Showing papers on "Excimer published in 2006"

Chloride selective calix[4]arene optical sensor combining urea functionality with pyrene excimer transduction.

Abstract: A neutral 2-site chloride selective compound has been developed (3), based on a 1,3-alternate tetrasubstituted calix[4]arene providing a preorganized supramolecular scaffold. The resultant supramolecular cavity is among the first to combine urea functional groups bridged with single methylene spacers to pyrene moieties. It combines a naturally and synthetically proven H-bonding system with the elegant ratiometric fluorescent signaling properties of an intramolecular pyrene excimer system, triggered by conformational changes upon anion coordination. The excimer emission of 3 is quenched, with a simultaneous rise in the monomer emission solely by the chloride anion among a wide variety of anions tested. 3 has an association constant of 2.4 x 10(4) M(-1) with chloride. The suitability and advantages of ratiometric optical sensor compounds like 3 for use in practical sensor devices is discussed. 3 has an LOD of 8 x 10(-6) M with chloride in acetonitrile-chloroform (95:5 v/v). A dynamic fluorescence study revealed a response time of < 3 s. A recently developed and simple HPLC-based purification method complimented conventional organic work up methods to yield pure product.

Pyrene binary probes for unambiguous detection of mRNA using time-resolved fluorescence spectroscopy

Abstract: We report here the design, synthesis and application of pyrene binary oligonucleotide probes for selective detection of cellular mRNA. The detection strategy is based on the formation of a fluorescent excimer when two pyrene groups are brought into close proximity upon hybridization of the probes with the target mRNA. The pyrene excimer has a long fluorescence lifetime (.40 ns) compared with that of cellular extracts (� 7 ns), allowing selective detection of the excimer using time-resolved emission spectra (TRES). Optimized probes were used to target a specific region of sensorin mRNA yielding a strong excimer emission peak at 485 nm in the presence of the target and no excimer emission in the absence of the target in buffer solution. While direct fluorescence measurement of neuronal extracts showed a strong fluorescent background, obscuring the detection of the excimer signal, time-resolved emission measurements indicated that the emission decay of the cellular extracts is � 8 times faster than that of the pyrene excimer probes. Thus, using TRES of the pyrene probes, we are able to selectively detect mRNA in the presence of cellular extracts, demonstrating the potential for application of pyrene excimer probes for imaging mRNAs in cellular environments that have background fluorescence.

Excimer-Based Peptide Beacons: A Convenient Experimental Approach for Monitoring Polypeptide−Protein and Polypeptide−Oligonucleotide Interactions

Abstract: While protein−polypeptide and nucleic acid−polypeptide interactions are of significant experimental interest, quantitative methods for the characterization of such interactions are often cumbersome. Here we described a relatively simple means of optically monitoring such interactions using excimer-based peptide beacons (PBs). The design of PBs is based on the observation that, whereas short peptides are almost invariably unfolded and highly dynamic, they become rigid when complexed with macromolecular targets. Using this binding-induced folding to segregate two pyrene moieties and therefore inhibit excimer formation, we have produced PBs directed against both anti-HIV antibodies and the retroviral transactive response (TAR) RNA hairpin. For both polypeptides, target recognition is accompanied by a roughly 2-fold decrease in excimer emission, thus allowing the detection of their respective targets at concentrations of a few nanomolar. Because excimer emission requires the formation of a tight, precisely or...

Pump-probe and pump-deplete-probe spectroscopies on carotenoids with N=9-15 conjugated bonds.

Abstract: A series of all-trans-carotenoids with N=9, 13, and 15 conjugated bonds has been studied by pump-probe and pump-deplete-probe spectroscopies to obtain a systematic analysis of the energy flow between the different electronic states. The ultrafast dynamics in the carotenoids are initialized by excitation to the S2 state and subsequently manipulated by an additional depletion pulse in the near-IR spectral range. The changes in the dynamics after depletion of the excited state population allowed differentiation of the excited state absorption into two components, a major one corresponding to the well known S1 state and the small contribution on the red wing of the S0-S2 absorption band originating from the hot ground state. We found no evidence for an additional electronically excited state, usually called S*. Instead, a deactivation mechanism that includes the hot ground state supports the observed results nicely in the framework of a simple three state model (S2, S1, and S0).

Vibrationally mediated photodissociation of ammonia: the influence of N-H stretching vibrations on passage through conical intersections.

