Intramolecular energy transfer in water

The evolution of the vibrational motion of a water molecule which has been excited locally is studied. An exact solution is obtained of a model Hamiltonian representing the non-harmonic behaviour of the molecule. Since this is obtained numerically it does not explain what is observed but it leads to a simplified model of the motion in which different aspects can be isolated and discussed. For many initial modes, especially those of higher energy, there is a large initial drop in the probability of finding the energy in the original local mode. This is due to dephasing. The factors involved in dephasing are discussed. A simple hypothesis is suggested which leads to a formula for this drop and this agrees substantially with the graphical evidence. The relation between the drop and the amplitude of the initial mode is also discussed.     

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.     

Controlling short- and long-range electron transfer processes in molecular dyads and triads

Novel pi-extended tetrathiafulvalene (exTTF)-based donor acceptor hybrids-dyads and triads-have been synthesized following a multistep synthetic procedure. Cyclic voltammetry and absorption spectroscopy, conducted in room temperature solutions, reveal features that are identical to the sum of the separate donor and acceptor moieties. Steady-state and time-resolved photolytic techniques confirm that upon photoexcitation of the fullerene chromophore, rapid (1.25 x 10(10) s(-1)) and efficient (67 %) charge separation leads to long-lived, charge-separated radical pairs. Typical lifetimes for the dyad ensembles range between 54 and 460 ns, with the longer values found in more polar solvents. This indicates that the dynamics are located in the 'normal region' of the Marcus curve. In the triads, subsequent charge shifts transform the adjacent radical pair into the distant radical pair, for which we determined lifetimes of up to 111 micros in DMF-values never previously accomplished in molecular triads. In the final charge-separated state, large donor-acceptor separation (center-to-center distances: approximately 30 A) minimizes the coupling between reduced acceptor and oxidized donor. Analysis of the charge recombination kinetics shows that a stepwise mechanism accounts for the unusually long lifetimes.     

Through-bond excited energy transfer mediated by an amidinium-carboxylate salt bridge in Zn-porphyrin free-base porphyrin dyads

Excited energy-transfer processes were investigated for a supramolecular Zn-porphyrin free-base porphyrin dyad, ZnPA-2 x FbPC-2, in which beta-octaalkylated meso-diarylporphyrins are connected through an amidinium-carboxylate salt bridge. The rate of energy transfer in the dyad (1.3 x 10(9) s(-1)) is substantially slower than that in the previously reported dyad, ZnPA-1FbPC-1 (4.0 x 10(9) s(-1)), in which meso-tetraarylporphyrins are connected through the same amidinium-carboxylate salt bridge. The F?rster-type mechanism can explain only minor parts of these rates (3.3 x 10(8) and 5.1 x 10(8) s(-1), respectively). Thus, Dexter-type through-bond energy transfer may be invoked. Indeed, bridge-mediated electronic processes would be favored in ZnPA-1 x FbPC-1 over ZnPA-2 x FbPC-2 on the basis of steric and electronic factors. Sterically, the phenyl groups in ZnPA-2 and FbPC-2 are more closely perpendicular to the porphyrin planes than those in ZnPA-1 and FbPC-1. Electronically, the energy and symmetry of the occupied frontier orbitals should favor ZnPA-1 x FbPC-1 over ZnPA-2 x FbPC-2 in terms of electronic interactions through the bridge. Therefore, the observed trend (ZnPA-1 x FbPC-1>ZnPA-2 x FbPC-2), consistent with these considerations, lends further support to the through-bond mechanism. Thus, the amidinium-carboxylate salt bridge is effective in mediating through-bond energy transfer even though the bond is noncovalent.     

Electronic energy transfer in a multiporphyrin-based molecular box.

