Fluorescent Chromophore Research Articles

Phosphorescence quenching as an approach for estimating the localization of triplet label in cotton fibers

The method based on the qualitative investigation of chromophore fluorescence (phosphorescence) quenching for instance, by stable nitroxide radical was first used to measure the depth of immersion of triplet label in cotton fiber as a molecular object. The concept of dynamic quenching of fluorescence in solutions and the empirical dependence of the parameters of static quenching between centers with fixed distances were used. The erythrosine triplet labels were incorporated in cotton fibers with subsequent measurement of the efficiency of label phosphorescence quenching and determination of temperature dependence of phosphorescence duration. Using above mentioned approach it became possible for the first time to estimate the depth of immersion of chromophore fragment of the labels (7.4-7.8 A) and study their molecular dynamics in the millisecond range of correlation times. Subtle differences in microstructure and molecular dynamics of the investigated samples were revealed. The proposed approach can be used for investigation of widespread biological and nonbiological objects.

Excitation energy transfer in GFP‐X‐CFP model peptides (X = amino acids): Direct Versus through‐bridge energy transfers

AbstractThe excitation energy transfer (EET) between a fluorescent resonance energy transfer (FRET) pair, cyan fluorescent protein chromophore (CFPc)/ green fluorescent protein chromophore (GFPc), is used for measuring molecular proximity in experimental studies. In this article, the role of the bridging protein media has been investigated using the quantum chemical calculations for the EET electronic coupling. We adopted a model peptide connecting GFPc and CFPc, a GFPc‐X‐CFPc model, and examined the X (amino acids) dependence. The major part of the EET coupling element arises from the direct interaction between GFPc and CFPc via the Förster mechanism. The magnitude of the through‐X interactions vary for the type of residues. The contribution of the X was, however, at most 10% of the total value. Together with the contributions from through‐peptide and charge‐transfer types, X gives minor modifications to the total coupling via the super‐exchange mechanism. © 2012 Wiley Periodicals, Inc.

Highly selective fluorescent chemosensor for detecting Hg(II) in water based on pyrene functionalized core–shell structured mesoporous silica

Novel pyrene functionalized mesoporous core–shell structured silica (denoted as SiO2@mSiO2/Py-Si) was designed and synthesized as a highly selective fluorescent chemosensor for detecting Hg2+ in water. The core–shell structured silica was prepared by a simple sol–gel process through coating SiO2 nanospheres with a layer of ordered mesoporous silica. The surface of outer mesoporous silica shell was then further functionalized by the fluorescent chromophore alkoxysilane modified pyrene (Py-Si). XRD data confirmed that the hexagonal ordered mesoporous structure was preserved after functionalization. The chemosensing material successfully exhibited a remarkable “turn on” response toward Hg2+ over miscellaneous metal ions. A good linear response towards Hg2+ in the concentration range of 10−8–10−4M was constructed with R2=0.9913. Most importantly, a satisfactory detection limit of 3.4×10−9gmL−1 (down to ppb level) was obtained, which is 100 times lower than our previous report of covalently grafted Py-OH to the bulk mesoporous silica SBA-15. These results indicated that SiO2@mSiO2/Py-Si can be used as a highly selective and sensitive fluorescence sensor for Hg2+.

Theoretical studies on the isomerization mechanism of the ortho-green fluorescent protein chromophore

We present a systematic theoretical investigation on the overall ground state and excited-state isomerization reaction mechanism of ortho-green fluorescent protein chromophore (o-HBDI) using the density functional theory and the multireference methods. The calculated results and subsequent analysis suggest the possible isomerization mechanism for o-HBDI. By comparison with experimental observation and detailed analysis, it is concluded that as initiated by the excited-state intramolecular proton transfer reaction, the conical intersection between the ground state and the excited state along the C4-C5 single-bond rotational coordinate is responsible for the rapid deactivation of o-HBDI.

