Ultrafast excited-state dynamics of oxazole yellow DNA intercalators

The excited-state dynamics of the DNA intercalator YO-PRO-1 and of three derivatives has been investigated in water and in DNA using ultrafast fluorescence spectroscopy. In the free form, the singly charged dyes exist both as monomers and as H-dimers, while the doubly charged dyes exist predominantly as monomers. Both forms are very weakly fluorescent: the monomers because of ultrafast nonradiative deactivation, with a time constant on the order of 3-4 ps, associated with large amplitude motion around the methine bridge, and the H-dimers because of excitonic interaction. Upon intercalation into DNA, large amplitude motion is inhibited, H-dimers are disrupted, and the molecules become highly fluorescent. The early fluorescence dynamics of these dyes in DNA exhibits substantial differences compared with that measured with their homodimeric YOYO analogues, which are ascribed to dissimilarities in their local environment. Finally, the decay of the fluorescence polarization anisotropy reveals ultrafast hopping of the excitation energy between the intercalated dyes. In one case, a marked change of the depolarization dynamics upon increasing the dye concentration is observed and explained in terms of a different binding mode.     

Subcellular distributions and excited-state processes of hypericin in neurons

The photodynamic drug, hypericin, is studied in fetal rat neurons using fluorescence microscopy. Hypericin has an extremely high affinity for the cell membrane and is found to a smaller extent in the nucleus. Fluorescent excitation of hypericin is shown to cause irreversible damage to the cell membranes of living neurons. Fixed cells were used to make ultrafast time-resolved measurements to avoid the deleterious effects of long-term exposure to intense light and room temperatures. To our knowledge, these are the first ultrafast time-resolved measurements of the fluorescence lifetime of hypericin in a subcellular environment. Nonexponential fluorescence decay is observed in hypericin in the neurons. This nonexponential decay is discussed in terms of other examples where nonexponential decay is induced in hypericin upon its binding to biomolecules. The nonradiative processes giving rise to the nonexponential hypericin decay are attributed to excited-state electron transfer, excited-state proton transfer or both.     

Nonradiative deactivation of excited hemicyanines studied with submolecular spatial resolution by time-resolved surface second harmonic generation at liquid-liquid interfaces

The excited-state dynamics of aminostilbazolium dyes is known to be dominated by nonradiative deactivation through large-amplitude motion. In order to identify the coordinate(s) responsible for this process, the excited-state lifetimes of two dialkylaminostyryl-methylpyridinium iodides have been measured at liquid-liquid interfaces using time-resolved surface second harmonic generation. We found that the decay time of the excited-states of both compounds was increasing with the viscosity of the apolar phase, consisting of n-alkanes of varying length, but was unaffected by that of the polar phase, made of water/glycerol mixtures. This indicates that the nonradiative deactivation is associated with the twist of the dialkylaniline group, which is located in the apolar part of the molecule.     

Microsolvation effects on the excited-state dynamics of protonated tryptophan

To better understand the complex photophysics of the amino acid tryptophan, which is widely used as a probe of protein structure and dynamics, we have measured electronic spectra of protonated, gas-phase tryptophan solvated with a controlled number of water molecules and cooled to approximately 10 K. We observe that, even at this temperature, the bare molecule exhibits a broad electronic spectrum, implying ultrafast, nonradiative decay of the excited state. Surprisingly, the addition of two water molecules sufficiently lengthens the excited-state lifetime that we obtain a fully vibrationally resolved electronic spectrum. Quantum chemical calculations at the RI-CC2/aug-cc-pVDZ level, together with TDDFT/pw based first-principles MD simulations of the excited-state dynamics, clearly demonstrate how interactions with water destabilize the photodissociative states and increase the excited-state lifetime.     

Ultrafast excited-state dynamics of eosin B: a potential probe of the hydrogen-bonding properties of the environment

The photophysics of two dyes from the xanthene family, eosin B (EB), and eosin Y (EY) has been investigated in various solvents by femtosecond transient absorption spectroscopy, first, to clarify the huge disparity of the EB fluorescence lifetimes reported in literature, and, second, to understand the mechanism responsible for the ultrafast excited-state deactivation of EB in water. The excited-state lifetime of EB was found to be much shorter in water and in other protic solvents, due to the occurrence of hydrogen-bond assisted nonradiative deactivation. This mechanism is associated with the hydrogen bonds between the solvent molecules and the nitro groups of EB, which become stronger upon optical excitation due to the charge-transfer character of the excited-state. This process is not operative with EY, where the nitro groups are replaced by bromine atoms. Therefore, the excited-state lifetime of EB in solution is directly related to the strength of the solvent as a hydrogen-bond donor, offering the possibility to build a corresponding scale based on the fluorescence quantum yield or lifetime of EB. This scale of hydrogen-bonding strength could be especially useful for studies of liquid interfaces by time-resolved surface second harmonic generation.     

