Single-molecule spectroscopy of a dendrimer-based host-guest system

The polar side of polyphenylene dendrimers

The site-specific functionalization of poly(phenylene) dendrimers can produce macromolecules with a range of different polarities.

Conjugated polyelectrolyte dendrimers: aggregation, photophysics, and amplified quenching

Conjugated polyelectrolyte dendrimers (CPDs) are monodisperse macromolecules that feature a fully π-conjugated dendrimer core surrounded on the periphery by ionic solubilizing groups. CPDs are soluble in water and polar organic solvents, and they exhibit photophysics characteristic of the π-conjugated chromophores comprising the dendrimer core. Here we describe the synthesis and photophysical characterization of series of three generations of CPDs based on a phenylene ethynylene repeat unit structure that is surrounded by an array of anionic sodium carboxylate groups. Molecular dynamics simulations indicate that the first-generation CPD is flat while the second- and third-generation CPDs adopt oblate structures. Photophysical studies, including absorption, fluorescence spectroscopy, and lifetimes, show that the ester protected precursor dendrimers exhibit highly efficient blue fluorescence in THF solution emanating from the phenylene ethynylene chromophore that is in the dendrimer core. By contrast, the water-soluble CPDs have much lower fluorescence quantum yields and the absorption and fluorescence spectra exhibit features of strong chromophore-chromophore interactions. The results are interpreted as suggesting that the CPDs exist as dimer or multimer aggregates, even in very dilute solution. Fluorescence quenching of the anionic CPDs with the dication electron acceptor N,N'-dimethylviologen (MV(2+)) is very efficient, with Stern-Volmer quenching constants (K(SV)) increasing with generation number. The third-generation CPD exhibits highly efficient amplified quenching, with K(SV) ∼ 5 × 10(6) M(-1).

Photochemical conversion of solar energy

Energy is the most important issue of the 21st century. About 85% of our energy comes from fossil fuels, a finite resource unevenly distributed beneath the Earth's surface. Reserves of fossil fuels are progressively decreasing, and their continued use produces harmful effects such as pollution that threatens human health and greenhouse gases associated with global warming. Prompt global action to solve the energy crisis is therefore needed. To pursue such an action, we are urged to save energy and to use energy in more efficient ways, but we are also forced to find alternative energy sources, the most convenient of which is solar energy for several reasons. The sun continuously provides the Earth with a huge amount of energy, fairly distributed all over the world. Its enormous potential as a clean, abundant, and economical energy source, however, cannot be exploited unless it is converted into useful forms of energy. This Review starts with a brief description of the mechanism at the basis of the natural photosynthesis and, then, reports the results obtained so far in the field of photochemical conversion of solar energy. The "grand challenge" for chemists is to find a convenient means for artificial conversion of solar energy into fuels. If chemists succeed to create an artificial photosynthetic process, "... life and civilization will continue as long as the sun shines!", as the Italian scientist Giacomo Ciamician forecast almost one hundred years ago.

Photoswitchable Dendritic Hosts: A Dendrimer with Peripheral Azobenzene Groups

We have studied the adducts formed by eosin (E) with a fourth generation dendrimer (D) that comprises 30 tertiary amine units in the interior and 32 naphthyl and 32 trans azobenzene units in the periphery. We have found that: (i) the all trans dendrimer D(32t) can be converted by irradiation with 365 nm light (Phi=0.12) into species containing, as an average, 4 trans and 28 cis azobenzene units, D(4t28c), that at 313 K undergoes a D(4t28c) --> D(32t) thermal back reaction (k = 7.0 x 10(-5) s(-1)); (ii) D(32t) and D(4t28c) extract 8 and, respectively, 6 eosin molecules from water at pH 7, yielding the species D(32t) subset 8E and D(4t28c) subset 6E; (iii) eosin uptake is significantly faster for D(32t) than for D(4t28c); (iv) irradiation at 365 nm of the D(32t) subset 8E species at 298 K leads to the release of two eosin molecules with formation of a photostable D(15t17c) subset 6E species (Phi = 0.15) that is also obtained from the back thermal reaction of D(4t28c) subset6E at 313 K (k = 2.7 x 10(-5) s(-1)); (v) thermal release of E from D(32t) subset 6E is much faster than from D(4t28c) subset 6E; and (vi) excitation of E in the adducts sensitizes the cis --> trans (but not the trans --> cis) isomerization. The results obtained show that the isomerization of the 32 peripheral azobenzene units controls to some extent the hosting capacity of the dendrimer and, viceversa, eosin molecules hosted in the dendrimer affect the isomerization process of its azobenzene units.

