Cavitand Complexes in Aqueous Solution: Collaborative Experimental and Computational Studies of the Wetting, Assembly, and Function of Nanoscopic Bowls in Water

Tetrafluororesorcin[4]arene Hexameric Capsule Enables the Expansion of the Reactivity Space in Supramolecular Catalysis

This study presents the development and catalytic applications of the tetrafluororesorcin[4]arene hexameric capsule (capsule II) as a novel supramolecular catalyst. It demonstrates unprecedented catalytic activity, enabling the β-selective glycosylation of glycals to 2-deoxy glycosides─a transformation that has not been achieved before in molecular and supramolecular catalysis. Mechanistic investigations, including experimental and computational studies, revealed that the high β-selectivity arises from a proton wire mechanism along the capsule's surface, coupling glycal protonation with nucleophile deprotonation. Control experiments confirmed the unique reactivity of capsule II compared to its nonfluorinated predecessor, capsule I, showcasing its potential to expand the boundaries of supramolecular catalysis.

Tuning Bro̷nsted Acidity by up to 12 pKa Units in a Redox-Active Nanopore Lined with Multifunctional Metal Sites

Electrostatic interactions, hydrogen bonding, and solvation effects can alter the free energies of ionizable functional groups in proteins and other nanoporous architectures, allowing such structures to tune acid-base chemistry to support specific functions. Herein, we expand on this theme to examine how metal sites (M = H2, ZnII, CoII, CoI) affect the pKa of benzoic acid guests bound in discrete porphyrin nanoprisms (M3TriCage) in CD3CN. These host-guest systems were chosen to model how porous metalloporphyrin electrocatalysts might influence H+ transfer processes that are needed to support important electrochemical reactions (e.g., reductions of H+, O2, or CO2). Usefully, the cavities of the host-guest complexes become hydrated at low water concentrations (10-40 mM), providing a good representation of the active sites of porous electrocatalysts in water. Under these conditions, Lewis acidic CoII and ZnII ions increase the Bro̷nsted acidities of the guests by 4 and 8 pKa units, respectively, while reduction of the CoII sites to anionic CoI sites produces an electrostatic potential that lowers acidity by ca. 4 units (8 units relative to the CoII state). Lacking functional metal sites, H6TriCage increases the acidity of the guests by just 2.5 pKa units despite the 12+ charge of this host and contributions from other factors (hydrogen bonding, hydration) that might stabilize the deprotonated guests. Thus, the metal sites have dominant effects on acid-base chemistry in the M3TriCages, providing a larger pKa range (12.75 to ≥24.5) for an encapsulated acid than attained via other confinement effects in proteins and artificial porous materials.

An updated synthesis of octa-acid

Octa-acid 1 is a water-soluble deep-cavity cavitand devised in our labs that has found utility in a number of research groups. The host has been used to investigate hydrophobic solvation and Hofmeister effects, control photophysical and physicochemical properties, modulate the reactivity of encapsulated guests, and as a tool to engender novel separation protocols. The synthesis of 1 has largely centered around its formation from cavitand 2, a host that is itself most readily synthesized on the multi-gram-scale but in a crude form (>75% purity). In this Methods Article we reveal improvements in the synthesis of 2, as well as a new synthetic strategy that efficiently converts crude 2 into pure 1. This new synthesis provides access to 1 in only a five-step linear sequence, shortening the total reaction time from previous methods, improving the purity, and increasing the final yield of pure 1. We therefore anticipate that the described protocols will be of interest to any research group seeking to utilize octa-acid in their studies.

Window[1]resorcin[3]arenes: A Novel Macrocycle Able to Self-Assemble to a Catalytically Active Hexameric Cage

The hexameric resorcin[4]arene capsule has been utilized as one of the most versatile supramolecular capsule catalysts. Enlarging its size would enable expansion of the substrate size scope. However, no larger catalytically active versions have been reported. Herein, we introduce a novel class of macrocycles, named window[1]resorcin[3]arene (wRS), that assemble to a cage-like hexameric host. The new host was studied by NMR, encapsulation experiments, and molecular dynamics simulations. The cage is able to bind tetraalkylammonium ions that are too large for encapsulation inside the hexameric resorcin[4]arene capsule. Most importantly, it retained its catalytic activity, and the accelerated conversion of a large substrate that does not fit the closed hexameric resorcin[4]arene capsule was observed. Thus, it will help to expand the limited substrate size scope of the closed hexameric resorcin[4]arene capsule.

