA1.5k-Se)2 micelles can be more sensitive drug carriers than (PEO2k-b-PFMA1.5k-S)2 micelles.

The Efficiency of Metabolic Labeling of DNA by Diels-Alder Reactions with Inverse Electron Demand: Correlation with the Size of Modified 2'-Deoxyuridines

A selection of four different 2'-deoxyuridines with three different dienophiles of different sizes was synthesized. Their inverse electron demand Diels-Alder reactivity increases from k₂ = 0.15 × 10^-2 M^-1 s^-1 to k₂ = 105 × 10^-2 M^-1 s^-1 with increasing ring strain of the dienophiles. With a fluorogenic tetrazine-modified cyanine-styryl dye as reactive counterpart the fluorescence turn-on ratios lie in the range of 21-48 suitable for wash-free cellular imaging. The metabolic DNA labeling was visualized by a dot blot on a semiquantitative level and by confocal fluorescence microscopy on a qualitative level. A clear correlation between the steric demand of the dienophiles and the incorporation efficiency of the modified 2'-deoxyuridines into cellular DNA was observed. Even 2'-deoxyuridines with larger dienophiles, such as norbornene and cyclopropene, were incorporated to a detectable level into the nascent genomic DNA. This was achieved by an optimized way of cell culturing. This expands the toolbox of modified nucleosides for metabolic labeling of nucleic acids in general.

Two-Factor Fluorogenicity of Tetrazine-Modified Cyanine-Styryl Dyes for Bioorthogonal Labelling of DNA

Two green fluorescent tetrazine-modified cyanine-styryl dyes were synthesized for bioorthogonal labelling of DNA by means of the Diels-Alder reaction with inverse electron demand. With DNA as target biopolymer the fluorescence of these dyes is released by two factors: (i) sterically by their interaction with DNA, and (ii) structurally via the conjugated tetrazine as quencher moiety. As a result, the reaction with bicyclononyne-modified DNA is significantly accelerated up to ≥284,000 M^-1  s^-1 , and the fluorescence turn-on is enhanced up to 560 by the two-factor fluorogenicity. These dyes are cell permeable even in low concentrations and undergo fluorogenic reactions with BCN-modified DNA in living HeLa cells. The two-factor fluorescence release improves the signal-to-noise ratio such that washing procedures prior to cell imaging are not needed, which is a great advantage for live cell imaging of DNA and RNA in the future.

Photomechanochemical control over stereoselectivity in the [2 + 2] photodimerization of acenaphthylene

Tuning solubility and mechanical activation alters the stereoselectivity of the [2 + 2] photochemical cycloaddition of acenaphthylene. Photomechanochemical conditions produce the syn cyclobutane, whereas the solid-state reaction in the absence of mechanical activation provides the anti. When the photochemical dimerization occurs in a solubilizing organic solvent, there is no selectivity. Dimerization in H2O, in which acenaphthylene is insoluble, provides the anti product. DFT calculations reveal that insoluble and solid-state reactions proceed via a covalently bonded excimer, which drives anti selectivity. Alternatively, the noncovalently bound syn conformer is more mechanosusceptible than the anti, meaning it experiences greater destabilization, thereby producing the syn product under photomechanochemical conditions. Cyclobutanes are important components of biologically active natural products and organic materials, and we demonstrate stereoselective methods for obtaining syn or anti cyclobutanes under mild conditions and without organic solvents. With this work, we validate photomechanochemistry as a viable new direction for the preparation of complex organic scaffolds.

Chemical strategies to engineer hydrogels for cell culture

Two-dimensional and three-dimensional cell culture systems are widely used for biological studies, and are the basis of the organoid, tissue engineering and organ-on-chip research fields in applications such as disease modelling and drug screening. The natural extracellular matrix of tissues, a complex scaffold with varying chemical and mechanical properties, has a critical role in regulating important cellular functions such as spreading, migration, proliferation and differentiation, as well as tissue morphogenesis. Hydrogels are biomaterials that are used in cell culture systems to imitate critical features of a natural extracellular matrix. Chemical strategies to synthesize and tailor the properties of these hydrogels in a controlled manner, and manipulate their biological functions in situ, have been developed. In this Review, we provide the rational design criteria for predictably engineering hydrogels to mimic the properties of the natural extracellular matrix. We highlight the advances in using biocompatible strategies to engineer hydrogels for cell culture along with recent developments to dynamically control the cellular environment by exploiting stimuli-responsive chemistries. Finally, future opportunities to engineer hydrogels are discussed, in which the development of novel chemical methods will probably have an important role.

