Fluorescent Chromophore Research Articles

Excited state dynamics of the isolated green fluorescent protein chromophore anion following UV excitation.

A combined frequency-, angle-, and time-resolved photoelectron spectroscopy study is used to unravel the excited state dynamics following UV excitation of the isolated anionic chromophore of the green fluorescent protein (GFP). The optically bright S3 state, which is populated for hv > 3.7 eV, is shown to decay predominantly by internal conversion to the S2 state that in turn autodetaches to the neutral ground state. For hv > 4.1 eV, a new and favorable autodetachment channel from the S2 state becomes available, which leads to the formation of the neutral in an excited state. The results indicate that the UV excited state dynamics of the GFP chromophore involve a number of strongly coupled excited states.

Multiple and configurable optical logic systems based on layered double hydroxides and chromophore assemblies.

Multiple and configurable fluorescence logic gates were fabricated via self-assembly of layered double hydroxides and various chromophores. These logic gates were operated by observation of different emissions with the same excitation wavelength, which achieve YES, NOT, AND, INH and INHIBIT logic operations, respectively.

Two-photon absorption of fluorescent protein chromophores incorporating non-canonical amino acids: TD-DFT screening and classical dynamics.

Two-photon spectroscopy of fluorescent proteins is a powerful bio-imaging tool characterized by deep tissue penetration and little damage. However, two-photon spectroscopy has lower sensitivity than one-photon microscopy alternatives and hence a protein with a large two-photon absorption cross-section is needed. We use time-dependent density functional theory (TD-DFT) at the B3LYP/6-31+G(d,p) level of theory to screen twenty-two possible chromophores that can be formed upon replacing the amino-acid Tyr66 that forms the green fluorescent protein (GFP) chromophore with a non-canonical amino acid. A proposed chromophore with a nitro substituent was found to have a large two-photon absorption cross-section (29 GM) compared to other fluorescent protein chromophores as determined at the same level of theory. Classical molecular dynamics are then performed on a nitro-modified fluorescent protein to test its stability and study the effect of the conformational flexibility of the chromophore on its two-photon absorption cross-section. The theoretical results show that the large cross-section is primarily due to the difference between the permanent dipole moments of the excited and ground states of the nitro-modified chromophore. This large difference is maintained through the various conformations assumed by the chromophore in the protein cavity. The nitro-derived protein appears to be very promising as a two-photon absorption probe.

Benchmarking two-photon absorption cross sections: performance of CC2 and CAM-B3LYP.

We investigate the performance of CC2 and TDDFT/CAM-B3LYP for the calculation of two-photon absorption (TPA) strengths and cross sections and contrast our results to a recent coupled cluster equation-of-motion (EOM-EE-CCSD) benchmark study [K. D. Nanda and A. I. Krylov, J. Chem. Phys., 2015, 142, 064118]. In particular, we investigate whether CC2 TPA strengths are significantly overestimated compared to higher-level coupled-cluster calculations for fluorescent protein chromophores. Our conclusion is that CC2 TPA strengths are only slightly overestimated compared to the reference EOM-EE-CCSD results and that previously published overestimated cross sections are a result of inconsistencies in the conversion of the TPA strengths to macroscopic units. TDDFT/CAM-B3LYP TPA strengths, on the other hand, are found to be 1.5 to 3 times smaller than the coupled-cluster reference for the molecular systems considered. The unsatisfactory performance of TDDFT/CAM-B3LYP can be linked to an underestimation of excited-state dipole moments predicted by TDDFT/CAM-B3LYP.

Confined chromophores in tobacco mosaic virus to mimic green fluorescent protein

Due to the nano-confinement effect, grafting green fluorescent protein-like chromophores on the interior surface of tobacco mosaic virus can greatly enhance its fluorescence emission in various solvents.

How far can a single hydrogen bond tune the spectral properties of the GFP chromophore?

Photoabsorption of the hydrogen-bonded complex of a neutral and an anionic Green Fluorescent Protein chromophore has been studied using a new dual-detection approach to action-absorption spectroscopy. Following absorption of one photon, dissociation through a single channel ensures that the full absorption spectrum is measured. Our theoretical account of the spectral shape reveals that the anionic 0-0 transition (464 nm) is blue-shifted compared to that of the wild-type protein (478 nm) due to the stronger H-bond in the dimer, and represents an upper bound for that of the isolated anion. At the same time, the apparent effect of the H-bond for the neutral chromophore is as large as 0.5 eV, red-shifting the absorption maximum of the isolated neutral (340 nm) to that measured in the dimer (393 nm) and various proteins (∼395 nm). This shift results from changes in the topography of potential-energy surfaces in the Franck-Condon region of the H-bonded systems.

