Molecular baskets form inclusion complexes with phenethylamine drugs in water

Molecular basket 16- comprising a nonpolar cavity and an anionic nest of six carboxylates at its rim was found to form inclusion complexes with (1R, 2S)-ephedrine, (1R, 2R)-pseudoephedrine, and (1S, 2R)-tranylcypromine. Experimental results (NMR) and theory (MM/DFT) suggest the basket encapsulates phenethylamines in unique and predictable fashion.

Dynamic and Assembly Characteristics of Deep-Cavity Basket Acting as a Host for Inclusion Complexation of Mitoxantrone in Biotic and Abiotic Systems

We describe the preparation, dynamic, assembly characteristics of vase-shaped basket 13- along with its ability to form an inclusion complex with anticancer drug mitoxantrone in abiotic and biotic systems. This novel cavitand has a deep nonpolar pocket consisting of three naphthalimide sides fused to a bicyclic platform at the bottom while carrying polar glycines at the top. The results of 1 H Nuclear Magnetic Resonance (NMR), 1 H NMR Chemical Exchange Saturation Transfer (CEST), Calorimetry, Hybrid Replica Exchange Molecular Dynamics (REMD), and Microcrystal Electron Diffraction (MicroED) measurements are in line with 1 forming dimer [12 ]6- , to be in equilibrium with monomers 1(R) 3- (relaxed) and 1(S) 3- (squeezed). Through simultaneous line-shape analysis of 1 H NMR data, kinetic and thermodynamic parameters characterizing these equilibria were quantified. Basket 1(R) 3- includes anticancer drug mitoxantrone (MTO2+ ) in its pocket to give stable binary complex [MTO⊂1]- (Kd =2.1 μM) that can be precipitated in vitro with UV light or pH as stimuli. Both in vitro and in vivo studies showed that the basket is nontoxic, while at a higher proportion with respect to MTO it reduced its cytotoxicity in vitro. With well-characterized internal dynamics and dimerization, the ability to include mitoxantrone, and biocompatibility, the stage is set to develop sequestering agents from deep-cavity baskets.

Crystalline Nanoparticles of Water-Soluble Covalent Basket Cages (CBCs) for Encapsulation of Anticancer Drugs

We herein describe the preparation, assembly, recognition characteristics, and biocompatibility of novel covalent basket cage CBC-11, composed of four molecular baskets linked to four trivalent aromatic amines through amide groups. The cage is tetrahedral in shape and similar in size to small proteins (Mw =8637 g/mol) with a spacious nonpolar interior for accommodating multiple guests. While 24 carboxylates at the outer surface of CBC-11 render it soluble in aqueous phosphate buffer (PBS) at pH=7.0, the amphiphilic nature prompts its assembly into nanoparticles (d=250 nm, DLS). Cryo-TEM examination of nanoparticles revealed their crystalline nature with wafer-like shapes and hexagonally arranged cages. Nanoparticulate CBC-11 traps anticancer drugs irinotecan and doxorubicin, with each cage binding up to four drug molecules in a non-cooperative manner. The inclusion complexation resulted in nanoparticles growing in size and precipitating. In media containing mammalian cells (HCT 116, human colon carcinoma), the IC50 value of CBC-11 was above 100 μM. While this work presents the first example of a large covalent organic cage operating in water at the physiological pH and forming crystalline nanoparticles, it also demonstrates its biocompatibility and potential to act as a polyvalent binder of drugs for their sequestration or delivery.

Rapid Access to Chiral and Tripodal Cavitands from β-Pinene

We report Pd-catalyzed cyclotrimerization of (+)-α-bromoenone, obtained from monoterpene β-pinene, into an enantiopure cyclotrimer. This C₃ symmetric compound has three bicyclo[3.1.1]heptane rings fused to its central benzene with each ring carrying a carbonyl group. The cyclotrimer undergoes diastereoselective threefold alkynylation with the lithium salts of five terminal alkynes (41-63 %, de=4-83 %). The addition enabled a rapid synthesis of a small library of novel chiral cavitands that, in shape, resemble a tripod stand. These molecular tripods include a tris-bicycloannelated benzene head attached to three alkyne legs twisted in one direction to form a nonpolar cavity with polar groups as feet. Tripods with methylpyridinium and methylisoquinolinium legs, respectively, form inclusion complexes with anti-inflammatory and chiral drugs (R)/(S)-ibuprofen and (R)/(S)-naproxen. The mode of binding shows drug molecules docked in the cavity of the host through ion-ion, cation-π, and C-H-π contacts that, in addition of desolvation, give rise to complexes having millimolar to micromolar stability in water. Our findings open the door to creating a myriad of enantiopure tripods with tunable functions that, in the future, might give novel chemosensors, catalysts or sequestering agents.

