A Conical Intersection Controls the Deactivation of the Bacterial Luciferase Fluorophore

The photophysics of flavins is highly dependent on their environment. For example, 4a‐hydroxy flavins display weak fluorescence in solution, but exhibit strong fluorescence when bound to a protein. To understand this behavior, we performed temperature‐dependent fluorescent studies on an N(5)‐alkylated 4a‐hydroxy flavin: the putative bacterial luciferase fluorophore. We find an increase in fluorescence quantum yield upon reaching the glass transition temperature of the solvent. We then employ multiconfigurational quantum chemical methods to map the excited‐state deactivation path of the system. The result reveals a shallow but barrierless excited state deactivation path that leads to a conical intersection displaying an orthogonal out‐of‐plane distortion of the terminal pyrimidine ring. The intersection structure readily explains the observed spectroscopic behavior in terms of an excited‐state barrier imposed by the rigid glass cavity.     

Ultrafast Relaxation Dynamics of the Excited States of 1‐Amino‐ and 1‐(N,N‐Dimethylamino)‐fluoren‐9‐ones

The dynamics of the excited states of 1‐aminofluoren‐9‐one (1AF) and 1‐(N,N‐dimethylamino)‐fluoren‐9‐one (1DMAF) are investigated by using steady‐state absorption and fluorescence as well as subpicosecond time‐resolved absorption spectroscopic techniques. Following photoexcitation of 1AF, which exists in the intramolecular hydrogen‐bonded form in aprotic solvents, the excited‐state intramolecular proton‐transfer reaction is the only relaxation process observed in the excited singlet (S₁) state. However, in protic solvents, the intramolecular hydrogen bond is disrupted in the excited state and an intermolecular hydrogen bond is formed with the solvent leading to reorganization of the hydrogen‐bond network structure of the solvent. The latter takes place in the timescale of the process of solvation dynamics. In the case of 1DMAF, the main relaxation pathway for the locally excited singlet, S₁(LE), or S₁(ICT) state is the configurational relaxation, via nearly barrierless twisting of the dimethylamino group to form the twisted intramolecular charge‐transfer, S₁(TICT), state. A crossing between the excited‐state and ground‐state potential energy curves is responsible for the fast, radiationless deactivation and nonemissive character of the S₁(TICT) state in polar solvents, both aprotic and protic. However, in viscous but strong hydrogen‐bond‐donating solvents, such as ethylene glycol and glycerol, crossing between the potential energy surfaces for the ground electronic state and the hydrogen‐bonded complex formed between the S₁(TICT) state and the solvent is possibly avoided and the hydrogen‐bonded complex is weakly emissive.     

The photochemistry of 6‐phenanthridinecarbonitrile II. The physical and photophysical properties

The physical and photophysical properties of 6‐phenanthridinecarbonitrile ( 1 ) have been examined. We previously reported that when 1 is irradiated in aqueous 2‐propanol, three products are formed [3]. These include dimethyl‐6‐phenanthridinylcarbinol (2), phenanthridine (3) and 6,6′‐biphenanthridine (4). Phenanthridinyl radical is formed in neutral media by hydrogen atom abstraction from an alcohol molecule by an excited state of 1 in a monophotonic process. The presents of acid effectively quenches all photochemical behavior. These products may all be explained assuming in‐cage and out‐of‐cage reactions. The free spin value, g_e, was determined at 125 K and found to be 2.0043 which is close to the theoretical value for that of a free electron. The total emission spectrum of 1 at 77 K shows a fluorescence maximum at 378 nm and a much weaker phosphorescence maximum at 502 nm which represented less than 3% of the total emission. When benzophenone is added to the reaction mixture, the triplet state of 1 is populated, but photosensitized product formation does not occur. The result supports a singlet reactive state. When cis/trans‐piperylene is added to the reaction mixtures, it quenches the fluorescence of 1 . The fluorescence quantum yield (Φ_f) was found to be 0.227 in neat 2‐propanol. The addition of water causes an increase in Φ_f and a decrease in the Pk_a of the medium. The excited state lifetime (τ) was determined in neat 2‐propanol, using oxygen quenching, and found to be 3.4 ns. This number increased with increasing water concentration. The photoreactive state of 1 appears to be its π,π* singlet state making its behavior more like that of the corresponding hydrocarbon parent.     