The molecular box 1 comprises of two zinc-porphyrin metallacycles connected by two free-base 4'-trans-dipyridylporphyrins, axially coordinated to the zinc centers. The photophysics of 1 were studied in chloroform by emission and ultrafast absorption spectroscopy. In the molecular box, fast singlet energy transfer (main component, tau=32 ps) is observed to occur from the zinc-porphyrin metallacycles to the free-base chromophores. From wavelength-dependent spectrofluorimetric data, the efficiency of the energy-transfer (ET) process is estimated as 0.5. The lower-than-unity value is tentatively attributed to the possibility of a competing electron-transfer quenching pathway. Molecular box 1 can be considered to be a simple, self-assembling, six-chromophore antenna system. It has an inner cavity, 11.4 Angstrom wide, that could be used, in principle, to host a variety of guest molecules and obtain higher-order assemblies.     

Intramolecular energy transfer in rhodamine–phthalocyanine conjugates

Conjugates of tetrasulphosubstituted zinc phthalocyanine with rhodamine 6G or rhodamine B have been synthesized and characterized to have four rhodamine 6G or average two rhodamine B residues per phthalocyanine molecule. The ionized conjugates (positive charge on the rhodamine part) are non-soluble in water. Photochemical and photophysical measurements, carried out in dimethylsulphoxide, have shown that the main result of conjugation is efficient intramolecular energy transfer from rhodamine to phthalocyanine part of molecular system. The conjugation results in about twofold decrease of quantum yields for photodegradation, fluorescence and singlet oxygen photogeneration.     

A novel design method of ratiometric fluorescent probes based on fluorescence resonance energy transfer switching by spectral overlap integral

A ratiometric measurement, namely, simultaneous recording of the fluorescence intensities at two wavelengths and calculation of their ratio, allows greater precision than measurements at a single wavelength, and is suitable for cellular imaging studies. Here we describe a novel method of designing probes for ratiometric measurement of hydrolytic enzyme activity based on switching of fluorescence resonance energy transfer (FRET). This method employs fluorescent probes with a 3'-O,6'-O-protected fluorescein acceptor linked to a coumarin donor through a linker moiety. As there is no spectral overlap integral between the coumarin emission and fluorescein absorption, the fluorescein moiety cannot accept the excitation energy of the donor moiety and the donor fluorescence can be observed. After cleavage of the protective groups by hydrolytic enzymes, the fluorescein moiety shows a strong absorption in the coumarin emission region, and then acceptor fluorescence due to FRET is observed. Based on this mechanism, we have developed novel ratiometric fluorescent probes (1-3) for protein tyrosine phosphatase (PTP) activity. They exhibit a large shift in their emission wavelength after reaction with PTPs. The fluorescence quenching problem that usually occurs with FRET probes is overcome by using the coumarin-cyclohexane-fluorescein FRET cassette moiety, in which close contact of the two dyes is hindered. After study of their chemical and kinetic properties, we have concluded that compounds 1 and 2 bearing a rigid cyclohexane linker are practically useful for the ratiometric measurement of PTPs activity. The design concept described in this paper, using FRET switching by spectral overlap integral and a rigid link that prevents close contact of the two dyes, should also be applicable to other hydrolytic enzymes by introducing other appropriate enzyme-cleavable groups into the fluorescein acceptor.     

Resonance energy transfer methods of RNA detection

Quantitation of RNA is important in diagnostics, environmental science, and basic biomedical research. RNA is considered a signature for pathogen identification, and its expression profile is linked with disease pathogenesis, allowing for biomarker identification. RNA-based diagnostics is an emerging field of research. This expansion of interest in studying RNA has generated demand for its accurate and sensitive detection. Several methods have therefore been developed to detect RNA. Resonance energy transfer methods of RNA detection are highly promising in terms of simplicity and high sensitivity. In this review, we have focused on the latest developments in resonance energy transfer methods of RNA detection that utilize various probe designs. The probe designs discussed here are molecular beacons, quenched autoligation probes, and linear oligonucleotide probes. Resonance energy transfer methods based on both fluorescence and bioluminescence detection are discussed.     

