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The design of the phosphorescent oxygen nanosensor is described, where two-photon (2P) light harvesting and intramolecular energy transfer (ET) are succeeded by the intersystem crossing within the acceptor chromophore to induce its phosphorescence, which is sensitive to oxygen. Various Pt phorphyrin-coumarin based sensors are synthesized and their characteristics are analyzed to study the proposed design.

Fluorescence quenching in solutions of a pendant-functionalized conjugated polymer chemosensor (ttp-PPETE) is evaluated in the presence of a variety of transition metal cations, including Ni(super 2+), Co(super 2+), Cu(super 2+), Fe(super 2+), and Cr(super 6+) is presented. Photophysical characterization for ttp-PPETE includes absorbance, emission, and single-photon counting lifetimes in the absence and presence of varying concentrations of the analytes.

Glycine betaine (GB) is a naturally occurring osmolyte that has been widely recognized as a protein protectant. Since GB consists of a methylated ammonium moiety, it can engage in strong cation–p interactions with aromatic amino acid sidechains. We hypothesize that such specific binding interactions would allow GB to decrease the stability of proteins that are predominantly stabilized by a cluster of aromatic amino acids. To test this hypothesis, we investigate the effect of GB on the stability of two b-hairpins (or mini-proteins) that contain such a cluster. We find that for both systems the stability of the folded state first decreases and then increases with increasing GB concentration. Such nonmonotonic dependence not only confirms that GB can act as a protein denaturant, but also underscores the complex interplay between GB’s stabilizing and destabilizing forces toward a given protein. While stabilizing osmolytes all have the tendency to be excluded from the protein surface which is the action underlying their stabilizing effect, our results suggest that in order to quantitatively assess the effect of GB on the stability of any given protein, specific cation–p binding interactions need to be explicitly considered. Moreover, our results show, consistent with other studies, that cation methylation can strengthen the respective cation–p interactions. Taken together, these findings provide new insight into the mechanism by which amino acid-based osmolytes interact with proteins. [ABSTRACT FROM AUTHOR]

A water-soluble triacetic acid cryptophane-A derivative (TAAC) is prepared and determined by isothermal calorimetry and fluorescence quenching assay in order to find out xenon association constant. Tris(triazole propionic acid)cryptophane-A derivative (TTPC) has showed the effect of solvation of the carboxylate anions on the aqueous behavior of the large, nonpolar cryptophane.

A model enhanced two-photon-absorbing (2PA) antenna-triplet core dyads is studied for identifying undesirable photinduced electron transfer (ET) processes and for evaluating their distance dependence. Guidelines are developed for designing the optimized-triplet core 2PA systems for biological applications.

Methods based on fluorescence resonance energy transfer (FRET) and photo-induced electron transfer (PET) are widely used in the biological sciences, employing mostly dye-based FRET and PET pairs. While very useful and important, dye-based reporters are not always applicable without concern, for example, in cases where the fluorophore size needs to be minimized. Therefore, development and characterization of smaller, ideally amino acid-based PET and FRET pairs will expand the biological spectroscopy toolbox to enable new applications. Herein, we show that, depending on the excitation wavelength, tryptophan and 4-cyanotrptophan can interact with each other via the mechanism of either energy or electron transfer, hence constituting a dual FRET and PET pair. The biological utility of this amino acid pair is further demonstrated by applying it to study the end-to-end collision rate of a short peptide, the mode of interaction between a ligand and BSA, and the activity of a protease. [ABSTRACT FROM AUTHOR]