Synthesis, structure and photophysical properties of a highly luminescent terpyridine-diphenylacetylene hybrid fluorophore and its metal complexes.

A new fluorescent terpyridyl-diphenylacetylene hybrid fluorophore 4'-[4-{(4-methoxyphenyl)ethynyl}phenyl]-2,2':6',2''-terpyridine, L, was synthesized via Sonogashira cross-coupling of 4'-(4-bromophenyl)-2,2':6',2''-terpyridine and 4-ethynylanisole in the presence of Pd(PPh3)4/CuI as a catalyst. The solid state structure of L shows a trans arrangement of pyridine nitrogen atoms along the interannular bond in the terpyridine domain. Five transition metal complexes of L, {[FeL2](CF3SO3)2 (1), [ZnL2](ClO4)2 (2), [CdL2](ClO4)2 (3), [RuL2](PF6)2 (4), and PtMe3IL (5)}, have also been synthesized and characterized by spectroscopic methods and single crystal X-ray analysis. The X-ray crystal structures of complexes 1-3 show a distorted octahedral MN6 arrangement with tridentate coordination of the two terpyridine ligands, whereas in complex 5 the ligand L binds in a bidentate fashion. The ligand L displays bright blue emission in the solid state and in both non-polar and polar organic media. The fluorescence quantum yield of L is exceptionally high for a monoterpyridine ligand of its kind, which can be rationalized with density functional theory calculations. The electronic structure of L shows that the fluorescence involves intramolecular charge transfer from the diphenylacetylene moiety to the terpyridine group, and it is not affected by the usual non-radiative relaxation processes such as pyridine rotation. The Fe(II), Ru(II) and Pt(IV) complexes of L were found to be non-emissive, whereas both Zn(II) and Cd(II) complexes displayed significant green emission attributed to intra-ligand charge transfer states. These results were supported by the observed red-shift of the emission maxima of complexes 2 and 3 with increasing the solvent polarity.

Probing the Internal and External Structure of Carbon Nanodots through Fluorescence Quenching

In past several years, there has been significant investigation into the various synthetic routes of carbon nanodots along with their associated photophysical properties [1-3]. Carbon nanodots are naturally fluorescing nanometer-sized particles with interesting and unique photophysical properties, which make them highly applicable for various applications in the life sciences [2-3]. Our lab has been investigating these particles produced by various combustion routes for many years, studying both the photophysical and plasmon-enhanced photophysical properties [1]. In order to fully understand the photophysical properties of carbon nanodots, in this poster we have examined the both the internal and external structure of these particles in an attempt to ascertain the origins of the fluorescence signature/s, using a combination of differently charged ions; which ultimately results in both static and dynamic quenching processes being observed. Our results reveal significant vibronic structure of the nanodots’ chromophore, which can readily be quenched by non-charged ions (acrylamide), suggesting a buried fluorescent chromophore center. [1] Y. Zhang, H. Gonçalves, J. C. G. Esteves Da Silva, and C. D. Geddes, “Metal-enhanced photoluminescence from carbon nanodots,” Chem. Commun. 47, 5313-5315 (2011). [2] S. Baker and G. Baker, “Luminescent Carbon Nanodots: Emergent Nanolights,” Angew, Chem. Int. Ed. 49, 6726-6744 (2010). [3] H. Li, Z. Kang, Y. Liu, and S-T. Lee, “Carbon nanodots synthesis, properties and applications,” J. Mater. Chem, 22, 24230-24253 (2010).

Fluorescent polymeric assemblies as stimuli-responsive vehicles for drug controlled release and cell/tissue imaging

Polymer assemblies with good biocompatibility, stimuli-responsive properties and clinical imaging capability are desirable carriers for future biomedical applications. Herein, we report on the synthesis of a novel anthracenecarboxaldehyde-decorated poly(N-(4-aminophenyl) methacryl amide-oligoethyleneglycolmonomethylether methacrylate) (P(MAAPAC-MAAP-MAPEG)) copolymer, comprising fluorescent chromophore and acid-labile moiety. This copolymer can assemble into micelles in aqueous solution and shows a spherical shape with well-defined particle size and narrow particle size distribution. The pH-responsive property of the micelles has been evaluated by the change of particle size and the controlled release of guest molecules. The intrinsic fluorescence property endows the micelles with excellent cell/tissue imaging capability. Cell viability evaluation with human hepatocellular carcinoma BEL-7402 cells demonstrates that the micelles are nontoxic. The cellular uptake of the micelles indicates a time-dependent behavior. The H22-tumor bearing mice treated with the micelles clearly exhibits the tumor accumulation. These multi-functional nanocarriers may be of great interest in the application of drug delivery.

