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A colorimetric sensing ensemble for heparin.

A receptor possessing ammoniums and a novel amino acid with a boronic acid side chain was designed and synthesized. The receptor shows good affinity and selectivity for heparin over similar polysaccharides possessing lower anionic charge density. The affinity for heparin is similar to that for a heparin disaccharide, indicating that disaccharidic units are the likely sites for binding to the receptor. The receptor has a potential use for creating a colorimetric assay for heparin.

Anticoagulants↗

Designing the selectivity of the fluorescent detection of amino acids: a chemosensing ensemble for histidine.

The imidazole group of histidine deprotonates and bridges the two CuII centers of a dimetallic polyamine macrocyclic complex, displacing the previously bound and quenched fluorescent indicator I. Thus, histidine recognition is signaled by the revival of the fluorescence of I. Selectivity with respect to other natural amino acids is achieved by choosing an indicator of tuned affinity toward the dicopper(II) receptor.

Amino Acids↗

Hydrogen bonding interfaces in fullerene*TTF ensembles.

Novel thermodynamically stable supramolecular donor-acceptor dyads have been synthesized. In particular, we assembled successfully C(60), as an electron acceptor, with the strong electron donor TTF through a complementary guanidinium-carboxylate ion pair. Two strong and well-oriented hydrogen bonds, in combination with ionic interactions, ensure the formation of stable donor-acceptor dyads. The molecular architecture has been fine-tuned by using chemical spacers of different lengths (i.e., phenyl versus biphenyl) and functional groups (i.e., ester versus amide), thus providing meaningful incentives to differentiate between through-bond and through-space electron-transfer scenarios. In electrochemical studies, both the donor and acceptor character of the TTF and C(60) units, respectively, have been clearly identified. Steady-state and time-resolved emission studies, however, show a solvent-dependent fluorescence quenching in C(60)*TTF dyads as well as the formation of the C(60)(*)(-)*TTF(*)(+) radical ion pairs, for which we determined lifetimes that are in the range of hundred of nanoseconds to microseconds. The complex network that connects C(60) with TTF in the dyads and the flexible nature of the spacer result in through-space electron-transfer processes. This first example of electron transfer in C(60)-based dyads, connected by strong hydrogen bonds, demonstrates that this approach can add outstanding benefits to the construction of artificial photosynthetic systems that bear a closer resemblance to the natural one.

Journal Article↗

Self-assembly of flexible supramolecular metallacyclic ensembles: structures and adsorption properties of their nanoporous crystalline frameworks.

The syntheses, structures, and N2 adsorption properties of six new supramolecular metallacycles are reported. Flexible ditopic linkers, 1-4, with systematically varied lengths and conformational degrees of freedom were synthesized utilizing ester linkages. They were used in combination with (dppp)M(OTf)2, where M = Pt(II) and Pd(II), and cis-(Me3P)2Pt(OTf)2 to form flexible supramolecular metallacycles 5-10 in 88-98% isolated yields. Their structures were characterized via multinuclear NMR and X-ray crystallography. The metallacycles stack to form porous structures in the crystalline state. The pore dimensions depend on both the phosphorus ligands attached to the metals and the flexible linkers. Adsorption studies on the porous materials show that 5a, 6, 8, and 9 held 11.7, 16.5, 5.7, and 6.8 cm3/g STP of N2 at 77 K, respectively. A guest-exchange study with nitromethane and toluene reveals that the nanopore in 5 is flexible, a property which was transferred from the linker to the supramolecular structure in the solid state.

Adsorption↗

Studying and switching electron transfer: from the ensemble to the single molecule.

We report here on the systematic investigation of photoinduced intramolecular electron transfer (IET) in a series of donor-bridge-acceptor molecules as a means of understanding electron transport through the bridge. Perylenebisimide chromophores connected by various oligophenylene bridges are studied because their electron-transfer behavior can readily be monitored by following changes in the fluorescence intensity. We find dramatic switching of the IET behavior as the solvent polarity (dielectric constant) is increased. By combining steady-state and time-resolved fluorescence spectroscopy in a variety of solvents at multiple temperatures with standard theories of electron transfer, we determine parameters governing the IET behavior of these dimers, such as the electronic coupling through the bridges. We also deploy available ab initio quantum chemical methods to calculate the through-space component of the electronic coupling matrix element. Single-molecule investigations of the electron-transfer behavior also show that IET can be switched reversibly by a similar mechanism in an isolated individual molecule.

Journal Article↗

Stabilization of charge-separated states in phthalocyanine-fullerene ensembles through supramolecular donor-acceptor interactions.