2E1610 Regulatory Mechanism of the fluorescence emission from Green Fluorescent Protein Chromophore(Proteins:Property II,Oral Presentation,The 50th Annual Meeting of the Biophysical Society of Japan)

2E1610 Regulatory Mechanism of the fluorescence emission from Green Fluorescent Protein Chromophore(Proteins:Property II,Oral Presentation,The 50th Annual Meeting of the Biophysical Society of Japan)

Highly fluorescent benzofuran derivatives of the GFP chromophore

Intramolecular cyclization reactions of Green Fluorescent Protein chromophores (GFPc) containing an arylethynyl ortho-substituent at the phenol ring provide new aryl-substituted benzofuran derivatives of the GFPc. Some of these heteroaromatic compounds exhibit significantly enhanced fluorescence at red-shifted emission wavelengths relative to the parent GFPc structure.

A theoretical study on photomagnetic fluorescent protein chromophore coupled diradicals and their possible applications

We have designed and theoretically studied three different pairs of green fluorescent protein chromophores and their different homologue-based diradicals coupled with imino nitroxides. To begin with, the geometries of all these diradicals have been optimized at high spin (HS) state in the gas phase, in a water medium and in a blood plasma medium. The process of calculations is straightforward and well-established in the case of the gas phase. However, for calculations in water, we have adopted our own N-layer integrated molecular orbital and molecular mechanics (ONIOM) method. Similarly for the blood phase calculations, the polarized continuum model (PCM) method has been adopted. With these optimized geometries the magnetic exchange coupling constant (J) values are estimated for these diradicals in different media using the broken symmetry (BS) approach in an unrestricted DFT framework. In order to obtain the BS solutions in the ONIOM method, we have carried out ONIOM-BS, where the BS calculations are done for the inner high-level layer (diradical system) keeping the outer water layer at low level. In a similar fashion, a PCM-BS technique has also been adopted for the BS calculations in the PCM method. We have found that these diradicals have an ability to change their magnetic nature from antiferromagnetic in the trans form to ferromagnetic in the cis form upon irradiation of light with the appropriate wavelength. Using a time-dependent DFT (TDDFT) technique, the required wavelengths of light by which non-fluorescent dark trans diradicals turn into their corresponding bright fluorescent cis isomers are determined for each pair of diradicals for the gas and water media. This color change is indeed a signature of the change in magnetic state of the diradicals concerned. Here, we have also calculated the zero field splitting (ZFS) parameter (D), rhombic ZFS parameter (E) and ZFS magnitude (a2). From our calculations we ambitiously expect that if these diradicals are synthesized then they might be used as a successful, non-hazardous magnetic resonance imaging contrast agent (MRICA) in place of other metal-based contrast agents.

Isomerization mechanism of the HcRed fluorescent protein chromophore

To understand how the protein achieves fluorescence, the isomerization mechanism of the HcRed chromophore is studied both under vacuum and in the solvated red fluorescent protein. Quantum mechanical (QM) and quantum mechanical/molecular mechanical (QM/MM) methods are applied both for the ground and the first excited state. The photoinduced processes in the chromophore mainly involve torsions around the imidazolinone-bridge bond (τ) and the phenoxy-bridge bond (φ). Under vacuum, the isomerization of the cis-trans chromophore essentially proceeds by τ twisting, while the radiationless decay requires φ torsion. By contrast, the isomerization of the cis-trans chromophore in HcRed occurs via simultaneous τ and φ twisting. The protein environment significantly reduces the barrier of this hula twist motion compared with vacuum. The excited-state isomerization barrier via the φ rotation of the cis-coplanar conformer in HcRed is computed to be significantly higher than that of the trans-non-coplanar conformer. This is consistent with the experimental observation that the cis-coplanar-conformation of the chromophore is related to the fluorescent properties of HcRed, while the trans-non-planar conformation is weakly fluorescent or non-fluorescent. Our study shows how the protein modifies the isomerization mechanism, notably by interactions involving the nearby residue Ile197, which keeps the chromophore coplanar and blocks the twisting motion that leads to photoinduced radiationless decay.