Closed Aromatic Tubes-Capsularenes

In this study, we describe a synthetic method for incorporating arenes into closed tubes that we name capsularenes. First, we prepared vase-shaped molecular baskets 4-7. The baskets comprise a benzene base fused to three bicycle[2.2.1]heptane rings that extend into phthalimide (4), naphthalimide (6), and anthraceneimide sides (7), each carrying a dimethoxyethane acetal group. In the presence of catalytic trifluoroacetic acid (TFA), the acetals at top of 4, 6 and 7 change into aliphatic aldehydes followed by their intramolecular cyclization into 1,3,5-trioxane (¹ H NMR spectroscopy). Such ring closure is nearly a quantitative process that furnishes differently sized capsularenes 1 (0.7×0.9 nm), 8 (0.7×1.1 nm;) and 9 (0.7×1.4 nm;) characterized by X-Ray crystallography, microcrystal electron diffraction, UV/Vis, fluorescence, cyclic voltammetry, and thermogravimetry. With exceptional rigidity, unique topology, great thermal stability, and perhaps tuneable optoelectronic characteristics, capsularenes hold promise for the construction of novel organic electronic devices.

Dissipative Formation of Covalent Basket Cages

Living systems use chemical fuels to transiently assemble functional structures. As a step toward constructing abiotic mimics of such structures, we herein describe dissipative formation of covalent basket cage CBC 5 by reversible imine condensation of cup‐shaped aldehyde 2 (i.e., basket) with trivalent aromatic amine 4. This nanosized [4+4] cage (V=5 nm³, M_w=6150 Da) has shape of a truncated tetrahedron with four baskets at its vertices and four aromatic amines forming the faces. Importantly, tris‐aldehyde basket 2 and aliphatic tris‐amine 7 undergo condensation to give small [1+1] cage 6. The imine metathesis of 6 and aromatic tris‐amine 4 into CBC 5 was optimized to bias the equilibrium favouring 6. Addition of tribromoacetic acid (TBA) as a chemical fuel perturbs this equilibrium to result in the transient formation of CBC 5, with subsequent consumption of TBA via decarboxylation driving the system back to the starting state.

A double-decker cage for allosteric encapsulation of ATP

In this work, we describe the preparation of double-decker cage [1-H₆]⁶⁺ comprising two binding pockets, each with three ammonium and three amide hydrogen bonding sites. This novel host possesses a high affinity for trapping two molecules of ATP in an allosteric fashion, with both experiments and theory suggesting the synergistic action of charged hydrogen bonds and π-π stacking in the encapsulation.

Picking on Carbonate: Kinetic Selectivity in the Encapsulation of Anions

Supramolecular hosts bind to inorganic anions at a fast rate and select them in proportion with thermodynamic stability of the corresponding [anion⊂host] complexes, forming in a reversible manner. In this study, we describe the action of hexapodal capsule 1 and its remarkable ability to select anions based on a large span of rates by which they enter this host. The thermodynamic affinity of 1 toward eighteen anions extends over eight orders of magnitude (0<K_a <10⁸  M^-1 ; ¹ H NMR spectroscopy). The capsule would retain CO₃ ^2- (K_a =10⁷  M^-1 ) for hours in the presence of eleven competing anions, including stronger binding SO₄ ^2- , HAsO₄ ^2- and HPO₄ ^2- (K_a =10⁷ -10⁸  M^-1 ). The observed selection resulted from 1 possessing narrow apertures (ca. 3×6 Å) comparable in size to anions (d=3.5-7.1 Å) slowing down the encapsulation to last from seconds to days. The unorthodox mode of action of 1 sets the stage for creating hosts that pick anions by their ability to access the host.