Non-adiabatic dynamics of isolated green fluorescent protein chromophore anion.

On-the-fly ab initio molecular dynamics calculations have been performed to investigate the relaxation mechanism of green fluorescent protein chromophore anion under vacuum. The CASSCF surface hopping simulation method based on Zhu-Nakamura theory is applied to present the real-time conformational changes of the target molecule. The static calculations and dynamics simulation results suggest that not only the twisting motion around bridging bonds between imidazolinone and phenoxy groups but the strength mode of C=O and pyramidalization character of bridging atom are major factors on the ultrafast fluorescence quenching process of the isolated chromophore anion. The abovementioned factors bring the molecule to the vicinity of conical intersections on its potential energy surface and to finish the internal conversion process. A Hula-like twisting pattern is displayed during the relaxation process and the entire decay process disfavors a photoswitching pattern which corresponds to cis-trans photoisomerization.

Chemistry and biology of pyoverdines, Pseudomonas primary siderophores.

Pyoverdine is the generic name given to a vast family of fluorescent green-yellowish pigments produced by Pseudomonas species. Pseudomonas aeruginosa is an opportunistic pathogen, particularly infecting humans with compromised natural defenses. These infections result in significantly higher morbidity, longer hospitalization, increased mortality rates and excess health care costs. P. aeruginosa is very difficult to eradicate because of an intrinsic coupled with an adaptive resistance to a wide variety of classical antibiotics. When subjected to iron starvation conditions, Pseudomonas bacteria synthesize pyoverdines, their primary siderophores, to acquire iron from the extracellular medium. These molecules are not only powerful iron(III) scavengers but efficient iron(III) transporters as well. Three distinct structural parts constitute pyoverdines, i.e. (i) the fluorescent chromophore, deriving from a dihydroxyquinoline, attached via its carbonyl group to (ii) a type-specific peptide composed of 6 to 14 amino acids and (iii) a small side chain corresponding to a carboxylic acid derivative. Their chemical structure show three bidentate chelating sites including a catechol and two hydroxamates, leading to an octahedral geometry when complexed to iron(III). While the chromophore group is common to all pyoverdines, their peptide moiety differs among strains and species by the number, length, composition and configuration of amino acids. Following chelation with iron(III), the newly formed pyoverdine-Fe complex is recognized by a specific outer membrane transporter, namely FpvA, and reenters the cell where the iron is released from the pyoverdine into the periplasm for further incorporation into bacterial proteins. The remaining apo-pyoverdine is then recycled and secreted back to the extracellular medium by efflux pumps. Besides, the role of pyoverdines in P. aeruginosa is not only limited to scavenge iron from the bacterial environment. Indeed, these siderophores act as signal molecules for the production of acute virulence factors and are involved in biofilm formation as well. The ongoing expanding pathogenicity of P. aeruginosa has become a major public health problem, and finding alternative strategies to classical antibiotics is urgently needed. Pyoverdines along with the iron pathway recently gained interest among academical researchers as potential new approaches to "fight" the bacteria. This review describes the classification of the nearly 60 pyoverdines identified so far, their structural and chemical properties and their (bio)synthesis. The different mechanisms underlying the steps of a pyoverdine's life in Pseudomonas are detailed as well: the affinity by which a pyoverdine chelates iron(III), the description of the interactions inducing the siderophore-receptor recognition, the specific transport of the pyoverdine-Fe(III) complex. As pyoverdine production and severe infections are linked, we will also report on situations where pyoverdines are considered as being P. aeruginosa Achilles heel: the propensity of FpvA to transport exo-pyoverdines, organic synthesis of pyoverdines and analogs, grafting of antibiotics on pyoverdines in a Trojan Horse strategy.

The effects of resonance delocalization and the extent of π system on ionization energies of model fluorescent proteins chromophores

Recent advances in the design and application of redox‐active fluorescent proteins (FPs) stimulated an interest in the electronic structure of the ionized/electron‐detached FP chromophores. Here, we report the results of a computational study of the electron‐detached and ionized states of model chromophores of green and red FPs. We focus on the analysis of the effects of the phenolate OH group position (ortho, meta, and para) on relative energies of the chromophores in the ground as well as in the ionized/detached electronic states. We found that, similarly to the green chromophore, the red chromophores with the OH group in meta position have lower vertical detachment energies (DE) and greater ionization energies relative to the ortho and para forms. Moreover, the effect is stronger for the red anionic chromophores. The differences in DE in meta species relative to their para counterparts are 0.47 and 0.25 eV for the red and green chromophores, respectively. The observed trends are due to a combined effect of resonance stabilization and the electronegativity of the acylimine group in the red chromophores. The analysis is supported by the computed charge and spin density delocalization patterns. © 2014 Wiley Periodicals, Inc.