Inverse-electron demand Diels Alder Reactions between glycals and tetrazines

The inverse-electron demand Diels Alder reaction (IEDDA) of substituted tetrazines with 2,3-unsaturated sugars (glycals) has been investigated to prepare novel carbohydrate-based heterocycles. The cycloaddition reactions occurred in moderate to good, isolated yields and gave acyclic, C-linked pyranose diazines as the major products (33-90%). The effects of variations in sugars, sugar protecting groups, and reaction solvents on the yields and products obtained in these reactions were studied. Lower yields of adducts were isolated for TBDMS-protected glucals and for 4,6-O-benzylidene protected glucals. When unprotected sugars were used, the reactions failed to give the desired cycloadducts. A range of substituted tetrazines were also evaluated in these reactions. For comparison, HOMO-[LUMO + 1] gaps for glycal-tetrazine pairs were calculated using Density Functional (DFT) calculations at the B3LYP/631G+ level.

Mechanism of Self-Healing Hydrogels and Application in Tissue Engineering

Self-healing hydrogels and traditional hydrogels both have three-dimensional polymeric networks that are capable of absorbing and retaining a large amount of water. Self-healing hydrogels can heal and restore damage automatically, and they can avoid premature failure of hydrogels caused by mechanical damage after implantation. The formation mechanism of self-healing hydrogels and the factors that hydrogels can load are various. Researchers can design hydrogels to meet the needs of different tissues through the diversity of hydrogels Therefore, it is necessary to summarize different self-healing mechanisms and different factors to achieve different functions. Here, we briefly reviewed the hydrogels designed by researchers in recent years according to the self-healing mechanism of water coagulation. Then, the factors for different functions of self-healing hydrogels in different tissues were statistically analyzed. We hope our work can provide effective support for researchers in the design process of self-healing hydrogel.

Photoaffinity labeling and bioorthogonal ligation: Two critical tools for designing "Fish Hooks" to scout for target proteins

Small molecules remain an important category of therapeutic agents. Their binding to different proteins can lead to both desired and undesired biological effects. Identification of the proteins that a drug binds to has become an important step in drug development because it can lead to safer and more effective drugs. Parent bioactive molecules can be converted to appropriate probes that allow for visualization and identification of their target proteins. Typically, these probes are designed and synthesized utilizing some or all of five major tools; a photoactivatable group, a reporter tag, a linker, an affinity tag, and a bioorthogonal handle. This review covers two of the most challenging tools, photoactivation and bioorthogonal ligation. We provide a historical and theoretical background along with synthetic routes to prepare them. In addition, the review provides comparative analyses of the available tools that can assist decision making when designing such probes. A survey of most recent literature reports is included as well to identify recent trends in the field.

2,6-exo-8,10-exo-4-Butyl-9-oxa-4-azatetracyclo[5.3.1.02,6.08,10]undecane-3,5-dione

The title epoxide was obtained by spontaneous epoxidation of the corresponding unsaturated imide in air or by peracid oxidation. Unambiguous assignment of the 1H- and 13C-NMR spectra is achieved by comparison between analogous compounds and its X-ray structure confirms the exo,exo-configuration.

Reversible Click Chemistry Tag for Universal Proteome Sample Preparation for Top-Down and Bottom-Up Analysis

Successful proteome analysis requires reliable sample preparation beginning with protein solubilization and ending with a sample free of contaminants, ready for downstream analysis. Most proteome sample preparation technologies utilize precipitation or filter-based separation, both of which have significant disadvantages. None of the current technologies are able to prepare both intact proteins or digested peptides. Here, we introduce a reversible protein tag, ProMTag, that enables whole proteome capture, cleanup, and release of intact proteins for top-down analysis. Alternatively, the addition of a novel Trypsin derivative to the workflow generates peptides for bottom-up analysis. We show that the ProMTag workflow yields >90% for intact proteins and >85% for proteome digests. For top-down analysis, ProMTag cleanup improves resolution on 2D gels; for bottom-up exploration, this methodology produced reproducible mass spectrometry results, demonstrating that the ProMTag method is a truly universal approach that produces high-quality proteome samples compatible with multiple downstream analytical techniques. Data are available via ProteomeXchange with identifier PXD027799.