Structural Perturbation of Superfolder GFP in the Presence of Guanidine Thiocyanate

The guanidine-thiocyanate-induced denaturation-renaturation of sfGFP was studied. It was shown that the disruption of sfGFP native structure occurs in the range of guanidine thiocyanate concentrations from 0.5 to 2.5 M. This process was accompanied by simultaneous changes of all recorded parameters. It was found that the small guanidine thiocyanate concentrations (less then 0.1-0.2 M) triggered local structural disturbances in protein which result in significant decrease of chromophore and tryptophan fluorescence intensity and change of protein visible absorption spectrum.

Excited states of the green fluorescent protein chromophore: Performance of ab initio and semi‐empirical methods

AbstractThe complex photophysical properties of fluorescent proteins give rise to a wide field of applications as markers in molecular biology. Understanding these properties is essential for rational genetic engineering of new fluorescent proteins. Here, theoretical models are required to support the interpretation of structural and spectroscopic experimental data. This requires the accurate and reliable prediction of excited‐state features of the chromophore and its interactions with the protein matrix. Here, we compare calculations of absorption and emission energies of semi‐empirical (OM2/MRCI, ZINDO/S, and TD‐DFTB) and ab initio (SORCI, CC2, and TDDFT) approaches for the HBDI chromophore in vacuo and wild‐type green fluorescent protein (GFP) using QM/MM models. We discuss the influence of electrostatic fields, the chromophore geometry, the size of the QM region, and methodological aspects, in particular charge‐transfer states in TDDFT and the applicability of real‐space TDDFT codes. We revisit previous opposing theoretical studies and benchmark gas‐phase measurements.magnified image Proton transfer wire of wild‐type green fluorescent protein (wt‐GFP).

ChemInform Abstract: Direct Synthesis of Fluorescent 1,3a,6a‐Triazapentalene Derivatives via Click—Cyclization—Aromatization Cascade Reaction.

An efficient and versatile method was established for the preparation of 1,3a,6a-triazapentalenes. The 1,3a,6a-triazapentalene skeleton without an additional fused ring system was discovered to be a compact and highly fluorescent chromophore, which exhibited various interesting fluorescent properties such as a noteworthy correlation of luminescent wavelength with the Hammett σp value and a strongly positive solvatofluorochromism.

Fluorescence excitation–emission matrix combined with regional integration analysis to characterize the composition and transformation of humic and fulvic acids from landfill at different stabilization stages

Fluorescence excitation–emission matrix spectroscopy (EEMs) combined with fluorescence regional integration (FRI) analysis was used to investigate the composition and transformation of humic acid (HA) and fulvic acid (FA) from landfill. The EEMs of HAs at different landfill ages were characterized by two typical fluorescence chromophores with Ex/Em pairs at Ex=420–470nm/Em=490–530nm and Ex=345–375nm/Em=450–465nm. EEMs of FA were featured by other two distinctly different fluorophores with Ex/Em pairs at Ex=315–335nm/Em=420–440nm and Ex=255–275nm/Em=425–455nm. The results show that HA extracted from the refuse disposed in the year of 1989 was formed by connecting small-condensed aromatic structures with protein-like chains. Compared with HA extracted from the refuse disposed in the year of 1992, HA extracted from the refuse of 1996 had a higher fluorescence intensity and lower r(B,A) (the ratio of the fluorescence intensities of peak B and peak A) value. It contained low molar mass components, low aromatic condensation degree, and more easily oxidized substituents. This indicates that the landfill time strongly affects the EEMs characteristics of HA, and that the humification degree of HA increases with the landfill time. A red shift to a longer wavelength region and an increase of fluorescence intensity were observed when the concentration of HA was increased, suggesting that concentration had a great influence on the fluorescence characteristics of HAs. pH (2–12) also had significant effects on the fluorescence intensity, although it exerted no effect on the peak position of fluorescence of HA and FA. The results of FRI show that increasing concentration lead to more interactions among various structure components and that small molecular weight units tend to aggregate or be masked into more complicated and larger structures. The pH influence on the fluorescence intensity of HA seems mainly through molecular configuration, while the fluorescence intensity change with pH may be due to various substituents of FA.

