Supramolecular Explorations: Exhibiting the Extent of Extended Cationic Cyclophanes.

Acting as hosts, cationic cyclophanes, consisting of π-electron-poor bipyridinium units, are capable of entering into strong donor-acceptor interactions to form host-guest complexes with various guests when the size and electronic constitution are appropriately matched. A synthetic protocol has been developed that utilizes catalytic quantities of tetrabutylammonium iodide to make a wide variety of cationic pyridinium-based cyclophanes in a quick and easy manner. Members of this class of cationic cyclophanes with boxlike geometries, dubbed Ex(n)Boxm(4+) for short, have been prepared by altering a number of variables: (i) n, the number of "horizontal" p-phenylene spacers between adjoining pyridinium units, to modulate the "length" of the cavity; (ii) m, the number of "vertical" p-phenylene spacers, to modulate the "width" of the cavity; and (iii) the aromatic linkers, namely, 1,4-di- and 1,3,5-trisubstituted units for the construction of macrocycles (ExBoxes) and macrobicycles (ExCages), respectively. This Account serves as an exploration of the properties that emerge from these structural modifications of the pyridinium-based hosts, coupled with a call for further investigation into the wealth of properties inherent in this class of compounds. By variation of only the aforementioned components, the role of these cationic receptors covers ground that spans (i) synthetic methodology, (ii) extraction and sequestration, (iii) catalysis, (iv) molecular electronics, (v) physical organic chemistry, and (vi) supramolecular chemistry. Ex(1)Box(4+) (or simply ExBox(4+)) has been shown to be a multipurpose receptor capable of binding a wide range of polycyclic aromatic hydrocarbons (PAHs), while also being a suitable component in switchable mechanically interlocked molecules. Additionally, the electronic properties of some host-guest complexes allow the development of artificial photosystems. Ex(2)Box(4+) boasts the ability to bind both π-electron-rich and -poor aromatic guests in different binding sites located within the same cavity. ExBox2(4+) forms complexes with C60 in which discrete arrays of aligned fullerenes result in single cocrystals, leading to improved material conductivities. When the substitution pattern of the Ex(n)Box(4+) series is changed to 1,3,5-trisubstituted benzenoid cores, the hexacationic cagelike compound, termed ExCage(6+), exhibits different kinetics of complexation with guests of varying sizes-a veritable playground for physical organic chemists. The organization of functionality with respect to structure becomes valuable as the number of analogues continues to grow. With each of these minor structural modifications, a wealth of properties emerge, begging the question as to what discoveries await and what properties will be realized with the continued exploration of this area of supramolecular chemistry based on a unique class of receptor molecules.

Cooperative Reactivity in an Extended-Viologen-Based Cyclophane.

A tetracationic pyridinium-based cyclophane with a box-like geometry, incorporating two juxtaposed alkyne functions, has been synthesized. The triple bonds are reactive through cycloadditions toward dienes and azides, promoted by the electron-withdrawing nature of the pyridinium rings, as well as by the strain inherent in the cyclophane. The cycloadditions proceeded in high yields, with the cyclophane reacting faster than its acyclic analogue. While the cyclophane contains two reactive triple bonds, there is no evidence for a stable monofunctional intermediate-only starting material and the difunctional product have been detected by (1)H NMR spectroscopy. Molecular modeling of the energy landscape reveals a lower barrier for the kinetically favored second cycloaddition compared with the first one. This situation results in tandem cascading reactions within rigid cyclophanes, where reactions at a first triple bond induce increased reactivity at a distal second alkyne.

Ultrafast Two-Electron Transfer in a CdS Quantum Dot-Extended-Viologen Cyclophane Complex.

Time-resolved optical spectroscopies reveal multielectron transfer from the biexcitonic state of a CdS quantum dot to an adsorbed tetracationic compound cyclobis(4,4'-(1,4-phenylene) bipyridin-1-ium-1,4-phenylene-bis(methylene)) (ExBox(4+)) to form both the ExBox(3+•) and the doubly reduced ExBox(2(+•)) states from a single laser pulse. Electron transfer in the single-exciton regime occurs in 1 ps. At higher excitation powers the second electron transfer takes ∼5 ps, which leads to a mixture of redox states of the acceptor ligand. The doubly reduced ExBox(2(+•)) state has a lifetime of ∼10 ns, while CdS(+•):ExBox(3+•) recombines with multiple time constants, the longest of which is ∼300 µs. The long-lived charge separation and ability to accumulate multiple charges on ExBox(4+) demonstrate the potential of the CdS:ExBox(4+) complex to serve as a platform for two-electron photocatalysis.

Allosteric Modulation of Substrate Binding within a Tetracationic Molecular Receptor.