Mechanisms for Fluorescence Depolarization in Dendrimers

We have investigated the fluorescence properties of dendrimers (Gn is the dendrimer generation number) containing four different luminophores, namely terphenyl (T), dansyl (D), stilbenyl (S), and eosin (E). In the case of T, the dendrimers contain a single p-terphenyl fluorescent unit as a core with appended sulfonimide branches of different size and n-octyl chains. In the cases of D and S, multiple fluorescent units are appended in the periphery of poly(propylene amine) dendritic structures. In the case of E, the investigated luminophore is noncovalently linked to the dendritic scaffold, but is encapsulated in cavities of a low luminescent dendrimer. Depending on the photophysical properties of the fluorescent units and the structures of the dendrimers, different mechanisms of fluorescence depolarization have been observed: (i) global rotation for GnT dendrimers; (ii) global rotation and local motions of the dansyl units at the periphery of GnD dendrimers; (iii) energy migration among stylbenyl units in G2S; and (iv) restricted motion when E is encapsulated inside a dendrimer, coupled to energy migration if the dendrimer hosts more than one eosin molecule.

From 3D to 2D: a review of the molecular imprinting of proteins

Molecular imprinting is a generic technology that allows for the introduction of sites of specific molecular affinity into otherwise homogeneous polymeric matrices. Commonly this technique has been shown to be effective when targeting small molecules of molecular weight <1500, while extending the technique to larger molecules such as proteins has proven difficult. A number of key inherent problems in protein imprinting have been identified, including permanent entrapment, poor mass transfer, denaturation, and heterogeneity in binding pocket affinity, which have been addressed using a variety of approaches. This review focuses on protein imprinting in its various forms, ranging from conventional bulk techniques to novel thin film and monolayer surface imprinting approaches.

Photo-induced protonation/deprotonation in the GFP-like fluorescent protein Dronpa: mechanism responsible for the reversible photoswitching

Recently, reversible photoswitching in bulk samples or in individual molecules of Dronpa, a mutant of a green fluorescent protein (GFP)-like fluorescent protein, has been demonstrated. Intense irradiation at 488 nm changed Dronpa in a dim protonated form, and weak irradiation at 405 nm restored it to the bright deprotonated form. Here, we report on the mechanism of photoswitching of Dronpa by means of ensemble and single-molecule spectroscopy. Ensemble spectroscopy shows that the photoswitching can be described, in first approximation, by a three-state model including a deprotonated (B), a protonated (A1), and a photoswitched protonated (A2) forms of the chromophore. While the B and the A1 forms are in a ground state acid-base equilibrium, the B and the A2 forms are reversibly photoswitched upon irradiation with 488 and 405 nm light. At the single-molecule level, the on-times in fluorescence intensity trajectories excited at 488 nm decrease with increasing the excitation power, consistent with the photoswitching from the B to A2 form. The on-times agree well with expected values, which are calculated based on the ensemble spectroscopic properties of Dronpa. The fluorescence trajectory obtained with simultaneous dual-color excitation at 488 and 405 nm demonstrates reversible photoswitching between the B and the A2 forms at the single-molecule level. The efficiency of the photoswitching from the A2 to B form increased with increasing the excitation power of the 405 nm light. Our results demonstrate that Dronpa holds its outstanding photoswitching properties, based on a photo-induced protonation/deprotonation process, even at the single-molecule level.

On the Use of Nonfluorescent Dye Labeled Ligands in FRET-Based Receptor Binding Studies

The efficiency of fluorescence resonance energy transfer (FRET) is dependent upon donor-acceptor proximity and spectral overlap, whether the acceptor partner is fluorescent or not. We report here on the design, synthesis, and characterization of two novel pirenzepine derivatives that were coupled to patent blue VF and pinacyanol dyes. These nonfluorescent compounds, when added to cells stably expressing enhanced green fluorescent protein (EGFP)-fused muscarinic M1 receptors, promote EGFP fluorescence extinction in a time-, concentration-, and atropine-dependent manner. They display nanomolar affinity for the muscarinic receptor, determined using either FRET or classical radioligand binding conditions. We provide evidence that these compounds behave as potent acceptors of energy from excited EGFP with quenching efficiencies comparable to those of analogous fluorescent bodipy or rhodamine red pirenzepine derivatives. The advantages they offer over fluorescent ligands are illustrated and discussed in terms of reliability, sensitivity, and wider applicability of FRET-based receptor binding assays.