Hydrogen Bonding in the Electronic Excited State

Because of its fundamental importance in many branches of science, hydrogen bonding is a subject of intense contemporary research interest. The physical and chemical properties of hydrogen bonds in the ground state have been widely studied both experimentally and theoretically by chemists, physicists, and biologists. However, hydrogen bonding in the electronic excited state, which plays an important role in many photophysical processes and photochemical reactions, has scarcely been investigated. Upon electronic excitation of hydrogen-bonded systems by light, the hydrogen donor and acceptor molecules must reorganize in the electronic excited state because of the significant charge distribution difference between the different electronic states. The electronic excited-state hydrogen-bonding dynamics, which are predominantly determined by the vibrational motions of the hydrogen donor and acceptor groups, generally occur on ultrafast time scales of hundreds of femtoseconds. As a result, state-of-the-art femtosecond time-resolved vibrational spectroscopy is used to directly monitor the ultrafast dynamical behavior of hydrogen bonds in the electronic excited state. It is important to note that the excited-state hydrogen-bonding dynamics are coupled to the electronic excitation. Fortunately, the combination of femtosecond time-resolved spectroscopy and accurate quantum chemistry calculations of excited states resolves this issue in laser experiments. Through a comparison of the hydrogen-bonded complex to the separated hydrogen donor or acceptor in ground and electronic excited states, the excited-state hydrogen-bonding structure and dynamics have been obtained. Moreover, we have also demonstrated the importance of hydrogen bonding in many photophysical processes and photochemical reactions. In this Account, we review our recent advances in electronic excited-state hydrogen-bonding dynamics and the significant role of electronic excited-state hydrogen bonding on internal conversion (IC), electronic spectral shifts (ESS), photoinduced electron transfer (PET), fluorescence quenching (FQ), intramolecular charge transfer (ICT), and metal-to-ligand charge transfer (MLCT). The combination of various spectroscopic experiments with theoretical calculations has led to tremendous progress in excited-state hydrogen-bonding research. We first demonstrated that the intermolecular hydrogen bond in the electronic excited state is greatly strengthened for coumarin chromophores and weakened for thiocarbonyl chromophores. We have also clarified that the intermolecular hydrogen-bond strengthening and weakening correspond to red-shifts and blue-shifts, respectively, in the electronic spectra. Moreover, radiationless deactivations (via IC, PET, ICT, MLCT, and so on) can be dramatically influenced through the regulation of electronic states by hydrogen-bonding interactions. Consequently, the fluorescence of chromophores in hydrogen-bonded surroundings is quenched or enhanced by hydrogen bonds. Our research expands our understanding of the nature of hydrogen bonding by delineating the interaction between hydrogen bonds and photons, thereby providing a basis for excited-state hydrogen bonding studies in photophysics, photochemistry, and photobiology.

ChemInform Abstract: Absorption Tuning of the Green Fluorescent Protein Chromophore: Synthesis and Studies of Model Compounds

AbstractReview: 25 refs.

Excited state relaxation dynamics of model green fluorescent protein chromophore analogs: evidence for cis-trans isomerism.

Two green fluorescent protein (GFP) chromophore analogs (4Z)-4-(N,N-dimethylaminobenzylidene)-1-methyl-2-phenyl-1,4-dihydro-5H-imidazolin-5-one (DMPI) and (4Z)-4-(N,N-diphenylaminobenzylidene)-1-methyl-2-phenyl-1,4-dihydro-5H-imidazolin-5-one (DPMPI) were investigated using femtosecond fluorescence up-conversion spectroscopy and quantum chemical calculations with the results being substantiated by HPLC and NMR measurements. The femtosecond fluorescence transients are found to be biexponential in nature and the time constants exhibit a significant dependence on solvent viscosity and polarity. A multicoordinate relaxation mechanism is proposed for the excited state relaxation behavior of the model GFP analogs. The first time component (τ(1)) was assigned to the formation of twisted intramolecular charge transfer (TICT) state along the rotational coordinate of N-substituted amine group. Time resolved intensity normalized and area normalized emission spectra (TRES and TRANES) were constructed to authenticate the occurrence of TICT state in subpicosecond time scale. Another picosecond time component (τ(2)) was attributed to internal conversion via large amplitude motion along the exomethylenic double bond which has been enunciated by quantum chemical calculations. Quantum chemical calculation also forbids the involvement of hula-twist because of high activation barrier of twisting. HPLC profiles and proton-NMR measurements of the irradiated analogs confirm the presence of Z and E isomers, whose possibility of formation can be accomplished only by the rotation along the exomethylenic double bond. The present observations can be extended to p-HBDI in order to understand the role of protein scaffold in reducing the nonradiative pathways, leading to highly luminescent nature of GFP.