Fluorescence excitation spectra of jet-cooled van der Waals complexes of the planar aromatic hydrocarbon perylene with the n-alkanes pentane, hexane, octane, and decane show in each case a single structural form. Rotational coherence transients observed for these species, spaced by 2.5–4.4 ns, are consistent with the n-alkane chain oriented parallel to the long axis of perylene and placed 3.6 Å above its surface. In contrast, the 1-chloropentane and 1-fluoropentane complexes of perylene both exhibit three conformational isomers (α,β,γ) in the electronic ground state. Rotational coherence experiments have measured the structures of these different species in the S1 state, via 000 excitation, proving the existence of three distinct isomers in each case. Dispersed emission spectra following vibronic excitation at 355 cm-1 (A10) indicate in each case that the γ structure relaxes to the α form. Knowledge of the structures of the different forms provides a basis to identify the photoisomerization trajectories. Rotational coherence spectroscopy (RCS) was also used to examine the structures following vibronic excitation. The n-alkane complexes each revealed at least one prominent recurrence transient, showing that vibronic excitation and subsequent vibrational redistribution processes do not necessarily cause rapid rotational dephasing. Similarly, an appreciable degree of rotational coherence persisted into the nanosecond domain for the α and β isomers of the fluoropentane and chloropentane complexes. On the other hand, loss of the γ form was confirmed via the RCS traces, since there were no recurrences for 355 cm-1 excitation. In this way, RCS measurements following vibronic excitation can provide a means to probe conformational stability. © 1994 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Picosecond time-resolved polarized fluorescence experiments involving time-correlated single-photon counting have studied rotational coherence phenomena of hydrogen-bonded and other molecular aggregates in their lowest excited singlet states. The experiments are supported by detailed simulations. Using the molecule 2,5-diphenyl-1,3,4-oxadiazole (PPD) as a host species, experiments have compared van der Waals aggregates with Ar1,2, (CH4)1,2, (H2O)1,2, (CH3OH)1,2, (C2H5OH)1, and (1-C3H7OH)1. Bare PPD, and the argon and methane aggregates all exhibit prominent J-type recurrences. The resulting sums of rotational constants (B+C) are consistent with center-of-mass-bound, three-dimensional structures, having out-of-plane distances for the attached species of 3.3–3.5 Å. The 1:2 aggregates involving argon and methane exhibit additive spectral shifts and nearly additive rotational recurrence times. This shows that the sites for addition of consecutive species are equivalent.Calculations of rotational constants confirm these findings. All except the Ar 1:2 cluster exist close to the prolate symmetric top limit. On the other hand, the excitation spectra of complexes involving hydrogen-bonding species all show small complexation shifts at the 1:1 level and disproportionately larger shifts at the 1:2 level. Similar nonadditive behavior is seen for the rotational recurrence transients. Hydrogen-bonded species differ from the nonpolar cases, since they show both prominent C-type and J-type transients. This shows that these species all differ significantly from prolate symmetric tops. Detailed simulations reveal that all of the hydrogen-bonding species produce aggregates that involve a single hydrogen bond to one of the PPD nitrogen atoms. This imposes a planar type of structure on the 1:1 water and methanol complexes. On the other hand, the aggregates methanol 1:2, ethanol 1:1, and propanol 1:1 all involve a distinct out-of-plane twist, consistent with the... [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations were performed for van der Waals clusters naphthalene·Arn, n=1 to 4. For all isomers and conformers of these clusters, dynamical quantities such as velocity autocorrelation functions, vibrational power spectra, and semiclassical electronic absorption spectra were calculated over a wide energy range, and averaged over a canonical distribution at temperatures in the range T=5 to 30 K. Electronic absorption spectra were calculated for the origin bands according to the semiclassical method [L. E. Fried and S. Mukamel, J. Chem. Phys. 96, 116 (1992)] and are compared with the corresponding experimental naphthalene·Arn R2PI spectra [T. Troxler and S. Leutwyler, J. Chem. Phys. 95, 4010 (1991)]. The appearance of distinct absorption bands due to specific isomers for a given cluster size, as observed experimentally, is well reproduced by the simulations. Comparison of calculated electronic shifts for different isomers allows clear assignments in the experimental spectra. Increasing the simulation temperature to T=15–25 K is accompanied by band broadening and the appearance of sidebands towards the blue. Especially strong sidebands appear for naph·Ar2 and all clusters containing the Ar2 subunit, due to large-amplitude surface rotation/translation of the argon dimer on the naphthalene surface, in agreement with experiment. For clusters containing the n=3 and n=4 subunits the spectral broadening is smaller. For the n=4 (4+0)-isomer, the calculated band shape increases less than for the other n=4 isomers, mainly due to the motional narrowing effect of cluster fluxionality. Above 25 K, isomerization between different possible topological structures also occurs by side-crossing motion of one or several argon atoms. [ABSTRACT FROM AUTHOR]

