Rim Binding of Cyclodextrins in Size-Sensitive Guest Recognition

Cinematographic study of stochastic chemical events at atomic resolution

The advent of single-molecule atomic-resolution time-resolved electron microscopy (SMART-EM) has created a new field of 'cinematic chemistry,' allowing for the cinematographic recording of dynamic behaviors of organic and inorganic molecules and their assembly. However, the limited electron dose per frame of video images presents a major challenge in SMART-EM. Recent advances in direct electron counting cameras and techniques to enhance image quality through the implementation of a denoising algorithm have enabled the tracking of stochastic molecular motions and chemical reactions with sub-millisecond temporal resolution and sub-angstrom localization precision. This review showcases the development of dynamic molecular imaging using the SMART-EM technique, highlighting insights into nanomechanical behavior during molecular shuttle motion, pathways of multistep chemical reactions, and elucidation of crystallization processes at the atomic level.

Spontaneous and Selective Macrocyclization in Nitroaldol Reaction Systems

Through a dynamic polymerization and self-sorting process, a range of lowellane macrocycles have been efficiently generated in nitroaldol systems composed of aromatic dialdehydes and aliphatic or aromatic dinitroalkanes. All identified macrocycles show a composition of two repeating units, resulting in tetra-β-nitroalcohols of different structures. The effects of the building block structure on the macrocyclization process have been demonstrated, and the influence from the solvent has been explored. In general, the formation of the lowellanes was amplified in response to phase-change effects, although solution-phase structures were, in some cases, favored.

Construction of molecular enrichment accelerators via assembly of enzyme surface grafted polymer and cyclodextrin achieving rapid and stable ester catalysis for biodiesel synthesis

Efficient and stable catalysis has always been the core concept of enzyme catalysis in industrial processes for manufacturing. Here, we constructed molecular enrichment accelerators to synergistically enhance enzyme activity and stability by assembling enzyme surface grafted polymer and cyclodextrin. At 40 °C, the enzyme activity of CalB-PNIPAM212/β-CD was 2.9 times that of CalB-PNIPAM212. The enzyme activity of CalB-PNIPAM428/γ-CD had reached 1.61 times that of CalB. At the same time, the stability of CalB-PNIPAM212/β-CD and CalB-PNIPAM428/γ-CD are slightly better than that of CalB under high temperature, organic solution and extreme pH conditions. The synergistic increase in activity and stability of the lipase-polymer assembly was achieved due to the structure of assembly, in which the role of cyclodextrin could enrich substrate affecting molecular diffusion. In addition, the lipase-polymer assembly proved to be an efficient catalyst for biodiesel synthesis, with a biodiesel conversion 1.4 times that of CalB at 60 °C. Therefore, this simple and low-cost lipase-polymer assembly provides new possibilities for the construction of high-efficiency industrial biocatalytic catalysts.

Complexation of Fluorofenidone by Cucurbit[7]uril and β-Cyclodextrin: Keto-Enol Tautomerization to Enhance the Solubility

This study is designed to compare drug encapsulation by cucurbit[7]uril and β-cyclodextrin, using fluorofenidone as a model drug. Single-crystal X-ray diffraction analysis was employed to successfully determine the crystal structures of fluorofenidone·H+@cucurbit[7]uril Form, fluorofenidone@cucurbit[7]uril Form, and fluorofenidone@β-cyclodextrin Form. Keto-enol tautomerization of fluorofenidone mediated by cucurbit[7]uril in acid solution is confirmed by crystal structures, pH titration, and nuclear magnetic resonance experiments. However, β-cyclodextrin cannot cause the keto-enol tautomerization of fluorofenidone under similar conditions. The phase solubility study demonstrates that cucurbit[7]uril has a much higher solubilization capacity for fluorofenidone than β-cyclodextrin in 0.1 M HCl since the Kc values of fluorofenidone with cucurbit[7]uril and β-cyclodextrin were 1223.97 ± 452.68 and 78.49 ± 10.56 M-1, respectively. Excellent solubility can be attributed to the keto-enol tautomerization of fluorofenidone under the conditions of cucurbit[7]uril in acid solution. The enol form of fluorofenidone is encapsulated by cucurbit[7]uril by hydrogen bonding interaction and hydrophobic interaction to increase binding affinity. Rat pharmacokinetic studies demonstrate that the area under the plasma concentration-time curve from time 0 to 7 h value of fluorofenidone@cucurbit[7]uril complex is 1.70-fold greater than that of free fluorofenidone, and the mean residence time from time 0 to 7 h is slightly prolonged from 1.29 to 1.76 h (P < 0.01) after oral administration. However, no significant difference is found between fluorofenidone and fluorofenidone@β-cyclodextrin complex. This work indicates that the induction of keto-enol tautomerization of drugs using macrocyclic molecules has the potential to be an effective method to improve their solubility and bioavailability, providing valuable insights for the application of macrocyclic molecules in the biomedical field.

