Synthesis and inverse electron demand Diels-Alder reactions of 3,6-bis(3,4-dimethoxybenzoyl)-1,2,4,5-tetrazine

Advances in the Synthesis of Bioorthogonal Reagents: s-Tetrazines, 1,2,4-Triazines, Cyclooctynes, Heterocycloheptynes, and trans-Cyclooctenes

Aligned with the increasing importance of bioorthogonal chemistry has been an increasing demand for more potent, affordable, multifunctional, and programmable bioorthogonal reagents. More advanced synthetic chemistry techniques, including transition-metal-catalyzed cross-coupling reactions, C-H activation, photoinduced chemistry, and continuous flow chemistry, have been employed in synthesizing novel bioorthogonal reagents for universal purposes. We discuss herein recent developments regarding the synthesis of popular bioorthogonal reagents, with a focus on s-tetrazines, 1,2,4-triazines, trans-cyclooctenes, cyclooctynes, hetero-cycloheptynes, and -trans-cycloheptenes. This review aims to summarize and discuss the most representative synthetic approaches of these reagents and their derivatives that are useful in bioorthogonal chemistry. The preparation of these molecules and their derivatives utilizes both classical approaches as well as the latest organic chemistry methodologies.

Palladium-Catalyzed Dearomatization of Benzothiophenes: Isolation and Functionalization of a Discrete Dearomatized Intermediate

A Pd-catalyzed decarboxylative dearomatization reaction of a heterocyclic substrate enables access to an uncommon reaction intermediate that rearomatizes in the presence of amine bases in a net C-H functionalization sequence. The dearomatized benzo[b]thiophene intermediate bears an exocyclic alkene that can be functionalized through cycloaddition and halogenation reactions to deliver complex heterocyclic products.

Triazine Chalcogenones from Thiocyanate or Selenocyanate Addition to Tetrazine Ligands in Ruthenium Arene Complexes

The chemistry of 1,2,4,5-tetrazines has attracted considerable interest both from a synthetic and applicative standpoint. Recently, regioselective reactions with alkynes and alkenes have been reported to be favored once the tetrazine ring is coordinated to Re(I), Ru(II), and Ir(III) centers. Aiming to further explore the effects of metal coordination, herein, we unveil the unexplored reactivity of tetrazines with chalcogenocyanate anions. Thus, ruthenium(II) tetrazine complexes, [RuCl{κ²N-3-(2-pyridyl)-6-R-1,2,4,5-tetrazine}(η⁶-arene)]⁺ (arene = p-cymene, R = H, [1a]⁺, R = Me, [1b]⁺, R = 2-pyridyl, [1c]⁺; arene = C₆Me₆, R = H, [1d]⁺, R = Me, [1e]⁺; PF₆^- salts), reacted quantitatively and in mild conditions with M(ECN) salts (M = Na, K, Bu₄N; E = O, S, Se). The addition of thiocyanate or selenocyanate to the tetrazine ligand is regioselective and afforded, via N₂ release, 1,2,4-triazine-5-chalcogenone heterocycles, the one with selenium being unprecedented. The novel ruthenium complexes [RuCl{κ²N-(2-pyridyl)}{triazine chalcogenone}(η⁶-arene)] 2a-e (sulfur), 3b, 3d, and 3e (selenium) were characterized by analytical (CHNS analyses, conductivity), spectroscopic (IR, multinuclear and two-dimensional (2D) NMR), and spectrometric (electrospray ionization mass spectrometry (ESI-MS)) techniques. According to density functional theory (DFT) calculations, the nucleophilic attack of SCN^- on the tetrazine ring is kinetically driven. Compound 2b is selectively and reversibly mono-protonated on the triazine ring by HCl or other strong acids, affording a single tautomer. When reactions of chalcogenocyanates were performed on the 2,2'-bipyridine (bpy) complex [RuCl(bpy)(η⁶-p-cymene)]⁺, the chloride substitution products [Ru(ECN)(bpy)(η⁶-p-cymene)]⁺ (E = O, [4]⁺; E = S, [5]⁺; E = Se, [6]⁺) were obtained in 82-90% yields (PF₆^- salts). Combined spectroscopic data (IR, ¹H/¹³C/⁷⁷Se NMR) was revealed to be a useful tool to study the linkage isomerism of the chalcogenocyanate ligand in [4-6]⁺.