Van der Waals (vdW) clusters of naphthalene with argon were synthesized in supersonic beam expansions. Mass-selective absorption spectroscopy was carried out by using fragmentation-free two-color resonant two-photon ionization with mass-spectrometric detection. Electronic spectra of naph·Arn (n≤6) were recorded at the vicinity of the naphthalene S1←S0 electronic origin (32 020 cm-1 ), and corresponding spectra for the 810 transition up to n=30. For n=3, the spectra due to two different isomers could be separated. Clear evidence for the existence of different cluster isomers was also found for n=6, 8, 9, 12–14, and 25–28. In comparison with most other solvent clusters M·Arn (M is the aromatic molecule), the spectral red shifts of 000 and vibronic bands of the naph·Arn clusters are very small. Analysis of the size dependence of the electronic spectral shifts indicates that the stepwise solvation of the naphthalene molecule proceeds predominantly on one side of the molecule. Two semicyclic trends in the spectral shifts are interpreted as successive wetting-nonwetting transitions which occur with increasing solvent cluster size. In the proposed mechanism for these transitions, part of the innermost solvent layer ‘‘unwets’’ the substrate, and moves to the second or third layer, thereby forming a nonwetting dropletlike cluster on one side of the naphthalene substrate. [ABSTRACT FROM AUTHOR]

Considerable efforts have been devoted to the development of spectroscopic probes that are sensitive to water and can be used to monitor, for example, biological and chemical processes involving dehydration or hydration. Continuing this line of research, herein we show that 7-cyanoindole can serve as a sensitive fluorescence probe of hydration as its fluorescence properties, including intensity, peak wavelength and lifetime, depend on the amount of water in nine water–organic solvent mixtures. Our results indicate that 7-cyanoindole is not only able to reveal the underlying microheterogeneity of these binary solvent systems, but also offers distinct advantages. These include: (1) its fluorescence intensity increases more than ten times upon going from a hydrated to a dehydrated environment; (2) its peak wavelength shifts as much as 35 nm upon dehydration; (3) its single-exponential fluorescence decay lifetime increases from 2.0 ns in water to 8–16 ns in water–organic binary mixtures, making it viable to distinguish between differently hydrated environments via fluorescence lifetime measurements; and (4) its absorption spectrum is significantly red-shifted from that of indole, making selective excitation of its fluorescence possible in the presence of naturally occurring amino-acid fluorophores. Moreover, we find that for seven binary mixtures the fluorescence lifetimes of 7-cyanoindole measured at solvent compositions where maximum microheterogeneity occurs correlate linearly with the peak wavenumbers of its fluorescence spectra obtained in the respective pure organic solvents. This suggests that the microheterogeneities of these binary mixtures bear certain similarity, a phenomenon that warrants further investigation. [ABSTRACT FROM AUTHOR]

The M2 proton channel of the influenza A virus has been the subject of extensive studies because of its critical role in viral replication. As such, we now know a great deal about its mechanism of action, especially how it selects and conducts protons in an asymmetric fashion. The conductance of this channel is tuned to conduct protons at a relatively low biologically useful rate, which allows acidification of the viral interior of a virus entrapped within an endosome, but not so great as to cause toxicity to the infected host cell prior to packaging of the virus. The dynamic, structural and chemical features that give rise to this tuning are not fully understood. Herein, we use a tryptophan (Trp) analog, 5-cyanotryptophan, and various methods, including linear and nonlinear infrared spectroscopies, static and time-resolved fluorescence techniques, and molecular dynamics simulations, to site-specifically interrogate the structure and hydration dynamics of the Trp41 gate in the transmembrane domain of the M2 proton channel. Our results suggest that the Trp41 sidechain adopts the t90 rotamer, the χ2 dihedral angle of which undergoes an increase of approximately 35° upon changing the pH from 7.4 to 5.0. Furthermore, we find that Trp41 is situated in an environment lacking bulk-like water, and somewhat surprisingly, the water density and dynamics do not show a measurable difference between the high (7.4) and low (5.0) pH states. Since previous studies have shown that upon channel opening water flows into the cavity above the histidine tetrad (His37), the present finding thus provides evidence indicating that the lack of sufficient water molecules near Trp41 needed to establish a continuous hydrogen bonding network poses an additional energetic bottleneck for proton conduction. [ABSTRACT FROM AUTHOR]

