Emission properties of cyclodextrin dimers linked with perylene diimide—effect of cyclodextrin tumbling

Solubility of Hydrophobes into Macrocyclic Hosts

The intrinsic nature of macrocyclic molecules to preferentially absorb a specific solute has been opening up supramolecular chemistry. Nevertheless, the determinant factor with molecular perspectives in promoting host-guest complexations remains inconclusive, due to the lack of rigorous thermodynamic examination on the guest solubility inside the host. Here, we quantify the solute-solvent energetic and entropic contributions between the end states and on the docking route during inclusion of noble gases in cucurbit[5]uril, cucurbit[6]uril, and α-cyclodextrin, using molecular dynamics simulations in combination with the potential distribution theorem. Results show that in all of the pairs examined both the solute-solvent energy and entropy favor the inclusion, while the former is rather dominant. The frequency of interior drying, which pertains to the entropic contribution, differs between the hosts and is controlled by the existence of lid water at portal and the flexibility of host framework. Moreover, the hosts exhibit various types of absorption manners, involving non-, single-, and double-free-energy barriers.

Guest-Mediated Reversal of the Tumbling Process in Phosphorus-Dendritic Compounds Containing β-Cyclodextrin Units: An NMR Study

The conformational study of dendritic platforms containing multiple β-cyclodextrin (βCD) units in the periphery is relevant to determine the availability of βCD cavities for the formation of inclusion complexes in aqueous biological systems. In this work, we performed a detailed conformational analysis in D2O, via 1D and 2D NMR spectroscopy of a novel class of phosphorus dendritic compounds of the type P3N3-[O-C6H4-O-(CH2)n-βCD]6 (where n = 3 or 4). We unambiguously demonstrated that a functionalized glucopyranose unit of at least one βCD unit undergoes a 360° tumbling process, resulting in a deep inclusion of the spacer that binds the cyclodextrin to the phosphorus core inside the cavity, consequently limiting the availability of the inner cavities. In addition, we confirmed through NMR titrations that this tumbling phenomenon can be reversed for all βCD host units using a high-affinity guest, namely 1-adamantanecarboxylic acid (AdCOOH). Our findings have demonstrated that it is possible to create a wide variety of multi-functional dendritic platforms.

Self-Inclusion and Dissociation of a Bridging β-Cyclodextrin Triplet

To understand the self-inclusion and the dissociation in a branched β-cyclodextrin (CD) system, we designed and synthesized a β-CD trimer in which each CD group is connected to one of bridging arms of a planar triphenylbenzene core through a CuAAC click reaction. Only one rather than two or all of the three host CDs was demonstrated to be in a self-including state in water, while no self-inclusion was observed to occur in dimethylsulfoxide (DMSO) via the characterization of ¹H and NOESY NMR spectra. The configuration structures of the CD groups in the self-included state were evaluated, and the dissociation to free state in water was investigated under various conditions like heating, increased acidity, and discharging versus the addition of competitive guests. While raised temperature and increased acidity did not break the self-inclusion, two adamantane guest molecules were found to show capability in driving the equilibrium to get back to free state against the self-inclusion. The inclusion process of the added guests was believed to involve in the dissociation of the self-inclusion and the occupation of the guests in CD cavity. The results of host-guest interaction study indicated that the stable combination of guests was favorable for blocking the structural overturning of glucose toward trapping the bridging group into the cavity.

How Does PHEMA Pass through the Cavity of γ-CDs to Create Mismatched Overfit Polypseudorotaxanes?

A syndiotactic-rich PHEMA oligomer ( rr = 74%, DP = 29, PDI = 1.19) was synthesized and subsequently subjected to self-assembly with a varying amount of γ-CDs in its aqueous solution to create mismatched overfit polypseudorotaxanes (PPRs). The inclusion complexation proceeded in an obvious mismatched manner between the cavity of γ-CDs and the cross-sectional area of an incoming PHEMA chain. The 2D-NOESY NMR analysis provided direct evidence indicating that two adjacent pendant hydroxyethyl groups in PHEMA preferably adopt a curled conformation to pass through the cavity of γ-CDs, giving the PPRs characteristics of a mismatched overfit instead of a matched tight-fit crystal structure. The results suggested that the mutual adaption of pendant side chains of HEMA units with the cavity geometry of γ-CDs would play a dominant role in this unfavorable overfit inclusion complexation besides the size of γ-CDs and the stereoregularity of the PHEMA chain.

