Foldamer-based pyridine-fullerene tweezer receptors for enhanced binding of zinc porphyrin

This paper reports the design and synthesis of a new series of hydrogen bonding-mediated foldamer-derived tweezer receptors that are used for efficient complexation of zinc porphyrin guest. One end of the rigidified aromatic amide backbone is incorporated with one fullerene unit, while another end is connected to one pyridine or imidazole unit. The ¹H NMR, UV-vis, and fluorescent investigations in chloroform revealed that, due to the intramolecular hydrogen bonding-driven preorganized folded conformation, the fullerene and pyridine units of the receptors are located with suitable spatial separation and consequently able to co-complex zinc porphyrin with remarkably increased stability. In contrast, the imidazole-incorporated receptor displays a weakened binding affinity possibly due to structural mismatching and large steric hindrance. The association constants of the complexes of the new receptors with zinc porphyrin have been determined.     

Recognition through self-assembly. A quadruply-hydrogen-bonded, strapped porphyrin cleft that binds dipyridyl molecules and a [2]rotaxane

Quadruply-hydrogen-bonded porphyrin homodimer Zn1.Zn1 has been designed, assembled, and evaluated as a supramolecular cleft-featured receptor for its ability to bind dipyridyl guests in chloroform-d. Monomer Zn1 consists of a 2-ureidopyrimidin-4(1H)-one unit, which was initially reported by Meijer et al., and a zinc porphyrin unit. The zinc porphyrin is strapped with an additional aliphatic chain for controlling the atropisomerization of porphyrin. The 2-ureidopyrimidin-4(1H)-one unit dimerizes exclusively in chloroform even at the dilute concentration of 10(-)(4) M, while the two "strapped" zinc porphyrin units of the homodimer provide additional binding sites for selective guest recognition. (1)H NMR studies indicate that the new homodimer Zn1.Zn1 adopts an S-type conformation due to strong donor-acceptor interaction between the electron-rich porphyrin units and the electron-deficient 2-ureidopyrimidin-4(1H)-one unit. (1)H NMR, UV-vis, and vapor pressure osmometry investigations reveal that Zn1.Zn1 could function as a new generation of assembled supramolecular cleft, to be able to not only efficiently bind linear dipyridyl molecules 14-17, resulting in the formation of stable termolecular complexes, with K(aasoc) values ranging from 3.8 x 10(6) to 8.9 x 10(7) M(-)(1), but also strongly complex a hydrogen-bond-assembled [2]rotaxane, 18, which consists of a rigid fumaramide thread and a pyridine-incorporated tetraamide cyclophane, with K(aasoc) = 1.2 x 10(4) M(-)(1). (1)H NMR competition experiments reveal that complexation to the dipyriyl guests also promotes the stability of the quadruply-hydrogen-bonded dimeric receptor.     

Synthesis and Aggregation Behavior of Chiral Naphthoquinoline Petroporphyrin Asphaltene Model Compounds

The synthesis of structurally relevant compounds that model the chemical behavior and supramolecular aggregation of the asphaltenes, the most polar and metal‐rich fraction of heavy petroleum, has been extended to include fusions of important petroleum biomarkers. The synthetic protocol features a multicomponent reaction to form a dyad composed of a fused steroidal naphthoquinoline, followed by a pyrrole cyclocondensation reaction to incorporate the dyad into a chiral triad containing a Ni^II‐porphyrin substituent. This synthetic protocol has been used to prepare large molecules that represent both “continental” and “archipelago” models of asphaltene composition. The steroid–naphthoquinoline–porphyrin triads have been studied by UV/Vis and circular dichroism (CD) spectroscopies, and the results suggest that the naphthoquinoline core, a tetrahydro[4]helicene, adopts a helical conformation, producing a CD signal electronically related to the characteristic Soret absorption band of the porphyrin subunit. Finally, supramolecular aspects of asphaltene aggregation have been examined on a molecular level through analysis of axial coordination of pyridine to the Ni‐porphyrin. The relative affinity of pyridine for binding to the Ni center of the porphyrin is evaluated by comparing binding propensities in a series of sterically differentiated substituted porphyrins.     