Fluorescence enhancement of covalently linked 1-cyano-1,2-diphenylethene chromophores with naphthalene-1,8-diyl linker units: analysis based on kinetic constants.

The fluorescence enhancement effect of covalently fixed fluorescent chromophores has been investigated by means of kinetic analysis of decay rate constants and theoretical calculations. Derivatives of 1-cyano-1,2-diphenylethene dimer have a distorted cyclic structure when both ends are clipped with two naphthalene-1,8-diyl linker units. In contrast to the reference monomer derivative, which exhibits only slight fluorescence in solution (Φf < 0.01, τf < 0.1 ns), the dimer derivative shows high fluorescence quantum yield (Φf = 0.55) and long lifetime (τf = 20.6 ns) in dilute solution owing to suppression of the nonradiative decay process (knr = 0.022 ns(-1)). A V-shaped derivative with a covalent linker on one side showed moderate quantum yield and lifetime (Φf = 0.12, τf = 4.9 ns). According to the wavelength shifts of the absorption/fluorescence bands and theoretical calculations by time-dependent density functional theory (TD-DFT), we propose an H-aggregate-type excimer interaction.

Diabatic Population Matrix Formalism for Performing Molecular Mechanics Style Simulations with Multiple Electronic States.

An accurate description of nonbonded interactions is important in investigating dynamics of molecular systems. In many situations, fixed point charge models are successfully applied to explaining various chemical phenomena. However, these models with conventional formulations will not be appropriate in elucidating the detailed dynamics during nonadiabatic events. This is mainly because the chemical properties of any molecule, especially its electronic populations, significantly change with respect to molecular distortions in the vicinity of the surface crossing. To overcome this issue in molecular simulations yet within the framework of the fixed point charge model, we define a diabatic electronic population matrix and substitute it for the conventional adiabatic partial charges. We show that this matrix can be readily utilized toward attaining more reliable descriptions of Coulombic interactions, in combination with the interpolation formalism for obtaining the intramolecular interaction potential. We demonstrate how the mixed formalism with the diabatic charges and the interpolation can be applied to molecular simulations by conducting adiabatic and nonadiabatic molecular dynamics trajectory calculations of the green fluorescent protein chromophore anion in aqueous environment.

Fast calcium sensor proteins for monitoring neural activity.

A major goal of the BRAIN Initiative is the development of technologies to monitor neuronal network activity during active information processing. Toward this goal, genetically encoded calcium indicator proteins have become widely used for reporting activity in preparations ranging from invertebrates to awake mammals. However, slow response times, the narrow sensitivity range of Ca2+ and in some cases, poor signal-to-noise ratio still limit their usefulness. Here, we review recent improvements in the field of neural activity-sensitive probe design with a focus on the GCaMP family of calcium indicator proteins. In this context, we present our newly developed Fast-GCaMPs, which have up to 4-fold accelerated off-responses compared with the next-fastest GCaMP, GCaMP6f. Fast-GCaMPs were designed by destabilizing the association of the hydrophobic pocket of calcium-bound calmodulin with the RS20 binding domain, an intramolecular interaction that protects the green fluorescent protein chromophore. Fast-GCaMP6f-RS06 and Fast-GCaMP6f-RS09 have rapid off-responses in stopped-flow fluorimetry, in neocortical brain slices, and in the intact cerebellum in vivo. Fast-GCaMP6f variants should be useful for tracking action potentials closely spaced in time, and for following neural activity in fast-changing compartments, such as axons and dendrites. Finally, we discuss strategies that may allow tracking of a wider range of neuronal firing rates and improve spike detection.

Resonantly Enhanced Multiphoton Ionization Spectrum of the Neutral Green Fluorescent Protein Chromophore.

The photophysics of the green fluorescent protein is governed by the electronic structure of the chromophore at the heart of its β-barrel protein structure. We present the first two-color, resonance-enhanced, multiphoton ionization spectrum of the isolated neutral chromophore in vacuo with supporting electronic structure calculations. We find the absorption maximum to be 3.65 ± 0.05 eV (340 ± 5 nm), which is blue-shifted by 0.5 eV (55 nm) from the absorption maximum of the protein in its neutral form. Our results show that interactions between the chromophore and the protein have a significant influence on the electronic structure of the neutral chromophore during photoabsorption and provide a benchmark for the rational design of novel chromophores as fluorescent markers or photomanipulators.