Click-functionalized hydrogel design for mechanobiology investigations

The advancement of click-functionalized hydrogels in recent years has coincided with rapid growth in the fields of mechanobiology, tissue engineering, and regenerative medicine. Click chemistries represent a group of reactions that possess high reactivity and specificity, are cytocompatible, and generally proceed under physiologic conditions. Most notably, the high level of tunability afforded by these reactions enables the design of user-controlled and tissue-mimicking hydrogels in which the influence of important physical and biochemical cues on normal and aberrant cellular behaviors can be independently assessed. Several critical tissue properties, including stiffness, viscoelasticity, and biomolecule presentation, are known to regulate cell mechanobiology in the context of development, wound repair, and disease. However, many questions still remain about how the individual and combined effects of these instructive properties regulate the cellular and molecular mechanisms governing physiologic and pathologic processes. In this review, we discuss several click chemistries that have been adopted to design dynamic and instructive hydrogels for mechanobiology investigations. We also chart a path forward for how click hydrogels can help reveal important insights about complex tissue microenvironments.

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.

Catalyst-free and additive-free reactions enabling C-C bond formation: a journey towards a sustainable future

This review focuses on the catalyst- and additive-free C-C bond forming reactions reported mostly from the year 2005 to date. C-C bond forming reactions are highly important as large and complex organic molecules can be derived from simpler ones via these reactions. On the other hand, catalyst- and additive-free reactions are economical, environmentally friendly and less sensitive to air/moisture, allow easy separation of products and are operationally simple. Hence, a large number of research articles have been published in this area. Though a few reviews are available on the catalyst-free organic reactions, most of them were published a few years ago. The current review excludes catalysts as well as additives and is specific to only C-C bond formation. Besides many organic name reactions, catalyst/additive-free C-H functionalizations, coupling reactions and UV-visible-light-promoted reactions are also discussed. Undoubtedly, the contents of this review will motivate readers to do more novel work in this area which will accelerate the journey towards a sustainable future.

Water as the reaction medium in organic chemistry: from our worst enemy to our best friend

A review presenting water as the logical reaction medium for the future of organic chemistry. A discussion is offered that covers both the "on water" and "in water" phenomena, and how water is playing unique roles in each, specifically with regard to its use in organic synthesis.

Bioorthogonal Reactions in Activity-Based Protein Profiling

Activity-based protein profiling (ABPP) is a powerful technique to label and detect active enzyme species within cell lysates, cells, or whole animals. In the last two decades, a wide variety of applications and experimental read-out techniques have been pursued in order to increase our understanding of physiological and pathological processes, to identify novel drug targets, to evaluate selectivity of drugs, and to image probe targets in cells. Bioorthogonal chemistry has substantially contributed to the field of ABPP, as it allows the introduction of tags, which may be bulky or have unfavorable physicochemical properties, at a late stage in the experiment. In this review, we give an overview of the bioorthogonal reactions that have been implemented in ABPP, provide examples of applications of bioorthogonal chemistry in ABPP, and share some thoughts on future directions.

Synthesis of 4H,5H-pyrano[3,2-c]pyrano-5-ones in aqueous media

The reaction of 4-hydroxy-6-methylpyran-2-one with substituted cinnamonitriles in water in the presence of triethylbenzylammonium chloride (TEBA) provide an efficient route to 2-amino-4-aryl-4H,5H-pyrano[3,2-c]pyran-5-one derivatives. The products were characterised by IR, 1H NMR, elemental analysis and were further confirmed by the X-ray crystal structure analysis.

Inverse electron demand Diels-Alder (IEDDA) reactions in peptide chemistry

Click chemistry is applied to selectively modify, lable and ligate peptides for their use as therapeutics, in biomaterials or analytical investigations. The inverse electron demand Diels-Alder (IEDDA) reaction is a catalyst-free click reaction with pronounced chemoselectivity and fast reaction rates. Applications and achievements of the IEDDA reaction in peptide chemistry since 2008 are described in this review.

The Emerging Role of Tetrazines in Drug-Activation Chemistries

Traditionally, prodrug activation has been limited to enzymatic triggers or gross physiological aberrations, such as pH, that offer low selectivity and control over dosage. In recent years, the field of prodrug activation chemistry has been transformed by the use of bioorthogonal reactions that can be carried out under biological conditions at sub-millimolar concentrations, with the tetrazine-mediated inverse electron demand Diels-Alder reaction amongst the most recognised. Their high reaction rates, chemoselectivity and excellent biocompatibility make tetrazines ideal small molecules for activating prodrugs. Recently the tetrazine moiety has been used as a prodrug for a pyridazine thus broadening the scope of prodrug systems. This article discusses the concept of using tetrazines as small-molecule activators for prodrugs, and provides an overview of tetrazine-based prodrug systems, with a particular focus on the recently reported prodrug-prodrug activation strategy.