Synthesis of meso-5-azaindolyl-appended Zn(II) porphyrins via Pd-catalyzed annulation

Pd-catalyzed annulation reaction of meso-hexynyl Zn(II) porphyrin with 4-amino-3-iodopyridine efficiently provides meso-3-(5-azaindolyl)-substituted Zn(II) porphyrin as a major product, which assembles to form a slipped cofacial dimer by the complementary coordination of the pyridine moiety to the Zn(II) center. 2-iodoaniline and 2-iodophenol also undergo this [3 + 2] annulation with the meso-hexynyl Zn(II) porphyrin to furnish meso-indolyl- and benzofuranyl-substituted Zn(II) porphyrins, respectively.     

A photoactive molecular triad as a nanoscale power supply for a supramolecular machine

A tetrathiafulvalene-porphyrin-fullerene (TTF-P-C(60)) molecular triad, which generates electrical current by harnessing light energy when self-assembled onto gold electrodes, has been developed. The triad, composed of three unique electroactive components, namely, 1) an electron-donating TTF unit, 2) a chromophoric porphyrin unit, and 3) an electron-accepting C(60) unit, has been synthesized in a modular fashion. A disulfide-based anchoring group was tagged to the TTF end of the molecule in order to allow its self-assembly on gold surfaces. The surface coverage by the triad in a self-assembled monolayer (SAM) was estimated to be 1.4 nm(2) per molecule, a density which is consistent with hexagonal close-packing of the spherical C(60) component (diameter approximately 1 nm). In a closed electronic circuit, a triad-SAM functionalized working-electrode generates a switchable photocurrent of approximately 1.5 microA cm(-2) when irradiated with a 413 nm Kr-ion laser, a wavelength which is close to the porphyrin chromophore's absorption maximum peak at 420 nm. The electrical energy generated by the triad at the expense of the light energy is ultimately exploited to drive a supramolecular machine in the form of a [2]pseudorotaxane comprised of a pi-electron-deficient tetracationic cyclobis(paraquat-p-phenylene) (CBPQT(4+)) cyclophane and a pi-electron-rich 1,5-bis[(2-hydroxyethoxy) ethoxy]naphthalene (BHEEN) thread. The redox-induced dethreading of the CBPQT(4+) cyclophane from the BHEEN thread can be monitored by measuring the increase in the fluorescence intensity of the BHEEN unit. A gradual increase in the fluorescence intensity of the BHEEN unit concomitant with the photocurrent generation, even at a potential (0 V) much lower than that required (-300 mV) for the direct reduction of the CBPQT(4+) unit, confirms that the dethreading process is driven by the photocurrent generated by the triad-SAM.     

Complex formation of mono-and binuclear dimeric cyclophane zinc diphenylporphyrinates with pyridine

The formation of host-guest complexes between zinc diphenylporphyrinates of dimeric diphenylporphyrins and pyridine in toluene has been studied by the spectrophotometric titration method and ¹H NMR spectroscopy. The zinc porphyrinates with pyridine form “internal” or “external” 1: 1 or 1: 2 complexes, depending on the length of binding ether O(CH₂)_nO bridges (n = 2, 3) of the cyclophane dimers and the reactant concentration. The stability constants of the porphyrinate-ligand complexes and concentration ranges of their formation have been determined.     

Catalytic Cyclophanes. Part VIII. Cytochrome P-450 activity of a porphyrin-bridged cyclophane