A phosphine-catalyzed preparation of 4-arylidene-5-imidazolones.

A simple and efficient method for constructing 4-arylidene-5-imidazolones was developed using a phosphine-catalyzed tandem umpolung addition and intramolecular cyclization of amidine pronucleophiles on arylpropiolates. The reaction offers a robust route to heterocycle analogues of the fluorescent protein chromophores.

The lineshape of the electronic spectrum of the green fluorescent protein chromophore, part II: solution phase.

The vibronic spectra of the green fluorescent protein chromophore analogues p-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI) and 3,5-tert-butyl-HBDI (35Bu) are similar in the vacuum, but very different in water or ethanol. To understand this difference, we have computed the vibrationally resolved solution spectra of these chromophores, using the polarizable continuum model (PCM) to account for solvent effects on the (harmonic) potential energy surfaces (PES). In agreement with experiment, we found that the vibrational progression increases with the polarity of the solvent, but we could neither reproduce the broadening, nor the large difference between the absorption spectra of HBDI and 35Bu. To account for the inhomogeneous broadening of the solution spectra, we used two approaches. In the first, we estimated the polar broadening from the solvent reorganization energy upon photo-excitation, using the state-specific PCM implementation. In the second, we estimated the broadening from the variance of the vertical excitation energies in molecular dynamics trajectories. Although we found good agreement for the lineshape of 35Bu in ethanol, and to a lesser extent in water, we highly underestimated the broadening for HBDI. To resolve this discrepancy, we explored the PES of HBDI in water and found that in contrast to the PCM result, the ground-state geometry is not planar in explicit solvent. We furthermore found that nonplanar geometries enhance the intramolecular charge transfer upon excitation. Therefore, the solvent reorganization and broadening are much larger and we speculate that the much broader spectrum of HBDI in water is due to the population of nonplanar geometries.

The lineshape of the electronic spectrum of the green fluorescent protein chromophore, part I: gas phase.

In this work we present the vibrationally resolved optical absorption spectrum of p-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI), the green fluorescent protein (GFP) chromophore, computed at several levels of theory, including time-dependent DFT with various functionals and basis sets, CASSCF, CASPT2 and XMCQDPT2. We also investigated what happens to the spectrum if the ground- and excited-state geometries are optimized at different levels of theory (mixed approach), as has been used previously. The vibrationally resolved absorption spectra obtained by DFT, CASPT2 and XMCQDPT2 are very similar and consist of a main absorption peak and a shoulder that is ∼1500 cm(-1) higher in energy. The vibrational progression increases moderately with temperature. These spectra are in qualitative agreement with experimental action spectra, but much narrower and lack the long tail in the blue, even at high temperatures. Because our calculated emission spectra, which are equally narrow, are in good agreement with the emission of green fluorescent protein at 253 K, we argue that the action spectrum are too broad to be considered as the absorption spectrum. The CASSCF method and the mixed approaches overestimate the vibrational progressions with respect to CAM-B3LYP, CASPT2 and XMCQDPT2, due to inaccuracies in the geometric S0 →S1 displacements. Finally, we computed the vibronic spectra of four chromophore analogues with different substitutions on the rings and found that these substitutions hardly affect the lineshape in vacuum.

Synthesis, structure, photoluminescence, and electroluminescence of siloles that contain planar fluorescent chromophores.

Herein, a new series of siloles that were 2,5-substituted with planar fluorescent chromophores (PFCs), including fluorene, fluoranthene, naphthalene, pyrene, and anthracene, were synthesized and characterized. These compounds showed weak emission in the solution state, owing to active intramolecular rotation (IMR), but the synergistic effect from electronic coupling between the PFC and the silole ring compensated for the emission quenching by the IMR process to some extent, thereby affording higher emission efficiencies than those of 2,3,4,5-tetraphenylsiloles in solution. These new siloles showed enhanced emission efficiencies in the aggregated state. The electroluminescence (EL) color and efficiency of new siloles were sensitive towards the PFC. Siloles containing naphthalene moieties showed green EL emission, whilst those containing anthracene moieties showed orange EL emission. The siloles containing pyrene moieties exhibited yellow EL emission at 546 nm, with a peak luminance of 49000 cd cm(-2) and a high current efficiency of 9.1 cd A(-1).