Synthesis of a pillar[5]arene dimer by co-oligomerization and its complexation with n-octyltrimethyl ammonium hexafluorophosphate

Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: II. regression and dielectric constant

End-point free energy calculations as a powerful tool have been widely applied in protein-ligand and protein-protein interactions. It is often recognized that these end-point techniques serve as an option of intermediate accuracy and computational cost compared with more rigorous statistical mechanic models (e.g., alchemical transformation) and coarser molecular docking. However, it is observed that this intermediate level of accuracy does not hold in relatively simple and prototypical host-guest systems. Specifically, in our previous work investigating a set of carboxylated-pillar[6]arene host-guest complexes, end-point methods provide free energy estimates deviating significantly from the experimental reference, and the rank of binding affinities is also incorrectly computed. These observations suggest the unsuitability and inapplicability of standard end-point free energy techniques in host-guest systems, and alteration and development are required to make them practically usable. In this work, we consider two ways to improve the performance of end-point techniques. The first one is the PBSA_E regression that varies the weights of different free energy terms in the end-point calculation procedure, while the second one is considering the interior dielectric constant as an additional variable in the end-point equation. By detailed investigation of the calculation procedure and the simulation outcome, we prove that these two treatments (i.e., regression and dielectric constant) are manipulating the end-point equation in a somehow similar way, i.e., weakening the electrostatic contribution and strengthening the non-polar terms, although there are still many detailed differences between these two methods. With the trained end-point scheme, the RMSE of the computed affinities is improved from the standard ~ 12 kcal/mol to ~ 2.4 kcal/mol, which is comparable to another altered end-point method (ELIE) trained with system-specific data. By tuning PBSA_E weighting factors with the host-specific data, it is possible to further decrease the prediction error to ~ 2.1 kcal/mol. These observations along with the extremely efficient optimized-structure computation procedure suggest the regression (i.e., PBSA_E as well as its GBSA_E extension) as a practically applicable solution that brings end-point methods back into the library of usable tools for host-guest binding. However, the dielectric-constant-variable scheme cannot effectively minimize the experiment-calculation discrepancy for absolute binding affinities, but is able to improve the calculation of affinity ranks. This phenomenon is somehow different from the protein-ligand case and suggests the difference between host-guest and biomacromolecular (protein-ligand and protein-protein) systems. Therefore, the spectrum of tools usable for protein-ligand complexes could be unsuitable for host-guest binding, and numerical validations are necessary to screen out really workable solutions in these 'prototypical' situations.

Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: I. Standard procedure

Despite the massive application of end-point free energy methods in protein-ligand and protein-protein interactions, computational understandings about their performance in relatively simple and prototypical host-guest systems are limited. In this work, we present a comprehensive benchmark calculation with standard end-point free energy techniques in a recent host-guest dataset containing 13 host-guest pairs involving the carboxylated-pillar[6]arene host. We first assess the charge schemes for solutes by comparing the charge-produced electrostatics with many ab initio references, in order to obtain a preliminary albeit detailed view of the charge quality. Then, we focus on four modelling details of end-point free energy calculations, including the docking procedure for the generation of initial condition, the charge scheme for host and guest molecules, the water model used in explicit-solvent sampling, and the end-point methods for free energy estimation. The binding thermodynamics obtained with different modelling schemes are compared with experimental references, and some practical guidelines on maximizing the performance of end-point methods in practical host-guest systems are summarized. Further, we compare our simulation outcome with predictions in the grand challenge and discuss further developments to improve the prediction quality of end-point free energy methods. Overall, unlike the widely acknowledged applicability in protein-ligand binding, the standard end-point calculations cannot produce useful outcomes in host-guest binding and thus are not recommended unless alterations are performed.

Neutral Isocyanide-Templated Assembly of Pillar[5]arene [2] and [3]Pseudorotaxanes

Unprecedented pillar[5]arene–isocyanide pseudorotaxane inclusion complexes are reported. Extensive 1H-NMR experiments reveal remarkably strong binding affinities of alkyl diisocyanide guests (Ka >105 M-1 in CDCl3) by pillar[5]arenes. Characterised by multinuclear 1H...