Following a known synthetic procedure, the porphyrin-cyclophane 1 having a porphyrin attached by two straps to an apolar cyclophane binding site was prepared. Upon metallation, the Zn^II and Fe^III derivatives 2 and 3 , respectively, were obtained in good yields. Treatment of 3 with base yielded the μ-oxo dimer 4 in which the two oxo-bridged porphyrins moieties are both capped by cyclophane binding sites. All compounds 1–4 are freely soluble in protic solvents such as MeOH and CF₃CH₂OH, and the Fe^III derivatives 3 and 4 are active cytochrome P-450 mimics in these protic environments. Strong inclusion complexation of polycyclic aromatic hydrocarbons by 1 and 3 in alcoholic solvents was observed and quantified by ¹H-NMR and UV/VIS titrations. Acenaphthylene binds in an ‘equatorial’ orientation which locates its reactive 1,2-double bond near the porphyrin center, whereas phenanthrene binds ‘axially’ with the reactive 9,10-double bond oriented away from the porphyrin. The reduction potential of 3 was not significantly altered by substrate binding. In the unbound form, the Fe^III center in porphyrin 3 was found by ESR and ¹H-NMR to prefer a high-spin state (S = 5.2). In CF₃CH₂OH, using iodosylbenzene as O-transfer agent, the Fe^III derivative 3 catalyzed the oxidation of acenaphthylene to acenaphthen-1-one ( 14 ). Phenanthrene inhibited the reaction, possibly as a result of strong but nonproductive binding. Under similar conditions, isotetralin ( 18 ) was aromatized with high turnover to 1,4-dihydronaphthalene. The μ-oxo dimer 4 also showed high activity in the oxidation of acenaphthylen in MeOH, a result which provides strong evidence for efficent supramolecular catalysis. Due to as yet unknown reaction channels leading to polymeric products, poor mass balances were generally obtained in the oxidations effected in MeOH and CF₃CH₂OH in the presence of PhIO.     

Effect of Bridging Units on Photophysical and DNA Binding Properties of a Few Cyclophanes

A few novel anthracene-based cyclophanes CP-1 , CP-2 and CP-3 were synthesized and their interactions with DNA were investigated employing photophysical and biophysical techniques. In methanol and acetonitrile, these systems exhibited optical properties characteristic of the anthracene chromophore. However, in the aqueous medium, the symmetric cyclophane CP-1 showed a dual emission having λ_max at 430 and 550 nm, due to the monomer and excimer, respectively. In contrast, the cyclophanes CP-2 and CP-3 in the aqueous medium showed structured anthracene absorption and emission spectra similar to those obtained in methanol and acetonitrile. DNA binding studies indicate that CP-1 undergoes efficient nonclassical partial intercalative interactions with DNA resulting in the exclusive formation of a sandwich-type excimer having enhanced emission intensity and lifetimes. The cyclophane CP-2 having one anthracene moiety exhibited nonclassical intercalative binding with DNA, albeit with less efficiency compared with CP-1 . In contrast, CP-3 , having sterically bulky viologen bridging group showed DNA electrostatic as well as groove binding interactions. These results demonstrate that the nature of the bridging unit plays an important role in the binding mode of the cyclophanes with DNA and in the formation of the novel sandwich-type excimer.     

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.     

Electromechanics of a redox-active rotaxane in a monolayer assembly on an electrode

A rotaxane monolayer consisting of the cyclophane, cyclobis(paraquat-p-phenylene) (2), threaded on a "molecular string" that includes a pi-donor diiminobenzene unit and stoppered by an adamantane unit is assembled on a Au electrode. The surface coverage of the electroactive cyclophane unit, E degrees = -0.43 V vs SCE, corresponds to 0.8 x 10(-10) mol.cm(-2). The cyclophane (2) is structurally localized on the molecular string by generating a pi-donor-acceptor complex with the diiminobenzene units of the molecular string. The cyclophane (2) acts as a molecular shuttle, revealing electrochemically driven mechanical translocations along the molecular wire. Reduction of the cyclophane (2) to the respective biradical-dication results in its dissociation from the pi-donor site, and the reduced cyclophane is translocated toward the electrode. Oxidation of the reduced cyclophane reorganizes 2 on the pi-donor-diiminobenzene sites. The positions of the oxidized and reduced cyclophane units are characterized by chronoamperometric and impedance measurements. Using double-step chronoamperometric measurements the dynamics of the translocation of the cyclophane units on the molecular string is characterized. The reduced cyclophane moves toward the electrode with a rate constant corresponding to k(1) = 320 s(-1), whereas the translocation of the oxidized cyclophane from the electrode to the pi-donor binding site proceeds with a rate constant of k(2) = 80 s(-1). Also, in situ electrochemical/contact angle measurements reveal that the electrochemically driven translocation of the cyclophane on the molecular string provides a means to reversibly control the hydrophilic and hydrophobic properties of the surface. The latter system demonstrates the translation of a molecular motion into the macroscopic motion of a water droplet.     