Divergent Reactivity of Phosphorylated and Related Allenes: [4 + 2] Cycloaddition with 3,6-Diphenyltetrazine, Self-Addition Leading to Dimers and [Pd]-Complex Formation

Phosphorus-based naphthalenes are formed by self-dimerization-cum-cyclization of α-aryl allenylphosphonates or allenylphosphine oxides using catalytic Pd(OAc)₂in the presence of PPh₃ and Et₃N . This reaction involves [4 + 2]-cycloaddition with the (β,γ) double bond of one allene as the dienophile; the double bonds at the α-aryl-(β',γ') group and (α,β)-carbons of the second allene act as the diene part. A subsequent proton shift also takes place. Upon treating allenylphosphine oxides with Pd(OAc)₂ [stoichiometry 2:1] in the presence of PPh₃/Ag₂CO₃, a [Pd]-complex is isolated and structurally characterized. This complex can be used as a catalyst for C-C bond-forming reactions of phosphorus-based allenes with 2-iodophenol. Densely substituted 3,6-diphenylpyridazines are conveniently obtained in excellent yields by a thermally induced regioselective Inverse Electron Demand Diels-Alder (IEDDA) reaction of allenes with 3,6-diphenyltetrazine, followed by a [1,3]-H shift.

Computational insights into the inverse electron-demand Diels-Alder reaction of norbornenes with 1,2,4,5-tetrazines: norbornene substituents' effects on the reaction rate

The study of the reaction rates and mechanism of click chemistry reactions still remains an interesting challenge in organic chemistry. In this regard, the inverse electron demand Diels-Alder (IEDDA) reaction represents a promising metal-free alternative with enhanced reaction rates compared to other reactions of the click chemistry toolbox. Among the different types of dienophiles used in the IEDDA reactions, norbornenes have been widely used given their high stability and fast reaction rates. The inverse electron-demand Diels Alder reaction of 3,6-dipyridin-2-yl-1,2,4,5-tetrazine with a series of norbornene derivatives was studied with quantum mechanical calculations at the M06-2X/6-311+G(d,p) level of theory. The theoretical predictions were confirmed with the experimental data and analyzed with the use of the distortion/interaction model. The obtained results will help in obtaining a better understanding of the factors that affect the relative cycloaddition rates of norbornenes with tetrazines, which are crucial for selectively tuning their efficacy.

Divergent, C-C Bond Forming Macrocyclizations Using Modular Sulfonylhydrazone and Derived Substrates

A divergent approach to C-C bond forming macrocycle construction is described. Modular sulfonylhydrazone and derived pyridotriazole substrates with three key building blocks have been constructed and cyclized to afford diverse macrocyclic frameworks. Broad substrate scope and functional group tolerance have been demonstrated. In addition, site-selective postfunctionalization allowed for further diversification of macrocyclic cores.

Boron Trifluoride-Mediated Cycloaddition of 3-Bromotetrazine and Silyl Enol Ethers: Synthesis of 3-Bromo-pyridazines

Pyridazines are important scaffolds for medicinal chemistry or crop protection agents, yet the selective preparation of 3-bromo-pyridazines with high regiocontrol remains difficult. We achieved the Lewis acid-mediated inverse electron demand Diels-Alder reaction between 3-monosubstituted s-tetrazine and silyl enol ethers and obtained functionalized pyridazines. In the case of 1-monosubstituted silyl enol ethers, exclusive regioselectivity was observed. Downstream functionalization of the resulting 3-bromo-pyridazines was demonstrated utilizing several cross-coupling protocols to synthesize 3,4-disubstituted pyridazines with excellent control over the substitution pattern.

Labelling of DNA and RNA in the cellular environment by means of bioorthogonal cycloaddition chemistry

Labelling of nucleic acids as biologically important cellular components is a crucial prerequisite for the visualization and understanding of biological processes. Efficient bioorthogonal chemistry and in particular cycloadditions fullfill the requirements for cellular applications. The broadly applied Cu(i)-catalyzed azide-alkyne cycloaddition (CuAAC), however, is limited to labellings in vitro and in fixed cells due to the cytotoxicity of copper salts. Currently, there are three types of copper-free cycloadditions used for nucleic acid labelling in the cellular environment: (i) the ring-strain promoted azide-alkyne cycloaddition (SPAAC), (ii) the "photoclick" 1,3-dipolar cycloadditions, and (iii) the Diels-Alder reactions with inverse electron demand (iEDDA). We review only those building blocks for chemical synthesis on solid phase of DNA and RNA and for enzymatic DNA and RNA preparation, which were applied for labelling of DNA and RNA in situ or in vivo, i.e. in the cellular environment, in fixed or in living cells, by the use of bioorthogonal cycloaddition chemistry. Additionally, we review the current status of orthogonal dual and triple labelling of DNA and RNA in vitro to demonstrate their potential for future applications in situ or in vivo.