The photochemistry of 6‐phenanthridinecarbonitrile I. Product analysis

When 6‐phenanthridinecarbonitrile ( 3 ) is irradiated at 2537 Å in neutral 9:1 2‐propanol/water, three major products are formed. These are dimethyl‐(6‐phenanthridinyl)methanol ( 4 ), phenanthridine ( 5 ) and 6,6′‐biphenanthridine ( 6 ). When benzophenone is present in the reaction mixture, diphenyl‐(6‐phenanthridinyl)‐methanol is also formed. 6‐Phenanthridinyl radical which is common to the formation of all these products, is formed by a monophotonic process involving hydrogen atom abstraction from an alcohol molecule by an excited state of 3 . Unlike what is generally found with other nitrogen‐heterocycles, the photochemistry of 3 appears to involve only a π,π* singlet state. The fluorescence of 3 is quenched with the triplet quencher cis/trans‐piperylene as a function of the concentration of the diene without the accompaniment of an exci‐plex emission.     

Time‐dependent density functional theory study on the electronic excited‐state geometric structure,infrared spectra,and hydrogen bonding of a doubly hydrogen‐bonded complex

The geometric structures and infrared (IR) spectra in the electronically excited state of a novel doubly hydrogen‐bonded complex formed by fluorenone and alcohols, which has been observed by IR spectra in experimental study, are investigated by the time‐dependent density functional theory (TDDFT) method. The geometric structures and IR spectra in both ground state and the S₁ state of this doubly hydrogen‐bonded FN‐2MeOH complex are calculated using the DFT and TDDFT methods, respectively. Two intermolecular hydrogen bonds are formed between FN and methanol molecules in the doubly hydrogen‐bonded FN‐2MeOH complex. Moreover, the formation of the second intermolecular hydrogen bond can make the first intermolecular hydrogen bond become slightly weak. Furthermore, it is confirmed that the spectral shoulder at around 1700 cm^?1 observed in the IR spectra should be assigned as the doubly hydrogen‐bonded FN‐2MeOH complex from our calculated results. The electronic excited‐state hydrogen bonding dynamics is also studied by monitoring some vibraitonal modes related to the formation of hydrogen bonds in different electronic states. As a result, both the two intermolecular hydrogen bonds are significantly strengthened in the S₁ state of the doubly hydrogen‐bonded FN‐2MeOH complex. The hydrogen bond strengthening in the electronically excited state is similar to the previous study on the singly hydrogen‐bonded FN‐MeOH complex and play important role on the photophysics of fluorenone in solutions. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009     

A detailed theoretical study on the excited‐state hydrogen‐bonding dynamics and the proton transfer mechanism for a novel white‐light fluorophore

In this work, density functional theory (DFT) and time‐dependent DFT (TDDFT) methods were used to investigate the excited‐state dynamics of the excited‐state hydrogen‐bonding variations and proton transfer mechanism for a novel white‐light fluorophore 2‐(4‐[dimethylamino]phenyl)‐7‐hyroxy‐6‐(3‐phenylpropanoyl)‐4H‐chromen‐4‐one ( 1 ). The methods we adopted could successfully reproduce the experimental electronic spectra, which shows the appropriateness of the theoretical level in this work. Using molecular electrostatic potential (MEP) as well as the reduced density gradient (RDG) versus the product of the sign of the second largest eigenvalue of the electron density Hessian matrix and electron density (sign[λ₂]ρ), we demonstrate that an intramolecular hydrogen bond O1–H2···O3 should be formed spontaneously in the S₀ state. By analyzing the chemical structures, infrared vibrational spectra, and hydrogen‐bonding energies, we confirm that O1–H2·O3 should be strengthened in the S₁ state, which reveals the possibility of an excited‐state intramolecular proton transfer (ESIPT) process. On investigating the excitation process, we find the S₀ → S₁ transition corresponding to the charge transfer, which provides the driving force for ESIPT. By constructing the potential energy curves, we show that the ESIPT reaction results in a dynamic equilibrium in the S₁ state between the forward and backward processes, which facilitates the emission of white light.     