Covalently bridged pillararene-based oligomers: from construction to applications

Covalently bridged pillararene-based oligomers (CBPOs) are formed by covalent bonding of pillararene monomers, and they play a critical role in expanding the multi-disciplinary application of pillararenes due to their excellent molecular complexing ability, specially designed geometry and multifunctional linking groups. This article provides a comprehensive review of the synthesis and applications of CBPOs. The design and synthetic strategies of a series of CBPOs (dimers, trimers, tetramers and others) are first introduced. Many CBPOs with multi-cavities and unique geometry are very attractive and efficient building blocks for constructing novel smart supramolecular polymers (SPs) with different topological structures through host-guest interactions. We describe the methods of constructing various SPs based on CBPOs in detail. Furthermore, the extensive applications of CBPOs and CBPO-based SPs in recognition and detection of ions and organic small molecules, selective adsorption and separation, artificial light-harvesting systems, catalysis, drug delivery systems, and others are systematically introduced. Finally, the future challenges and perspectives for CBPOs are also highlighted.

Anion-Responsive Pseudo[3]rotaxane from a Difunctionalized Pillar[4]arene[1]quinone and a Bis-Imidazolium Cation

Synthesis of a new functionalized pillar[4]arene[1]quinone and its host-guest complexation with a bis-imidazolium dication was demonstrated. 1D/2D NMR spectroscopic analyses and high-resolution mass spectrometric analyses showed the formation of the pseudo[3]rotaxane assembly upon host-guest complexation. ¹H NMR titration experiments revealed the role of hydrogen bonding motifs in bringing positive cooperativity by comparing the binding constants for the host-guest complexation of pillar[4]arene[1]quinone with a bis-imidazolium guest. Anion-responsiveness of the pseudo[3]rotaxane assembly was also demonstrated.

Oxacalix[4]arene-bridged pillar[5]arene dimers: syntheses, planar chirality and construction of chiral rotaxanes

Conformationally fixed oxacalix[4]arene-bridged pillar[5]arene dimers comprising a pair of enantiomers and a meso isomer were designed and synthesized. Furthermore, chiral [2]rotaxanes and [3]rotaxanes were constructed. Two pairs of enantiomers for [2]rotaxanes, one pair of enantiomers and a meso isomer for [3]rotaxanes were found, respectively.

Controllable hierarchical self-assembly of porphyrin-derived supra-amphiphiles

Control of self-assembly is significant to the preparation of supramolecular materials and illustration of diversities in either natural or artificial systems. Supra-amphiphiles have remarkable advantages in the construction of nanostructures but control of shape and size of supramolecular nanostructures is still a great challenge. Here, we fabricate a series of supra-amphiphiles by utilizing the recognition motifs based on a heteroditopic porphyrin amphiphile and its zinc complex. These porphyrin amphiphiles can bind with a few guests including Cl^-, coronene, C₆₀, 4,4'-bipyridine and 2,4,6-tri(pyridin-4-yl)-1,3,5-triazine, which are further applied to facilitate the controllable self-assembly. Addition of these guests result in the formation of various supra-amphiphiles with well-defined structures, thus induce the generation of different aggregates. A diverse of aggregation morphologies including nanospheres, nanorods, films, spheric micelles, vesicles and macrowires are constructed upon the influence of specific complexation, which highlights the present work with abundant control on the shapes and dimensions of self-assemblies.