A novel ZnPc-C60 dyad (3), in which two photoactive units are brought together by a phenylenevinylene spacer has been synthesized. The synthetic strategy en route toward 3 involves a Heck reaction to attach 4-vinylbenzaldehyde to a monoiodophthalocyanine precursor, followed by standard cycloaddition of azomethine ylides (generated from the formylPc derivative and N-methylglycine) to one of the double bonds of C60. Electrochemical studies reveal that in 3 the ZnPc is about 39 mV more difficult to oxidize than in the corresponding ZnPc reference, which points to appreciable electronic communication between ZnPc and C60 in the ground state. In the excited state, photoexcitation leads to the formation of a charge-separated ZnPc*+-C60*- state, for which a lifetime of 130 ns was determined in THF. Hetero-association between complementary Pcs (1 and 2 or 3 and 2), which carry different peripheral functionalities (i.e., either electron-donating alkoxy groups or electron-deficient alkylsulfonyl chains) was assessed by different techniques. They provided evidence for donor-acceptor 1:1 complex formation with a stability constant of ca. 10(5) M(-1) in CHCl3. Interestingly, hetero-association of ZnPc-C60 dyad 3 with an electron-deficient PdPc (2) allowed the construction of supramolecular triads, in which a substantial stabilization of the radical pair is seen relative to that of the covalently linked dyad ZnPc-C60 (3).

Biomimetic Materials↗

Supramolecular bis(rutheniumphthalocyanine)-Perylenediimide ensembles: simple complexation as a powerful tool toward long-lived radical ion pair states.

A novel supramolecular electron donor-acceptor hybrid (1) has been designed through axial coordination of a perylenebisimide moiety [BPyPDI], bearing two 4-pyridyl substituents at the imido positions, to the ruthenium(II) metal centers of two phthalocyanines [Ru(CO)Pc]. This modular protocol enables access to electron donor-acceptor hybrids with potentially great design flexibility. The new array (1) has been characterized by standard spectroscopic methods, and its photophysical behavior has been established by using ultrafast and fast time-resolved techniques. Photoexcitation of either chromophore leads to a product that is essentially identical for both pathways, that is, evolving from the [Ru(CO)Pc] or [BPyPDI] singlet excited state. Features of the photoproduct are new transient maxima at 530 and 725 nm, plus transient minima at 580 nm and 650 nm. Based on the radiolytically generated [BPyPDI*-] (i.e., one-electron reduction of [BPyPDI]) and [Ru(CO)Pc*+] (i.e., one-electron oxidation of [Ru(CO)Pc]) features, which in the 300 and 900 nm range remarkably resemble those noted for photoexcited 1, we attribute the photolytically generated species to the composite spectrum of the [Ru(CO)Pc*+ -BPyPDI*- -RuCOPc] radical ion pair state. Its lifetime, which is on the order of 115 +/- 5 ns, reveals a significant stabilization and confirms that the strongly exothermic charge recombination dynamics are placed deeply in the inverted region of the Marcus parabola.

Journal Article↗

A computational ensemble pharmacophore model for identifying substrates of P-glycoprotein.

P-glycoprotein (P-gp) functions as a drug efflux pump, mediating multidrug resistance and limiting the efficacy of many drugs. Clearly, identification of potential P-gp substrate liability early in the drug discovery process would be advantageous. We describe a multiple-pharmacophore model that can discriminate between substrates and nonsubstrates of P-gp with an accuracy of 63%. The application of this filter allows large virtual libraries to be screened efficiently for compounds less likely to be transported by P-gp.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

Molecular engineering of C60-based conjugated oligomer ensembles: modulating the competition between photoinduced energy and electron transfer processes.

A series of novel and soluble C60-(pi-conjugated oligomer) dyads were synthesized, starting from suitably functionalized oligomer precursors (i.e., dihexyloxynaphthalene, dihexyloxynaphthalene-thiophene, and dihexyloxybenzene-thiophene). A systematic change in the nature of the oligomeric component allowed (i) tailoring the light absorption of the chromophore by shifting the ground-state absorption from the ultraviolet to the visible region and (ii) varying the oxidation potential of the donor. The resulting electro- and photoactive dyads were examined by electrochemical and photophysical means. In general, both singlet-singlet energy transfer and intramolecular electron transfer were found to take place and, most importantly, to compete with each other in the overall deactivation of the photoexcited oligomer. The selection of polar solvents in combination with the dihexyloxybenzene-thiophene donor shifted the reactivity from an all energy (1a; dihexyloxynaphthalene) to an all electron-transfer scenario (1d, dihexyloxybenzene-thiophene). Encouraged by the favorable electron-transfer properties of dyad 1d, we prepared photodiodes by embedding 1d between asymmetric metal contacts, which showed external monochromatic efficiencies (IPCE) close to 10% at the maximum absorption of the molecule.

