The critical size of hydrogen-bonded alcohol clusters as effective Brønsted bases in solutions.

The alkyl oxonium ion, which is a protonated alcohol, has long been proposed as a key reaction intermediate in alcohol dehydration. Nonetheless, the dynamics and structure of this simple but important intermediate species have not been adequately examined due to the transient nature of the oxonium ion. Here, we devised a model system for the key step in the alcohol dehydration reaction, in which a photoacid transfers a proton to alcohols of different basicity in the acetonitrile solvent. Using time-resolved spectroscopy and computation, we have found that the linkage of at least two alcohol molecules via hydrogen bonding is critical for their enhanced reactivity and extraction of the proton from the acid. This finding addresses the cooperative role of the simplest organic protic compounds, namely alcohols, in nonaqueous acid-base reactions.

Biphasic tautomerization dynamics of excited 7-hydroxyquinoline in reverse micelles.

The excited-state tautomerization dynamics of 7-hydroxyquinoline in the water pools of reverse micelles has been investigated by monitoring time-resolved fluorescence spectra and kinetics as well as static absorption and emission spectra with a variation of water content and isotopic fractionation. The normal and the tautomeric species are found to reside preferentially in the bound- and the free-water regions of the micelles, respectively. The excited-state tautomerization of the normal species in the bound-water layers is suggested to occur via two different channels, depending on rotamers at the moment of excitation. The cis tautomerizes via proton relay from the enol group to the imino group along a hydrogen-bonded water bridge, unusual in water but common in alcohols, whereas the trans tautomerizes via the stepwise individual acid-base reactions of two prototropic groups as found in bulk water. Proton relay can take place because water in the pools has substantially reduced polarity and disrupted hydrogen-bond networks compared with bulk water.

Photoinduced strong acid-weak base reactions in a polar aprotic solvent.

The excited-state proton transfer (ESPT) of the strong photoacid, N-methyl-7-hydroxyquinolinium, was studied in the presence of different weak bases such as methanol, ethanol, and dimethyl sulfoxide in an aprotic solvent of acetonitrile. Here, we present chemical kinetics analysis of the ESPT mechanism to explain biphasic fluorescence decay of the parent photoacid and the sign reversal of the rise and decay of the resulting conjugate-base fluorescence. The ESPT of the free photoacid showed a molecularity of 2 with reacting alcohol molecules. In the ground state, it was found that a fraction of the photoacid formed 1 : 2 hydrogen-bonded complexes with the residual water present in the aprotic solvent or 1 : 1 complexes with the additive alcohols. In the excited state, these adducts underwent proton transfer when complexed further with diffusing alcohol molecules.

A blue-to-red energy-transfer thymidine analogue that functions in DNA.

The thymidine analogue 1 is a blue-to-red energy transfer cassette designed to absorb UV light in the 300 nm region and emit it as fluorescence at around 520 nm. When incorporated into DNA, the fluorescence intensity of this modified nucleobase is not significantly reduced by the surrounding structure in the oligonucleotides. [structure--see text]

Syntheses, photophysical properties, and application of through-bond energy-transfer cassettes for biotechnology.

We have designed fluorescent "through-bond energy-transfer cassettes" that can harvest energy of a relatively short wavelength (e.g., 490 nm), and emit it at appreciably longer wavelengths without significant loss of intensity. Probes of this type could be particularly useful in biotechnology for multiplexing experiments in which several different outputs are to be observed from a single excitation source. Cassettes 1-4 were designed, prepared, and studied as model systems to achieve this end. They were synthesized through convergent routes that feature coupling of specially prepared fluorescein- and rhodamine-derived fragments. The four cassettes were shown to emit strongly, with highly efficient energy transfer. Their emission maxima cover a broad range of wavelengths (broader than the four dye cassettes currently used for most high-throughput DNA sequencing), and they exhibit faster energy-transfer rates than a similar through-space energy-transfer cassette. Specifically, energy-transfer rates in these cassettes is around 6-7 ps, in contrast to a similar through-space energy-transfer system shown to have a decay time of around 35 ps. Moreover, the cassettes are considerably more stable to photobleaching than fluorescein, even though they each contain fluorescein-derived donors. This was confirmed by bulk fluorescent measurements, and in single-molecule-detection studies. Modification of a commercial automated DNA-sequencing apparatus to detect the emissions of these four energy-transfer cassettes enabled single-color dye-primer sequencing.

Ultrashort-lived excited states of aminophthalimides in fluid solution.

The Sn-->S0 ultraviolet fluorescence spectra (270-380 nm) of 4-aminophthalimide (4AP) and its N-methyl derivative 4-amino-N-methylphthalimide (4ANMP) are reported, following the absorption of two laser pulses. In polar but non-hydrogen-bonding solvents, both molecules exhibit a principal emission maximum near 290 nm, whereas solutions in hydrogen-bonding solvents display two prominent emission bands, near 300 and 350 nm. The relative intensities of these bands depend on solvent type and, in a pump-probe experiment, on the wavelengths and temporal spacing of two ultrashort pulses. Experiments covering the range approximately 0.1-100 ps showed evidence for at least two distinct ultrashort relaxation processes, the rates of which depend on solvent. Fluorescence upconversion experiments at < 0.2 ps resolution have shown that the longer-duration process correlates with the fluorescence Stokes shift, and provide evidence that the solvent-dependent shift of the S1-->S0 fluorescence spectrum is reflected in the fluorescence quantum efficiency of a nearby electronic state.

Anthracene-BODIPY cassettes: syntheses and energy transfer.

Compounds based on the 4,4-difluoro-1,3,5,7-tetramethyl-4-bora-3a,4a-diaza-s-indacene (BODIPY) framework are excellent fluorescent markers. When BODIPY dyes of this type are conjugated to functionalities that absorb at relatively short wavelengths, those functionalities can, in some molecules, transmit the absorbed energy to the BODIPY which then fluoresces. In such cases the BODIPY fragment acts as an acceptor while the other group serves as a donor. Energy transfer efficiencies in such donor-acceptor cassette systems must vary with the relative orientation of the two components, and with the structure of the linkers that attach them. This study was designed to probe these issues for the special case in which the linkers between the donor and acceptor fragments are conjugated. To do this, the cassettes 3-10 were prepared. Electrochemical studies were performed to provide insight into the degree of donor-acceptor conjugation in these systems. X-ray Crystallographic studies on single crystals of compounds 7 and 9 revealed the favored conformations of the donor and acceptor fragments in the solid state. Absorption, fluorescence, and time-resolved fluorescence spectra of the compounds were recorded, and quantum yields for the cassettes excited at the donor lambda(max) were measured. Fluorescence steady-state anisotropy data were determined for cassettes 3 and 9 to provide information about the mutual direction of the transition dipole moments.