Experimental model design: exploration and optimization of customized polymerization conditions for the preparation of targeted smart materials by the Diels Alder click reaction

The experimental model design proposed herein has proved to be an indispensable tool to rapidly and easily elucidate the optimal polymerization conditions in the preparation of tailor-made responsive materials for biomedical applications.

Inverse electron demand Diels-Alder reactions in chemical biology

The emerging inverse electron demand Diels-Alder (IEDDA) reaction stands out from other bioorthogonal reactions by virtue of its unmatchable kinetics, excellent orthogonality and biocompatibility. With the recent discovery of novel dienophiles and optimal tetrazine coupling partners, attention has now been turned to the use of IEDDA approaches in basic biology, imaging and therapeutics. Here we review this bioorthogonal reaction and its promising applications for live cell and animal studies. We first discuss the key factors that contribute to the fast IEDDA kinetics and describe the most recent advances in the synthesis of tetrazine and dienophile coupling partners. Both coupling partners have been incorporated into proteins for tracking and imaging by use of fluorogenic tetrazines that become strongly fluorescent upon reaction. Selected notable examples of such applications are presented. The exceptional fast kinetics of this catalyst-free reaction, even using low concentrations of coupling partners, make it amenable for in vivo radiolabelling using pretargeting methodologies, which are also discussed. Finally, IEDDA reactions have recently found use in bioorthogonal decaging to activate proteins or drugs in gain-of-function strategies. We conclude by showing applications of the IEDDA reaction in the construction of biomaterials that are used for drug delivery and multimodal imaging, among others. The use and utility of the IEDDA reaction is interdisciplinary and promises to revolutionize chemical biology, radiochemistry and materials science.

Fine-Tuning Strain and Electronic Activation of Strain-Promoted 1,3-Dipolar Cycloadditions with Endocyclic Sulfamates in SNO-OCTs

The ability to achieve predictable control over the polarization of strained cycloalkynes can influence their behavior in subsequent reactions, providing opportunities to increase both rate and chemoselectivity. A series of new heterocyclic strained cyclooctynes containing a sulfamate backbone (SNO-OCTs) were prepared under mild conditions by employing ring expansions of silylated methyleneaziridines. SNO-OCT derivative 8 outpaced even a difluorinated cyclooctyne in a 1,3-dipolar cycloaddition with benzylazide. The various orbital interactions of the propargylic and homopropargylic heteroatoms in SNO-OCT were explored both experimentally and computationally. The inclusion of these heteroatoms had a positive impact on stability and reactivity, where electronic effects could be utilized to relieve ring strain. The choice of the heteroatom combinations in various SNO-OCTs significantly affected the alkyne geometries, thus illustrating a new strategy for modulating strain via remote substituents. Additionally, this unique heteroatom activation was capable of accelerating the rate of reaction of SNO-OCT with diazoacetamide over azidoacetamide, opening the possibility of further method development in the context of chemoselective, bioorthogonal labeling.

Effects of Solvent and Side-Chain Length on the Cycloaddition of Cyclopentadiene to N-alkylmaleimides: A Dft Study

Quantum chemistry calculations have been performed to investigate the kinetics and mechanism of the cycloaddition reaction between cyclopentadiene and N-alkylmaleimides in the gas phase and different solvents. To investigate the effects of side-chain length on the cycloaddition reaction, the rate constants and kinetic parameters of the reaction between cyclopentadiene with N-methyl-, N-ethyl-, N-propyl- and N-butyl-maleimide were calculated. The results obtained indicate that the reaction in solvents is faster than in the gas phase. Moreover, the dipole moments of the transition states are larger than those of the reactants. Therefore, the reactions in the most polar solvent (water) are faster than in ethanol, n-hexane, 2,2,2-trifluoroethanol (TFE) and acetonitrile. Quantum mechanics-molecular mechanics (QM/MM) calculations on the reactions using the explicit solvent model for water and TFE indicate that hydrogen bond interactions of the solvents have a key role in the rate of the reaction and these are more important than the polarity of the solvent. Natural bond orbital analysis reveals that the charge transfer between the reactants in solvents is more than in the gas phase. Finally, HOMO–LUMO analysis indicates that solvents increase the reactivity of the reactants in comparison to the gas phase.