A molecular electron density theory study of the participation of tetrazines in aza-Diels–Alder reactions

The reactions of eight tetrazines of increased electrophilic character with nucleophilic tetramethyl ethylene (TME) and with electrophilic tetracyanoethylene (TCE) have been studied using Molecular Electron Density Theory. These reactions are domino processes comprising an aza-Diels–Alder (ADA) reaction followed by an extrusion of molecular nitrogen, yielding a dihydropyridazine. Analysis of the conceptual DFT (CDFT) indices showed an increase of the electrophilicity and a decrease of the nucleophilicity of tetrazines with an increase of the electron-withdrawing character of the substituent. A very good correlation between the global electron density transfer at the transition structures and the activation enthalpies for the ADA reactions involving TME was found. However, tetrazines have no tendency to react with electrophilic ethylenes such as TCE. Bonding Evolution Theory (BET) analysis of the ADA reaction of dinitro tetrazine with TME showed that the activation energy is mainly associated with the continuous depopulation of the C–C and C–N double bonds.

The electron-withdrawing substituents on the tetrazine favour aza-Diels–Alder reactions towards nucleophilic ethylenes, but they do not react with electrophilic ethylenes.

Metal-Free Formal Inverse-Electron-Demand Diels-Alder Reaction of 1,2-Diazines with Ynamides

A highly effective metal-free formal inverse-electron-demand Diels-Alder reaction of 1,2-diazines with ynamides has been developed. This catalytic protocol is more environmentally friendly and allows for the construction of 2-aminonaphthalenes and 2-aminoanthracenes from 1,2-diazines and ynamides in good to high yields with wide diversity and functional group tolerance.

Synthesis, Characterization, and Rapid Cycloadditions of 5-Nitro-1,2,3-triazine

The synthesis, characterization, and a study of the cycloaddition reactions of 5-nitro-1,2,3-triazine (3) are reported. The electron-deficient nature of 3 permits rapid cycloaddition with a variety of electron-rich dienophiles, including amidines, enamines, enol ethers, ynamines, and ketene acetals in high to moderate yields. ¹H NMR studies of a representative cycloaddition reaction between 3 and an amidine revealed a remarkable reaction rate and efficiency (1 mM, <60 s, CD₃CN, 23 °C, >95%).

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.

iEDDA Reaction of the Molecular Iodine-Catalyzed Synthesis of 1,3,5-Triazines via Functionalization of the sp3 C-H Bond of Acetophenones with Amidines: An Experimental Investigation and DFT Study

The present work reports an inverse electron demand Diels-Alder (iEDDA)-type reaction to synthesize 1,3,5-trizines from acetophenones and amidines. The use of molecular iodine in a catalytic amount facilitates the functionalization of the sp³ C-H bond of acetophenones. This is a simple and efficient methodology for the synthesis of 1,3,5-triazines in good to excellent yields under transition-metal-free and peroxide-free conditions. The reaction is believed to take place via an in situ iodination-based oxidative elimination of formaldehyde. DFT calculations at the M062X/6-31+G(d,p) level were employed to investigate the reaction mechanism. Reaction barriers for the cycloaddition as well as a formaldehyde expulsion steps were computed, and a multistep mechanism starting with the nucleophilic attack by benzamidine on an in situ generated imine intermediate has been proposed. Both local and global reactivity descriptors were used to study the regioselectivity of the addition steps.

Direct Synthesis of β-Aminoenals through Reaction of 1,2,3-Triazine with Secondary Amines

Simple and direct nucleophilic addition of secondary amines, including imidazole, to 1,2,3-triazine under mild reaction conditions (THF, 25-65 °C, 12-48 h), requiring no additives, cleanly provides β-aminoenals 4 in good yields (21 examples, 31-79%). The reaction proceeds by amine nucleophilic addition to C4 of the 1,2,3-triazine, in situ loss of N₂, and subsequent imine hydrolysis to provide 4.

