Structure and conformation of cyclopentene, cycloheptene and trans-cyclooctene

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.

Indane Based Molecular Motors: UV-Switching Increases Number of Isomers

We describe azophenylindane based molecular motors (aphin-switches) which have two different rotamers of trans-configuration and four different rotamers of cis-configuration. The behaviors of these motors were investigated both experimentally and computationally. The conversion of aphin-switch does not yield single isomer but a mixture of these. Although the trans to cis conversion leads to the increase of the system entropy some of the cis-rotamers can directly convert to each other while others should convert via trans-configuration. The motion of aphin-switches resembles the work of a mixing machine with indane group serving as a base and phenol group serving as a beater. The aphin-switches presented herein may provide a basis for promising applications in advanced biological systems or particularly in cases where on demand disordering of molecular packing has value, such as lipid bilayers.

A Cleavable C2-Symmetric trans-Cyclooctene Enables Fast and Complete Bioorthogonal Disassembly of Molecular Probes

Bioorthogonal chemistry is bridging the divide between static chemical connectivity and the dynamic physiologic regulation of molecular state, enabling in situ transformations that drive multiple technologies. In spite of maturing mechanistic understanding and new bioorthogonal bond-cleavage reactions, the broader goal of molecular ON/OFF control has been limited by the inability of existing systems to achieve both fast (i.e., seconds to minutes, not hours) and complete (i.e., >99%) cleavage. To attain the stringent performance characteristics needed for high fidelity molecular inactivation, we have designed and synthesized a new C2-symmetric trans-cyclooctene linker (C2TCO) that exhibits excellent biological stability and can be rapidly and completely cleaved with functionalized alkyl-, aryl-, and H-tetrazines, irrespective of click orientation. By incorporation of C2TCO into fluorescent molecular probes, we demonstrate highly efficient extracellular and intracellular bioorthogonal disassembly via omnidirectional tetrazine-triggered cleavage.

Chemoselectivity in the Oxidation of Cycloalkenes with a Non-Heme Iron(IV)-Oxo-Chloride Complex: Epoxidation vs. Hydroxylation Selectivity

We report and analyze chemoselectivity in the gas phase reactions of cycloalkenes (cyclohexene, cycloheptene, cis-cyclooctene, 1,4-cyclohexadiene) with a non-heme iron(IV)-oxo complex [(PyTACN)Fe(O)(Cl)]⁺, which models the active species in iron-dependent halogenases. Unlike in the halogenases, we did not observe any chlorination of the substrate. However, we observed two other reaction pathways: allylic hydrogen atom transfer (HAT) and alkene epoxidation. The HAT is clearly preferred in the case of 1,4-cyclohexadiene, both pathways have comparable reaction rates in reaction with cyclohexene, and epoxidation is strongly favored in reactions with cycloheptene and cis-cyclooctene. This preference for epoxidation differs from the reactivity of iron(IV)-oxo complexes in the condensed phase, where HAT usually prevails. To understand the observed selectivity, we analyze effects of the substrate, spin state, and solvation. Our DFT and CASPT2 calculations suggest that all the reactions occur on the quintet potential energy surface. The DFT-calculated energies of the transition states for the epoxidation and hydroxylation pathways explain the observed chemoselectivity. The SMD implicit solvation model predicts the relative increase of the epoxidation barriers with solvent polarity, which explains the clear preference of HAT in the condensed phase.

Bent Singlet Cyclobutylcarbene: Computed Geometry, Properties, and Product Selectivity of a Nonclassical Carbene

Ab initio computations of cyclobutylcarbene (c-C₄H₇CH) were performed using the UMP4(fc)/6-311++G(2df,2p)//UMP2(full)/6-311++G(d,p) theoretical model. The carbene's most striking feature is its :CH-group. It is markedly bent toward the elongated C1'-C2' bond in the singlet ground-state but not in the triplet state, which is at least 1.1 kcal/mol higher in energy. Nonclassical 3C2E bonding among the C1, C1', and C2' atoms is prominent in the HOMO{-1}. The electron-donating ability of the nonbonding HOMO is thereby enhanced. The intensified nucleophilicity of the singlet carbene is manifested in quantifiable ways. For example, its hard and soft acid and base (HSAB) hardness, HSAB absolute electronegativity, and gas-phase proton affinity rival those of ylide-stabilized N-heterocyclic carbenes. It is computed to act as a nucleophile toward alkenes with higher HSAB hardness values. Transition states from singlet cyclobutylcarbene to bicyclo[2.1.0]pentane, cyclopentene, and methylenecyclobutane were computed and confirmed by intrinsic reaction coordinate calculations. Activation energies depend on the singlet's conformation with regard to c-C₄H₇ ring-puckering, :CH-group rotation, and :CH-group bending. The singlet's bent :CH-group favors bicyclo[2.1.0]pentane and cyclopentene formation.