A TD‐DFT study on the cyanide‐chemosensing mechanism of 8‐formyl‐7‐hydroxycoumarin

Proton transfer (PT) and excited‐state PT process are proposed to account for the fluorescent sensing mechanism of a cyanide chemosensor, 8‐formyl‐7‐hydroxycoumarin. The time‐dependent density functional theory method has been applied to investigate the ground and the first singlet excited electronic states of this chemosensor as well as its nucleophilic addition product with cyanide, with a view to monitoring their geometries and spectrophotometrical properties. The present theoretical study indicates that phenol proton of the chemosensor transfers to the formyl group along the intramolecular hydrogen bond in the first singlet excited state. Correspondingly, the nucleophilic addition product undergoes a PT process in the ground state, and shows a similar structure in the first singlet excited state. This could explain the observed strong fluorescence upon the addition of the cyanide anion in the relevant fluorescent sensing mechanism. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

QM/MM study of the role of the solvent in the formation of the charge separated excited state in 9,9'-bianthryl

In this paper the role of the solvent in the formation of the charge-separated excited state of 9,9'-bianthryl (BA) is examined by means of mixed molecular mechanical/quantum mechanical (QM/MM) calculations. It is shown that in weakly polar solvents a relaxed excited state is formed with an interunit angle that is significantly smaller than 90 degrees . This relaxed excited state has a considerable dipole moment even in weakly polar solvents; for benzene and dioxane dipole moments of ca. 6 D were calculated, which is close to experimental data. These dipoles are induced by the solvent in the highly polarizable relaxed excited state of BA, and the dipole relaxation time is governed by solvent reorganizations. In polar solvent the charge separation is driven to completion by the stronger dipoles in the solvent and a fully charged separated excited state is formed with an interunit angle of 90 degrees.     

Bioluminophore and Flavin Mononucleotide Fluorescence Quenching of Bacterial Bioluminescence—A Theoretical Study

Bacterial bioluminescence with continuous glow has been applied to the fields of environmental toxin monitoring, drug screening, and in vivo imaging. Nonetheless, the chemical form of the bacterial bioluminophore is still a bone of contention. Flavin mononucleotide (FMN), one of the light‐emitting products, and 4a‐hydroxy‐5‐hydro flavin mononucleotide (HFOH), an intermediate of the chemical reactions, have both been assumed candidates for the light emitter because they have similar molecular structures and fluorescence wavelengths. The latter is preferred in experiments and was assigned in our previous density functional study. HFOH displays weak fluorescence in solutions, but exhibits strong bioluminescence in the bacterial luciferase. FMN shows the opposite behavior; its fluorescence is quenched when it is bound to the luciferase. This is the first example of flavin fluorescence quenching observed in bioluminescent systems and is merely an observation, both the quenching mechanism and quencher are still unclear. Based on theoretical analysis of high‐level quantum mechanics (QM), combined QM and molecular mechanics (QM/MM), and molecular dynamics (MD), this paper confirms that HFOH in its first singlet excited state is the bioluminophore of bacterial bioluminescence. More importantly, the computational results indicate that Tyr110 in the luciferase quenches the FMN fluorescence via an electron‐transfer mechanism.     

Étude de réactions photochimiques—XXVI: Réactions photochimiques de diènes transoïdes en série stéroïdes

A mechanism accounting for the products from excited transoid dienes is proposed. In the singlet excited state, these dienes are deactivated by an intramolecular path which competes with a bimolecular process. In the triplet excited state, dienes undergo a unique bimolecular process. The multiplicity of the excited state controls the “product” formation through the conformation of the excited dienes.     

CHEMIEXCITATION IN THE PEROXIDATIVE METABOLISM OF N- METHYLCARBAZOLE: MECHANISTIC IMPLICATIONS

Abstract –The peroxidative metabolism of TV-methylcarbazole emits light independently of the presence of oxygen. It is likely that two chemiexcited transients are formed by electron transfer to the activated peroxidase, the cation radical by one electron transfer and a cation biradical by two electron transfer consistent with the failure to observe horseradish peroxidase-II in the steady state of the reaction. In the spectral range investigated (390–700 nm) the observed emission (570–700 nm) is ascribed to the biradical, as the latter is equivalent to an excited state of the postulated iminium cation.
While lipoxygenase has no effect upon JV-methylcarbazole, it markedly enhances the emission if peroxidase is present. This effect requires oxygen and is ascribed to an excited product formed by lipoxygenase acting upon an intermediate hydroperoxide of the aerobic process promoted by peroxidase.     