Size-matched hydrogen bonded hydroxylammonium frameworks for regulation of energetic materials

Size matching molecular design utilizing host-guest chemistry is a general, promising strategy for seeking new functional materials. With the growing trend of multidisciplinary investigations, taming the metastable high-energy guest moiety in well-matched frameworks is a new pathway leading to innovative energetic materials. Presented is a selective encapsulation in hydrogen-bonded hydroxylammonium frameworks (HHF) by screening different sized nitrogen-rich azoles. The size-match between a sensitive high-energy guest and an HHF not only gives rise to higher energetic performance by dense packing, but also reinforces the layer-by-layer structure which can stabilize the resulting materials towards external mechanic stimuli. Preliminary assessment based on calculated detonation properties and mechanical sensitivity indicates that HHF competed well with the energetic performance and molecular stability (detonation velocity = 9286 m s−1, impact sensitivity = 50 J). This work highlights the size-matched phenomenon of HHF and may serve as an alternative strategy for exploring next generation advanced energetic materials.

Time-Resolved Atomistic Imaging and Statistical Analysis of Daptomycin Oligomers with and without Calcium Ions

Daptomycin (DP) is effective against multiple drug-resistant Gram-positive pathogens because of its distinct mechanism of action. An accepted mechanism includes Ca²⁺-triggered aggregation of the DP molecule to form oligomers. DP and its oligomers have so far defied structural analysis at a molecular level. We studied the ability of DP molecule to aggregate by itself in water, the effects of Ca²⁺ ions to promote the aggregation, and the connectivity of the DP molecules in the oligomers by the combined use of dynamic light scattering in water and atomic-resolution cinematographic imaging of DP molecules captured on a carbon nanotube on which the DP molecule is installed as a fishhook. We found that the DP molecule aggregates weakly into dimers, trimers, and tetramers in water, and strongly in the presence of calcium ions, and that the tetramer is the largest oligomer in homogeneous aqueous solution. The dimer remains as the major species, and we propose a face-to-face stacked structure based on dynamic imaging using millisecond and angstrom resolution transmission electron microscopy. The tetramer in its cyclic form is the largest oligomer observed, while the trimer forms in its linear form. The study has shown that the DP molecule has an intrinsic property of forming tetramers in water, which is enhanced by the presence of calcium ions. Such experimental structural information will serve as a platform for future drug design. The data also illustrate the utility of cinematographic recording for the study of self-organization processes.

Ionization and electron excitation of C60 in a carbon nanotube: A variable temperature/voltage transmission electron microscopic study

The destruction of specimen molecules by an electron beam (e-beam) is either beneficial, as in mass spectrometry capitalizing on ion formation, or deleterious, as in electron microscopy. In the latter application, the e-beam not only produces the specimen image, but also causes information loss upon prolonged irradiation. However, the atomistic mechanism of such loss has been unclear. Performing single-molecule kinetic analysis of C₆₀ dimerization in a carbon nanotube (CNT) under variable-temperature/voltage conditions, we identified three reactive species—that is, radical cation, singlet, and triplet excited states—reacting competitively as the voltage and the properties of the CNT were changed. The key enabler was in situ continuous recording of the whole reaction process, suggesting an upcoming new era of “cinematic chemistry.”

There is increasing attention to chemical applications of transmission electron microscopy, which is often plagued by radiation damage. The damage in organic matter predominantly occurs via radiolysis. Although radiolysis is highly important, previous studies on radiolysis have largely been descriptive and qualitative, lacking in such fundamental information as the product structure, the influence of the energy of the electrons, and the reaction kinetics. We need a chemically well-defined system to obtain such data and have chosen as a model a variable-temperature and variable-voltage (VT/VV) study of the [2 + 2] dimerization of a van der Waals dimer [60]fullerene (C₆₀) to C₁₂₀ in a carbon nanotube (CNT), as studied for several hundred individual reaction events at atomic resolution. We report here the identification of five reaction pathways that serve as mechanistic models of radiolysis damage. Two of them occur via a radical cation of the specimen generated by specimen ionization, and three involve singlet or triplet excited states of the specimen, as initiated by electron excitation of the CNT, followed by energy transfer to the specimen. The [2 + 2] product was identified by measuring the distance between the two C₆₀ moieties, and the mechanisms were distinguished by the pre-exponential factor and the Arrhenius activation energy—the standard protocol of chemical kinetic studies. The results illustrate the importance of VT/VV kinetic analysis in the studies of radiation damage and show that chemical ionization and electron excitation are inseparable, but different, mechanisms of radiation damage, which has so far been classified loosely under the single term “ionization.”