An Affordable Topography-Based Protocol for Assigning a Residue's Character on a Hydropathy (PARCH) Scale

The hydropathy of proteins or quantitative assessment of protein-water interactions has been a topic of interest for decades. Most hydropathy scales use a residue-based or atom-based approach to assign fixed numerical values to the 20 amino acids and categorize them as hydrophilic, hydroneutral, or hydrophobic. These scales overlook the protein's nanoscale topography, such as bumps, crevices, cavities, clefts, pockets, and channels, in calculating the hydropathy of the residues. Some recent studies have included protein topography in determining hydrophobic patches on protein surfaces, but these methods do not provide a hydropathy scale. To overcome the limitations in the existing methods, we have developed a Protocol for Assigning a Residue's Character on the Hydropathy (PARCH) scale that adopts a holistic approach to assigning the hydropathy of a residue. The parch scale evaluates the collective response of the water molecules in the protein's first hydration shell to increasing temperatures. We performed the parch analysis of a set of well-studied proteins that include the following─enzymes, immune proteins, and integral membrane proteins, as well as fungal and virus capsid proteins. Since the parch scale evaluates every residue based on its location, a residue may have very different parch values inside a crevice versus a surface bump. Thus, a residue can have a range of parch values (or hydropathies) dictated by the local geometry. The parch scale calculations are computationally inexpensive and can compare hydropathies of different proteins. The parch analysis can affordably and reliably aid in designing nanostructured surfaces, identifying hydrophilic and hydrophobic patches, and drug discovery.

Biomimetic tail-to-head terpene cyclizations using the resorcin[4]arene capsule catalyst

The tail-to-head terpene (THT) cyclization is a biochemical process that gives rise to many terpene natural product skeletons encountered in nature. Historically, it has been difficult to achieve THT synthetically without using an enzyme. In this protocol, a hexameric resorcin[4]arene capsule acts as an artificial enzyme mimic to carry out biomimetic THT cyclizations and related carbocationic rearrangements. The precursor molecule bears a leaving group (usually an alcohol or acetate group) and undergoes the THT reaction in the presence of the capsule catalyst and HCl as a cocatalyst. Careful control of several parameters (including water content, amount of HCl cocatalyst, temperature and solvent) is crucial to successfully carrying out the reaction. To facilitate the application of this unique capsule-catalysis methodology, we therefore developed a very detailed procedure that includes the preparation and analysis of all reaction components. In this protocol, we describe how to prepare two different terpenes: isolongifolene and presilphiperfolan-1β-ol. The two procedures differ in the water content required for efficient product formation, and thus exemplify the two common use cases of this methodology. The influence of other crucial reaction parameters and means of precisely controlling them are described. A commercially available substrate, nerol, can be used as simple test substrate to validate the reaction setup. Each synthetic procedure requires 5-7 d, including 1-5 h of hands-on time. The protocol applies to the synthesis of many complex terpene natural products that would otherwise be difficult to access in synthetically useful yields.

Exploring the Glycosylation Reaction Inside the Resorcin[4]arene Capsule

In the past decade, there has been an increased interest in applying supramolecular capsule and cage catalysis to the current challenges in synthetic organic chemistry. In this context, we recently reported the resorcin[4]arene capsule-catalyzed conversion of α-glycosyl halides into β-glycosides with high selectivity. Interestingly, this methodology enabled the formation of a wide range of β-pyranosides as well as β-furanosides, although these two donor classes exhibit different reactivities and usually require different reaction conditions and catalysts. Evidence was provided that a proton wire plays a key role in this reaction by enabling dual activation of the glycosyl donor and acceptor. Here, we describe a detailed investigation of several aspects of this reactivity. Besides a mechanistic study, we elucidated the size limitation, the origin of catalytic turnover, and the electrophile scope of nonglycosylic halides. Moreover, a screening of the sensitivity to changes in the reaction conditions provides guidelines to facilitate reproducibility. Furthermore, we demonstrate the compatibility with environmentally benign solvent alternatives, including the renewable solvent limonene.

Host Dynamics under General-Purpose Force Fields

Macrocyclic hosts as prototypical receptors to gaseous and drug-like guests are crucial components in pharmaceutical research. The external guests are often coordinated at the center of these macromolecular containers. The formation of host-guest coordination is accompanied by the broken of host-water and host-ion interactions and sometimes also involves some conformational rearrangements of the host. A balanced description of various components of interacting terms is indispensable. However, up to now, the modeling community still lacks a general yet detailed understanding of commonly employed general-purpose force fields and the host dynamics produced by these popular selections. To fill this critical gap, in this paper, we profile the energetics and dynamics of four types of popular macrocycles, including cucurbiturils, pillararenes, cyclodextrins, and octa acids. The presented investigations of force field definitions, refitting, and evaluations are unprecedently detailed. Based on the valuable observations and insightful explanations, we finally summarize some general guidelines on force field parametrization and selection in host-guest modeling.