Reaction of Aldehydes/Ketones with Electron-Deficient 1,3,5-Triazines Leading to Functionalized Pyrimidines as Diels-Alder/Retro-Diels-Alder Reaction Products: Reaction Development and Mechanistic Studies

Catalytic inverse electron demand Diels-Alder (IEDDA) reactions of heterocyclic aza-dienes are rarely reported since highly reactive and electron-rich dienophiles are often found not compatible with strong acids such as Lewis acids. Herein, we disclose that TFA-catalyzed reactions of electron-deficient 1,3,5-triazines and electron-deficient aldehydes/ketones can take place. These reactions led to highly functionalized pyrimidines as products in fair to good yields. The reaction mechanism was carefully studied by the combination of experimental and computational studies. The reactions involve a cascade of stepwise inverse electron demand hetero-Diels-Alder (ihDA) reactions, followed by retro-Diels-Alder (rDA) reactions and elimination of water. An acid was required for both ihDA and rDA reactions. This mechanism was further verified by comparing the relative reactivity of aldehydes/ketones and their corresponding vinyl ethers in the current reaction system.

Vinyl Ether/Tetrazine Pair for the Traceless Release of Alcohols in Cells

The cleavage of a protecting group from a protein or drug under bioorthogonal conditions enables accurate spatiotemporal control over protein or drug activity. Disclosed herein is that vinyl ethers serve as protecting groups for alcohol‐containing molecules and as reagents for bioorthogonal bond‐cleavage reactions. A vinyl ether moiety was installed in a range of molecules, including amino acids, a monosaccharide, a fluorophore, and an analogue of the cytotoxic drug duocarmycin. Tetrazine‐mediated decaging proceeded under biocompatible conditions with good yields and reasonable kinetics. Importantly, the nontoxic, vinyl ether duocarmycin double prodrug was successfully decaged in live cells to reinstate cytotoxicity. This bioorthogonal reaction presents broad applicability and may be suitable for in vivo applications.

Microwave-Assisted Synthesis of Bioactive Six-Membered Heterocycles and Their Fused Analogues

This review describes the formation of six-membered heterocyclic compounds and their fused analogues under microwave activation using modern organic transformations including cyclocondensation, cycloaddition, multicomponents and other modular reactions. The review is divided according to the main heterocycle types in order of increasing complexity, starting with heterocyclic systems containing one, two and three heteroatoms and their fused analogues. Recent microwave applications are reviewed, with special focus on the chemistry of bioactive compounds. Selected examples from the 2006 to 2015 literature are discussed.

Cycloadditions of 1,2,3-Triazines Bearing C5-Electron Donating Substituents: Robust Pyrimidine Synthesis

The examination of the cycloaddition reactions of 1,2,3-triazines 17-19, bearing electron-donating substituents at C5, are described. Despite the noncomplementary 1,2,3-triazine C5 substituents, amidines were found to undergo a powerful cycloaddition to provide 2,5-disubstituted pyrimidines in excellent yields (42-99%; EDG = SMe > OMe > NHAc). Even select ynamines and enamines were capable of cycloadditions with 17, but not 18 or 19, to provide trisubstituted pyridines in modest yields (37-40% and 33% respectively).

Regiospecific synthesis of neuroprotective 1,4-benzoxazine derivatives through a tandem oxidation–Diels–Alder reaction

Highly functionalized 1,4-benzoxazine derivatives have been synthesized at room temperature, with complete regiochemical control, through a tandem oxidation–Diels–Alder reaction.

Cycloadditions of noncomplementary substituted 1,2,3-triazines

The scope of the [4 + 2] cycloaddition reactions of substituted 1,2,3-triazines, bearing noncomplementary substitution with electron-withdrawing groups at C4 and/or C6, is described. The studies define key electronic and steric effects of substituents impacting the reactivity, mode (C4/N1 vs C5/N2), and regioselectivity of the cycloaddition reactions of 1,2,3-triazines with amidines, enamines, and ynamines, providing access to highly functionalized heterocycles.

Total syntheses of (-)-pyrimidoblamic acid and P-3A

Total syntheses of (-)-pyrimidoblamic acid and P-3A are disclosed. Central to the convergent approach is a powerful inverse electron demand Diels-Alder reaction between substituted electron-deficient 1,2,3-triazines and a highly functionalized and chiral primary amidine, which forms the pyrimidine cores and introduces all necessary stereochemistry in a single step. Intrinsic in the convergent approach is the potential it provides for the late stage divergent synthesis of modified analogs bearing deep-seated changes in either the pyrimidine cores or the highly functionalized C2 side chain common to both natural products. The examination of the key cycloaddition reaction revealed that the inherent 1,2,3-triazine mode of cycloaddition (C4/N1 vs C5/N2) as well as the amidine regioselectivity were unaffected by introduction of two electron-withdrawing groups (-CO2R) at C4 and C6 of the 1,2,3-triazine even if C5 is unsubstituted (Me or H), highlighting the synthetic potential of the powerful pyrimidine synthesis.

