Synthesis and Evaluation of a Cyclophane Receptor for Acetic Acid

A bicyclic cyclophane ( 2 ) containing one pyridine nitrogen and four amide N-H groups oriented toward the interior of the cavity was synthesized. The binding constants of various carboxylic acids with 2 were measured by UV/Vis spectroscopy. Acetic acid bound to 2 with a K a of 980 - 90 M m 1 in chloroform while branched carboxylic acids showed significantly lower binding. The data indicate that acetic acid was bound within the cavity of 2 . Only one acetic acid binds to two control hosts, whereas 2 shows definitive 1:1 binding. The results suggest that selectivity in the binding of carboxylic acids can be achieved via size constraints dictated by the receptor cavity, and that the same size restrictions lead to only one carboxylic acid bound to the cyclophane. The crystal structure of 2 is reported.     

Tuneable side-chain supramolecular polymer

[reaction: see text] A random copolymer containing 1,5-dialkyloxynaphthalene moieties has been synthesized using atom-transfer radical polymerization. We have shown that this polymer has the ability to form complexes with the tetracationic cyclophane cyclobis(paraquat-p-phenylene) (CBPQT(4+)) and that electrochemical reduction of the cyclophane or the addition of a competing guest for the cavity of the cyclophane results in disassembly of the supramolecular polymer.     

Synthesis of a polypseudorotaxane, polyrotaxane, and polycatenane using ‘click’ chemistry

The synthesis of a polypseudorotaxane, polyrotaxane, and polycatenane containing the electron-deficient cyclophane cyclobis(paraquat-p-phenylene) (CBPQT⁴⁺) subunit in the side chain is described. These interlocked supramolecular polymers have been prepared from an azide-functionalized polystyrene derivative and an acetylene-functionalized [2]rotaxane, [2]catenane and their parent tetracationic cyclophane via Cu(I)-catalyzed 1,3 dipolar cycloadditions (‘click chemistry’). The synthesis and characterization of the polymers and intermediates has been described using IR, ¹H NMR, UV spectroscopies, and voltammetry. We have shown that the CBPQT⁴⁺ unit of the side chain polystyrene derivative has the ability to reversibly undergo complexation with a complementary dialkoxynaphthalene derivative.     

Fluorophore appended saccharide cyclophane: self-association, fluorescent properties, heterodimers with cyclodextrins, and cross-linking behavior with peanut agglutinin of dansyl-modified saccharide cyclophane

A saccharide cyclophane bearing an environment-sensitive fluorophore (1) was prepared by introducing not only three branches with a terminal galactose residue but also one with a dansyl moiety into a tetraaza[6.1.6.1]paracyclophane skeleton. Self-association behavior of the dansyl-appended saccharide cyclophane was characterized in aqueous media by fluorescence spectroscopy and dynamic light scattering measurements. At least in the concentrations below 1.0 x 10(-5) M, saccharide cyclophane 1 existed in a monomeric state, whereas it tended to form self-aggregated complexes in the higher concentration. Solvent polarity dependency on the emission spectra of 1 was examined by fluorescence spectroscopy. With increasing dioxane contents in dioxane/water solvents, the fluorescence intensity originating from the dansyl moiety of 1 increased along with a concomitant blue shift of the fluorescence maximum (lambda(em)). In the monomeric state of 1 in water, the dansyl moiety of 1 was not fully included into its cyclophane cavity but partially exposed to the bulk aqueous phase. In the higher concentration ranges in an aggregate state, however, the dansyl group of 1 was located in the apolar cyclophane cavity whose microenvironment was equivalent to the polarity of 1-butanol evaluated on the basis of a correlation between lambda(em) and solvent polarity. This indicates an intermolecular inclusion of the dansyl moiety within the cyclophane. When cyclodextrin (CD) was mixed with 1, the dansyl group of 1 was bound to an internal cavity of CD such as gamma-CD, beta-CD, 6-O-alpha-glucosyl-beta-CD, and 6-O-alpha-maltosyl-beta-CD with binding constants of 7.5 x 10(2), 7.8 x 10(2), 7.7 x 10(2), and 6.0 x 10(2) M(-1), respectively. Such a supramolecular assembling of dansyl-modified cyclophane 1 and CDs caused changes of the fluorescence spectra as well as appearance of induced CD bands in aqueous media. Furthermore, saccharide cyclophane 1 was selectively bound to peanut agglutinin (PNA), galactoside-binding lectin, which was readily monitored by a visible turbidity of the solution due to a cross-linking agglutination of these components, as well as by fluorescence spectroscopy.     