Ultrafast dynamics of epicocconone, a second generation fluorescent protein stain

Femtosecond upconversion experiment has been carried out for epicocconone and its butylamine adduct in acetonitrile and tert-butanol. An ultrafast component is found to dominate the decay of fluorescence of epicocconone in acetonitrile solution. Upon reacting with butylamine, a model for the epicocconone-protein adduct, this ultrafast component remains almost unaffected but an additional rise time occurs, indicating the formation of a highly emissive species from the locally excited state. This phenomenon is central to the extraordinary applications of epicocconone in biotechnology. The magnitude of the rise time of the butylamine adduct is similar to that of the longer component of the decay of epicocconone in acetonitrile, suggesting that the dynamics of epicocconone and its butylamine adduct are similar. The ultrafast component is slowed upon increasing the viscosity of the solvent. This results in a marked increase in quantum yield and suggests that it corresponds to rapid bond isomerization, leading to a nonradiative decay. Surprisingly, in water/sucrose mixtures, the ultrafast component remains unaffected but there is still an increase in quantum yield, suggesting that there are at least two nonradiative pathways, one involving bond isomerization and another involving proton transfer. The correct interpretation of these data will allow the design of second generation protein stains based on the epicocconone scaffold with increased quantum yields and photostability.     

Origin of ultrafast excited state dynamics of 1-nitropyrene

Time-resolved emission measurements in subpicosecond time domain have been carried out for 1-nitropyrene in different solvents to understand the mechanism for the observed ultrafast decay of its first excited singlet state. Excited-state dynamics of 1-nitropyrene is found to be independent of the solvent viscosity. This result contradicts the proposition in the literature (J. Phys. Chem. A 2007, 111, 552) that the ultrafast decay in 1-nitropyrene is due to the large amplitude torsional motion of the nitro group around the pyrene moiety. Excited-state dynamics of 1-nitropyrene in solvents with different dielectric constants shows that excited-state lifetime suddenly increases after a certain value of the dielectric constant. Detailed quantum chemical calculations have been carried out to understand the process that is responsible for the observed effect of the dielectric constant on the excited-state dynamics of 1-nitropyrene. It is seen that the excited-state lifetime and the singlet-triplet energy gap follow similar variation with the dielectric constant of the medium. Such a correlation between the excited-state lifetime and the singlet-triplet energy gap supports the fact that the observed ultrafast decay for 1-nitropyrene is due to an efficient intersystem crossing rather than to the torsional motion of the nitro group as proposed in the literature.     

Hybridization‐Sensitive On–Off DNA Probe: Application of the Exciton Coupling Effect to Effective Fluorescence Quenching

The design of dyes that emit fluorescence only when they recognize the target molecule, that is, chemistry for the effective quenching of free dyes, must play a significant role in the development of the next generation of functional fluorescent dyes. On the basis of this concept, we designed a doubly fluorescence‐labeled nucleoside. Two thiazole orange dyes were covalently linked to a single nucleotide in a DNA probe. An absorption band at approximately 480 nm appeared strongly when the probe was in a single‐stranded state, whereas an absorption band at approximately 510 nm became predominant when the probe was hybridized with the complementary strand. The shift in the absorption bands shows the existence of an excitonic interaction caused by the formation of an H aggregate between dyes, and as a result, emission from the probe before hybridization was suppressed. Dissociation of aggregates by hybridization with the complementary strand resulted in the disruption of the excitonic interaction and strong emission from the hybrid. This clear change in fluorescence intensity that is dependent on hybridization is useful for visible gene analysis.     