Fluoride anion sensing mechanism of a BODIPY‐linked hydrogen‐bonding probe

The sensing mechanism of a fluoride‐anion probe BODIPY‐amidothiourea ( 1c ) has been elucidated through the density functional theory (DFT) and time‐dependent density functional theory (TDDFT) calculations. The theoretical study indicates that in the DMSO/water mixtures the fluorescent sensing has been regulated by the fluoride complex that formed between the probe 1c /two water molecules and the fluoride anion, and the excited‐state intermolecular hydrogen bond (H‐B) plays an important role in the fluoride sensing mechanism. In the first excited state, the H‐Bs of the fluoride complex 1cFH₂ are overall strengthened, which induces the weak fluorescence emission. In addition, molecular orbital analysis demonstrates that 1cFH₂ has more obvious intramolecular charge transfer (ICT) character in the S₁ state than 1cH₂ formed between the probe 1c and two water molecules, which also gives reason to the weaker fluorescence intensity of 1cFH₂ . Further, our calculated UV‐vis absorbance and fluorescence spectra are in accordance with the experimental measurements. © 2018 Wiley Periodicals, Inc.     

Correlated,Dual‐Beam Optical Gating in Coupled Organic–Inorganic Nanostructures

An optical switch with two distinct resonances is formed by combining PbS nanocrystals and the conductive polymer poly[sodium 2‐(2‐ethynyl‐4‐methoxyphenoxy)acetate] (PAE) into a hybrid thin film. Infrared excitation of the nanocrystals invokes charge transfer and consecutive polaron formation in the PAE, which activates the switch for excited‐state absorption at visible frequencies. The optical modulation of the photocurrent response of the switch exhibits highly wavelength‐selective ON/OFF ratios. Transient absorption spectroscopy shows that the polaron formation is correlated with the excited state of the nanocrystals, opening up new perspectives for photonic data processing. Such correlated activated absorption can be exploited to enhance the sensitivity for one optical signal by a second light source of different frequency as part of an optical amplifier or a device with AND logic.     

A Molecular Nanotube with Three‐Dimensional π‐Conjugation

A π‐conjugated twelve‐porphyrin tube is synthesized in 32 % yield by a template‐directed coupling reaction that joins together six porphyrin dimers, forming twelve new C? C bonds. The nanotube has two bound templates, enclosing an internal volume of approximately 4.5 nm³. Its UV/Vis/NIR absorption and fluorescence spectra resemble those of a previously reported six‐porphyrin ring, but are red‐shifted by approximately 300 cm^?1, reflecting increased conjugation. Ultrafast fluorescence spectroscopy demonstrates extensive excited‐state delocalization. Transfer of electronic excitation from an initially formed state polarized in the direction of the nanotube axis (z axis) to an excited state polarized in the xy plane occurs within 200 fs, resulting in a negative fluorescence anisotropy on excitation at 742 nm.     

Correlated,Dual‐Beam Optical Gating in Coupled Organic–Inorganic Nanostructures

An optical switch with two distinct resonances is formed by combining PbS nanocrystals and the conductive polymer poly[sodium 2‐(2‐ethynyl‐4‐methoxyphenoxy)acetate] (PAE) into a hybrid thin film. Infrared excitation of the nanocrystals invokes charge transfer and consecutive polaron formation in the PAE, which activates the switch for excited‐state absorption at visible frequencies. The optical modulation of the photocurrent response of the switch exhibits highly wavelength‐selective ON/OFF ratios. Transient absorption spectroscopy shows that the polaron formation is correlated with the excited state of the nanocrystals, opening up new perspectives for photonic data processing. Such correlated activated absorption can be exploited to enhance the sensitivity for one optical signal by a second light source of different frequency as part of an optical amplifier or a device with AND logic.     