Synthesis of a novel cyclic donor-acceptor conjugate for selective recognition of ATP

[reaction and structures: see text] Novel cyclophane 1 was synthesized, and its interactions with phosphate, adenosine, AMP, ADP, and ATP have been investigated. With addition of ATP, significant decrease in absorbance of 1 was observed, whereas other guest molecules showed negligible effect. The complex between 1 and ATP was confirmed through cyclic voltammetry and 1H NMR. The uniqueness of the system is that it complexes selectively with ATP in a cavity and involves synergistic effects of both electrostatic and pi-pi stacking interactions.     

Molecular Pacman: folding, inclusion, and X-ray structures of tri- and tetraamino piperazine cyclophanes

Reaction of piperazine and 1,3-bis(bromomethyl)-2-nitrobenzene under high-dilution conditions yields cyclic trimeric trinitro, tetrameric tetranitro, and pentameric pentanitro piperazine cyclophanes. Reduction of the nitro groups with SnCl(2) under acidic conditions produces the corresponding triamino and tetraamino piperazine cyclophanes. The solution studies of both nitro and amino piperazine cyclophanes at 30 degrees C by (1)H NMR spectroscopy shows symmetrical structures owing to the fast conformational exchange, whereas the low temperature studies of the tetraamino piperazine cyclophane reveals interesting dynamic behavior that indicates additional intramolecular interactions. Careful crystallizations of the trimeric trinitro and triamino and the tetrameric tetraamino cyclophanes resulted in crystals suitable for X-ray diffraction studies. In the crystalline state the amino-functionalized cyclophanes manifest an extraordinary circular intramolecular hydrogen-bonding network that leads to a fixed 3D structure. Hydrogen bonding in the triamino trimer leads to orientation of all three of the amino groups on the same side of the macrocycle, namely, the rcc conformation, whereas the tetraamino tetramer folds into a more compact shell-like conformation. During the crystallization process one acetonitrile guest is enclosed into the cavity of the tetraamino cyclophane, which gives a crystalline inclusion complex with remarkable resemblance to the famous Pacman motif. The folding, which mimics the behavior of some cyclic peptides and pyrroles, is induced by intramolecular hydrogen bonding from the amino groups to the tertiary amine groups of the piperazines. The cavity of the tetraamino tetramer is markedly smaller than in the corresponding, but nonfolded, tetranitro tetramer and the guest/host volume ratio (packing coefficient) for the acetonitrile and the cavity is approximately 50 %, which indicates a good size match for acetonitrile inclusion.     

The electrochemically-driven decomplexation/recomplexation of inclusion adducts of ferrocene derivatives with an electron-accepting receptor

The tetracationic cyclophane, cyclobis(paraquat-4,4'-biphenylene), binds 1,1'-disubstituted ferrocene-based polyethers as a result of (i) [pi...pi] stacking between the pi-electron-deficient bipyridinium units and the pi-electron-rich cyclopentadienyl rings and (ii) [C-H...O] hydrogen bonds between the alpha-bipyridinium hydrogen atoms and the polyether oxygen atoms. However, even the presence of a bulky tetraarylmethane group--which is too large to thread through the cavity of the cyclophane host--at the end of each of the two polyether substituents of the ferrocene-containing guest does not discourage adduct formation of the inclusion type. Thus, in these adducts, the ferrocene unit of the guest is located inside the cavity of the host with its two polyether chains protruding outward from the same side of the host. The alternative pseudorotaxane geometry is not observed in solutions of these 1:1 adducts. The host-guest adducts display absorption bands in the visible spectral region, characteristic of charge-transfer interactions. In the case of one of these adducts, reversible decomplexation/recomplexation takes place upon electrochemical oxidation/reduction of the ferrocene-based unit or upon reduction/oxidation of the tetracationic cyclophane.     