1,3-Dipolar Cycloaddition with Diazo Groups: Noncovalent Interactions Overwhelm Strain

Like azides, diazoacetamides undergo 1,3-dipolar cycloadditions with oxanorbornadienes (OND) in a reaction that is accelerated by the relief of strain in the transition state. The cycloaddition of a diazoacetamide with unstrained ethyl 4,4,4-trifluoro-2-butynoate is, however, 35-fold faster than with the analogous OND because of favorable interactions with the fluoro groups. Its rate constant (k = 0.53 M(-1) s(-1) in methanol) is comparable to those of strain-promoted azide-cyclooctyne cycloadditions.

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.

On the mechanism of retro-Diels–Alder reaction of partially saturated 2-pyrones to produce biorenewable chemicals

Partially saturated 2-pyrone molecules undergo ring-opening and decarboxylation via retro-Diels–Alder (rDA) reaction.

Organic synthesis reactions on-water at the organic–liquid water interface

Organic synthesis on-water has shown surprising successful synthetic methods. This review discusses the array of chemistry, which has been adapted with this methodology.

How does aqueous solubility of organic reactant affect a water-promoted reaction?

It was widely reported that under the "on water" condition, various water-promoted organic reactions can proceed with very high speed. Thus, it is considered that the aqueous solubility of reactant is not an important issue in these reactions. Three types of water-promoted organic reactions were investigated in the current study to distinguish whether the reaction rate of an aqueous reaction was affected by the aqueous solubilities of the reactants. The results showed that, for a Diels-Alder reaction which was fast under the neat conditions, the aqueous solubilities of reactants had little influence on the reaction. However, for the reactions which proceeded slowly under the neat conditions, such as [2σ+2σ+2π] cycloaddition reactions and epoxide aminolysis reactions, the reactants with good aqueous solubilities proceeded fast in water. Poorly aqueous soluble reactants reacted slowly or did not react under the "on water" condition, and an appropriate amount of organic cosolvent was needed to make the reaction become efficient. This evidence suggested that for these two types of reactions, the dissolution of the reactants in water was required.

“On water” hydroformylation of 1-hexene using Rh/PAA (PAA = polyacrylic acid) as catalyst

Efficient hydroformylation of 1-hexene was performed in water using rhodium catalyst and hydrophobic phosphine.

Quantitative structure-activation barrier relationship modeling for Diels-Alder ligations utilizing quantum chemical structural descriptors

Background

In the present study, we show the correlation of quantum chemical structural descriptors with the activation barriers of the Diels-Alder ligations. A set of 72 non-catalysed Diels-Alder reactions were subjected to quantitative structure-activation barrier relationship (QSABR) under the framework of theoretical quantum chemical descriptors calculated solely from the structures of diene and dienophile reactants. Experimental activation barrier data were obtained from literature. Descriptors were computed using Hartree-Fock theory using 6-31G(d) basis set as implemented in Gaussian 09 software.

Results

Variable selection and model development were carried out by stepwise multiple linear regression methodology. Predictive performance of the quantitative structure-activation barrier relationship (QSABR) model was assessed by training and test set concept and by calculating leave-one-out cross-validated Q² and predictive R² values. The QSABR model can explain and predict 86.5% and 80% of the variances, respectively, in the activation energy barrier training data. Alternatively, a neural network model based on back propagation of errors was developed to assess the nonlinearity of the sought correlations between theoretical descriptors and experimental reaction barriers.

Conclusions

A reasonable predictability for the activation barrier of the test set reactions was obtained, which enabled an exploration and interpretation of the significant variables responsible for Diels-Alder interaction between dienes and dienophiles. Thus, studies in the direction of QSABR modelling that provide efficient and fast prediction of activation barriers of the Diels-Alder reactions turn out to be a meaningful alternative to transition state theory based computation.

On water: silver-catalyzed domino approach for the synthesis of benzoxazine/oxazine-fused isoquinolines and naphthyridines from o-alkynyl aldehydes

An operationally simple domino approach for the silver-catalyzed synthesis of oxazine/benzoxazine-fused isoquinolines 5a-q and naphthyridines 6a-v by the reaction of o-alkynyl aldehydes 3a-aa with amines having embedded nucleophiles 4a-d under mild reaction condition in water is described. The reaction shows selective C-N bond formation on the more electrophilic alkynyl carbon resulting in the formation of 6-endo-dig cyclized product. The competitive experiments show the viability of an intramolecular nucleophilic attack over an intermolecular attack of the external nucleophile. This methodology accommodates wide functional group variation, which proves to be useful for structural and biological assessment.