Molecular Recognition in an Aqueous Medium Using Water-Soluble Prismarene Hosts

The synthesis of water-soluble prism[n]arenes (n = 5 and 6) bearing anionic carboxylato groups on the rims is described. The binding properties of this novel class of water-soluble hosts are studied by nuclear magnetic resonance and calorimetry. The complexation of singly and doubly charged ammonium guests with the more rigid pentamer is enthalpically driven by secondary interactions, while the thermodynamic fingerprint for the larger hexamer reveals driving forces that strongly depend on the guest charge and/or size.

Atomic-number (Z)-correlated atomic sizes for deciphering electron microscopic molecular images

Atomic resolution transmission electron microscopy (TEM) has opened up a new era of molecular science by providing atomic video images of dynamic motions of single organic and inorganic molecules. However, the images often look different from the images of molecular models, because these models are designed to visualize the electronic properties of the molecule instead of nuclear electrostatic potentials that are felt by the e-beam in TEM imaging. Here, we propose a molecular model that reproduces TEM images using atomic radii correlated to atomic number (Z). The model serves to provide a priori a useful idea of how a single molecule, molecular assemblies, and thin crystals of organic or inorganic materials look in TEM.

With the advent of atomic resolution transmission electron microscopy (AR-TEM) achieving sub-Ångstrom image resolution and submillisecond time resolution, an era of cinematic molecular science where chemists can visually study the time evolution of molecular motions and reactions at atomistic precision has arrived. However, the appearance of experimental TEM images often differs greatly from that of conventional molecular models, and the images are difficult to decipher unless we know in advance the structure of the specimen molecules. The difference arises from the fundamental design of the molecular models that represent atomic connectivity and/or the electronic properties of molecules rather than the nuclear charge of atoms and electrostatic potentials that are felt by the e-beam in TEM imaging. We found a good correlation between the atomic number (Z) and the atomic size seen in TEM images when we consider shot noise in digital images. We propose Z-correlated (ZC) atomic radii for modeling AR-TEM images of single molecules and ultrathin crystals with which we can develop a good estimate of the molecular structure from the TEM image much more easily than with conventional molecular models. Two parameter sets were developed for TEM images recorded under high-noise (ZC_HN) and low-noise (ZC_LN) conditions. The molecular models will stimulate the imaginations of chemists planning to use AR-TEM for their research.

Hydrophobic Localized Enrichment of Co-reactants to Enhance Electrochemiluminescence of Conjugated Polymers for Detecting SARS-CoV-2 Nucleocapsid Proteins

The enrichment of co-reactants is one of the keys to improving the sensitivity of electrochemiluminescence (ECL) detection. This work developed a novel hydrophobic localized enrichment strategy of co-reactants utilizing the inner hydrophobic cavity of β-cyclodextrin (β-CD). Pt nanoparticles (Pt NPs) were grown in situ on the coordination sites for metal ions of β-CD to prepare the β-CD-Pt nanocomposite, which could not only enrich co-reactant 3-(dibutylamino) propylamine (TDBA) highly efficiently through its hydrophobic cavity but also immobilize TDBA via the Pt-N bond. Meanwhile, the carboxyl-functionalized poly[2,5-dioctyl-1,4-phenylene] (PDP) polymer nanoparticles (PNPs) were developed as excellent ECL luminophores. With SARS-CoV-2 nucleocapsid protein (ncovNP) as a model protein, the TDBA-β-CD-Pt nanocomposite combined PDP PNPs to construct a biosensor for ncovNP determination. The PDP PNPs were modified onto the surface of a glassy carbon electrode (GCE) to capture the first antibody (Ab1) and further capture antigen and secondary antibody complexes (TDBA-β-CD-Pt@Ab2). The resultant biosensor with a sandwich structure achieved a highly sensitive detection of ncovNP with a detection limit of 22 fg/mL. TDBA-β-CD-Pt shared with an inspiration in hydrophobic localized enrichment of co-reactants for improving the sensitivity of ECL detection. The luminophore PDP PNPs integrated TDBA-β-CD-Pt to provide a promising and sensitive ECL platform, offering a new method for ncovNP detection.

Efficient Persistent Luminescence Tuning Using a Cyclodextrin Inclusion Complex as Efficient Light Conversion Materials

Developing an appropriate method to broaden the color of long persistent luminescence materials has important scientific significance and practical value but remains a great challenge. Herein, we have developed a unique strategy to fine-tune the persistent luminescence using the inclusion complex of rhodamine 6G with (2-hydroxypropyl)-β-cyclodextrin as efficient light conversion materials. The emitting color of the novel persistent luminescence material could be tuned from green to orange by changing the concentration of the light conversion agent. Furthermore, afterglow decay measurements showed that the initial afterglow brightness is 9.65 cd/m², and the initial afterglow brightness gradually decreased as the cyclodextrin inclusion compound coating increased. This design concept introduces a new perspective for broadening the luminescence color of afterglow phosphors, which may open up new opportunities for persistent luminescence materials toward many emerging applications.