Supramolecular Capsule Catalysis Enables the Exploration of Terpenoid Chemical Space Untapped by Nature

Terpenes represent the largest and the most diverse class of natural compounds. This is remarkable as the whole variety is accessed from just a handful of highly conserved linear precursors. Modification of the cyclization precursors would enable a dramatic expansion of the accessible chemical space. However, natural enzymes do not enable us to tap into this potential, as they do not tolerate larger deviations from the prototypical substrate structure. Herein we report that supramolecular capsule catalysis enables facile access to diverse and novel terpenoid skeletons that formally can be traced back to C3-phenyl, benzyl, and homoprenyl derivatives of farnesol. Novel skeletons related to the presilphiperfolane core structure, as well as novel neoclovene derivatives were accessed efficiently in only four synthetic steps. Importantly, the products obtained carry functional groups that may be readily derivatized further.

A New Application of Spin and Fluorescence Double-Sensor Molecules

EPR imaging techniques are known to be successful tools for mapping living bodies, especially because of the high transparency of tissues in the microwave range. This technique assumes the presence of radicals whose in vivo transport is also controlled by serum albumins. Accordingly, in this study, the interactions between 3-hydroxymethyl-1-oxyl-4-(pyren-1-yl)-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrole radical and the human serum albumin molecules were investigated. To clarify the adsorption processes of this radical onto the surface of human serum albumin (HSA), the interaction of the OMe derivative of the radical was also examined parallel with the studies on the radical—HSA interactions. Considering the solubility issues and also to modulate the transport, inclusion complexes of the radical with a cavitand derivative were also studied. The latter interactions were observed through fluorescence spectroscopy, fluorescence polarization, and by EPR spectroscopy. As a double-sensor molecule, we found that the fluorophore nitroxide is a good candidate as it gave further information about host-guest interactions (fluorescence, fluorescence polarization, and EPR). We also found that in the presence of a cavitand, a complex with greater stability was formed between the sensor molecule and the human serum albumin. Based on these observations, we can conclude that applying this double-sensor (spin, fluorescent) molecule is useful in cases when different interactions can affect the EPR measurements.

Supramolecular Capsule-Catalyzed Highly β-Selective Furanosylation Independent of the SN1/SN2 Reaction Pathway

The resorcin[4]arene capsule was found to catalyze β-selective furanosylation reactions for a variety of different furanosyl donors: α-d- and α-l-arabinosyl-, α-l-fucosyl-, α-d-ribosyl-, α-d-xylosyl-, and even α-d-lyxosyl fluorides. The scope is only limited by the inherently finite volume inside the closed capsular catalyst. The catalyst is readily available on a multi-100 g scale and can be recycled for at least seven rounds without significant loss in activity, yield, and selectivity. The mechanistic investigations indicated that the furanosylation mechanism is shifted toward an SN1 reaction on the mechanistic continuum between the prototypical SN1 and SN2 substitution types, as compared to the pyranosylation reaction inside the same catalyst. This is especially true for the lyxosyl donor, as indicated by the nucleophile reaction order of 0.26, and supported by metadynamics calculations. The mechanistic shift toward SN1 is of high interest as it indicates that this catalyst not only enables β-selective furanosylations and pyranoslyations independently of the substrate configuration but in addition also independently of the operating mechanism. To our knowledge, there is no alternative catalyst available that displays such properties.

Megalo-Cavitands: Synthesis of Acridane[4]arenes and Formation of Large, Deep Cavitands for Selective C70 Uptake

Deep cavitands, concave molecular containers, represent an important supramolecular host class that has been explored for a variety of applications ranging from sensing, switching, purification and adsorption to catalysis. A major limitation in the field has been the cavitand volume that is restricted by the size of the structural platform utilized (diameter approx. 7 Å). We here report the synthesis of a novel, unprecedentedly large structural platform, named acridane[4]arene (diameter approx. 14 Å), suitable for the construction of cavitands with volumes of up to 814 Å3 . These megalo-cavitands serve as size-selective hosts for fullerenes with mM to sub-μM binding affinity for C60 and C70 . Furthermore, the selective binding of fullerene C70 in the presence of C60 was demonstrated.