The Chemistry of Organic Nanomaterials

The development of nanotechnology using organic materials is one of the most intellectually and commercially exciting stories of our times. Advances in synthetic chemistry and in methods for the investigation and manipulation of individual molecules and small ensembles of molecules have produced major advances in the field of organic nanomaterials. The new insights into the optical and electronic properties of molecules obtained by means of single-molecule spectroscopy and scanning probe microscopy have spurred chemists to conceive and make novel molecular and supramolecular designs. Methods have also been sought to exploit the properties of these materials in optoelectronic devices, and prototypes and models for new nanoscale devices have been demonstrated. This Review aims to show how the interaction between synthetic chemistry and spectroscopy has driven the field of organic nanomaterials forward towards the ultimate goal of new technology.

Polyphenylene dendrimers as scaffolds for shape-persistent multiple peptide conjugates

The present work describes synthetic concepts for the coupling of peptides to polyphenylene dendrimers (PPDs). Novel functionalized cyclopentadienones have been synthesized whose Diels-Alder cycloaddition with various core molecules leads to polyphenylene dendrimers possessing (protected) amino or carboxyl groups. In addition, the resulting functionalized molecules exhibit the characteristic shape-persistence and monodispersity of PPDs. Their functions have been used for the attachment of polylysine to the dendritic scaffold. Three different methods for the decoration of dendrimers with polypeptides are presented. First, polylysine segments are grafted from the surface of the dendrimers employing alpha-amino acid N-carboxyanhydride (NCA) polymerization. Second, the C-terminal carboxyl groups of protected polypeptides are activated and then coupled to the amino groups on the surface of the PPD. Finally, cysteine terminated, unprotected peptide sequences are attached to polyphenylene dendrimers utilizing the addition of the sulfhydryl group of a cysteine to the maleimide functions on the dendrimer surface. Moreover, Diels-Alder cycloaddition of suitably functionalized cyclopentadienons to a desymmetized core molecule allows the design of a dendritic scaffold with a specific number of different anchor groups on its periphery. These approaches are important for the tailoring of new, shape-persistent, polyfunctional multiple antigen conjugates.

Carbocyanine dyes as efficient reversible single-molecule optical switch

We demonstrate that commercially available unmodified carbocyanine dyes such as Cy5 (usually excited at 633 nm) can be used as efficient reversible single-molecule optical switch, whose fluorescent state after apparent photobleaching can be restored at room temperature upon irradiation at shorter wavelengths. Ensemble photobleaching and recovery experiments of Cy5 in aqueous solution irradiating first at 633 nm, then at 337, 488, or 532 nm, demonstrate that restoration of absorption and fluorescence strongly depends on efficient oxygen removal and the addition of the triplet quencher beta-mercaptoethylamine. Single-molecule fluorescence experiments show that individual immobilized Cy5 molecules can be switched optically in milliseconds by applying alternating excitation at 633 and 488 nm between a fluorescent and nonfluorescent state up to 100 times with a reliability of >90% at room temperature. Because of their intriguing performance, carbocyanine dyes volunteer as a simple alternative for ultrahigh-density optical data storage. Measurements on single donor/acceptor (tetramethylrhodamine/Cy5) labeled oligonucleotides point out that the described light-driven switching behavior imposes fundamental limitations on the use of carbocyanine dyes as energy transfer acceptors for the study of biological processes.

Spider-web amphiphiles as artificial lipid clusters: design, synthesis, and accommodation of lipid components at the air-water interface

As a novel category of two-dimensional lipid clusters, dendrimers having an amphiphilic structure in every unit were synthesized and labeled "spider-web amphiphiles". Amphiphilic units based on a Lys-Lys-Glu tripeptide with hydrophobic tails at the C-terminal and a polar head at the N-terminal are dendrically connected through stepwise peptide coupling. This structural design allowed us to separately introduce the polar head and hydrophobic tails. Accordingly, we demonstrated the synthesis of the spider-web amphiphile series in three combinations: acetyl head/C16 chain, acetyl head/C18 chain, and ammonium head/C16 chain. All the spider-web amphiphiles were synthesized in satisfactory yields, and characterized by 1H NMR, MALDI-TOFMS, GPC, and elemental analyses. Surface pressure (pi)-molecular area (A) isotherms showed the formation of expanded monolayers except for the C18-chain amphiphile at 10 degrees C, for which the molecular area in the condensed phase is consistent with the cross-sectional area assigned for all the alkyl chains. In all the spider-web amphiphiles, the molecular areas at a given pressure in the expanded phase increased in proportion to the number of units, indicating that alkyl chains freely fill the inner space of the dendritic core. The mixing of octadecanoic acid with the spider-web amphiphiles at the air-water interface induced condensation of the molecular area. From the molecular area analysis, the inclusion of the octadecanoic acid bears a stoichiometric characteristic; i.e., the number of captured octadecanoic acids in the spider-web amphiphile roughly agrees with the number of branching points in the spider-web amphiphile.