Molecular Structure of 1-Isocyano-1-silacyclopent-3-ene: A Combined Microwave Spectral and Theoretical Study

The microwave spectrum of 1-isocyano-1-silacyclopent-3-ene has been obtained from broad-band chirped-pulse Fourier transform microwave spectroscopy. The rotational constants (RCs) for the standard abundant isotopic species are A = 3328.4182(23), B = 1017.69404(53), and C = 1012.33297(58) MHz. The symmetric quartic centrifugal distortion constants, using the I^r representation in C_S symmetry for Δ_J,Δ_JK, Δ_K, and δ_J, have been evaluated; similarly, the ¹⁴N nuclear quadrupole coupling has been determined. Several singly substituted isotopologues observed in natural abundance enabled most of the heavy atom substructure to be determined. The five-membered ring is close to planar, but the orientation of the isocyanate unit, derived from the N¹³CO spectrum, unexpectedly lies above the ring center in a cis C_2,5-Si-N═C conformation. Our initial equilibrium structural searches led to a trans orientation of the C_2,5-Si-N═C unit, i.e., bending away from the ring. When the cis conformation was applied, the final equilibrium structure, assuming C_S symmetry, gave RC values of 3221.3 ( A), 1037.0 ( B), and 1031.3 ( C) MHz, very close to the MW values. This enabled the full-equilibrium structure to be determined with confidence. The principal bond lengths were 1.7157 (Si-N), 1.8696 (Si-C), 1.1998 (N═C), and 1.1737 (C═O) Å, with angles 163.3 (Si-N═C), 178.1 (N═C═O), 96.5 (C-Si-C), and 118.7° (C-C═C), respectively. The extensive widening of the SiNC angle is particularly notable; the SiNCO unit has a trans dihedral angle. The cis orientation implies a (weak) attractive force between the ring and isocyanate groups by a through-space interaction. An atoms in molecule study, where the local minima of electron density are determined, fails to disclose the exact nature of the interaction; however, a highly polarized skeleton was obtained. A systematic theoretical study of the Si-N═C angle potential energy surface (PES) relative to the ring gave a very shallow double minimum with the barrier being less than 1 cm^-1; a polynomial fit to the surface shows major contributions of both harmonic and quartic components. A similar study of the XSiN angle, where X is at the ring center, also gave a PES with considerable quartic character.

C-H Activation in Primary 3-Phenylpropylamines: Synthesis of Seven-Membered Palladacycles through Orthometalation. Stoichiometric Preparation of Benzazepinones and Catalytic Synthesis of Ureas

The dimeric cyclometalated complexes [Pd2{κ(2)C,N-C6H4CH2CH2C(R)(Me)NH2-2}2(μ-Cl)2] (R = Me (1a), H (1b)) are prepared by reacting 1,1-dimethyl-3-phenylpropylammonium or 1-methyl-3-phenylpropylammonium triflate with Pd(OAc)2 in a 1:1 molar ratio and subsequent treatment with excess NaCl. The mononuclear derivatives [Pd{κ(2)C,N-C6H4CH2CH2C(R)(Me)NH2-2}Cl(L)] (L = PPh3, R = Me (3a), H (3b); L = 4-picoline (4-pic), R = Me (4a), H (4b)) were prepared from 1a,b by splitting the chloro bridges with the neutral ligands L. A conformational analysis of the mononuclear palladacycles in solution has been carried out. Insertion of CO takes place into the Pd-C bond of complexes 1a,b, affording Pd(0) and the tetrahydro-benzazepinone 5a or 5b, which possesses potential pharmacological interest. Additionally, the triflate salt A or B undergoes catalytic carbonylation with CO to afford the corresponding N,N'-dialkylurea, using Pd(OAc)2/Cu(OAc)2, in boiling acetonitrile. The crystal structures of 3a·(1)/2H2O, 3b, 4b·CHCl3, and 5a were determined by X-ray diffraction studies.