A computational study of competing conformational selection and induced fit in an abiotic system

Host-guest complexations can be described by two competing mechanisms, conformational selection (CS) and induced fit (IF). In this work, we used a combination of nudged elastic band (NEB), adaptive steered molecular dynamics (ASMD), and density functional theory (DFT, with a correction for dispersion) to study the dynamics of the pathways (IF/CS) by which two conformers of basket B(+) and B(-) interconvert and trap CX₄ guests (X = Cl and Br). While the results from NEB/DFT studies disclosed host-guest noncovalent contacts reducing the basket's conformational dynamics, ASMD methodology suggested an associative mechanism for the guest complexation. With theory in excellent agreement with experiments, NEB and ASMD emerge as the methods of choice for studying dynamics of supramolecular systems.

Enantioselective Construction of Modular and Asymmetric Baskets

The precise positioning of functional groups about the inner space of abiotic hosts is a challenging task and of interest for developing more effective receptors and catalysts akin to those found in nature. To address it, we herein report a synthetic methodology for preparing basket-like cavitands comprised of three different aromatics as side arms with orthogonal esters at the rim for further functionalization. First, enantioenriched A (borochloronorbornene), B (iodobromonorbornene), and C (boronorbornene) building blocks were obtained by stereoselective syntheses. Second, consecutive A-to-B and then AB-to-C Suzuki-Miyaura (SM) couplings were optimized to give enantioenriched ABC cavitand as the principal product. The robust synthetic protocol allowed us to prepare (a) an enantioenriched basket with three benzene sides and each holding either tBu, Et, or Me esters, (b) both enantiomers of a so-called "spiral staircase" basket with benzene, naphthalene, and anthracene groups surrounding the inner space, and (c) a photo-responsive basket bearing one anthracene and two benzene arms.

Molecular Recognition of Nerve Agents and Their Organophosphorus Surrogates: Toward Supramolecular Scavengers and Catalysts

Nerve agents are tetrahedral organophosphorus compounds (OPs) that were developed in the last century to irreversibly inhibit acetylcholinesterase (AChE) and therefore impede neurological signaling in living organisms. Exposure to OPs leads to a rapid development of symptoms from excessive salivation, nasal congestion and chest pain to convulsion and asphyxiation which if left untreated may lead to death. These potent toxins are prepared on a large scale from inexpensive staring materials, making it feasible for terrorist groups or states to use them against military and civilians. The existing antidotes provide limited protection and are difficult to apply to a large number of affected individuals. While new prophylactics are currently being developed, there is still need for therapeutics capable of both preventing and reversing the effects of OP poisoning. In this review, we describe how the science of molecular recognition can expand the pallet of tools for rapid and safe sequestration of nerve agents.

From Selection to Instruction and Back: Competing Conformational Selection and Induced Fit Pathways in Abiotic Hosts

Two limiting cases of molecular recognition, induced fit (IF) and conformational selection (CS), play a central role in allosteric regulation of natural systems. The IF paradigm states that a substrate "instructs" the host to change its shape after complexation, while CS asserts that a guest "selects" the optimal fit from an ensemble of preexisting host conformations. With no studies that quantitatively address the interplay of two limiting pathways in abiotic systems, we herein and for the first time describe the way by which twisted capsule M-1, encompassing two conformers M-1(+) and M-1(-), trap CX₄ (X=Cl, Br) to give CX₄ ⊂M-1(+) and CX₄ ⊂M-1(-), with all four states being in thermal equilibrium. With the assistance of 2D EXSY, we found that CBr₄ would, at its lower concentrations, bind M-1 via a M-1(+)→M-1(-)→CBr₄ ⊂M-1(-) pathway corresponding to conformational selection. For M-1 complexing CCl₄ though, data from 2D EXSY measurements and 1D NMR line-shape analysis suggested that lower CCl₄ concentrations would favor CS while the IF pathway prevailed at higher proportions of the guest. Since CS and IF are not mutually exclusive, we reason that our work sets the stage for characterizing the dynamics of a wide range of already existing hosts to broaden our fundamental understanding of their action. The objective is to master the way in which encapsulation takes place for designing novel and allosteric sequestering agents, catalysts and chemosensors akin to those found in nature.