The synthesis and recognition phenomena of a tetracationic molecular receptor that possesses a nanometer-sized molecular cavity are described. The host-guest properties of the molecular receptor can be tuned and modulated allosterically, where the association of a heterotropic effector at the periphery of the molecule serves to modulate its affinity for the globular, electron-rich guest that resides within its molecular cavity. This stimuli-responsive host-guest behavior was observed in both the solution phase and the crystalline solid state, and can be reversed with high fidelity by sequestration of the effector molecule.

Catenation through a Combination of Radical Templation and Ring-Closing Metathesis.

Synthesis of an electrochemically addressable [2]catenane has been achieved following formation by templation of a [2]pseudorotaxane employing radically enhanced molecular recognition between the bisradical dication obtained on reduction of the tetracationic cyclophane, cyclobis(paraquat-p-phenylene), and the radical cation generated on reduction of a viologen disubstituted with p-xylylene units, both carrying tetraethylene glycol chains terminated by allyl groups. This inclusion complex was subjected to olefin ring-closing metathesis, which was observed to proceed under reduced conditions, to mechanically interlock the two components. Upon oxidation, Coulombic repulsion between the positively charged and mechanically interlocked components results in the adoption of a co-conformation where the newly formed alkene resides inside the cavity of the tetracationic cyclophane. (1)H NMR spectroscopic analysis of this hexacationic [2]catenane shows a dramatic upfield shift of the resonances associated with the olefinic and allylic protons as a result of them residing inside the tetracationic component. Further analysis shows high diastereoselectivity during catenation, as only a single (Z)-isomer is formed.

Energy and Electron Transfer Dynamics within a Series of Perylene Diimide/Cyclophane Systems.

Artificial photosynthetic systems for solar energy conversion exploit both covalent and supramolecular chemistry to produce favorable arrangements of light-harvesting and redox-active chromophores in space. An understanding of the interplay between key processes for photosynthesis, namely light-harvesting, energy transfer, and photoinduced charge separation and the design of novel, self-assembling components capable of these processes are imperative for the realization of multifunctional integrated systems. We report our investigations on the potential of extended tetracationic cyclophane/perylene diimide systems as components for artificial photosynthetic applications. We show how the selection of appropriate heterocycles, as extending units, allows for tuning of the electron accumulation and photophysical properties of the extended tetracationic cyclophanes. Spectroscopic techniques confirm energy transfer between the extended tetracationic cyclophanes and perylene diimide is ultrafast and quantitative, while the heterocycle specifically influences the energy transfer related parameters and the acceptor excited state.

Semiconducting single crystals comprising segregated arrays of complexes of C60.

Although pristine C60 prefers to adopt a face-centered cubic packing arrangement in the solid state, it has been demonstrated that noncovalent-bonding interactions with a variety of molecular receptors lead to the complexation of C60 molecules, albeit usually with little or no control over their long-range order. Herein, an extended viologen-based cyclophane­ExBox2(4+)­has been employed as a molecular receptor which, not only binds C60 one-on-one, but also results in the columnar self-assembly of the 1:1 inclusion complexes under ambient conditions. These one-dimensional arrays of fullerenes stack along the long axis of needle-like single crystals as a consequence of multiple noncovalent-bonding interactions between each of the inclusion complexes. The electrical conductivity of these crystals is on the order of 10(-7) S cm(-1), even without any evacuation of oxygen, and matches the conductivity of high-quality, unfunctionalized C60-based materials that typically require stringent high-temperature vaporization techniques, along with the careful removal of oxygen and moisture, prior to measuring their conductance.

Active site profiling reveals coupling between domains in SRC-family kinases.

Protein kinases, key regulators of intracellular signal transduction, have emerged as an important class of drug targets. Chemical proteomic tools that facilitate the functional interrogation of protein kinase active sites are powerful reagents for studying the regulation of this large enzyme family and performing inhibitor selectivity screens. Here we describe a new crosslinking strategy that enables rapid and quantitative profiling of protein kinase active sites in lysates and live cells. Applying this methodology to the SRC-family kinases (SFKs) SRC and HCK led to the identification of a series of conformation-specific, ATP-competitive inhibitors that have a distinct preference for the autoinhibited forms of these kinases. Furthermore, we show that ligands that have this selectivity are able to modulate the ability of the regulatory domains of SRC and HCK to engage in intermolecular binding interactions. These studies provide insight into the regulation of this important family of tyrosine kinases.

Modulating the binding of polycyclic aromatic hydrocarbons inside a hexacationic cage by anion-π interactions.