Abstract: Velocity map ion imaging of the H atoms formed in the photodissociation of vibrationally excited ammonia molecules measures the extent of adiabatic and nonadiabatic dissociation for different vibrations in the electronically excited state. Decomposition of molecules with an excited symmetric N–H stretch produces primarily ground state NH2 along with a H atom. The kinetic energy release distribution is qualitatively similar to the ones from dissociation of ammonia excited to the electronic origin or to several different levels of the bending vibration and umbrella vibration. The situation is very different for electronically excited molecules containing a quantum of antisymmetric N–H stretch. Decomposition from that state produces almost solely electronically excited NH2*, avoiding the conical intersection between the excited state and ground state surfaces. These rotationally resolved measurements agree with our previous inferences from lower resolution Doppler profile measurements. The production of NH2*...

Molecular simulation of excimer fluorescence in polystyrene and poly(vinylcarbazole).

Abstract: In fluorescence emission spectra of poly(vinylcarbazole) (PVK), two types of excimers are observed, the fully and the partially overlapped excimers, namely, excimers and exciplexes. In this work, we investigated the structural changes induced by the transition between electronic levels S(0) and S(1). Furthermore, the widely used assumption of similar potential energy surfaces in the S(0) and S(1) states and its use in molecular dynamics simulations are thoroughly examined for PVK and polystyrene (PS). The ground-state and excited-state intermolecular potentials between phenyl or carbazyl substituents in PS or PVK, respectively, are computed from high-level ab initio calculations and fit to analytic potentials. Finally, molecular dynamics simulations are performed at room temperature for PS and for isotactic and syndiotactic PVK. This treatment enabled the decoupling of excimer and exciplex contributions from the simulated spectra.

Toward the understanding of DNA fluorescence: the singlet excimer of cytosine.

Abstract: By using the multiconfigurational second-order perturbation method CASPT2, including corrections for the basis set superposition error, the lowest-singlet excited state of the face-to-face π-stacked cytosine homodimer is revealed to be bound by about half an eV, being the source of an emissive feature consistent with the observed redshifted fluorescence.

Intramolecular Exciplex and Intermolecular Excimer Formation of 1,8-Naphthalimide−Linker−Phenothiazine Dyads

Abstract: Steady-state fluorescence spectra were measured for 1,8-naphthahlimide−linker−phenothiazine dyads (NI−L−PTZ, where L = octamethylenyl ((CH2)8) and 3,6,9-trioxaundecyl ((CH2CH2O)3C2H4)), NI−C8−PTZ and NI−O−PTZ, as well as the NI derivatives substituted on the nitrogen atom with various linker groups without PTZ as the reference NI molecule in n-hexane. Normal fluorescence peaks were observed at 367−369 nm in all NI molecules together with a broader emission around 470 nm, which is assigned to the excimer emission between the NI in the singlet excited state (1NI*) and the NI moiety of another NI molecule (1[NI/NI]*). In addition, a broad peak around 600 nm was observed only for NI−L−PTZ, which is assigned to an intramolecular exciplex emission between donor (PTZ) and acceptor (NI) moieties in the excited singlet state, 1[NI−L−NI]*. The formation of an intramolecular exciplex corresponds to the existence of a conformer with a weak face-to-face interaction between the NI and PTZ moieties in the excited state ...

Fluorescence from aromatic compounds isolated in the solid state by double intercalation using layered polymer crystals as the host solid

Abstract: Poly(muconic acid)s, stereoregular polymer crystals obtained by topochemical polymerization using supramolecular control, function as the layered host solids for organic intercalation, in which alkylamines as the guest species are reversibly inserted into them through an acid-base interaction. We now report a double-intercalation method using alkylamine and pyrene as the guests to control the fluorescence property in the solid state. An aromatic compound can be separately introduced into the hydrophobic layers of the ammonium polymer crystals. The aromatic molecules, which are sandwiched between two alkyl layers, show fluorescence emission from the single molecule but not the excimer. This method can be applied to various organic photofunctional materials showing unique fluorescence properties.

Enzymatic Synthesis of Fluorescent Oligomers Assembled on a DNA Backbone

Abstract: A number of research laboratories have investigated the properties of multichromophore molecules and their applications in materials science and in biotechnology. Previous approaches for preparing such molecules have involved traditional organic synthesis. Here we describe the one-step enzymatic synthesis of such a multichromophore species by using a DNA-polymerizing enzyme (terminal deoxynucleotidyl transferase (TdT)). We find that a nucleotide-like molecule with pyrene replacing the DNA base (dPTP) can be accepted as a substrate for this enzyme to produce discrete chromophores that have 3 or 4 pyrenes consecutively, depending on which anomer (alpha or beta) is used. Products were characterized by gel electrophoresis, mass spectrometry, and fluorescence. The reaction was found to change the fluorescence emission of the chromophore from a maximum at 375 nm (the monomer nucleotide) to 490 nm in the oligomeric product. This new green-white emission is consistent with the formation of a pyrene excimer between adjacent pyrene glycosides, which exhibit a large Stokes shift of 130 nm. The enzymatic synthesis of the pyrene excimer might have applications in homogeneous biological assays for DNA fragments, such as those that arise during apoptosis.