A Molecular Capsule with Revolving Doors Partitioning Its Inner Space

Covalent capsule 1 was designed to include two molecular baskets linked with three mobile pyridines tucked into its inner space. On the basis of both theory (DFT) and experiments (NMR and X-ray crystallography), we found that the pyridine "doors" split the chamber (380 ų ) of 1 so that two equally sizeable compartments (190 ų ) became joined through a conformationally flexible aromatic barrier. The compartments of such unique host could be populated with CCl₄ (88 ų ; PC=46 %), CBr₄ (106 ų ; 56 %) or their combination CCl₄ /CBr₄ (PC=51 %), with thermodynamic stabilities ΔG° tracking the values of packing coefficients (PC). Halogen (C-X⋅⋅⋅π) and hydrogen bonding (C-H⋅⋅⋅X) contacts held the haloalkane guests in the cavities of 1. The consecutive complexations were found to occur in a negative allosteric manner, which we propose to result from the induced-fit mode of complexation. Newly designed 1 opens a way for probing the effects of inner conformational dynamics on noncovalent interactions, reactivity and intramolecular translation in confined spaces of hollow molecules.

A highly diastereoselective synthesis of deep molecular baskets

We describe a preparative method for directing Mizoroki-Heck cyclotrimerization of enantioenriched bromonorbornenes into molecular baskets having increasingly deeper and extendable aromatic cavities. Such diastereoselective cyclotrimerizations of the bromo-olefinic substrates resulted from prevalent β migratory insertions without the formation of palladacycle intermediate(s). The facile access to multigram quantity of a new series of basket-like hosts clears the way for creating novel supramolecular materials for storage, sequestration and catalysis.

One-Pot Aldol Cascade for the Preparation of Isospiropyrans, Flavylium Salts, and bis-Spiropyrans

We probed tandem aldol condensations of sixteen o-hydroxyacetophenones, carrying electron-withdrawing and -donating groups at positions 4 and 5, using five molar equivalents of SiCl₄ in anhydrous ethanol. Substrates carrying electron-withdrawing groups (EWGs) (0 < ∑σ > 0.63) populated the equilibria with isospiropyrans (12-74% yield), while those carrying electron-donating groups (EDGs) (∑σ < -0.31) gave flavylium salts (50-80%) or thermochromic bis-spiropyrans (73%). The results are of interest for developing novel organic materials possessing switchable photochromic and thermochromic characteristics.

Tuning the allosteric sequestration of anticancer drugs for developing cooperative nano-antidotes

Dual-cavity baskets, carrying six γ-aminobutyric acids sequester anticancer anthracyclines in a cooperative manner to be of interest for creating nano-antidotes.

Photoinduced interruption of interannular cooperativity for delivery of cationic guests in water

Photoinduced decarboxylation of two hexaanionic baskets, surrounding a divalent cationic guest, reduced the interannular cooperativity (i.e. multivalency) holding the complex together to result in the release of guests.

An easily accessible isospiropyran switch

In the presence of SiCl4, three molecules of 5'-bromo-2'-hydroxyacetophenone underwent an unexpected tandem aldol condensation to give a novel isospiropyran switch (69%), with X-ray crystallography confirming its structure. The strong Brønsted acid CH3SO3H turned the colorless isospiropyran into its protonated and open form possessing red color. This process was reversed using the Et3N base, with the acid/base toggling repeatable for at least six times (UV-Vis). When printed on a silica plate, however, the isospiropyran formed a blue-colored product due to, as posited, its stabilization by hydrogen bonding (HB) to silica. An exposure to HB-competing ethyl acetate temporarily "erased" the print only to be brought back by subjecting the plate to a higher temperature for evaporating the solvent. The isospiropyran described here is an easily accessible, chromic, modular and switchable compound that one can incorporate into dynamic materials or use for building chemosensors, molecular machines and organic electronic devices.