Tetrathiafulvalenenaphthalenophanes: planar chirality and cis/trans photoisomerization

A cyclophane incorporating one 1,5-dioxynaphthalene ring system and one tetrathiafulvalene (TTF) unit bridged by [SCH(2)CH(2)O] linkages has been synthesized. In this cyclophane, the TTF unit can adopt either cis or trans configurations. In addition, the 1, 5-dioxynaphthalene ring system imposes one element of planar chirality on this cyclophane. A second element of planar chirality is introduced by the trans form of the TTF unit. Thus, the cyclophane exists in diastereoisomeric forms as three pairs of enantiomers. The enantiomeric pairs associated with the cis form of the TTF unit, as well as one of those associated with the trans form, have been isolated by crystallization, and their structures assigned in the solid state by single-crystal X-ray analyses. In solution, cis/trans isomerization occurs when either the cis or the trans form of the cyclophane is exposed to light. The photoisomerization reaction can be followed by (1)H NMR and UV-vis spectroscopies, as well as by HPLC. The photoisomerization quantum yield has been measured at two different excitation wavelengths (406 and 313 nm). In both cases, the trans --> cis process (Phi = 0.20 at 406 nm) is much more efficient than the reverse cis --> trans process (Phi = 0.030 at 406 nm). Since the absorption spectra of the trans and cis isomers are different and the quantum yield of the trans --> cis photoisomerization reaction depends on the excitation wavelength, the mole fraction of the two diastereoisomers present at the photostationary state depends on the wavelength of the exciting light. No isomerization occurs when the solutions, regardless of the mole fraction of the two diastereoisomers, are stored in the dark.     

Temperature-dependent and friction-controlled electrochemically induced shuttling along molecular strings associated with electrodes.

The temperature and solvent composition dependence of the electrochemically stimulated rate of shuttling of the redox-active cyclophane, cyclobis(paraquat-p-phenylene), on a molecular string has been studied. The molecular string includes a pi-donor diiminebenzene-site that is associated on one side with an electrode, and stoppered on the other side with an adamantane unit. The cyclophane rests on the pi-donor site, owing to stabilizing pi-donor-acceptor interactions. Electrochemical reduction of the cyclophane units, to the bis-radical cation cyclophane, results in the shuttling of the reduced cyclophane towards the electrode, a process that is driven by the removal of the stabilizing donor-acceptor interactions, and the electrostatic attraction of the reduced product by the electrode. The latter process is energetically downhill, and is temperature-independent. Upon oxidation of the reduced cyclophane that is associated with the electrode, the energetically uphill shuttling of the oxidized cyclophane to the pi-donor site proceeds. The rate of this translocation process has been found to be temperature-dependent, and controlled by the solvent composition. The experimental results have been theoretically analyzed in terms of Kramers' molecular friction model. The theoretical fitting of the experimental results, using solutions of variable composition, reveals that the rate-constants for the uphill reaction in a pure aqueous solution follow the temperature-dependence of the viscosity of water. The results demonstrate the significance of friction phenomena in shuttling processes within molecular machines.     

Synthesis, characterization and ion transportation studies of some novel cyclophane amides

Various novel cyclophane amides with a large cavity have been synthesized. The structures of cyclophane amides 14 and 15 were resolved using XRD studies. Cyclophane amide 28 shows a shift in λ_max in the UV/Vis. spectra when treated with Cu (II) ion as well as with Pb (II) ion. Ion transportation studies were carried out with cyclophane amide 14 which proved that the Na⁺ ion passes through the cavity while K⁺ ions are retained.     

Syntheses of chiral bishomodiazacalix[4]arenes incorporating amino acid residues: Molecular recognition for racemic ammonium ions by the macrocycles possessing tyrosine residues

Chiral bishomodiazacalix[4]arenes containing amino acid residues were prepared. The ¹H and ¹³C nmr spectra indicated that the macrocycles preferably adopted a cone conformation, which suggested that the cyclophane moiety was in a chiral twisted form. Circular dichroism spectra supported the existence of the chirality of the cyclophane unit, and showed that intramolecular hydrogen bonding plays an important role in the transmission of the chirality from the amino acid residues to the cyclophane moiety. Macrocycles bearing a tyrosine residue have a π‐base cavity large enough to include the ammonium ion, and can serve as a shift reagent for the racemic ammonium ions upon complexation during a ¹H nmr analysis.     