Ultrafast Excited State Dynamics of Spatially Confined Organic Molecules

This Feature Article highlights the role of spatial confinement in controlling the fundamental behavior of molecules. Select examples illustrate the value of using space as a tool to control and understand excited-state dynamics through a combination of ultrafast spectroscopy and conventional steady-state methods. Molecules of interest were confined within a closed molecular capsule, derived from a cavitand known as octa acid (OA), whose internal void space is sufficient to accommodate molecules as long as tetracene and as wide as pyrene. The free space, i.e., the space that is left following the occupation of the guest within the host, is shown to play a significant role in altering the behavior of guest molecules in the excited state. The results reported here suggest that in addition to weak interactions that are commonly emphasized in supramolecular chemistry, the extent of empty space (i.e., the remaining void space within the capsule) is important in controlling the excited-state behavior of confined molecules on ultrafast time scales. For example, the role of free space in controlling the excited-state dynamics of guest molecules is highlighted by probing the cis-trans isomerization of stilbenes and azobenzenes within the OA capsule. Isomerization of both types of molecule are slowed when they are confined within a small space, with encapsulated azobenzenes taking a different reaction pathway compared to that in solution upon excitation to S₂. In addition to steric constraints, confinement of reactive molecules in a small space helps to override the need for diffusion to bring the reactants together, thus enabling the measurement of processes that occur faster than the time scale for diffusion. The advantages of reducing free space and confining reactive molecules are illustrated by recording unprecedented excimer emission from anthracene and by measuring ultrafast electron transfer rates across the organic molecular wall. By monitoring the translational motion of anthracene pairs in a restricted space, it has been possible to document the pathway undertaken by excited anthracene from inception to the formation of the excimer on the excited-state surface. Similarly, ultrafast electron transfer experiments pursued here have established that the process is not hindered by a molecular wall. Apparently, the electron can cross the OA capsule wall provided the donor and acceptor are in close proximity. Measurements on the ultrafast time scale provide crucial insights for each of the examples presented here, emphasizing the value of both "space" and "time" in controlling and understanding the dynamics of excited molecules.

Enantioselective Tail-to-Head Terpene Cyclizations by Optically Active Hexameric Resorcin[4]arene Capsule Derivatives

Molecular capsules enable the conversion of substrates inside a closed cavity, mimicking to some extent enzymatic catalysis. Chirality transfer from the molecular capsule onto the encapsulated substrate has been only studied in a few cases. Here we demonstrate that chirality transfer is possible inside a rather large molecular container of approximately 1400 Å3 . Specifically, we present 1) the first examples of optically active hexameric resorcin[4]arene capsules, 2) their ability to enantioselectively catalyze tail-to-head terpene cyclizations, and 3) the surprisingly high sensitivity of enantioselectivity on the structural modifications.

On the Nature of Guest Complexation in Water: Triggered Wetting-Water-Mediated Binding

The complexity of macromolecular surfaces means that there are still many open questions regarding how specific areas are solvated and how this might affect the complexation of guests. Contributing to the identification and classification of the different possible mechanisms of complexation events in aqueous solution, and as part of the recent SAMPL8 exercise, we report here on the synthesis and conformational properties of TEEtOA 2, a cavitand with conformationally flexible ethyl groups at its portal. Using a combination of ITC and NMR spectroscopy, we report the binding affinities of a series of carboxylates to 2 and compare it to a related cavitand TEMOA 1. Additionally, we report MD simulations revealing how the wetting of the pocket of 2 is controlled by the conformation of its rim ethyl groups and, correspondingly, a novel triggered wetting, guest complexation mechanism, whereby the approaching guest opens up the pocket of the host, inducing its wetting and ultimately allows the formation of a hydrated host-guest complex (H·G·H2O). A general classification of complexation mechanisms is also suggested.

Chiral Water-Soluble Molecular Capsules With Amphiphilic Interiors

We present the synthesis of new chiral water-soluble dimeric capsules by the multicomponent Mannich reaction between charged amino acids (glutamic acid or arginine), resorcinarene, and formaldehyde and by subsequent self-assembly. The zwitterionic character of the backbones enables electrostatic interactions between arms and induces self-assembly of dimeric capsules, namely, (L-ArgR)₂ and (L-GluR)₂, in water with a wide range of pH, as demonstrated by NMR, diffusion coefficient measurement, and circular dichroism. The assembly/disassembly processes are fast on the NMR timescale. This mode of dimerization leaves side chains available for additional interactions and creates chiral cavities of mixed hydrophobic/hydrophilic character. According to this characteristic, capsules do not bind fully nonpolar or fully polar guests but effectively encapsulate a variety of chiral molecules with mixed polar/apolar characters (aliphatic and aromatic aldehydes, epoxides, alcohols, carboxylic acids, amines, and amino acids) with moderate strength. We also demonstrate the formation of heterocapsules (GluR) (ArgR) (homo- and heterochiral) that utilize additional interactions between charged acidic and basic side chains and have better encapsulation properties than those of the homodimers.