A Ratiometric Fluorescent Probe for Imaging of the Activity of Methionine Sulfoxide Reductase A in Cells

Methionine sulfoxide reductase A (MsrA) is an enzyme involved in redox balance and signaling, and its aberrant activity is implicated in a number of diseases (for example, Alzheimer's disease and cancer). Since there is no simple small molecule tool to monitor MsrA activity in real time in vivo, we aimed at developing one. We have designed a BODIPY‐based probe called (S)‐Sulfox‐1, which is equipped with a reactive sulfoxide moiety. Upon reduction with a model MsrA (E. coli), it exhibits a bathochromic shift in the fluorescence maximum. This feature was utilized for the real‐time ratiometric fluorescent imaging of MsrA activity in E. coli cells. Significantly, our probe is capable of capturing natural variations of the enzyme activity in vivo.     

Intramolecular dimers: a new design strategy for fluorescence-quenched probes

Fluorogenic probes dual-labeled with reporter and quencher dyes use a change in fluorescence to monitor biochemical events (e.g., substrate binding or enzyme digestion). Such events change the reporter-quencher distance, which affects fluorescence. Recently, it is has been shown that static quenching through intramolecular dimers is an important mechanism that can sometimes be more efficient than F?rster resonance energy transfer (FRET).     

On the mechanism of d-f energy transfer in RuII/LnIII and OsII/LnIII dyads: Dexter-type energy transfer over a distance of 20 A

We have used time-resolved luminescence methods to study rates of photoinduced energy transfer (PEnT) from [M(bipy)3]2+ (M=Ru, Os) chromophores to Ln(III) ions with low-energy f-f states (Ln=Yb, Nd, Er) in d-f dyads in which the metal fragments are separated by a saturated -CH2CH2- spacer, a p-C6H4 spacer, or a p-(C6H4)2 spacer. The finding that d-->f PEnT is much faster across a conjugated p-C6H4 spacer than it is across a shorter CH2CH2 spacer points unequivocally to a Dexter-type energy transfer, involving electronic coupling mediated by the bridging ligand orbitals (superexchange) as the dominant mechanism. Comparison of the distance dependence of the Ru-->Nd energy-transfer rate across different conjugated spacers [p-C6H4 or p-(C6H4)2 groups] is also consistent with this mechanism. Observation of Ru-->Nd PEnT (as demonstrated by partial quenching of the RuII-based 3MLCT emission (MLCT=metal-to-ligand charge transfer), and the growth of sensitised NdIII-based emission at 1050 nm) over approximately 20 A by an exchange mechanism is a departure from the normal situation with lanthanides, in which long-range energy transfer often involves through-space Coulombic mechanisms.     

Intramolecular triplet energy transfer in donor-acceptor molecules linked by a crown ether bridge

Bichromophoric compounds BP-C-NP and BP-C-NBD were synthesized with benzophenone chromophore (BP) as the donor, and 2-naphthyl (NP) and norbornadiene group (NBD) as the acceptor, respectively. Their intramolecular triplet energy transfer was examined. The bridges linking the donor and acceptors in these molecules involve a crown ether moiety complexing a sodium ion. Phosphorescence quenching, flash photolysis and photosensitized isomerization experiments indicate that intramolecular triplet energy transfer occurs with rate constants of about 3.3 x 10(5) and 4.8 x 10(5) s(-1) and efficiencies of about 33 and 42 % for BP-C-NP and BP-C-NBD, respectively. Theoretical calculations indicate that these molecules adopt conformations below room temperature which allow their two-end chromophores conducive to through-space energy transfer.     

Reversible Fluorescent Probes for Biological Redox States

The redox chemistry of the cell is key to its function and health, and the development of chemical tools to study redox biology is important. While fluxes in oxidative state are essential for healthy cell function, a chronically elevated oxidative capacity is linked to disease. It is therefore essential that probes of biological redox states distinguish between these two conditions by the reversible sensing of changes over time. In this review, we discuss the current progress towards such probes, and identify key directions for future research in this nascent field of vital biological interest.