Fluorescence of molecular micro- and nanocrystals prepared with Bodipy derivatives

Abstract: Trimesitylbodipy (TMB), a new 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene derivative with bulky side groups, was synthesized in order to develop nanostructured fluorescent devices. Fluorescence properties of TMB were studied in dichloromethane, in amorphous films prepared by rapid evaporation of a solution and in micro- and nanocrystals. It was compared to the spectroscopy of Mesitylbodipy (MB) to see if the mesityl groups of TMB modify fluorescence in the solid state. A set-up including a space and time correlated photon-counting photo-multiplier was used to record fluorescence intensity and lifetime images of solids. For both dyes, the formation of fluorescent excimers was observed. There is evidence to suggest energy transfer from monomer to both fluorescent and non-fluorescent excimers. MB fluorescence is still quenched in the crystalline state but in TMB monocrystals the fluorescence comes from only one excimer with a lifetime of 9.5 ns. TMB nanocrystals with a monoexponential fluorescence decay were also prepared.

Intramolecular excimer formation and sensing behavior of new fluorimetric probes and their interactions with metal cations and barbituric acids

Abstract: A new family of compounds able to promote host–guest interactions with specific molecules (e.g., cyanuric and parabanic acids) and to coordinate metal ions, namely Zn(II) and Cu(II), has been synthesized and fully characterized. The new probes derive from the attachment of two methylaminopyrene units to the carbonyl precursor 2,6-bis(2-formylphenoxymethyl)pyridine. Its signalling properties result from the fluorescence emission properties, which reveal the existence of intramolecular excimer formation. The compounds have showed to be highly sensitive to the solvent and hydrogen ion concentration of the medium. Depending on these, different monomer-to-excimer fluorescence ratio is displayed by the two probes. The compound with a single pyrene unit revealed absence of excimer formation and was used as model compound. The overall results are discussed on the basis of the studied probes as potentially revealing molecular movements, off–on–off fluorescent photoinduced electron transfer (PET), host–guest interactions with specific compounds and of sensing metal ions.

Theoretical study of the ground and excited states of 7-methyl guanine and 9-methyl guanine: comparison with experiment.

Abstract: The keto–enol tautomerization of 7-methyl-guanine and 9-methyl-guanine in the excited state was investigated using the time-dependent DFT (TDDFT) method. For both species, the potential energy surfaces of the ground state and two lowest singlet excited states (due to π → π* and n → π* transitions) have been investigated and their features discussed in terms of consequences on the excited state dynamics. The findings suggest that, for both species, the state due to the n → π* transition, suspected to be an intermediate in the excited state deactivation, exhibits two minima with the second minimum characterized by an elongated N1–H distance. This structure, intermediate between enol and keto tautomers, might play a role in the excited state relaxation. The existence of this second well, however, is observed in both 7- and 9-methyl-guanine, which suggests that it cannot account alone for the different photophysical behavior of these species.

Excimer laser material processing : State of the art and new approaches in microsystem technology

Abstract: In this paper the current state of the art and new trends in excimer laser processing of polymer materials are presented. Two processing regimes are of general interest: below and above the ablation threshold. The modification of polymer surface can be carried out by laser processing below ablation threshold. This is successfully demonstrated for the fabrication of optical singlemode waveguides in PMMA for the visible optical range and for 1550 nm. The obtained structures reveal absorption losses in the order of 1.4 dB/cm up to 5 dB/cm. Laser exposure using contact masks or direct scanning of planar structures are appropriate methods for the integration of optical waveguides in PMMA sensor devices (Y-branch). Above the ablation threshold excimer laser micromachining is a powerful tool for a rapid manufacturing of complex three-dimensional micro-structures in polymer surfaces with depths between 0.1 μm and 1000 μm and aspect ratios up to 10. Typical application fields are presented in micro-optics, micro-fluidics and rapid tooling. Micro-Laser-LIGA is established in order to fabricate nebulizer membranes, micro-fluidic devices and integrated single mode waveguides. Furthermore, the fabrication of 3d-shapes in metallic mold inserts is successfully demonstrated. Debris formation is completely suppressed. Polymer structuring with a low power short pulse excimer laser with high repetition rates up to 500 Hz is compared to the structuring with a "conventional" high power excimer laser with a repetition rate of about 10-100Hz as well as with a UV-Nd:YAG (1-2 kHz). These "high-repetition-rateexcimer lasers" with relatively small pulse energies but with much shorter laser pulse duration (< 6 ns) provide a significant improvement of pattern quality. Furthermore, the high repetition rate enables a fast material processing which is discussed in detail for several application fields.