Electrical detection of amine ligation to a metalloporphyrin via a hybrid SOI-MOSFET

A close-packed monolayer of zinc 5,10,15,20-tetrakis(3-carboxyphenyl)porphyrin has been prepared and deposited on the thin native oxide covering the surface of an SOI-MOSFET (silicon-on-insulator metal-oxide-semiconductor field effect transistor) using Langmuir-Blodgett techniques. When the device is exposed to amine vapors in a nitrogen atmosphere, the amine coordinates to the zinc atom. The resulting change in electron distribution within the porphyrin leads to a large change in the drain current of the transistor, biased via a back gate. This change is sensitive to both the amount of amine present and the base strength of the amine. Only very small changes in drain current were observed with a monolayer of free base porphyrin or palmitic acid. After exposure to high pyridine concentrations, the device response saturates, but partially recovers after overnight exposure to flowing nitrogen gas. Interestingly, the device response is instantaneously reset by exposure to visible light, suggesting that photode-ligation occurs. An electrical model for the hybrid device that describes its response to ligand binding in terms of a change in the work function of the porphyrin monolayer has been developed. A transistor response to a few hundred attomoles of bound pyridine can be readily detected. This extreme sensitivity, coupled with the ability to reset the device using light, suggests that such systems might be useful as sensors.     

Molecular modeling of cationic porphyrin-anthraquinone hybrids as DNA topoisomerase IIβ inhibitors

Human DNA Topoisomerase II has been regarded as a promising target in anticancer drug discovery. In the present study, we designed six porphyrin-anthraquinone hybrids bearing pyrazole or pyridine group as meso substituents and evaluated their potentials as DNA Topoisomerase IIβ inhibitor. First, we investigated the binding orientation of porphyrin hybrids into DNA topoisomerase IIβ employing AutoDock 4.2 and then performed 20-ns molecular dynamics simulations to see the dynamic stability of each porphyrin-Topo IIβ complex using Amber 14. We found that the binding of porphyrin hybrids occured through intercalation and groove binding mode in addition interaction with the amino acid residues constituting the active cavity of Topo IIβ. Each porphyrin-Topo IIβ complex was stabilized during 20-ns dynamics simulations. The MM-PBSA free energy calculation shows that the binding affinities of porphyrin hybrids were modified with the number of meso substituent. Interestingly, the affinity of all porphyrin hybrids to Topo IIβ was stronger than that of native ligand (EVP), indicating the potential of the designed porphyrin to be considered in experimental research.     

Self-assembled coordination cage derived from small-sized pyridinophane

The dithia[3.3]pyridinophane consisting of two pyridine rings has been found out to assume the syn-structure by the X-ray crystallography, meaning the two nitrogen atoms point in the same direction. From this cyclophane and cis-protected palladium(II), the self-assembled coordination molecular cage has been constructed.     

Study on the interaction of new water-soluble porphyrin with DNA

A porphyrin meso-tetrakis{[4-(1-pyridyl)propoxy]phenyl}porphyrin (TPyPP) and its Ni complex (TPyPP(Ni)) have been synthesized and characterized by 1H NMR, UV-vis spectra. The interaction of two porphyrins with calf thymus-DNA (CT-DNA) has been explored by UV-vis, fluorescence and circular dichroic spectroscopy and viscosity measurements. The results suggest that these porphyrins can bind to DNA by the same binding mode. TPyPP outside binds by self-stack with DNA both at low drug load r (=[porphyrin]/[DNA]) and high drug load. Though TPyPP(Ni) has center metal nickel, binding mode with DNA has little difference compared with TPyPP, dominating out-binding mode with different direction along DNA. The binding constants of the TPyPP and TPyPP(Ni) to DNA were 4.65 x 10(5) M(-1) and 3.2 x 10(5) M(-1), respectively. A colored precipitate was found after time in two porphyrin's viscosity measurement. The reasonable interpretation is the porphyrins with alkyl connected N-position of pyridine can strongly interact with the anionic phosphates of DNA and lead to hydrophobic complex.     