Biological and related applications of pillar[n]arenes

Pillar[n]arenes are a new class of synthetic supramolecular macrocycles streamlined by their particular pillar-shaped architecture which consists of an electron-rich cavity and two fine-tuneable rims. The ease and diversity of the functionalization of the two rims open possibilities for the design of new architectures, topological isomers, and scaffolds. Significantly, this emerging class of macrocyclic receptors offers a unique platform for biological purposes. This review article covers the most recent contributions from the pillar[n]arene field in terms of artificial membrane transport systems, controlled drug delivery systems, biomedical imaging, biosensors, cell adhesion, fluorescent sensing, and pesticide detection based on host-guest interactions. The review also uniquely describes the properties of sub-units that make pillar[n]arenes suitable for biological applications and it provides a detailed outline for the design of new innovative pillar-like structures with specific properties to open up a new avenue for pillar[n]arene chemistry.

Recent advances in pillar[n]arenes: synthesis and applications based on host-guest interactions

Pillar[n]arenes (n = 5-15) are a novel class of macrocyclic molecules with hydroquinone as the repeating unit linked by methylene bridges at para-positions. Introduced by T. Ogoshi for the first time in 2008, pillararenes have attracted increasing interest and have been widely studied during the last eight years, due to their unique structural advantages as host molecules, such as symmetrical rigid architecture, electron-rich cavities and facile functional modification. In this review, we first describe the syntheses of pillar[n]arenes including cyclooligomerization of pillar[n]arenes and modification of pillar[n]arenes after cyclooligomerization, summarising almost twenty different kinds of guest motifs and dividing them into three types: cationic, neutral and anionic motifs. The main section of this review examines the applications of pillar[n]arenes based on the host-guest interactions in different research fields, including biology, materials science and environmental science. Finally, future research directions and potential for novel applications are discussed.

A multi-stimuli responsive metallosupramolecular polypseudorotaxane gel constructed by self-assembly of a pillar[5]arene-based pseudo[3]rotaxane via zinc ion coordination and its application for highly sensitive fluorescence recognition of metal ions

A novel pillar[5]arene-based metallosupramolecular polypseudorotaxane gel has been successfully prepared.

Novel rare earth fluorescent supramolecular polymeric assemblies constructed by orthogonal pillar[5]arene-based molecular recognition, Eu(iii)-coordination and π–π donor–acceptor interactions

Linear rare earth fluorescent supramolecular polymer is easily constructed by pillar[5]arene-based molecular interaction.

Pillar-Shaped Macrocyclic Hosts Pillar[n]arenes: New Key Players for Supramolecular Chemistry

In 2008, we reported a new class of pillar-shaped macrocyclic hosts, known as "pillar[n]arenes". Today, pillar[n]arenes are recognized as key players in supramolecular chemistry because of their facile synthesis, unique pillar shape, versatile functionality, interesting host-guest properties, and original supramolecular assembly characteristics, which have resulted in numerous electrochemical and biomedical material applications. In this Review, we have provided historical background to macrocyclic chemistry, followed by a detailed discussion of the fundamental properties of pillar[n]arenes, including their synthesis, structure, and host-guest properties. Furthermore, we have discussed the applications of pillar[n]arenes to materials science, as well as their applications in supramolecular chemistry, in terms of their fundamental properties. Finally, we have described the future perspectives of pillar[n]arene chemistry. We hope that this Review will provide a useful reference for researchers working in the field and inspire discoveries concerning pillar[n]arene chemistry.

Synthesis of a disulfide-bridged bispillar[5]arene and its application in supramolecular polymers

A disulfide-bridged bispillar[5]arene was synthesized efficiently and applied to fabricate supramolecular polymers, which were redox-responsive and could be used to prepare fluorescent water-dispersible nanospheres.