On the encapsulation and assembly of anticancer drugs in a cooperative fashion

In this study, we report the remarkable recognition and assembly characteristics of D 3h symmetric basket 1 6- containing two adjoining and nonpolar cavities with six biocompatible GABA residues at their northern and southern termini. From the results of experimental (1H NMR, fluorescence and UV-Vis spectroscopies) and computational (MM-MC/OPLS3e) investigations, we deduced that hexaanionic 1 6- captured two molecules of anticancer drug doxorubicin 2 + in water and accommodated them in its two deep cavities. The formation of stable 1 6-⊂2 2 2+ (K a = 3 × 1012 M-2) was accompanied by the exceptional homotopic cooperativity (α = 4K 2/K 1 = 112) in which K 1 = 3.2 ± 0.8 × 105 M-1 and K 2 = 9 ± 1 × 106 M-1. Furthermore, bolaamphiphilic 1 6-⊂2 2 2+ assembled into spherical nanoparticles (DLS, cryo-TEM and TEM) possessing 41% drug loading. The preorganization of abiotic receptor 1 6- and its complementarity to 2 + have been proposed to play a part in the positive cooperativity in which ten favorable noncovalent contacts (i.e. hydrogen bonds, salt bridges, C-H···π and π-π contacts) are formed between doxorubicin and the dual-cavity host. In the case of topotecan 3 +, however, the absence of multiple and favorable basket⊂drug interactions resulted in the predominant formation of a binary 1 6- ⊂ 3 + complex (K 1 = 2.12 ± 0.01 × 104 M-1) and the negative homotopic allostery (α ≪ 1). To summarize, our study lays out a roadmap for creating a family of novel, accessible and multivalent hosts capable of complexing anticancer agents in a cooperative manner. As basket⊂drug complexes organize into highly loaded nanoparticles, the reported soft material is amenable to the bottom-up construction of stimuli-responsive nanomedicine capable of effective scavenging and/or delivery of drugs.

Stereo- and Regioselective Synthesis of Molecular Baskets

We describe a stereoselective method for obtaining multigram quantities of molecular basket 1 _syn in overall 11% yield, using inexpensive cyclopentadiene and diethyl fumarate as starting materials. First, an asymmetric synthesis of enantioenriched bromo(trimethylstannyl)alkene (-)-8 was accomplished by the stereoselective bromination of dibromonorbornene (+)-4 guided by anchimeric assistance and subsequent syn- exo-elimination of tetrabromonorbornane (-)-5a as the key steps. Subsequent Cu(I)-catalyzed cyclotrimerization of (-)-8 was optimized to give 1 _{syn/ anti} in 85% yield and 1:1 ratio of diastereomers. Importantly, the results of our mechanistic experiments were in line with the cyclotrimerization occurring in a chain-type fashion with racemization of a Cu(I) homochiral dimeric intermediate, reducing the stereoselectivity of the transformation. Enabled by more facile access to molecular baskets of type 1 _syn, a range of recognition studies can now be completed for producing novel supramolecular catalysts, organophosphorus scavengers, and nanostructured materials.

Stackable molecular chairs

Molecular chairs, carrying three amino acids or peptides, stack in an antiparallel fashion to give hexavalent assemblies for bottom-up construction of novel soft materials and therapeutics.

Photo-induced formation of organic nanoparticles possessing enhanced affinities for complexing nerve agent mimics

Organic nanoparticles, composed of molecular baskets, could act as nanocarriers for selective “mopping” of toxic CWAs or pesticides, after being assembled by a light stimulus.

Examining the Scope and Thermodynamics of Assembly in Nesting Complexes Comprising Molecular Baskets and TPA Ligands

Molecular baskets capture various tris(2-pyridylmethyl)amine ligands, with and without zinc(II) cation, to form nesting complexes. The results of our computational (MD) and experimental (¹H NMR/ITC) studies suggest that the assembly is driven by the hydrophobic effect with the charge of complementary molecular components playing an important role in the formation of nesting complexes. In brief, the complexation only takes place when the basket and the ligand carry either oppositely charged or noncharged groups.

