High binding yet accelerated guest rotation within a cucurbit[7]uril complex. Toward paramagnetic gyroscopes and rolling nanomachines

Cucurbit[7]uril Enhances Distance Measurements of Spin-Labeled Proteins

We report complex formation between the chloroacetamide 2,6-diazaadamantane nitroxide radical (ClA-DZD) and cucurbit[7]uril (CB-7), for which the association constant in water, Ka = 1.9 × 106 M-1, is at least 1 order of magnitude higher than the previously studied organic radicals. The radical is highly immobilized by CB-7, as indicated by the increase in the rotational correlation time, τrot, by a factor of 36, relative to that in the buffer solution. The X-ray structure of ClA-DZD@CB-7 shows the encapsulated DZD guest inside the undistorted CB-7 host, with the pendant group protruding outside. Upon addition of CB-7 to T4 Lysozyme (T4L) doubly spin-labeled with the iodoacetamide derivative of DZD, we observe the increase in τrot and electron spin coherence time, Tm, along with the narrowing of interspin distance distributions. Sensitivity of the DEER measurements at 83 K increases by a factor 4-9, compared to the common spin label such as MTSL, which is not affected by CB-7. Interspin distances of 3 nm could be reliably measured in water/glycerol up to temperatures near the glass transition/melting temperature of the matrix at 200 K, thus bringing us closer to the goal of supramolecular recognition-enabled long-distance DEER measurements at near physiological temperatures. The X-ray structure of DZD-T4L 65 at 1.12 Å resolution allows for unambiguous modeling of the DZD label (0.88 occupancy), indicating an undisturbed structure and conformation of the protein.

Cucurbit[7]uril Enhances Distance Measurements of Spin-Labeled Proteins

We report complex formation between the chloroacetamide 2,6-diazaadamantane nitroxide radical (ClA-DZD) and cucurbit[7]uril (CB-7), for which the association constant in water, Ka = 1.9 × 106 M-1, is at least one order of magnitude higher than the previously studied organic radicals. The radical is highly immobilized by CB-7, as indicated by the increase of the rotational correlation time, τrot, by a factor of 36, relative to that in the buffer solution. The X-ray structure of ClA-DZD@CB-7 shows the encapsulated DZD guest inside the undistorted CB-7 host, with the pendant group protruding outside. Upon addition of CB-7 to T4 Lysozyme (T4L) doubly spin-labeled with the iodoacetamide derivative of DZD, we observe the increase in τrot and electron spin coherence time, Tm, along with the narrowing of inter-spin distance distributions. Sensitivity of the DEER measurements at 83 K increases by a factor 4 - 9, compared to the common spin label such as MTSL, which is not affected by CB-7. Inter-spin distances of 3-nm could be reliably measured in water/glycerol up to temperatures near the glass transition/melting temperature of the matrix at 200 K, thus bringing us closer to the goal of supramolecular recognition-enabled long-distance DEER measurements at near physiological temperatures. The X-ray structure of DZD-T4L 65 at 1.12 Å resolution allows for unambiguous modeling of the DZD label (0.88 occupancy), indicating undisturbed structure and conformation of the protein.

Spirocyclic Nitroxides as Versatile Tools in Modern Natural Sciences: From Synthesis to Applications. Part I. Old and New Synthetic Approaches to Spirocyclic Nitroxyl Radicals

Spirocyclic nitroxyl radicals (SNRs) are stable paramagnetics bearing spiro-junction at a-, b-, or g-carbon atom of the nitroxide fragment, which is part of the heterocyclic system. Despite the fact that the first representatives of SNRs were obtained about 50 years ago, the methodology of their synthesis and their usage in chemistry and biochemical applications have begun to develop rapidly only in the last two decades. Due to the presence of spiro-function in the SNRs molecules, the latter have increased stability to various reducing agents (including biogenic ones), while the structures of the biradicals (SNBRs) comprises a rigid spiro-fused core that fixes mutual position and orientation of nitroxide moieties that favors their use in dynamic nuclear polarization (DNP) experiments. This first review on SNRs will give a glance at various strategies for the synthesis of spiro-substituted, mono-, and bis-nitroxides on the base of six-membered (piperidine, 1,2,3,4-tetrahydroquinoline, 9,9'(10H,10H')-spirobiacridine, piperazine, and morpholine) or five-membered (2,5-dihydro-1H-pyrrole, pyrrolidine, 2,5-dihydro-1H-imidazole, 4,5-dihydro-1H-imidazole, imidazolidine, and oxazolidine) heterocyclic cores.

ESR, STESR, DFT, and MD Study of the Dynamical Structure of Cucurbituril[7]-Spin Probe Guest-Host Complexes

We study the molecular dynamics and structures of the guest-host complexes of cucurbituril, CB[7], with spin probes through the conventional electron spin resonance (ESR), saturation transfer ESR (STESR), density functional theory (DFT), and molecular dynamics (MD) computations. Protonated TEMPOamine (I), a derivative of TEMPO having a positive charge and an octyl group on the quaternary nitrogen atom (II), and the neutral spin-labeled indole (III) are used as guests. To eliminate the overall complex rotation, the solutions of complexes in a solid CB[7] matrix were prepared. Resultantly, for all of the spin probes, the combined study of the conventional ESR and STESR spectra indicates the librational character of the rotational motion within the CB[7] cavity as opposed to the diffusional rotation over the whole solid angle. The kinetic accessibilities of the reporter NO groups to the paramagnetic complexes in aqueous solutions, determined by Heisenberg exchange broadening of the ESR spectra, together with the environment polarities from the hyperfine interaction values, as well as DFT computation results and MD simulations, were used to estimate the spin probe location relative to CB[7]. Utilizing the concept of the aqueous clusters surrounding the spin probes and CB[7] molecules and MD simulations has allowed the application of DFT to estimate the aqueous environment effects on the complexation energy and spatial structure of the guest-host complexes.