Validation and Comparison of Force Fields for Native Cyclodextrins in Aqueous Solution

Molecular dynamics simulations of native α-, β-, and γ-cyclodextrin in aqueous solution have been conducted with the goal to investigate the performance of the CHARMM36 force field, the AMBER-compatible q4md-CD force field, and five variants of the GROMOS force field. The properties analyzed are structural parameters derived from X-ray diffraction and NMR experiments as well as hydrogen bonds and hydration patterns, including hydration free enthalpies. Recent revisions of the torsional-angle parameters for carbohydrate systems within the GROMOS family of force fields lead to a significant improvement of the agreement between simulated and experimental NMR data. Therefore, we recommend using the variant 53A6_GLYC instead of 53A6 and 56A6_{CARBO_R} or 2016H66 instead of 56A6_CARBO to simulate cyclodextrins in solution. The CHARMM36 and q4md-CD force fields show a similar performance as the three recommended GROMOS parameter sets. A significant difference is the more flexible nature of the cyclodextrins modeled with the CHARMM36 and q4md-CD force fields compared to the three recommended GROMOS parameter sets.

Experimental Studies on A New Fluorescent Ensemble of Calix[4]pyrrole and Its Sensing Performance in the Film State

The supramolecular approach plays a pivotal role in the construction of smart and functional materials due to the reversible nature of noncovalent interactions. In the present work, two compounds, cholesterol-functionalized calix[4]pyrrole (CCP) and perylene bisimide diacid (PDA), were synthesized. Little fluorescence is observed in the ethanol solution of the mixture of CCP and PDA, while the solution turns fluorescent upon introduction of ammonia, which is attributed to the formation of a supramolecular ensemble, PDA/(CCP)₂/NH₃. The fluorescence emission of the as-formed ensemble is sensitive to the presence of phenol, an electron-rich analyte. Interestingly, the sensing can also be observed in the film state, and the relevant detection limit (DL) is lower than 1 ppb. Moreover, the sensing could also be performed in a visualized manner. Upon the basis of the findings, a sensor device with instant response and good reversibility was developed. Further studies revealed that the as-developed fluorescent ensemble is also sensitive to the presence of TNT, an electron-poor compound. The DL for this sensing is ∼80 nM. To our knowledge, this is the first report that a fluorescent sensor could be used for phenol sensing in the vapor state, and for sensing of both electron-rich and electron-poor analytes in solution state. It is believed that the present study presents a distinctive example that demonstrates how smart sensing is realized via combination of the host-guest chemistry of calix[4]pyrrole and the aggregation and disaggregation property of PBI derivatives.

Rational Design for Rotaxane Synthesis through Intramolecular Slippage: Control of Activation Energy by Rigid Axle Length

We describe a new concept for rotaxane synthesis through intramolecular slippage using π-conjugated molecules as rigid axles linked with organic soluble and flexible permethylated α-cyclodextrins (PM α-CDs) as macrocycles. Through hydrophilic-hydrophobic interactions and flipping of PM α-CDs, successful quantitative conversion into rotaxanes was achieved without covalent bond formation. The rotaxanes had high activation barrier for their de-threading, so that they were kinetically isolated and derivatized even under conditions unfavorable for maintaining the rotaxane structures. (1) H NMR spectroscopy experiments clearly revealed that the restricted motion of the linked macrocycle with the rigid axle made it possible to control the kinetic stability by adjusting the length of the rigid axle in the precursor structure rather than the steric bulkiness of the stopper unit.