Journal Article↗

Denatured-state ensemble and the early-stage folding of the G29A mutant of the B-domain of protein A.

The folding mechanism of the G29A mutant of the B-domain of protein A (BdpA) has been studied by all-atom molecular dynamics simulation using AMBER force field (ff03) and generalized Born continuum solvent model. Started from the extended chain conformation, a total of 16 simulations (400 ns each) at 300 K captured some early folding events of the G29A mutant of BdpA. In one of the 16 trajectories, the G29A mutant folded within 2.8 A (root mean square) of the wild-type NMR structure. We observed that the fast burial of hydrophobic residues was the driving force to bring the distant residues into close proximity. The initiation of the helix I and III occurred during the stage of hydrophobic collapse. The initiation and growth of the helix II was slow. Both the secondary structure formation and the development of the native tertiary contacts suggested a multistage folding process. Clustering analysis indicated that two helix species (helices I and III) could be intermediates. Further analysis revealed that the hydrophobic residues of partially folded helix II formed nativelike hydrophobic contacts with helices I and III that stabilized a nativelike state and delayed the completion of folding of the entire protein. The details of the early folding process were compared with other theoretical and experimental studies. It was found that a nativelike hydrophobic cluster was formed by residues including F(30), I(31), L(34), L(44), L(45), and A(48) that prevented further development of the native structures, and breaking the hydrophobic cluster like this one contributed to the rate-limiting step. This was in complete agreement with the recent kinetic measurements in which mutations of these residues to Gly and Ala substantially increased the folding rates by as much as 60 times. Apparently, destabilization of nonnative states dramatically enhanced the folding rates.

Cluster Analysis↗

Carboxy SNARF-4F as a fluorescent pH probe for ensemble and fluorescence correlation spectroscopies.

The optical spectroscopic properties of 1,4(and 5)-benzenedicarboxylic acid, 2-[10-(dimethylamino)-4-fluoro-3-oxo-3H-benzo[c]xanthen-7-yl] (carboxy SNARF-4F), a commercial promising fluorescent pH probe, are investigated in buffered aqueous solutions in the 5.6-8.2 pH range by steady-state and time-resolved spectroscopy. A multiexponential global analysis of the picosecond time-resolved data is performed. The nonprotonated A species decays monoexponentially (0.73 ns), while the protonated species AH decays following a biexponential law with time constants of 0.40 and 1.87 ns. A kinetic scheme is proposed to explain the observations, which involves AH in equilibrium with a species denoted Y. The nature of Y is discussed in terms of a possible structural change in the molecule producing the lactone form, although the formation of a hydrogen-bonded complex to the solvent cannot be ruled out. Finally, the ability of the dye to probe pH at the single-molecule level is explored using fluorescence correlation spectroscopy.

Absorption↗

Electronic interplay on illuminated aqueous carbon nanohorn-porphyrin ensembles.

Tetracationic water-soluble porphyrin (H(2)P(4+)) has been immobilized by pi-pi stacking interactions onto the skeleton of carbon nanohorns (CNH), without disrupting their pi-electronic network. The stable aqueous solution of the CNH-H(2)P(4+) nanoensemble was examined by both electron microscopy and spectroscopic techniques. The efficient fluorescence quenching of the H(2)P(4+) moiety in the CNH-H(2)P(4+) nanoensemble was probed by steady-state as well as time-resolved fluorescence emission spectroscopy, suggesting charge separation from the photoexcited H(2)P(4+) to CNH. In the presence of methyl viologen dication (MV(2+)) and a hole trap, accumulation of the reduced species of methyl viologen was observed by the photoillumination of CNH-H(2)P(4+), suggesting that the electron migration from the initially formed charge-separated state takes place. Transient absorption spectroscopy gave further insights on the transient species such as the charge-separated state (CNH(*-))-(H(2)P(4+))(*+), which was consumed in the presence of MV(2+) and hole shifter, leaving the reduced methyl viologen.

Letter↗

Membrane surface dynamics of DNA-threaded nanopores revealed by simultaneous single-molecule optical and ensemble electrical recording.