The C≡N stretching frequency and fluorescence quantum yield of p-cyanophenylalanine are sensitive to environment. As such, this unnatural amino acid has found broad applications, ranging from studying how proteins fold to determining the local electric field of membranes. Herein, we demonstrate that the fluorescence of p-cyanophenylalanine can be quenched by selenomethionine through an electron transfer process occurring at short distances, thus further expanding its spectroscopic utility. Using this fluorophore–quencher pair, we are able to show that short polyproline peptides (1–4 prolines) are not rigid; instead, they sample a bimodal conformational distribution. [ABSTRACT FROM AUTHOR]

The anti-AIDS drug rilpivirine undergoes conformational changes to bind HIV-1 reverse transcriptase (RT), which is an essential enzyme for the replication of HIV. These changes allow it to retain potency against mutations that otherwise would render the enzyme resistant. Here we report that water molecules play an essential role in this binding process. Femtosecond experiments and theory expose the molecular level dynamics of rilpivirine bound to HIV-1 RT. Two nitrile substituents, one on each arm of the drug, are used as vibrational probes of the structural dynamics within the binding pocket. Two-dimensional vibrational echo spectroscopy reveals that one nitrile group is unexpectedly hydrogen-bonded to a mobile water molecule, not identified in previous X-ray structures. Ultrafast nitrile-water dynamics are confirmed by simulations. A higher (1.51 Å) resolution X-ray structure also reveals a water-drug interaction network. Maintenance of a crucial anchoring hydrogen bond may help retain the potency of rilpivirine against pocket mutations despite the structural variations they cause. [ABSTRACT FROM AUTHOR]

Cylcodextrin sugars are cyclic sugars that have a hydrophilic exterior and a hydrophobic center. This enables cyclodextrins to solubilize hydrophobic molecules in aqueous media. Cyclodextrins may inhibit aggregation by intercalating surface aromatic residues and competing with interprotein aromatic clusters (π-π interactions). In order to investigate this concept, the interaction of hydroxypropyl-β-cyclodextrin (HPBCD) with melittin is studied with steady-state and time-resolved fluorescence, fluorescence polarization, circular dichroism, and IR spectroscopy. HPBCD inhibits the aggregation of melittin. This inhibition and the spectroscopic results are consistent with the lone aromatic tryptophan of the peptide being intercalated within HPBCD. Proteins 2004. © 2004 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]

Free base and Pd porphyrin derivatives of horseradish peroxidase show long-lived excited states that are quenched by the presence of the peroxidase inhibitor, benzhydroxamic acid. The relaxation times of the excited-state luminescence and the rates of the quenching reaction for these derivatives of peroxidase were monitored as a function of pH, temperature, and viscosity with the view of examining how protein dynamics affect the quenching reaction. As solvent viscosity increases, the rate decreases, but at the limit of very high viscosity (i.e., high glycerol or sugar glass) the quenching still occurs. A model is presented that is consistent with the known structure of the enzyme-inhibitor complex. It is considered that the inhibitor is held at an established position but that solvent-dependent and independent motions allow a limited diffusion of the two reactants. Since there is a steep dependence upon distance and orientation, the diffusion toward the favorable position for reaction enhances the reaction rate. The solvent viscosity dependent and independent effects were separated and analyzed. The importance of internal reaction dynamics is demonstrated in the observation that rigidity of solvent imposed by incorporating the protein into glass at room temperature allows the reaction to occur, while the reaction is inhibited at low temperature. The results emphasize that protein dynamics plays a role in determining reaction rates. [ABSTRACT FROM AUTHOR]