Activities, Kinetics and Emission Spectra of Bacterial Luciferase‐Fluorescent Protein Fusion Enzymes

A new approach to alter bacterial bioluminescence color was developed by fusing Vibrio harveyi luciferase with the coral Discosoma sp. fluorescent protein mOrange, a homolog of the Aequorea green fluorescent protein. Attachment of mOrange to the N- or C-terminus of luciferase α or β subunit, via a 5 or 10 residue linker, produced fully active fusion enzymes. However, only the fusion of mOrange to the N-terminus of luciferase α produced a new 560 nm emission. The differences in emission color by two such fusion enzymes from that of the wild-type luciferase (λ(max) 490 nm) were evident by eye or photographically with the aid of cut-off optical filters. In nonturnover reactions, light decay rates of fusion enzyme remained the same when monitored as the full-spectrum light or at 480 nm (from the luciferase emitter) or 570 nm (from mOrange). No 560 nm emission component was observed with a mixture of luciferase and free mOrange. These findings support that the 560 nm emission by the fusion enzyme was due to bioluminescence resonance energy transfer from luciferase to mOrange. We believe that the same approach could also alter the bacterial bioluminescence color by covalent attachment of other suitable fluorescent proteins or chromophores to luciferase.

Excited-State Intramolecular Proton Transfer Molecules Bearing o-Hydroxy Analogues of Green Fluorescent Protein Chromophore

o-Hydroxy analogues, 1a-g, of the green fluorescent protein chromophore have been synthesized. Their structures and electronic properties were investigated by X-ray single-crystal analyses, electrochemistry, and luminescence properties. In solid and nonpolar solvents 1a-g exist mainly as Z conformers that possess a seven-membered-ring hydrogen bond and undergo excited-state intramolecular proton transfer (ESIPT) reactions, resulting in a proton-transfer tautomer emission. Fluorescence upconversion dynamics have revealed a coherent type of ESIPT, followed by a fast vibrational/solvent relaxation (<1 ps) to a twisted (regarding exo-C(5)-C(4)-C(3) bonds) conformation, from which a fast population decay of a few to several tens of picoseconds was resolved in cyclohexane. Accordingly, the proton-transfer tautomer emission intensity is moderate (0.08 in 1e) to weak (∼10(-4) in 1a) in cyclohexane. The stronger intramolecular hydrogen bonding in 1g suppresses the rotation of the aryl-alkene bond, resulting in a high yield of tautomer emission (Φ(f) ≈ 0.2). In the solid state, due to the inhibition of exo-C(5)-C(4)-C(3) rotation, intense tautomer emission with a quantum yield of 0.1-0.9 was obtained for 1a-g. Depending on the electronic donor or acceptor strength of the substituent in either the HOMO or LUMO site, a broad tuning range of the emission from 560 (1g) to 670 nm (1a) has been achieved.

Rapid chemoselective bioconjugation through oxidative coupling of anilines and aminophenols.

A highly efficient protein bioconjugation method is described involving addition of anilines to o-aminophenols in the presence of sodium periodate. The reaction takes place in aqueous buffer at pH 6.5 and can reach high conversion in 2-5 min. The major product was characterized using X-ray crystallography, which revealed that an unprecedented oxidative ring contraction occurs after the coupling step. The compatibility of the reaction with protein substrates has been demonstrated through attachment of small molecules, polymer chains, and peptides to p-aminophenylalanine residues introduced into viral capsids through amber stop codon suppression. Coupling of anilines to o-aminophenol groups derived from tyrosine residues is also described. The compatibility of this method with thiol modification chemistry is shown through attachment of a near-IR fluorescent chromophore to cysteine residues inside the viral capsid shells, followed by attachment of integrin-targeting RGD peptides to anilines on the exterior surface.