Excited-state dynamics of nitroperylene in solution: solvent and excitation wavelength dependence

The photophysics and excited-state dynamics of nitroperylene (NPe) in solvents of various polarities and viscosities, including a room-temperature ionic liquid, have been investigated by femtosecond-resolved transient absorption spectroscopy. The excited-state absorption spectrum was found to depend substantially on solvent polarity. In the most polar solvents, it is very similar to that of the NPe radical cation generated upon bimolecular quenching by an electron acceptor, denoting a substantial charge-transfer character of the S1 state. Contrary to smaller nitroaromatic compounds, NPe in the S1 state does not undergo ultrafast intersystem crossing (ISC) but decays mainly by internal conversion (IC). In nonprotic solvents, IC involves low-frequency modes with large amplitude motion associated with the nitro group and depends on both the solvent viscosity and polarity. It takes place on a 100 ps time scale in acetonitrile, while in cyclohexane, it is slow enough for ISC to become competitive. Moreover, both the fluorescence quantum yield and the excited-state dynamics were found to differ, depending on which side of the S0-S1 absorption band excitation was performed. This dependence is explained by the inhomogeneous nature of the absorption spectrum arising from a distribution of twist angles of the nitro group relative to the aromatic plane. On the other hand, such excitation wavelength effects were not observed in protic solvents, where the excited-state lifetime was found to be substantially shorter than that in nonprotic solvents. This behavior is rationalized in terms of a H-bonding interaction, which limits the torsional disorder of NPe and favors ultrafast nonradiative deactivation of the excited state. Transient absorption measurements performed for comparative purpose with nitropyrene in acetonitrile confirm the occurrence of ultrafast ISC in smaller nitroaromatic compounds.     

Femtosecond fluorescence studies of self-assembled helical aggregates in solution

For the diamino-bipyridine based C(3)-symmetrical disk molecule, TAB, (sub)picosecond fluorescence transients have been observed by means of femtosecond fluorescence upconversion and picosecond time-correlated photon counting techniques. The dodecyl peripheral side chains of the synthetic compound are large enough to allow, in apolar solvents, self-assembling of the discotic molecules to helical aggregates. In polar solvents, the hydrogen bonding and pi-pi interactions pertaining to the chiral aggregation are compensated by solvation and self-assembling of the disklike molecules is disrupted. For comparison, time-resolved fluorescence measurements have been performed for the subgroup molecule, DAC, which is the (asymmetric) building block for TAB. It is concluded that, after pulsed photoexcitation, TAB and DAC exhibit excited-state intramolecular double proton transfer (ESIDPT) with a typical time of approximately 200-300 fs, irrespective of the degree of aggregation. Picosecond components in the fluorescence of TAB and DAC, ranging from 3 to 25 ps, are representative of vibrational cooling effects in the excited product state. Only aggregated TAB shows a rapid ( approximately 1 ps) decay of its fluorescence anisotropy. This component is attributed to excited-state energy transfer within the aggregate. Finally, the excited-state lifetime of TAB in the aggregated form is found to be an order of magnitude longer than that for TAB in its nonaggregated form. It is inferred that aggregation diminishes the influence of low-frequency twisting motions in the radiationless decay of the excited state.     

The guanine tautomer puzzle: quantum chemical investigation of ground and excited states

Combined density functional and multireference configuration interaction methods have been employed to explore the ground and low-lying electronically excited states of the most important tautomeric and rotameric forms of guanine with the purpose of resolving the conflicting assignments of IR-UV bands found in the literature. The calculations predict sharp 1(pi-->pi*) origin transitions for the RN1 rotamer of the 7H-amino-hydroxy species and the RN7 rotamer of the 9H-amino-hydroxy species. The other 9H-amino-hydroxy rotamer, RN1, undergoes ultrafast nonradiative decay and is thus missing in the UV spectra. Because of its very small Franck-Condon factor and the presence of a conical intersection close by, it appears questionable, whether the 1(pi-->pi*) origin transition of 9H-amino-oxo-guanine can be observed experimentally. Vibrational overlap is more favorable for the 1(pi-->pi*) origin transition of the 7H- amino-oxo form, but also this tautomer is predicted to undergo ultrafast nonradiative decay of the 1(pi-->pi*) population. The good agreement of calculated IR frequencies of the amino-oxo species with recent IR spectra in He droplets and their mismatch with peaks observed in IR-UV spectra indicate that none of the bands stem from 7H- or 9H-amino-oxo guanine. Instead, our results suggest that these bands originate from 7H-imino-oxo guanine tautomers. In the excited-state dynamics of the biologically relevant 9H-amino-oxo tautomer, a diffuse charge transfer state is predicted to play a significant role.     