Interpretation of unusual absorption bandwidths and resonance Raman intensities in excited state mixed valence.

Abstract: Excited state mixed valence (ESMV) occurs in molecules in which the ground state has a symmetrical charge distribution but the excited state possesses two or more interchangeably equivalent sites that have different formal oxidation states. Although mixed valence excited states are relatively common in both organic and inorganic molecules, their properties have only recently been explored, primarily because their spectroscopic features are usually overlapped or obscured by other transitions in the molecule. The mixed valence excited state absorption bands of 2,3-di-p-anisyl-2,3-diazabicyclo[2.2.2]octane radical cation are well-separated from others in the absorption spectrum and are particularly well-suited for detailed analysis using the ESMV model. Excited state coupling splits the absorption band into two components. The lower energy component is broader and more intense than the higher energy component. The absorption bandwidths are caused by progressions in totally symmetric modes, and the difference in bandwidths is caused by the coordinate dependence of the excited state coupling. The Raman intensities obtained in resonance with the high and low energy components differ significantly from those expected based on the oscillator strengths of the bands. This unexpected observation is a result of the excited state coupling and is explained by both the averaging of the transition dipole moment orientation over all angles for the two types of spectroscopies and the coordinate-dependent coupling. The absorption spectrum is fit using a coupled two-state model in which both symmetric and asymmetric coordinates are included. The physical meaning of the observed resonance Raman intensity trends is discussed along with the origin of the coordinate-dependent coupling. The well-separated mixed valence excited state spectroscopic components enable detailed electronic and resonance Raman data to be obtained from which the model can be more fully developed and tested.

Pyrene fluorescence at air/sodium dodecyl sulfate solution interface.

Abstract: The dependence of pyrene fluorescence spectra on the concentration of sodium dodecyl sulfate (SDS) was observed, where the solution was prepared from water saturated with pyrene. The values of the I1/I3 ratio from the bulk solution and from the upper meniscus region in an optical cell were similar but decreased rapidly around the critical micelle concentration (cmc) of SDS, indicating that pyrene molecules preferred to be solubilized in the micelles having a lower dielectric constant. The fluorescence intensity of the excimer indicated the concentration of pyrene molecules at the air/solution interface or the surface activity of pyrene molecules. In addition, the intensity from the meniscus region is much larger than that from the bulk at the concentrations below the cmc, whereas there was no difference in the intensity between the bulk and the meniscus above 8 mmol dm-3 of SDS. The analysis of the fluorescence intensity from the excimer strongly suggests the presence of molecular aggregates that are favo...

Investigation of excimer ultraviolet sources from dielectric barrier discharge in krypton and halogen mixtures

Abstract: The characteristics of the emission spectra of Kr/Br2 and Kr/I2 mixtures driven by dielectric barrier discharge as a function of gas pressure were respectively investigated. It was found that the KrBr* excimer lamp provided an intense narrow band ultraviolet (UV) radiation at λ=207 nm, whose intensity was strongly influenced by gas pressure and buffer gas. The excimer radiation at λ=191 nm generated by the KrI* excimer lamp was very weak and less dependent on gas pressure due to predissociation which was confirmed by the strong emission of the atomic iodine line at λ=183 nm.

A calixarene based fluorescent Sr2+ and Ca2+ probe

Abstract: A fluorescent probe, PyCalix, which has two pyrene moieties at the lower rim of a calix[4]arene fixed in the cone conformation was synthesized and its complexation behavior with alkali and alkaline earth cations was studied by fluorescence spectrometry. The compound showed intramolecular excimer emission at approximately 480 nm in the fluorescence spectra. Upon complexation with alkaline earth metal cations, a decrease of excimer emission was observed. The decrease of excimer emission was accompanied by an increase of monomer emission of pyrenes at 397 nm. The order of complexation constants of PyCalix with metal ions was Sr2+ ∼ Ca2+ > Ba2+ > Mg2+ > K+ > Na+ > Cs+ for all reagents. PyCalix doped polyvinyl chloride (PVC) membrane was fabricated and our results showed that this membrane can be used for selective detection of Sr2+.