Molecular dynamics of a dendrimer-dye guest-host system

We use molecular dynamics to investigate the instantaneous structure of a fourth generation (dansyl terminated) dendrimer of propylene amine dissolved in CH(2)Cl(2), and of the same system upon the subsequent encapsulation of several eosin Y dyes. Calculations, in a cubic box with up to approximately 3500 solvent molecules and a maximum of 12 eosins, show that one of the effects of the presence of the guest molecules is to "close" the structure of the box where they are contained. Multiple entrances-exits of the guest molecules in the dendrimer are observed in less than a nanosecond, until the excess eosins are irreversibly expelled and their number is finally brought down to the experimental limit of 6. The guest molecules are distributed at two main distances from the center of the dendrimer and their surroundings are far from static. Eosins move inside the hyperbranched molecule in a way similar to what the solvent molecules do and sometimes aggregate.

Excitation energy transfer in dendritic host-guest donor-acceptor systems

We report on a study of a physically formed host-guest system, which was designed to be investigated by fluorescence energy transfer. All donor and acceptor molecules used were cyanine dyes. Investigation was performed at the ensemble level as well as at the single-molecule level. The ensemble measurements revealed a distribution of binding sites as well for the donor as for the acceptor. Accordingly, we found a distribution of the energy transfer efficiency. At the single-molecule level, these distributions are still present. We could discriminate entities that show very efficient energy transfer, some that do not show any energy transfer and systems whose energy transfer efficiency is only about 50%. The latter allowed the time-resolved detection of energy transfer of single entities through the acceptor decay. Finally, we discuss the observation that the energy transfer efficiency fluctuates as a function of time.

Synthesis and properties of water-soluble asterisk molecules

An asterisk is comprised of six semirigid arms projecting from a benzene nucleus. In the case at hand, asterisks were synthesized with one, two, or three aromatic rings (connected by sulfur atoms) in each of the six arms. A phosphomonoester at the termini of each arm solubilized the asterisks in water. The colloidal properties of these amphiphilic molecules were investigated by UV-vis and fluorescence spectroscopy, calorimetry, light scattering, surface tensiometry, and pulse-gradient spin-echo NMR. Solubility, solubilization, metal binding, and micelle "seeding" experiments were also carried out. Chain-conformation and supramolecular assembly into remarkable molecular "scrolls" were investigated by X-ray analysis and electron microscopy, respectively. One of the more interesting properties of the asterisks is that they remain monomeric in water despite having as many as 19 hydrophobic aromatic rings exposed to the water. The reasons for this behavior, and the possibility of exploiting it for constructing enzyme models free from aggregation equilibria, are discussed.

Luminescent lanthanide ions hosted in a fluorescent polylysin dendrimer. Antenna-like sensitization of visible and near-infrared emission

We have investigated the complexation of the luminescent Nd(3+), Eu(3+), Gd(3+), Tb(3+), Er(3+), and Yb(3+) ions by a polylysin dendrimer containing 21 amide groups in the interior and, in the periphery, 24 chromophoric dansyl units which show an intense fluorescence band in the visible region. Most of the experiments were performed in 5:1 acetonitrile/dichloromethane solution at 298 K. On addition of the lanthanide ions to dendrimer solutions, the fluorescence of the dansyl units is quenched; in Nd(3+), Er(3+), and Yb(3+), a sensitized near-infrared emission of the lanthanide ion is observed. At low metal ion concentrations, each dendrimer hosts only one metal ion and when the hosted metal ion is Nd(3+) or Eu(3+), the fluorescence of all the 24 dansyl units of the dendrimer is quenched with unitary efficiency. Quantitative measurements were performed in a variety of experimental conditions, including protonation of the dansyl units and measurements in rigid matrix at 77 K where a sensitized Eu(3+) emission could also be observed. The results obtained have been interpreted on the basis of the energy levels and redox potentials of dendrimer and metal ions.