Promising Ultraviolet Absorbers—Novel Guanine Analogs Having Significantly Improved Ultraviolet Absorption Capacity and Dissipating the Energy of Absorbed Photons by Nonradiative Decay Mechanism

Structural properties of nucleobase underlie their ultrafast excited-state dynamics and low fluorescence quantum yields, which cause effectively nonradiative decay process and render them like sunscreens. Thus, eight guanine analogs[N-2-(2'-nitrobenzoyl)-guanine, N-2-(3'-nitrobenzoyl)-guanine, N-2-(4'-nitrobenzoyl)-guanine, N-2-(2'-hydroxybenzoyl)-guanine, N-2-(4'-methoxylbenzoyl)-guanine, N-2-(4'-chloricbenzoyl)-guanine, N-2-(4'- methylicbenzoyl)- guanine and N-2-(3',5'-dinitrobenzoyl)-guanine] with different substituted benzoyls, except N-2-(4'-chloricbenzoyl)-guanine, were newly synthesized. In contrast with guanine, they exhibit wider ultraviolet absorbent range, higher molar extinction coefficient and lower fluorescence intensity.     

Excitonic interaction: another photophysical process for fluorescence‐controlled nucleic acid sensing

An excitonic interaction caused by the H‐aggregation of fluorescent dyes is a new type of useful photophysical process for fluorescence‐controlled nucleic acid sensing. We designed a fluorescence‐labeled nucleotide in which two thiazole orange dyes were linked covalently. A DNA strand containing this fluorescence‐labeled nucleotide showed absorption at 480 nm before hybridization, whereas an absorption band at 510 nm became predominant when the DNA was hybridized with the complementary strand. The shift in the absorption bands shows the existence of an excitonic interaction between dyes in the nucleotide, and as a result, emission from the doubly thiazole orange‐labeled DNA was well controlled. This clear change in fluorescence intensity depending on hybridization is applicable to multicolor RNA imaging in living cells. © 2010 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 10: 188–196; 2010: Published online in Wiley InterScience ( www.interscience.wiley.com ) DOI 10.1002/tcr.201000003     

Structural control of the photodynamics of boron-dipyrrin complexes

Boron-dipyrrin chromophores containing a 5-aryl group with or without internal steric hindrance toward aryl rotation have been synthesized and then characterized via X-ray diffraction, static and time-resolved optical spectroscopy, and theory. Compounds with a 5-phenyl or 5-(4-tert-butylphenyl) group show low fluorescence yields (approximately 0.06) and short excited-singlet-state lifetimes (approximately 500 ps), and decay primarily (>90%) by nonradiative internal conversion to the ground state. In contrast, sterically hindered analogues having an o-tolyl or mesityl group at the 5-position exhibit high fluorescence yields (approximately 0.9) and long excited-state lifetimes (approximately 6 ns). The X-ray structures indicate that the phenyl or 4-tert-butylphenyl ring lies at an angle of approximately 60 degrees with respect to the dipyrrin framework whereas the angle is approximately 80 degrees for mesityl or o-tolyl groups. The calculated potential energy surface for the phenyl-substituted complex indicates that the excited state has a second, lower energy minimum in which the nonhindered aryl ring rotates closer to the mean plane of the dipyrrin, which itself undergoes some distortion. This relaxed, distorted excited-state conformation has low radiative probability as well as a reduced energy gap from the ground state supporting a favorable vibrational overlap factor for nonradiative deactivation. Such a distorted conformation is energetically inaccessible in a complex bearing the sterically hindered o-tolyl or mesityl group at the 5-position, leading to a high radiative probability involving conformations at or near the initial Franck-Condon form of the excited state. These combined results demonstrate the critical role of aryl-ring rotation in governing the excited-state dynamics of this class of widely used dyes.     

Photoinduced intramolecular charge transfer in 9-aminoacridinium derivatives assisted by intramolecular H-bond

Fluorochromic dyes derived from 9-aminoacridinium containing a vinylene function with electron withdrawing groups such as diethyl [(acridinium-9-ylamino)methylene]malonate (I), ethyl [(acridinium-9-ylamino)methylene]cyanoacetate (II), [(acridinium-9-ylamino)methylene]malononitrile (III), are prepared and studied in their monoprotonated form. Absorption spectra of the new dyes are red shifted compared to that of the precursor dye. The observed dual fluorescence and multiexponential decay are ascribed to normal emission from the acridinium chromophore in addition to excited-state intramolecular charge transfer (ESICT) process. However, biexponential decay character is observed only for the dicyano derivative (compound III), whereas for the two other systems, more complex kinetics and a three-component decay is recovered. The analysis of the fluorescence decays in different solvents for the first two compounds reveals two short-lived components in the range of 160-350 ps and 1.1-3.0 ns, related to formation and decay of the ESICT state, plus a third one with decay time of about 9 ns, which is ascribed to the normal emission from the acridinium chromophore as an enol tautomer or as an intramolecular H-bond conformer (closed form tautomer). For the dicyano derivative, in which the absence of carbonyl group precludes the H-bond interaction, the biexponential fitting reveals a slightly fast formation rate of the ESICT state with values on the order of 10(10) s(-1), whereas its decay time is between 0.6 and 3.2 ns, depending on the solvent used.     