An intramolecular inverse electron demand Diels-Alder approach to annulated α-carbolines

Intramolecular inverse electron demand cycloadditions of isatin-derived 1,2,4-triazines with acetylenic dienophiles tethered by amidations or transesterifications proceed in excellent yields to produce lactam- or lactone-fused α-carbolines. Beginning with various isatins and alkynyl dienophiles, a pilot-scale library of eighty-eight α-carbolines was prepared by using this robust methodology for biological evaluation.

Synthesis and evaluation of a series of 1,2,4,5-tetrazines for bioorthogonal conjugation

1,2,4,5-Tetrazines have been established as effective dienes for inverse electron demand [4 + 2] Diels-Alder cycloaddition reactions with strained alkenes for over 50 years. Recently, this reaction pair combination has been applied to bioorthogonal labeling and cell detection applications; however, to date, there has been no detailed examination and optimization of tetrazines for use in biological experiments. Here, we report the synthesis and characterization of 12 conjugatable tetrazines. The tetrazines were all synthesized in a similar fashion and were screened in parallel to identify candidates most ideally suited for biological studies. In depth follow-up studies revealed compounds with varying degrees of stability and reactivity that could each be useful in different bioorthogonal applications. One promising, highly stable, and water-soluble derivative was used in pretargeted cancer cell labeling studies, confirming its utility as a bioorthogonal moiety.

Inverse electron demand Diels-Alder reactions of 1,2,3-triazines: pronounced substituent effects on reactivity and cycloaddition scope

A systematic study of the inverse electron demand Diels-Alder reactions of 1,2,3-triazines is disclosed, including an examination of the impact of a C5 substituent. Such substituents were found to exhibit a remarkable impact on the cycloaddition reactivity of the 1,2,3-triazine without altering, and perhaps even enhancing, the intrinsic cycloaddition regioselectivity. The study revealed not only that the reactivity may be predictably modulated by a C5 substituent (R = CO(2)Me > Ph > H) but also that the impact is of a magnitude to convert 1,2,3-triazine (1) and its modest cycloaddition scope into a heterocyclic azadiene system with a reaction scope that portends extensive synthetic utility, expanding the range of participating dienophiles. Significantly, the studies define a now powerful additional heterocyclic azadiene, complementary to the isomeric 1,2,4-triazines and 1,3,5-triazines, capable of dependable participation in inverse electron demand Diels-Alder reactions, extending the number of complementary heterocyclic ring systems accessible with implementation of the methodology.

Scope of the inverse electron demand Diels-Alder reactions of 1,2,3-triazine

An examination of the scope of the inverse electron demand Diels-Alder reactions of the parent unsubstituted 1,2,3-triazine is described including the first report of its unique capabilities for participating in previously unexplored [4 + 2] cycloaddition reactions with heterodienophiles.

Theoretical investigation on carbon-centered tri-s-tetrazine and its 10 derivatives

A novel species, carbon-centered tri-s-tetrazine (C(4)N(9)H(3)), and its 10 derivatives (C(4)N(9)R(3), where R=OH, F, CN, N(3), NH(2), NO(2), N=NH, N(2)H(3), C triple bond CH, and CH=CH(2)) have been studied computationally. Density functional theory (DFT) has been used to study the geometries, electronic structure, harmonic vibrational frequencies, ionization energies of the 11 compounds at the restricted (for neutrals) and the unrestricted (for cations) B3LYP/cc-pVDZ level of theory. Atoms in molecule (AIM) and natural bond orbital (NBO) analyses have been used to obtain the bonding properties. Valence bond (VB) theory is applied to explain the unusual pyramidal structure around the carbon-center and electron arrangements of orbitals. We found: (1) All the species possess novel bonding features and geometrical structures. The atoms on the periphery of each species are sp(2) hybridized. Each of these atoms offers an orbital to form an extensive conjugation system (12)pi(15) (a pi system consisting of 12 centers and 15 electrons). The central carbon atom C13 is sp(3) hybridized, which makes the non-planar molecule shape like a straw-hat. Atom C13 also participates in the conjugated pi system with its sp(3) hybridized orbital, thus forming an extensive (13)pi(16) conjugate pi system covering the whole C(4)N(9) framework. (2) The change of charge on C13 is the largest among all the atoms when the species is ionized and the atomic charges are redistributed. In other words, C13 is the attack center for electrophilic agents. Thus, the species is carbanion-like. (3) All the species have low ionization energies (IEs). The electron ionized mainly comes from C13. They may have wide applications in organic chemistry, in organometallic chemistry and in alkyl lithium chemistry once they are synthesized.