We report the template-directed synthesis of BlueCage(6+), a macrobicyclic cyclophane composed of six pyridinium rings fused with two central triazines and bridged by three paraxylylene units. These moieties endow the cage with a remarkably electron-poor cavity, which makes it a powerful receptor for polycyclic aromatic hydrocarbons (PAHs). Upon forming a 1:1 complex with pyrene in acetonitrile, however, BlueCage⋅6 PF6 exhibits a lower association constant Ka than its progenitor ExCage⋅6 PF6. A close inspection reveals that the six PF6(-) counterions of BlueCage(6+) occupy the cavity in a fleeting manner as a consequence of anion-π interactions and, as a result, compete with the PAH guests. This conclusion is supported by a one order of magnitude increase in the Ka value for pyrene in BlueCage(6+) when the PF6(-) counterions are replaced by much bulkier anions. The presence of anion-π interactions is supported by X-ray crystallography, and confirms the presence of a PF6(-) counterion inside its cavity.

ExCage.

Cyclophanes, especially those where pyridinium units in conjugation with each other are linked up face-to-face within platforms that are held approximately 7 Å apart by rigid linkers, are capable of forming inclusion complexes with polycyclic aromatic hydrocarbons (PAHs) with high binding affinities as a result of a combination of noncovalent bonding interactions, including face-to-face [π···π] stacking and orthogonal [C-H···π] interactions. Here, we report the template-directed, catalyst-assisted synthesis of a three-fold symmetric, extended pyridinium-based, cage-like host (ExCage(6+)) containing a total of six π-electron-deficient pyridinium units connected in a pairwise fashion by three bridging p-xylylene linkers, displayed in a trigonal (1,3,5) fashion around two opposing and parallel 1,3,5-tris(4-pyridinium)benzene platforms. The association constants (K(a)) of eight complexes have been measured by isothermal titration calorimetry (ITC) in acetonitrile and were found to span the range from 2.82 × 10(3) for naphthalene up to 5.5 × 10(6) M(-1) for perylene. The barriers to decomplexation, which were measured in DMF-d7 for phenanthrene, pyrene, triphenylene, and coronene by dynamic (1)H NMR spectroscopy undergo significant stepwise increases from 11.8 → 13.6 → 15.5 → >18.7 kcal mol(-1), respectively, while complexation experiments using rapid injection (1)H NMR spectroscopy in DMF-d7 at -55 °C revealed the barriers to complexation for pyrene and coronene to be 6.7 and >8 kcal mol(-1), respectively. The kinetic and thermodynamic data reveal that, in the case of ExCage(6+), while the smaller PAHs form complexes faster than the larger ones, the larger PAHs form stronger complexes than the smaller ones. It is also worthy of note that, as the complexes become stronger in the case of the larger and larger PAHs, the Rebek 55% solution formula for molecular recognition in the liquid state becomes less and less relevant.

Relative contractile motion of the rings in a switchable palindromic [3]rotaxane in aqueous solution driven by radical-pairing interactions.

Artificial muscles are an essential component for the development of next-generation prosthetic devices, minimally invasive surgical tools, and robotics. This communication describes the design, synthesis, and characterisation of a mechanically interlocked molecule (MIM), capable of switchable and reversible linear molecular motion in aqueous solution that mimics muscular contraction and extension. Compatibility with aqueous solution was achieved in the doubly bistable palindromic [3]rotaxane design by using radical-based molecular recognition as the driving force to induce switching.

Ex(2)Box: interdependent modes of binding in a two-nanometer-long synthetic receptor.

Incorporation of two biphenylene-bridged 4,4'-bipyridinium extended viologen units into a para-phenylene-based cyclophane results in a synthetic receptor that is ~2 nm long and adopts a box-like geometry. This cyclophane, Ex(2)Box(4+), possesses the ability to form binary and ternary complexes with a myriad of guest molecules ranging from long π-electron-rich polycyclic aromatic hydrocarbons, such as tetracene, tetraphene, and chrysene, to π-electron-poor 2,6-dinitrotoluene, 1,2,4-trichlorobenzene, and both the 9,10- and 1,4-anthraquinone molecules. Moreover, Ex(2)Box(4+) is capable of forming one-to-one complexes with polyether macrocycles that consist of two π-electron-rich dioxynaphthalene units, namely, 1,5-dinaphtho[38]crown-10. This type of broad molecular recognition is possible because the electronic constitution of Ex(2)Box(4+) is such that the pyridinium rings located at the "ends" of the cyclophane are electron-poor and prefer to enter into donor-acceptor interactions with π-electron-rich guests, while the "middle" of the cyclophane, consisting of the biphenylene spacer, is more electron-rich and can interact with π-electron-poor guests. In some cases, these different modes of binding can act in concert to generate one-to-one complexes which possess high stability constants in organic media. The binding affinity of Ex(2)Box(4+) was investigated in the solid state by way of single-crystal X-ray diffraction and in solution by using UV-vis and NMR spectroscopy for 12 inclusion complexes consisting of the tetracationic cyclophane and the corresponding guests of different sizes, shapes, and electronic compositions. Additionally, density functional theory was carried out to elucidate the relative energetic differences between the different modes of binding of Ex(2)Box(4+) with anthracene, 9,10-anthraquinone, and 1,4-anthraquinone in order to understand the degree with which each mode of binding contributes to the overall encapsulation of each guest.