Porphyrin/Quinoidal‐Bithiophene‐Based Macrocycles and Their Dications: Template‐Free Synthesis and Global Aromaticity

We report the template‐free synthesis and characterization of a new type of porphyrin/quinoidal‐bithiophene‐based conjugated macrocycle. X‐ray crystallographic analysis of the dimer ( 2MC ) revealed a cyclophane‐like geometry with large dihedral angles between the porphyrin and the neighboring thiophene rings, and NMR measurements and theoretical calculations confirmed a localized aromatic character of the porphyrin/thiophene rings and quinoidal character of the bithiophene linkers. Restricted rotation of the thiophene rings linked to the porphyrin unit was observed by variable‐temperature NMR measurements. The dication ( 2MC²⁺ ) adopts a chair‐shaped conformation to facilitate π‐electron delocalization around the whole macrocycle. As a result, the molecule is globally aromatic, with a dominant 54 π conjugation pathway. The trimer ( 3MC ) also shows localized aromatic character of porphyrin rings and conformational flexibility, but its dication ( 3MC²⁺ ) is rigid and globally aromatic with a dominant 82 π conjugation pathway.     

Restricted rotation in a tetrakis(para-substituted phenyl) porphyrin bearing four porphyrin-fullerene substituents

A porphyrin substituted with four porphyrin-fullerene moieties has been prepared and variable-temperature NMR studies revealed a high barrier to free rotation about the four para-substituted phenyl groups of the central porphyrin core.     

The binding energy of nitrogen 1<Emphasis Type="Italic">s</Emphasis> electrons in pyridine derivatives: Substituent effects in N-centered radical cations

The effect of substituents on the binding energy of nitrogen 1s electrons in 2-, 3-, and 4-substituted pyridine derivatives, as measured by X-ray photoelectron spectroscopy and calculated by quantum chemistry methods, was analyzed. It has been first shown that the binding energy depends not only on the inductive and resonance effects, but also on the polarization effect of the substituents.     

Characterization of cationic glycoporphyrins by electrospray tandem mass spectrometry

Novel cationic porphyrin derivatives having a galactose or a bis(isopropylidene)galactose unit linked directly to a pyridine or to an aminophenyl group were characterized by electrospray tandem mass spectrometry (ESI-MS/MS). The electrospray mass spectra (ESI-MS) show the M(+) ions, since these porphyrins are already monocharged in solution. The fragmentation of these ions under ESI-MS/MS conditions was studied and it was found that elimination of the sugar residue as a radical (-163 or -243 Da) is a common fragmentation pathway. Loss of the sugar unit as a neutral fragment (-162 or -242 Da) and cross-ring fragmentations typical of glyco-derivatives are also observed for the pyridinium glycoporphyrins, but they are absent in the case of ammonium glycoporphyrins. The cationic beta-pyridiniumvinyl porphyrins show an atypical fragmentation due to the cleavage of the C(5)-C(6) bond of the sugar unit. Overall, the different patterns of fragmentation observed in the ESI-MS/MS spectra of the sugar pyridinium porphyrins and of the sugar ammonium phenyl porphyrins can give important information about the type of spacer between the porphyrin and the sugar unit.     

Molecular sensors using a resonance Raman template

The potential use of resonance Raman spectroscopy as a molecular sensing tool is illustrated using a metalloporphyrin template and pyridine as an analyte. The equilibrium binding constant for the axial binding of pyridine to zinc tetraphenylporphyrin has been measured using resonance Raman spectroscopy. Although no new peaks are observed and the porphyrin peaks do not shift position, the quantification is made possible by the selective resonance enhancement of the template vibrations. The value for log k was determined by resonance Raman to be 3.65 +/- 0.32, which compares well with previously published values estimated using absorption data. Values for log k were determined for a series of related compounds, the picolines, and these also compare favourably with those previously reported.     

Synthesis and characterization of new porphyrin/4-quinolone conjugates

New porphyrin/4-quinolone conjugates were synthesized from the Suzuki-Miyaura coupling reaction of a β-borylated porphyrin with bromo-4-quinolones containing N-ethyl and N-d-ribofuranosyl substituents. The use of electrospray ionization tandem mass spectrometry showed important information about the fragmentation pathways of the new compounds. It was possible to distinguish between those compounds with the porphyrin moiety linked at the 6-position of the quinolone unit from their 7-substituted isomers. The new compounds showed to be good singlet oxygen generators.