Multivalent and Photoresponsive Assembly of Dual-Cavity Baskets in Water

Large unilamellar vesicles [1]_n , composed of bolaamphiphilic baskets 1, were found to complex photoresponsive guest 3 and divalent 4 to, respectively, give stable vesicular assemblies [1₂ -3]_n and [1₂ -4₃ ]_n . With the assistance of ¹ H NMR spectroscopy, electron microscopy, and dynamic light scattering, it was deduced that [1₂ -3]_n vesicles comprise ternary [1₂ -3] organized into a curved membrane in which a pair of baskets entraps a laterally positioned dicationic 3. In the case of [1₂ -4₃ ]_n vesicles, however, the spectroscopic results suggest that three guest molecules 4 insert vertically between four baskets 1 to give pentanary [1₂ -4₃ ] packed into the membrane of [1₂ -4₃ ]_n . Importantly, nanostructured [1₂ -3]_n and [1₂ -4₃ ]_n retain rhodamine B (RhB) in their reservoir (fluorescence microscopy) and can be switched from one into another using UV light, with a disproportionate release of RhB dye. The reported complexes, organized into photoresponsive capsular materials, are rather unprecedented, demonstrating the potential of multivalency for creating functional structures of great interest in the areas of catalysis and delivery.

Assembly and Folding of Twisted Baskets in Organic Solvents

A synthetic method for obtaining enantiopure and twisted baskets of type (P)-3 is described. These chiral cavitands were found to fold quinoline gates, at the rim of their twisted platform, in acetonitrile and give molecular capsules that assemble into large unilamellar vesicles. In a less polar dichloromethane, however, cup-shaped (P)-3 packed into vesicles but with the quinoline gates in an unfolded orientation. The ability of twisted baskets to form functional nanostructured materials could be of interest for building stereoselective sensors and catalysts.

Gated molecular baskets

In this review, we describe the construction of gated molecular baskets, discuss their mechanism of action in regulating the exchange of guests and illustrate the potential of these concave hosts to act as catalysts for controlling chemical reactions. Importantly, a number of computational and experimental studies have suggested that gated baskets ought to unfold their gates at the rim for permitting the passage of guests to/from their inner space. These dynamic hosts are therefore offered as useful models for investigating the process of gating in artificial systems. Furthermore, gated baskets should permit examining the benefit of controlling the rate by which reactants access a gated catalyst for promoting chemical reactions occurring in its confined space.

Twisted baskets

A preparative procedure for obtaining a pair of twisted molecular baskets, each comprising a chiral framework with either right ((P)-1syn) or left ((M)-1syn) sense of twist and six ester groups at the rim has been developed and optimized. The racemic (P/M)-1syn can be obtained in three synthetic steps from accessible starting materials. The resolution of (P/M)-1syn is accomplished by its transesterification with (1R,2S,5R)-(-)-menthol in the presence of a Ti(IV) catalyst to give diastereomeric 8(P) and 8(M). It was found that dendritic-like cavitands 8(P) and 8(M), in CD2Cl2, undergo self-inclusion ((1)H NMR spectroscopy) with a menthol moiety occupying the cavity of each host. Importantly, the degree of inclusion of the menthol group was ((1)H NMR spectroscopy) found to be greater in the case of 8(P) than 8(M). Accordingly, it is suggested that different folding characteristic of 8(P) and 8(M) ought to affect the physicochemical characteristics of the hosts to permit their effective separation by column chromatography. The absolute configuration of 8(P)/8(M), encompassing right- and left-handed "cups", was determined with the exciton chirality method and also verified in silico (DFT: B3LYP/TZVP). Finally, the twisted baskets are strongly fluorescent due to three naphthalene chromophores, having a high fluorescence quantum yield within the rigid framework of 8(P)/8(M).

Fulleropyrrolidine molecular dumbbells act as multi-electron-acceptor triads. Spectroscopic, electrochemical, computational and morphological characterizations

Three novel fulleropyrrolidine dumbbells consisting three electron acceptor moieties joined by alkyl linker displaying tunable electrical and morphological properties were synthesized and characterized.

On the nature of the transition state characterizing gated molecular encapsulations

Gated molecular encapsulations, with baskets of type 1, are postulated to occur by the mechanism in which solvent molecule penetrates the inner space of 1, through one of its apertures, while the residing guest simultaneously departs the cavity. In the transition state of the exchange, three pyridine-based gates are proposed to assume an open position with both incoming solvent and departing guest molecules interacting with the concave surface of the host. The More O'Ferrall-Jencks diagram and linear free energy relationships (LFERs) suggest a more advanced departure of the guest when bigger solvents partake in the displacement.