When Molecules Meet in Water-Recent Contributions of Supramolecular Chemistry to the Understanding of Molecular Recognition Processes in Water

Molecular recognition processes in water differ from those in organic solvents in that they are mediated to a much greater extent by solvent effects. The hydrophobic effect, for example, causes molecules that only weakly interact in organic solvents to stay together in water. Such water-mediated interactions can be very efficient as demonstrated by many of the synthetic receptors discussed in this review, some of which have substrate affinities matching or even surpassing those of natural binders. However, in spite of considerable success in designing such receptors, not all factors determining their binding properties in water are fully understood. Existing concepts still provide plausible explanations why the reorganization of water molecules often causes receptor-substrate interactions in water to be strongly exothermic rather than entropically favored as predicted by the classical view of the hydrophobic effect.

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.

Organic pollutants in water-soluble cavitands and capsules: contortions of molecules in nanospace

We report on the binding properties of deep cavitand for various industrial pollutants in water. Depending on the guest type, monomeric cavitands, dimeric capsules or both acted as receptors and...

The role of electric field, peripheral chains, and magnetic effects on significant 1H upfield shifts of the encapsulated molecules in chalcogen-bonded capsules

The chalcogen-bonded homo-cavitand and hetero-cavitand AY+AY' capsules (Y, Y' = Se, Te), as well as their encapsulated complexes with one or two guest molecules have been studied theoretically via density functional theory (DFT), while the ¹H NMR spectra of the homo-cavitand encapsulated complexes (in ASe+ASe) have been measured experimentally. There is excellent agreement between theoretical and experimental spectra. In all cases, we found significant ¹H upfield shifts which are more intense in the ASe+ASe cage compared to the ATe+ATe and ASe+ATe cages. The non-uniform electron distribution which gives rise to an inherent electric field and a non-zero electric dipole moment of the encapsulated complexes, the induced electric field effects, the magnetic anisotropy which is enhanced due to the polarizability of chalcogen atoms, and the peripheral chains, which are responsible for the solubility of the cages, increase the upfield shifts of ¹H of the encapsulated molecules; the peripheral chains lead to an increase of the upfield shifts by up to 1.8 ppm for H of the rim and up to 1.2 ppm for the terminal H in the interior of the cage. Hence, substantial ¹H upfield chemical shifts of the guests in these capsules are consequences of (i) the enhanced aromaticity of the walls of the capsules due to the polarizability of chalcogen atoms, (ii) the induced and inherent electric field effects, and (iii) the peripheral chains.

Evolution of the Free Energy Landscapes of n-Alkane Guests Bound within Supramolecular Complexes

Confinement within nanoscale spaces can dramatically alter the ensemble of conformations flexible species explore. For example, chaperone complexes take advantage of confinement to fold misfolded proteins, while viral capsids transport genomic materials in tight packings. Here we examine the free energy landscapes of n-alkanes confined within supramolecular dimeric complexes of deep-cavity cavitand octa-acid, which have been experimentally demonstrated to force these chains with increasing length to adopt extended, helical, hairpin, and spinning top conformational motifs, using molecular simulations. Alkanes up to n-docosane in both vacuum and water predominantly exhibit a free energy minimum for elongated conformations with a majority of trans dihedrals. Within harmonically sealed cavitand dimers, however, the free energy landscapes as a function of the end-to-end distance between their terminal methyl units exhibit minima that evolve with the length of the alkane. Distinct free energy basins are observed between the helical and hairpin motifs and between the hairpin and chicane motifs whose relative stability changes with the number of carbons in the bound guest. These changes are reminiscent of two state-like protein folding, although the observed alkane conformations confined are more insensitive to temperature perturbation than proteins are. While the chicane motif within the harmonically sealed dimers has not been observed experimentally, this conformation relaxes to the observed spinning top motif once the harmonic restraints are released for the complexes in aqueous solution, indicating that these motifs are related to one another. We do not observe distinct minima between the confined extended and helical motifs, suggesting these conformers are part of a larger linear motif family whose population of gauche dihedral angles grows in proportion to the number of carbons in the chain to ultimately form a helix that fits the alkane within the complex.