Self-complementary

Three [3]catenanes with cavities large enough to accommodate aromatic guests have been designed and synthesized (yields = 5-20 %) by means of kinetically controlled self-assembly processes. The X-ray structural analysis of one of three [3]catenanes confirmed the presence of a rectangular cavity (dimensions = 7 x 11 A) lined by pi-electron-rich recognition sites and hydrogen-bond acceptor groups. In spite of their apparently ideal recognition features, none of these [3]catenanes bind guests incorporating a pi-electron-deficient bipyridinium unit. However, the template-directed syntheses of the [3]catenanes also produce, in yields of 2-23%, [2]catenanes incorporating a 1,5-dioxynaphtho[38]crown-10 interlocked with a bipyridinium-based tetracationic cyclophane. The X-ray structural analyses of two of these [2]catenanes revealed that a combination of [pi...pi] and [C-H...pi] interactions is responsible for the formation of supramolecular homodimers in the solid state. 1H NMR spectroscopic investigations of the four [2]catenanes demonstrated that supramolecular homodimers are also formed (Ka= 17-31M(-1), T= 185 K) in (CD3)2CO solutions. Dynamic 1H NMR spectroscopy revealed that the 1,5-dioxynaphtho[38]crown-10 and tetracationic cyclophane components in the four [2]catenanes and in the three [3]catenanes circumrotate (deltaGc(not equal to) = 9-14 kcal mol(-1)) through each other's cavity in (CD3)2CO. Similarly, the 1,5-dioxynaphthalene and the bipyridinium ring systems rotate (deltaGc(not equal to) =10-14 kcal mol(-1)) about their [O...O] and [N...N] axes, respectively, in solution.     

Magnetic face-to-face interaction and electrocommunication in chromium sandwich compounds

The reaction of [{(C5Me5)CrCl2}2] with [2.2](1,4)cyclophane gave [(C5Me5)Cr{[2.2](1,4)cyclophane}] (1) and [(C5Me5)Cr{[2.2](1,4)cyclophane}Cr(C5Me5)] (2), depending on the reaction conditions. X-ray structure analysis showed 2 to be a ministack which in turn is stacked in the lattice. The chromium atoms are 6.035 A apart, and the distortion of the benzene rings to boat-shaped moieties is less pronounced than in parent [2.2](1,4)cyclophane. The NMR and EPR spectra were consistent with a S=1/2 ground state for 1 and with two interacting S=1/2 centers in 2. Spin density was found in the ligand pi systems, where its sign was negative when the pi system was adjacent to chromium, while on the nonbonded benzene moiety of 1 it was positive. Cyclic voltammograms showed reductions to 1- and 2(2-), as well as oxidations to 1+, 2+, and 2(2+) which were quasireversible, whereas oxidations to 1(2+) and 2(3+) were irreversible. Interaction between the metal ions was revealed by a 260 mV separation of the redox waves belonging to 2+, and 2(2+). Both cations were isolated as [B(C6H5)4]- salts, which in solution decomposed to [2.2](1,4)cyclophane and [(C5Me5)Cr{(eta6-C6H5)B(C6H5)3}] (3). The 1H and 13C NMR spectra of 3 were in accordance with an S=1 ground state. Solid-state magnetic measurements of the dimetallic compounds showed antiferromagnetic interaction with J=-122 cm-1 for 2, J=-31 cm-1 for 2+ (ground state S=1/2), and J=-23.5 cm-1 for 2(2+) (with H=-JS1S2). The decrease of J in the series 2, 2+, and 2(2+) was traced to the number of unpaired electrons and, for the mixed-valent cation 2+, to additional double exchange.     