Chromosulfine, a novel cyclopentachromone sulfide produced by a marine-derived fungus after introduction of neomycin resistance

The discovery of chromosulfine, a novel cyclopentachromone sulfide generated by activating silent fungal pathways in a marine-derived fungus, was reported.

The isolation and synthesis of neodolastane diterpenoids

This account summarises the progress in isolation, characterisation and synthesis of diterpenoids sharing a tricyclic neodolastane skeleton as well as their biogenetic origin and diverse biological activities.

Ammonium-directed olefinic epoxidation: kinetic and mechanistic insights

The ammonium-directed olefinic epoxidations of a range of differentially N-substituted cyclic allylic and homoallylic amines (derived from cyclopentene, cyclohexene, and cycloheptene) have been investigated, and the reaction kinetics have been analyzed. The results of these studies suggest that both the ring size and the identity of the substituents on nitrogen are important in determining both the overall rate and the stereochemical outcome of the epoxidation reaction. In general, secondary amines or tertiary amines with nonsterically demanding substituents on nitrogen are superior to tertiary amines with sterically demanding substituents on nitrogen in their ability to promote the oxidation reaction. Furthermore, in all cases examined, the ability of the (in situ formed) ammonium substituent to direct the stereochemical course of the epoxidation reaction is either comparable or superior to that of the analogous hydroxyl substituent. Much slower rates of ring-opening of the intermediate epoxides are observed in cyclopentene-derived and cycloheptene-derived allylic amines as compared with their cyclohexene-derived allylic and homoallylic amine counterparts, allowing for isolation of these intermediates in both of the former cases.

Design and synthesis of highly reactive dienophiles for the tetrazine-trans-cyclooctene ligation

Computation was used to design a trans-cyclooctene derivative that displays enhanced reactivity in the tetrazine-trans-cycloctene ligation. The optimized derivative is an (E)-bicyclo[6.1.0]non-4-ene with a cis-ring fusion, in which the eight-membered ring is forced to adopt a highly strained 'half-chair' conformation. Toward 3,6-dipyridyl-s-tetrazine in MeOH at 25 °C, the strained derivative is 19 and 27 times more reactive than the parent trans-cyclooctene and 4E-cyclooct-4-enol, respectively. Toward 3,6-diphenyl-s-tetrazine in MeOH at 25 °C, the strained derivative is 160 times more reactive than the parent trans-cyclooctene.

Ammonium-directed oxidation of cyclic allylic and homoallylic amines

The ammonium-directed olefinic oxidation of a range of cyclic allylic and homoallylic amines has been investigated. Functionalization of a range of allylic 3-(N,N-dibenzylamino)cycloalk-1-enes with m-CPBA in the presence of Cl(3)CCO(2)H gives exclusively the corresponding syn-epoxide for the 5-membered ring (>99:1 dr), the anti-epoxide for the 8-membered ring (>99:1 dr), and predominantly the anti-epoxide for the 7-membered ring (94:6 dr). Oxidation of the homoallylic amines 3-(N-benzylamino)methylcyclohex-1-ene and 3-(N,N-dibenzylamino)methylcyclohex-1-ene gave, in both cases, the corresponding N-protected 1,2-anti-2,3-syn-3-aminomethylcyclohexane-1,2-diol with high levels of diastereoselectivity (>or=90:10 dr). The versatile synthetic intermediates resulting from these oxidation reactions are readily transformed into a range of amino diols.

A photochemical synthesis of functionalized trans-cyclooctenes driven by metal complexation

Described is a scalable procedure for driving photochemical sytheses of trans-cyclooctene derivatives through metal complexation. During photoirradiation, reaction mixtures are continuously pumped through a column of a AgNO3-impregnated silica gel. The trans-cyclooctene derivative is selectively retained by the AgNO3-impregnated silica, but the cis-isomer elutes from the column back to the reaction flask, where it is photoisomerized and recirculated through the column. The method provides access to a range of usefully functionalized derivatives of trans-cyclooctene, including a derivative of 5-aza-trans-cyclooctene that underwent transannular cyclization upon treatment with bromine. The alkene stereochemistry is transferred with high fidelity to the hexahydropyrrolizine framework in the transannular cyclization.