Host-guest interaction of nitroxide radicals with water-soluble pillar[6]arenes

The host-guest interaction of nitroxide radicals with water-soluble pillar[n]arenes was studied for the first time by electron paramagnetic resonance spectroscopy and NMR spectroscopy. Our results showed that this interaction strongly depended on the 4-substituents of nitroxides and the cavity size of pillar[n]arenes. The host-guest interaction with water-soluble pillar[6]arene WP6 effectively increased the thermodynamic and kinetic stability of nitroxide radical 4-AT toward ascorbic acid, thus expanding its potential biomedical applications.

EPR Spectroscopy: A Powerful Tool to Analyze Supramolecular Host•Guest Complexes of Stable Radicals with Cucurbiturils

Stable organic free radicals are increasingly studied compounds due to the multiple and unusual properties imparted by the single electron(s). However, being paramagnetic, classical methods such as NMR spectroscopy can hardly be used due to relaxation and line broadening effects. EPR spectroscopy is thus better suited to get information about the immediate surroundings of the single electrons. EPR has enabled obtaining useful data in the context of host•guest chemistry, and a classical example is reported here for the stable (2,2,6,6-tetramethyl-4-oxo-piperidin-1-yl)oxyl or 4-oxo-TEMPO nitroxide (TEMPONE) inside the macrocycle host cucurbit[7]uril (CB[7]). Generally and also observed here, a contraction of the spectrum is observed as a result of the reduced nitrogen coupling constant due to inclusion complexation in the hydrophobic cavity of the host. Simulations of EPR spectra allowed determining the corresponding binding constant pointing to a weaker affinity for CB[7], compared to TEMPO with CB[7]. We complement this work by the results of EPR spectroscopy of a biradical: bis-TEMPO-bis-ketal (bTbk) with cucurbit[8]uril (CB[8]). Initial investigations pointed to very weak effects on the spectrum of the guest and incorrectly led us to conclude an absence of binding. However, simulations of EPR spectra combined with NMR data of reduced bTbk allowed showing inclusion complexation. EPR titrations were performed, and the corresponding binding constant was determined. ¹H NMR spectra with reduced bTbk suggested a shuttle mechanism, at nearly one equivalent of CB[8], for which the host moves rapidly between two stations.

Kinetic Stabilization of Carbazole Nitroxides by Inclusion in a Macrocage and Their Electron Spin Resonance Characterization

Some nitroxides, for example, tetramethylpyridiniumoxide, are known as stable radicals; however, carbazole nitroxide is less stable. The kinetic stabilization of labile radicals by introduction of bulky substituents is usually effective to investigate intrinsic properties of the molecule because of small electronic perturbation induced by the substituents. In this study, macrocage molecules with a carbazole nitroxide connected by covalent bonds were newly designed as kinetically stabilized carbazole nitroxides. The nitroxides were prepared and characterized by electron spin resonance spectroscopy. The caged nitroxides presented long half-lives (∼50 h) by kinetic analysis.

Triangular Regulation of Cucurbit[8]uril 1:1 Complexes

Triangular shapes have inspired scientists over time and are common in nature, such as the flower petals of oxalis triangularis, the triangular faces of tetrahedrite crystals, and the icosahedron faces of virus capsids. Supramolecular chemistry has enabled the construction of triangular assemblies, many of which possess functional features. Among these structures, cucurbiturils have been used to build supramolecular triangles, and we recently reported paramagnetic cucurbit[8]uril (CB[8]) triangles, but the reasons for their formation remain unclear. Several parameters have now been identified to explain their formation. At first sight, the radical nature of the guest was of prime importance in obtaining the triangles, and we focused on extending this concept to biradicals to get supramolecular hexaradicals. Two sodium ions were systematically observed by ESI-MS in trimer structures, and the presence of Na⁺ triggered or strengthened the triangulation of CB[8]/guest 1:1 complexes in solution. X-ray crystallography and molecular modeling have allowed the proposal of two plausible sites of residence for the two sodium cations. We then found that a diamagnetic guest with an H-bond acceptor function is equally good at forming CB[8] triangles. Hence, a guest molecule containing a ketone function has been precisely triangulated thanks to CB[8] and sodium cations as determined by DOSY-NMR and DLS. A binding constant for the triangulation of 1:1 to 3:3 complexes is proposed. This concept has finally been extended to the triangulation of ditopic guests toward network formation by the reticulation of CB[8] triangles using dinitroxide biradicals.

Metal Actuated Ring Translocation Switches in Water

Among a series of metal ions in water, silver is the only one to remotely and reversibly switch cucurbit[7]uril (CB[7]) movements (translocation or uptake) on a rigid and linear three-station viologen-phenylene-imidazole ( V-P-I) derivative, avoiding undesired pH actuation. ¹H NMR, UV-vis spectroscopy, mass spectrometry, ITC, and modeling were combined to show that ring translocation or uptake along a molecular thread is possible in water by Ag⁺ as a metal stimulus.

Effects of cucurbit[n]uril (n = 7, 8, 10) hosts on the formation and stabilization of a naphthalenediimide (NDI) radical anion

The binding interactions of a NDI diammonium dichloride salt with cucurbit[n]uril (CB[n], n = 7,8, 10) and the formation process of a NDI radical anion upon photoexcitation of the NDI derivative in the presence of a CB[n] host have been investigated.