The H93G myoglobin cavity mutant as a versatile template for modeling heme proteins: ferrous, ferric, and ferryl mixed-ligand complexes with imidazole in the cavity

One of the difficulties in preparing accurate ambient-temperature model complexes for heme proteins, particularly in the ferric state, has been the generation of mixed-ligand adducts: complexes with different ligands on either side of the heme. The difference in the accessibility of the two sides of the heme in the H93G cavity mutant of myoglobin (Mb) provides a potential general solution to this problem. To demonstrate the versatility of H93G Mb for the preparation of heme protein models, numerous mixed-ligand adducts of ferrous, ferric, and ferryl imidazole-ligated H93G (H93G(Im) Mb) have been prepared. The complexes have been characterized by electronic absorption and magnetic circular dichroism (MCD) spectroscopy in comparison to analogous derivatives of wild type Mb. The starting ferric H93G(Im) Mb state spectroscopically resembles wild-type ferric Mb as expected for a complex containing a single imidazole in the proximal cavity and water bound on the distal side. Addition of a sixth ligand to ferric H93G(Im) Mb, whether charge neutral (imidazole) or anionic (cyanide and azide), results in formation of six-coordinate low-spin complexes with MCD characteristics similar to those of parallel derivatives of wild-type ferric Mb. Reduction of ferric H93G(Im) Mb and subsequent exposure to either CO, NO, or O2 produces ferrous complexes (deoxy, CO, NO, and O2) that consistently exhibit MCD spectra similar to the analogous ferrous species of wild-type ferrous Mb. Most interestingly, reaction of ferric H93G(Im) Mb with H2O2 results in the formation of a stable high-valent oxoferryl complex with MCD characteristics that are essentially identical to those of oxoferryl wild-type Mb. The generation of such a wide array of mixed-ligand heme complexes demonstrates the efficacy of the H93G Mb cavity mutant as a template for the preparation of heme protein model complexes.     

The H93G Myoglobin Cavity Mutant as a Versatile Scaffold for Modeling Heme Iron Coordination Structures in Protein Active Sites and Their Characterization with Magnetic Circular Dichroism Spectroscopy

Preparation of heme model complexes is a challenging subject of long-standing interest for inorganic chemists. His93Gly sperm whale myoglobin (H93G Mb) has the proximal His replaced with the much smaller non-coordinating Gly. This leaves a cavity on the proximal side of the heme into which a wide variety of exogenous ligands can be delivered. The end result is a remarkably versatile scaffold for the preparation of model heme adducts to mimic the heme iron coordination structure of native heme proteins. In this review, we first summarize the quantitative evidence for differential ligand binding affinities of the proximal and distal pockets of the H93G Mb cavity mutant that facilitates the preparation of mixed-ligand derivatives. Then we review our use of magnetic circular dichroism and electronic absorption spectroscopy to characterize nitrogen-, oxygen-, and sulfur-donor-ligated H93G Mb adducts with an emphasis on species not easily prepared by other heme model system approaches and those that serve as spectroscopic models for native heme proteins.     

8,16,24,32,40,48-Hexamethoxy[2.6]metacyclophane-1,9,17,25,33,41-hexayne: a novel near-planar ammonium-selective ionophore

The titled cyclophane (cyclic [6]metaphenylacetylene) with six methoxy groups inside the cavity has a nearly planar carbon framework, forms open-channel structures in the crystal, and exhibits an ammonium-selective ionophoric property in spite of the considerably large cavity.     

Switching of pseudorotaxanes and catenanes incorporating a tetrathiafulvalene unit by redox and chemical inputs