Spectroscopic Properties of Nanotube–Chromophore Hybrids

Recently, individual single-walled carbon nanotubes (SWNTs) functionalized with azo-benzene chromophores were shown to form a new class of hybrid nanomaterials for optoelectronics applications. Here we use a number of experimental and computational techniques to understand the binding, orientation, and nature of coupling between chromophores and the nanotubes, all of which are relevant to future optimization of these hybrid materials. We find that the binding energy between chromophores and nanotubes depends strongly on the type of tether that is used to bind the chromophores to the nanotubes. The pyrene tethers form a much stronger attachment to nanotubes compared to anthracene or benzene rings, resulting in more than 80% retention of bound chromophores post-processing. Density functional theory (DFT) calculations show that the binding energy of the chromophores to the nanotubes is maximized for chromophores parallel to the nanotube sidewall, even with the use of tethers; optical second harmonic generation measurements show that there is nonetheless a partial radial orientation of the chromophores on the nanotubes. We find weak electronic coupling between the chromophores and the SWNTs, consistent with noncovalent binding. This weak coupling is still sufficient to quench the chromophore fluorescence through a combination of static and dynamic processes. Photoluminescence measurements show a lack of significant energy transfer from the chromophores to isolated semiconducting nanotubes.

Collapse and Recovery of Green Fluorescent Protein Chromophore Emission through Topological Effects

Housed within the 11-stranded β-barrel of the green fluorescent protein (GFP) is the arylideneimidazolidinone (AMI) chromophore, the component responsible for fluorescence. This class of small-molecule chromophore has drawn significant attention for its remarkable photophysical and photochemical properties, both within the intact protein and after its denaturation. All of the proteins so far isolated that have visible light fluorescence have been found to contain an AMI chromophore. These proteins comprise an extensive rainbow, ranging from GFP, which contains the simplest chromophore, p-hydroxybenzylideneimidazolidinone (p-HOBDI), to proteins having molecules with longer conjugation lengths and a variety of intraprotein interactions. The fluorescence invariably almost vanishes upon removal of the protective β-barrel. The role of the barrel in hindering internal conversion has been the subject of numerous studies, especially in our laboratories and those of our collaborators. A better understanding of these chromophores has been facilitated by the development of numerous synthetic protocols. These syntheses, which commonly use the Erlenmeyer azlactone method, have evolved in recent years with the development of a [2 + 3] cycloaddition exploited in our laboratory. The synthetic AMI chromophores have allowed delineation of the complex photophysics of GFP and its derivatives. Upon denaturation, AMI chromophores are marked by 4 orders of magnitude of diminution in emission quantum yield (EQY). This result is attributed to internal conversion resulting from conformational freedom in the released chromophore, which is not allowed within the restrictive β-barrel. To date, the photophysical properties of the AMI chromophore remain elusive and have been attributed to a variety of mechanisms, including cis-trans isomerization, triplet formation, hula twisting, and proton transfer. Advanced studies involving gas-phase behavior, solvent effects, and protonation states have significantly increased our understanding of the chromophore photophysics, but a comprehensive picture is only slowly emerging. Most importantly, mechanisms in structurally defined chromophores may provide clues as to the origin of the "blinking" behavior of the fluorescent proteins themselves. One approach to examining the effect of conformational freedom on rapid internal conversion of the chromophores is to restrict the molecules, both through structural modifications and through adjustments of the supramolecular systems. We thus include here a discussion of studies involving the crystalline state, inclusion within natural protein-binding pockets, complexation with metal ions, and sequestration within synthetic cavities; all of this research affirms the role of restricting conformational freedom in partially restoring the EQY. Additionally, new photochemistry is observed within these restricted systems. Many of the studies carried out in our laboratories show promise for these molecules to be adapted as molecular probes, wherein inclusion turns on the fluorescence and provides a signaling mechanism. In this Account, we present an overview of the AMI chromophores, including synthesis, overall photophysics, and supramolecular behavior. A significant amount of work remains for researchers to fully understand the properties of these chromophores, but important progress achieved thus far in photophysics and photochemistry is underscored here.