Amino-functionalized pillar[5]arene

The recently introduced pillar[n]arenes have provided chemists with receptors that, when incorporated into materials, confer unique properties upon them. The symmetrical rims and cylindrical shape of pillar[5]arene begs the question--can these pillar-like receptors be linked covalently end-to-end in order to create tubular structures by a growth-from-template approach? In our efforts to produce these one-dimensional extended structures, we have developed a new method of functionalizing pillar[5]arene in which one of the five hydroquinone units is converted into a diaminobenzoquinone analogue. The resulting diaminopillar[5]arene derivative, which undergoes a stereochemical inversion process that is slow on the (1)H NMR timescale, can be chemically modified yet further in a direction that is orthogonal to the plane of its methylene bridging carbons through the formation of oxazole heterocycles. This strategy has been employed to create rigid oligomers that resemble one-dimensional tubular arrays. As a proof-of-principle, a rigid pillar[5]arene dimer has been isolated and characterized in the solution state as a 1:1 complex with an extended viologen for which it acts as a receptor.

Theoretical investigations on vibrational spectra of pillar[5]arene-bis(pyridinium) complexes

Electronic structure and vibrational spectra of pillar[5]arene (P5) complexes with bis(pyridinium) derivatives viz., 1,2-ethylenedipyridine (edpy), 1,2-propylenedipyridine (3-pdpy), 1,2-butylenedipyridine (bdpy), 1,2-pentamethylenedipyridine (pdpy) and 1,2-hexamethylenedipyridine (hdpy) are investigated employing density functional theory. B3LYP based density functional calculations predicted that interaction energies for complexation decreases steadily with increasing alkyl chain of bis(pyridinium) guest. The calculations have shown that O-H⋯O hydrogen bonded and non-bonded hydroxyls in the host led to distinct vibrations at the 3515 cm(-1) and 3681 cm(-1), respectively in the vibrational spectra. Complexation of bis(pyridinium) guest engenders frequency down-shift for aromatic C-H(α) vibrations owing to C-H⋯O interactions with P5 portals. Moreover, C-H⋯π interactions are inferred in edpy@P5 and 3-pdpy@P5 complexes which results in frequency up-shift (blue shift) of nearly 22-15 cm(-1) for the corresponding C-H(α) vibration.

Syntheses of a pillar[4]arene[1]quinone and a difunctionalized pillar[5]arene by partial oxidation

A pillar[4]arene[1]quinone and a difunctionalized pillar[5]arene have been synthesized by partial oxidation.

Pillararenes, a new class of macrocycles for supramolecular chemistry

Because of the importance of novel macrocycles in supramolecular science, interest in the preparation of these substances has grown considerably. However, the discovery of a new class of macrocycles presents challenges because of the need for routes to further functionalization of these molecules and good host-guest complexation. Furthermore, useful macrocylic hosts must be easily synthesized in large quantities. With these issues in mind, the recently discovered pillararenes attracted our attention. These macrocycles contain hydroquinone units linked by methylene bridges at para positions. Although the composition of pillararenes is similar to that of calixarenes, they have different structural characteristics. One conformationally stable member of this family is pillar[5]arene, which consists of five hydroquinone units. The symmetrical pillar architecture and electron-donating cavities of these macrocycles are particularly intriguing and afford them with some special and interesting physical, chemical, and host-guest properties. Due to these features and their easy accessibility, pillararenes, especially pillar[5]arenes, have been actively studied and rapidly developed within the last 4 years. In this Account, we provide a comprehensive overview of pillararene chemistry, summarizing our results along with related studies from other researchers. We describe strategies for the synthesis, isomerization, and functionalization of pillararenes. We also discuss their macrocyclic cavity sizes, their host-guest properties, and their self-assembly into supramolecular polymers. The hydroxyl groups of the pillararenes can be modified at all positions or selectively on one or two positions. Through a variety of functionalizations, researchers have developed many pillararene derivatives that exhibit very interesting host-guest properties both in organic solvents and in aqueous media. Guest molecules include electron acceptors such as viologen derivatives and (bis)imidazolium cations and alkyl chain derivatives such as n-hexane, alkanediamines, n-octyltrimethyl ammonium, and neutral bis(imidazole) derivatives. These host-guest studies have led to the fabrication of (pseudo)rotaxanes or poly(pseudo)rotaxanes, supramolecular dimers or polymers, artificial transmembrane proton channels, fluorescent sensors, and other functional materials.