Nonradiative relaxation in thiophene-S,S-dioxide derivatives: the role of the environment

The intramolecular radiative and nonradiative relaxation processes of three thiophene-S,S-dioxide derivatives with different molecular rigidity are investigated in different solutions and in inert matrix. We show that the fluorescence quantum efficiency and the relaxation dynamics are strongly dependent on the environment viscosity, whereas they are almost independent of the environment polarity. We demonstrate that this strong dependence is due to an environment dependent nonradiative decay rate, whereas no relevant variations of the radiative decay rate are observed. We demonstrate that the dipole coupling with the solvent does not provide an efficient nonradiative decay channel and that the S(n) - S(1) vibrational relaxation is very efficient in all of the molecules and for all of the investigated environments. Moreover first-principles time-dependent density-functional theory calculations in the correct, i.e., excited-state, molecular conformation, suggest that significant contributions of intersystem crossing to the triplet manifold can be excluded. We then conclude that the main nonradiative process determining the fluorescence quantum efficiency of this class of molecules is S(1) - S(0) internal conversion (IC). An explanation for the IC rate dependence in terms of the environment viscosity, molecular rigidity, S(1) - S(0) energy-gap, and molecular volume is presented.     

Real-time probing of structural dynamics by interaction between chromophores

We present an investigation of structural dynamics in excited-state cations probed in real-time by femtosecond time-resolved ion photofragmentation spectroscopy. From photoelectron spectroscopy data on 1,3-dibromopropane we conclude that the pump pulse ionizes the molecule, populating an excited electronic state of the radical cation. In this state a coherent torsional vibration of the bromomethylene groups with a period of 700 fs is started and probed by photoinduced fragmentation of the molecular cation. The vibrational coherence dephases with the decay of the excited state to the ground state of the cation in 1.6 ps. The real-time probing of the excited-state dynamics is made possible by exploiting the interaction between the two bromine chromophores and its dependence on molecular conformation. This experiment therefore illustrates the applicability of the concept of probing ultrafast molecular dynamics using the intramolecular interaction between two chromophores.     

Solvent effect on the singlet excited-state dynamics of 5-fluorouracil in acetonitrile as compared with water

The excited-state dynamics of 5-fluorouracil in acetonitrile has been investigated by femtosecond fluorescence upconversion spectroscopy in combination with quantum chemistry TD-DFT calculations ((PCM/TD-PBE0). Experimentally, it was found that when going from water to acetonitrile solution the fluorescence decay of 5FU becomes much faster. The calculations show that this is related to the opening of an additional decay channel in acetonitrile solution since the dark n/pi* excited state becomes near degenerate with the bright pi/pi* state, forming a conical intersection close to the Franck-Condon region. In both solvents, a S1-S0 conical intersection, governed by the out-of-plane motion of the fluorine atom, is active, allowing an ultrafast internal conversion to the ground state.     

Ultrafast excited-state deactivation and energy transfer in guanine-cytosine DNA double helices

The DNA double helix poly(dGdC).poly(dGdC) is studied by fluorescence upconversion spectroscopy with femtosecond resolution. It is shown that the excited-state relaxation of the duplex is faster than that of the monomeric components dGMP and dCMP. This contrasts with the behavior of duplexes composed exclusively of adenine-thymine base pairs, for which an overall lengthening of the fluorescence lifetimes with respect to that of an equimolar mixture of dAMP and TMP was reported previously. Despite the difference in the excited-state deactivation rate between the two types of duplexes, the signature of ultrafast energy transfer is present in both of them. It is attested by the decrease of fluorescence anisotropy decay of the duplexes on the subpicosecond time scale, where molecular motions are inhibited, and is corroborated by the fact that their steady-state fluorescence spectra do not change with the excitation wavelength. Energy transfer involves excited states delocalized over at least two bases, whose existence is revealed by the UV absorption spectrum of the duplex, clearly different from that of an equimolar spectrum of dGMP and dCMP.