An acyclic polyether 1a, incorporating a central tetrathiafulvalene (TTF) electron donor unit and two 4-tert-butylphenoxy groups at its termini, has been synthesized. Two macrocyclic polyethers containing two different electron donors, namely a TTF unit with, in one case, a 1,4-dioxybenzene ring (2a), and, in the other case (2b), a 1,5-dioxynaphthalene ring system, have also been synthesized. These two macrocyclic polyethers have been mechanically interlocked in kinetically controlled template-directed syntheses with cyclobis(paraquat-p-phenylene) cyclophane (3(4+)) to afford the [2]catenanes 2a/3(4+) and 2b/3(4+), respectively. X-ray crystallography reveals that the [2]-catenane 2b/3(4+) has the TTF unit of 2b located inside the cavity of 3(4+). The spectroscopic (UV/vis and 1H NMR) and electrochemical properties of compounds 1a, 2a, 2b, 2a/3(4+), and 2b/3(4+) and of the [2]pseudorotaxane 1a.3(4+) were investigated. The absorption and emission properties of the mono- and dioxidized forms of the TTF unit in these various species have also been studied. The results obtained in acetonitrile solution can be summarized as follows. (a) While TTF2+ exhibits a strong fluorescence, no emission can be observed for the TTF2+ units contained in the polyethers and in their pseudorotaxanes and catenanes. (b) A donor-acceptor absorption band is observed upon two-electron oxidation of the TTF unit in the macrocyclic polyethers 2a and 2b. (c) The spontaneous self-assembly of 1a and 3(4+) to give the [2]pseudorotaxane 1a.3(4+) is strongly favored (Kass. = 5 x 10(5) L mol-1) but slow (at 296 K, k = 11.3 L mol-1 s-1 and delta G++ = 15.9 kcal mol-1) because of the steric hindrance associated with the bulky end groups of 1a. (d) In the pseudorotaxane 1a.3(4+), the reversible displacement of the cyclophane from the TTF unit in the threadlike substrate occurs on oxidation/reduction of its electroactive components. (e) Switching between the two translational isomers of the catenanes 2a/3(4+) and 2b/3(4+) occurs by cyclic oxidation and reduction of the TTF unit contained in 2a and in 2b, respectively. (f) Addition of o-chloroanil to the pseudorotaxane 1a.3(4+) and to the catenanes 2a/3(4+) and 2b/3(4+) causes the displacement of the TTF unit from the cavity of the cyclophane 3(4+) because of the formation of an adduct between the TTF unit and o-chloroanil.     

Effect of remote substituents on solid state packing interactions in macrocyclic crownophanes derived from 1,3,5-triaroylbenzenes

A series of four structurally related crownophanes has been prepared and characterized by X-ray crystallography. The crownophanes are based upon a 1,3,5-triaroylbenzene framework and were synthesized via enaminone/alkyne cyclotrimerization. The crownophanes differ in the identity of a peripheral substituent attached to a remote arene ring that is not part of the cyclophane macrocycle. Solid state structural characterization reveals that crownophanes with remote phenyl and phenol substituents self-assemble to form centrosymmetric dimers. Incorporation of remote alkoxy groups (methoxy or ethoxy) disrupts dimerization and leads to catameric networks. Each crownophane crystallized as an inclusion complex or a hydrate and, in one instance, water was found to occupy the macrocyclic cavity.     

Selenolate complexes of CYP101 and the heme-bound hHO-1/H25A proximal cavity mutant

Thiolate and selenolate complexes of CYP101 (P450cam) and the H25A proximal cavity mutant of heme-bound human heme oxygenase-1 (hHO-1) have been examined by UV-vis spectroscopy. Both thiolate and selenolate ligands bound to the heme distal side in CYP101 and gave rise to characteristic hyperporphyrin spectra. Thiolate ligands also bound to the proximal side of the heme in the cavity created by the H25A mutation in hHO-1, giving a Soret absorption similar to that of the H25C hHO-1 mutant. Selenolate ligands also bound to this cavity mutant under anaerobic conditions but reduced the heme iron to the ferrous state, as shown by the formation of a ferrous CO complex. Under aerobic conditions, the selenolate ligand but not the thiolate ligand was rapidly oxidized. These results indicate that selenocysteine-coordinated heme proteins will not be stable species in the absence of a redox potential stabilizing effect.     

Syntheses and structures of isomeric [6.6]- and [8.8]cyclophanes with 1,4-dioxabut-2-yne and 1,6-dioxahexa-2,4-diyne bridges

All three isomers (ortho, meta, and para) of [8.8]cyclophane bearing 1,6-dioxahexa-2,4-diyne bridges have been synthesized and structually characterized by single-crystal X-ray crystallography to determine the conformation of the cyclophanes and their cavity dimensions. The three isomeric [6.6]cyclophanes bearing 1,4-dioxabut-2-yne bridges have also been synthesized from but-2-yne-1,4-diol ditosylate and the isomeric dihydroxybenzenes. The [6.6]orthocyclophane has been structurally characterized by single-crystal X-ray crystallography. The energy-minimized structures from the semiempirical AM1 calculations of these cyclophanes compare very well with the structures obtained by X-ray crystallography.