Host-guest interactions derived multilayer perylene diimide thin film constructed on a scaffolding porphyrin monolayer

The development of methods to grow well-ordered chromophore thin films on solid substrates is of importance because such surface-associated arrays have potential applications in the generation of functional electronic and optical materials and devices. In this article, we demonstrate a straightforward layer-by-layer (LBL) supramolecular deposition strategy to prepare numerous layers (up to 19) of functionalized perylene diimide (PDI) chromophores built upon a covalent scaffolding multivalent porphyrin monolayer. Our thin film formation strategy employs water as the immersion solvent and exploits the β-cyclodextrin-adamantane host-guest couple in addition to PDI based aromatic stacking. Within the resultant film the porphyrin scaffold is oriented close to parallel to the glass substrate while the PDI chromophores are aligned closer to the surface normal. Together, the porphyrin monolayer and the multi-PDI layers exhibit a large absorption bandwidth in the visible spectrum. Importantly, because a self-assembly strategy was utilized, when a single monolayer of PDI is deposited on the porphyrin scaffolding layer, this PDI monolayer can be readily disassembled by washing with DMF leading to the regeneration of the porphyrin monolayer. The PDI thin film can subsequently be regrown from the regenerated porphyrin surface. The reported LBL strategy will be of broad interest for researchers developing well-organized chromophoric films and materials due to its simplicity as well as the added advantage of being performed in sustainable and cost-effective aqueous media.

A switchable bis-branched [1]rotaxane featuring dual-mode molecular motions and tunable molecular aggregation

A multifunctional bis-branched [1]rotaxane containing a perylene bisimide (PBI) core and two identical bistable[1]rotaxane arms terminated with ferrocene units was prepared and characterized by (1)H NMR, (13)C NMR, and 2D ROESY NMR spectroscopies and by HR-ESI spectrometry. The system is shown to possess several key features: (1) In acetone solution, external acid-base stimuli can result in relative mechanical movements of its ring and thread, which can induce extension and contraction movements of the whole system accompanied by a rotational movement of the ferrocene units, thus realizing dual-mode molecular motions, and the optimized conformations at different states are obtained through molecular dynamics simulations employing the general Amber force field. (2) The introduction of PBI enables the system fluorescence encoding through distance-dependent photoinduced electron transfer process from the ferrocene units to the PBI fluorophore. (3) The addition of Zn(2+) can increase the degree of aggregation of the system, while adding base hinders aggregation because of the movement of the macrocycle. The tunable aggregated nanostructural morphologies of [1]rotaxane were examined by scanning electron microscopy. These results can pave the way to achieve precise control of integrated and coupling nanomechanical motions at a single-molecule level and provide more insight into controlling the aggregate behavior of switchable mechanically interlocked molecules.

Staudinger ligation towards cyclodextrin dimers in aqueous/organic media. Synthesis, conformations and guest-encapsulation ability

β-Cyclodextrin (β-CD) dimers have been prepared using the bioorthogonal Staudinger ligation for the first time. In addition to a known linker, methyl 2-(diphenylphosphanyl)terephthalate, a doubly active linker was specifically developed that enabled connection of two β-CD units in a single step and in aqueous/organic media, under mild conditions and with good yields. A three-carbon spacer between the β-CD torus and the azido group was required for facile dimer formation. The products, as studied by NMR spectroscopy, were found to adopt closed conformations by intramolecular self-inclusion. On the other hand, association via intermolecular binding was also observed in aqueous solution, confirmed by DOSY NMR experiments. Despite self-inclusion, the β-CD cavities were capable of guest encapsulation, as shown by titration experiments: the binding constant with 1-adamantylamine was similar to that of natural β-CD. Theoretical calculations for isolated molecules (PM3 level of theory) and in the presence of solvent [water, PM3(COSMO)] as well as DFT calculations suggested that the compounds prefer to adopt conformations which bring the phenyl groups either inside the β-CD cavity (inclusion) or over its narrow side (vicinal). Thus, Staudinger ligation could be the method of choice for linking CDs exhibiting (i) ease of preparation in aqueous media, in short steps, under mild conditions and in good yields, (ii) satisfactory aqueous solubility and independent binding capacity of the cavities.

Cyclodextrin-based molecular machines

This chapter overviews molecular machines based on cyclodextrins (CDs). The categories of CD-based molecular machines, external stimuli for CD-based molecular machines, and typical examples of CD-based molecular machines are briefly described.