The intermolecular Pauson-Khand reaction

Five membered carbocycles are important building blocks for many biologically active molecules. Moreover, substituted cyclopentenones (e.g. cyclopentenone prostaglandins) exhibit characteristic biological activity. The efficiency and atom economy of the Pauson-Khand reaction render this process potentially one of the most attractive methods for the synthesis of such compounds. Although it was discovered in its intermolecular form, the scope of the intermolecular Pauson-Khand reaction has always been limited by the poor reactivity and selectivity of the alkene component. The past decade, especially the last three years, has seen concerted efforts to broaden the scope of this reaction. In this overview, we provide a comprehensive and critical coverage of the intermolecular Pauson-Khand reaction based on the reactivity characteristics of different classes of alkenes and a rationalization of successes and misfortunes in this area.

Addition of Cyclopropyl Alkynes to a Brook Silene: Definitive Evidence for a Biradical Intermediate

The addition of three newly developed mechanistic probes, (trans-2-phenylcyclopropyl)ethyne, (trans,trans-2-methoxy-3-phenylcyclopropyl)ethyne, and (trans,trans-2-methoxy-1-methyl-3-phenylcyclopropyl)ethyne, 1a-c, to a Brook silene, 2-tert-butyl-2-trimethylsiloxy-1,1-bis(trimethylsilyl)-1-silene, 10, was examined. When alkyne 1a was added to silene 10 products derived from a formal ene reaction were obtained. When alkynes 1b-c were added to silene 10, in addition to the typical silacyclobutenes, a variety of silacycloheptenes were obtained in which the cyclopropyl ring had clearly opened. Formal ene-addition products were also produced from the addition of 1b to 10. Based on the relative positions of the phenyl and methoxy substituents within the seven-membered ring of the silacycloheptenes and the known behavior of the alkyne probes under both radical and ionic conditions, it was concluded that a biradical intermediate was formed during the addition of alkynes 1b-c to silene 10. In the addition of alkynes 1a-b to silene 10, the ene products are most likely formed by a competitive pericyclic reaction. We also present a straightforward method for the unambiguous determination of the regiochemistry of silacyclobutenes derived from the cycloaddition of terminal alkynes to silenes.

A cryosolution infrared and ab initio study of the van der Waals complexes of cyclopentene with hydrogen chloride and boron trifluoride

The formation of weak molecular complexes of cyclopentene with HCl and BF3, dissolved in liquid argon is investigated using infrared spectroscopy. Evidence is found for the formation of 1:1 complexes in which the Lewis acid under study binds to the CC double bond. At higher concentrations of HCl, weak absorption bands due to 1:2 species are also observed. From spectra recorded at different temperatures between 92 and 127 K, the complexation enthalpies for CP.HCl and CP.BF3 are determined to be -9.5(3) and -16.1(9) kJ mol-1, while for CP.(HCl)2 a value of -17.0(6) kJ mol-1 is obtained. For the 1:1 and 1:2 complexes, structural and spectral information is obtained from ab initio calculations at the MP2/6-31+G(d) level. Using free energy perturbation Monte Carlo simulations to calculate the solvation enthalpies and statistical thermodynamics to account for zero-point vibrational and thermal contributions, the complexation energies for CP.HCl and CP.(HCl)2 are estimated from the experimental complexation enthalpies to be -17.4(14) and -34.0(20) kJ mol-1, while the value for CP.BF3 was derived to be -23.4(22) kJ mol-1. The experimental complexation energies are compared with the theoretical values derived from the MP2/6-31+G(d) potential energy surfaces and with single point energies calculated at the MP2/6-311++G(3df,2pd) level.

An alpha,alpha'-dioxothione and its

In the reaction of Ninhydrin (1a)/1,2,3-indantrione (1b) with potassium thiotosylate, 1,4-oxathiin 6 is formed in up to 63% yield as the trapping product of the intermediary alpha,alpha'-dioxothione 1c with trans-cyclooctene (3a). Additionally, up to 18% of the available sulfur is transferred to olefin 3a to thiirane 3b through the intermediary oxathiirane.