We describe a method for simultaneous single-molecule optical and electrical characterization of membrane-based sensors that contain ion-channel nanopores. The technique is used to study the specific and nonspecific interactions of streptavidin-capped DNA polymers with lipid bilayers composed of diphytanoyl phosphatidylcholine and diphytanoyl phosphatidylglycerol. Biotinylated DNA that is bound to fluorescently labeled streptavidin is electrophoretically driven into, or away from, the lumen of alpha hemolysin (alphaHL) ion channels by an external electric field. Confocal microscopy simultaneously captures single-molecule fluorescence dynamics from the membrane interface at different applied potentials. Fluorescence correlation analysis is used to determine the surface number density and diffusion constant of membrane-associated complexes. The dual optical and electrical approach can detect membrane-associated species at a surface coverage below 10(-5) monolayers of streptavidin, a sensitivity that surpasses most other in vitro surface analysis techniques. By comparing the change in transmembrane current to the number of fluorescent molecules leaving the bilayer when the electrical potential is reversed, we demonstrate the general utility of the approach within the context of nanopore-based sensing and discuss a mechanism by which DNA-streptavidin complexes can be nonspecifically retained at the membrane interface.

Biotinylation↗

Photoconductive cadmium sulfide hemicylindrical shell nanowire ensembles.

We report the synthesis and characterization of hemicylindrical shell nanowires (HSNWs) composed of nanocrystalline cadmium sulfide (CdS). CdS HSNWs were synthesized by first electrodepositing microcrystalline cadmium (Cd) nanowires by electrochemical step-edge decoration on graphite electrode surfaces and then converting these Cd nanowires into CdS by exposure to H2S at elevated temperature. These nanowires had a hemicylindrical shell morphology that was produced by the Kirkendall effect, involving disparate rates for diffusion of Cd and S atoms within the nascent CdS layer during the conversion from Cd to CdS. The outer diameter of the CdS HSNWs was 1.6-2.4 times that of Cd precursor nanowires and was adjustable over the range from 116 to 550 nm. CdS HSNWs showed strong, band-edge photoluminescence at 2.45 eV and a fast, reversible, and stable photoconductivity response in air characterized by "on" and "off" times of less than 15 ms.

Journal Article↗

Energy transfer processes in novel subphthalocyanine-fullerene ensembles.

A series of subphthalocyanine-C(60) dyads in which the two subunits are placed at different distances have been prepared and their electrochemical properties measured. Photophysical measurements reveal energy transfer events following the initial photoexcitation of the subphthalocyanine chromophore.

Journal Article↗

A colorimetric boronic acid based sensing ensemble for carboxy and phospho sugars.

[structure: see text] A cadmium-centered tris-boronic acid receptor was synthesized, and its binding properties toward various anionic sugars were determined. This receptor shows high affinity for different anionic sugars, especially gluconic acid, which has an association constant near approximately 10(7) M(-)(1) at neutral pH. Further, using an indicator displacement assay, a color change of pyrocatechol violet was observed upon addition of anionic sugars. This colorimetric test was used as a facile screening technique to qualitatively analyze guest affinities.

Boronic Acids↗

Determination of the populations and structures of multiple conformers in an ensemble from NMR data: multiple-copy refinement of nucleic acid structures using floating weights.

A new algorithm is presented for determination of structural conformers and their populations based on NMR data. Restrained Metropolis Monte Carlo simulations or restrained energy minimizations are performed for several copies of a molecule simultaneously. The calculations are restrained with dipolar relaxation rates derived from measured NOE intensities via complete relaxation matrix analysis. The novel feature of the algorithm is that the weights of individual conformers are determined in every refinement step, by the quadratic programming algorithm, in such a way that the restraint energy is minimized. Its design ensures that the calculated populations of the individual conformers are based only on experimental restraints. Presence of internally inconsistent restraints is the driving force for determination of distinct multiple conformers. The method is applied to various simulated test systems. Conformational calculations on nucleic acids are carried out using generalized helical parameters with the program DNAminiCarlo. From different mixtures of A- and B-DNA, minor fractions as low as 10% could be determined with restrained energy minimization. For B-DNA with three local conformers (C2'-endo, O4'-exo, C3'-endo), the minor O4'-exo conformer could not be reliably determined using NOE data typically measured for DNA. The other two conformers, C2'-endo and C3'-endo, could be reproduced by Metropolis Monte Carlo simulated annealing. The behavior of the algorithm in various situations is analyzed, and a number of refinement protocols are discussed. Prior to application of this algorithm to each experimental system, it is suggested that the presence of internal inconsistencies in experimental data be ascertained. In addition, because the performance of the algorithm depends on the type of conformers involved and experimental data available, it is advisable to carry out test calculations with simulated data modeling each experimental system studied.

Algorithms↗