Synthesis of Ex(n)Box cyclophanes.

A rapid and efficient synthesis of the extended bipyridinium-based class of cyclophanes--that is, Ex(n)Box(4+) (n = 0-3), where n is the number of p-phenylene rings inserted between the pyridinium rings--is demonstrated, resulting in much higher yields of products along with a reduced output of oligomeric byproducts. Although each cyclophane can be synthesized readily without the use of a precise stoichiometric amount of template, ExBox(4+) can be prepared in 66% yield (following crystallization) using six equivalents of pyrene in a template-directed protocol. This new methodology has been employed to synthesize, in modest yield, a nearly 2.5 nm long cyclophane consisting of 12 aromatic rings.

Multiple binding modes of isothiocyanates that inhibit macrophage migration inhibitory factor.

Macrophage migration inhibitory factor (MIF) is a pleiotropic cytokine that has roles in the innate immune response, and also contributes to inflammatory disease. While the biological properties of MIF are closely linked to protein-protein interactions, MIF also has tautomerase activity. Inhibition of this activity interferes with the interaction of MIF with protein partners e.g. the CD74 receptor, and tautomerase inhibitors show promise in disease models including multiple sclerosis and colitis. Isothiocyanates inhibit MIF tautomerase activity via covalent modification of the N-terminal proline. We systematically explored variants of benzyl and phenethyl isothiocyanates, to define determinants of inhibition. In particular, substitution with hydroxyl, chloro, fluoro and trifluoro moieties at the para and meta positions were evaluated. In assays on treated cells and recombinant protein, the IC50 varied from 250 nM to >100 µM. X-ray crystal structures of selected complexes revealed that two binding modes are accessed by some compounds, perhaps owing to strain in short linkers between the isothiocyanate and aromatic ring. The variety of binding modes confirms the existence of two subsites for inhibitors and establishes a platform for the development of potent inhibitors of MIF that only need to target one of these subsites.

Induced-fit catalysis of corannulene bowl-to-bowl inversion.

Stereoelectronic complementarity between the active site of an enzyme and the transition state of a reaction is one of the tenets of enzyme catalysis. This report illustrates the principles of enzyme catalysis (first proposed by Pauling and Jencks) through a well-defined model system that has been fully characterized crystallographically, computationally and kinetically. Catalysis of the bowl-to-bowl inversion processes that pertain to corannulene is achieved by combining ground-state destabilization and transition-state stabilization within the cavity of an extended tetracationic cyclophane. This synthetic receptor fulfils a role reminiscent of a catalytic antibody by stabilizing the planar transition state for the bowl-to-bowl inversion of (ethyl)corannulene (which accelerates this process by a factor of ten at room temperature) by an induced-fit mechanism first formulated by Koshland.

Development of Toxoplasma gondii calcium-dependent protein kinase 1 (TgCDPK1) inhibitors with potent anti-toxoplasma activity.

Toxoplasmosis is a disease of prominent health concern that is caused by the protozoan parasite Toxoplasma gondii. Proliferation of T. gondii is dependent on its ability to invade host cells, which is mediated in part by calcium-dependent protein kinase 1 (CDPK1). We have developed ATP competitive inhibitors of TgCDPK1 that block invasion of parasites into host cells, preventing their proliferation. The presence of a unique glycine gatekeeper residue in TgCDPK1 permits selective inhibition of the parasite enzyme over human kinases. These potent TgCDPK1 inhibitors do not inhibit the growth of human cell lines and represent promising candidates as toxoplasmosis therapeutics.

Multiple determinants for selective inhibition of apicomplexan calcium-dependent protein kinase CDPK1.

Diseases caused by the apicomplexan protozoans Toxoplasma gondii and Cryptosporidium parvum are a major health concern. The life cycle of these parasites is regulated by a family of calcium-dependent protein kinases (CDPKs) that have no direct homologues in the human host. Fortuitously, CDPK1 from both parasites contains a rare glycine gatekeeper residue adjacent to the ATP-binding pocket. This has allowed creation of a series of C3-substituted pyrazolopyrimidine compounds that are potent inhibitors selective for CDPK1 over a panel of human kinases. Here we demonstrate that selectivity is further enhanced by modification of the scaffold at the C1 position. The explanation for this unexpected result is provided by crystal structures of the inhibitors bound to CDPK1 and the human kinase c-SRC. Furthermore, the insight gained from these studies was applied to transform an alternative ATP-competitive scaffold lacking potency and selectivity for CDPK1 into a low nanomolar inhibitor of this enzyme with no activity against SRC.