Multiple Photoluminescent Processes from Pyrene Derivatives with Aggregation‐ and Mechano‐Induced Excimer Emission

Two novel pyrene‐based isocyanide gold(I) complexes have been designed and synthesized. The different structures lead to distinct and diverse photophysical properties both in solution and in the aggregate state. Multiple photoluminescence, involving monomer emission, locally excited emission and excimer emission, are observed. Notably, an excimer is formed by aggregation in solution and external mechanical stimulation in the solid state, showing aggregation‐ and mechano‐induced excimer emission.     

Porphyrin–Phthalocyanine/Pyridylfullerene Supramolecular Assemblies

The synthesis and photophysical properties of several porphyrin (P)–phthalocyanine (Pc) conjugates (P–Pc; 1 – 3 ) are described, in which the phthalocyanines are directly linked to the β‐pyrrolic position of a meso‐tetraphenylporphyrin. Photoinduced energy‐ and electron‐transfer processes were studied through the preparation of H₂P–ZnPc, ZnP–ZnPc, and PdP–ZnPc conjugates, and their assembly through metal coordination with two different pyridylfulleropyrrolidines ( 4 and 5 ). The resulting electron‐donor–acceptor hybrids, which were formed by axial coordination of compounds 4 and 5 with the corresponding phthalocyanines, mimicked the fundamental processes of photosynthesis; that is, light harvesting, the transduction of excited‐state energy, and unidirectional electron transfer. In particular, photophysical studies confirmed that intramolecular energy‐transfer resulted from the S₂ excited state as well as from the S₁ excited state of the porphyrins to the energetically lower‐lying phthalocyanines, followed by an intramolecular charge‐transfer to yield P–Pc^.+ ? C₆₀^.?. This unique sequence of processes opens the way for solar‐energy‐conversion processes.     

FLUORESCENT POLYENE ALIPHATICS AS SPECTROSCOPIC AND MECHANISTIC PROBES FOR BACTERIAL LUCIFERASE: EVIDENCE AGAINST CARBONYL PRODUCT FROM ALDEHYDE AS THE PRIMARY EXCITED SPECIES

The fluorescent α-parinaric acid (α-PAC) and β-parinaric acid (β-PAC) were converted to the corresponding aldehydes and alcohols all of which exhibited absorption and fluorescence properties closely resembling those of the parent acids. α-PAC and β-PAC each binds to luciferase in competition with aldehyde. The hydrophobic nature of the aldehyde site was indicated by the enhanced fluorescence quantum yields of the bound α-PAC and β-PAC. These two polyene acids and the β-parinaryl alcohol were shown to stabilize the luciferase flavin-peroxide intermediate. α-Parinaraldehyde (α-PAD) and bt-parinaraldehyde (β-PAD) were active substrates for Vibrio harveyi and Vibrio fischeri luciferases and, for the former enzyme, exhibited K_m, values similar to and quantum yields about20–30% as those for decanal and dodecanal. For the V. harveyi luciferase with reduced FMN as a co-substrate, the α-PAD- or β-PAD-initiated luminescence was indistinguishable from the normal emission obtained with octanal (γ_max 495 nm) showing no additional 430-nm component correlatable with emission from excited α-PAC or β-PAC. In reactions using reduced 2-thioFMN for V. harveyi luciferase or reduced FMN for V. fischeri luciferase plus yellow fluorescent protein, the replacement of octanal by β-PAD again resulted in no additional 430-nm emission. The lack of any emission correlatable with excited α-PAC, β-PAC, or equivalent carbonyl product was not due to the quenching of the polyene moiety by chemical transformation, binding to luciferase, or a 100% energy transfer to the flavin 4a-hydroxide emitter. These results strongly favor singlet state of flavin 4a-hydroxide rather than singlet or triplet carbonyl product from aldehyde as the primary excited species in the normal luciferase reaction in the absence of any additional fluorescent protein.     

Squaraine Rotaxane as a Reversible Optical Chloride Sensor

A mechanically interlocked squaraine rotaxane is comprised of a deep‐red fluorescent squaraine dye inside a tetralactam macrocycle. NMR studies show that Cl^? binding to the rotaxane induces macrocycle translocation away from the central squaraine station, a process that is completely reversed when the Cl^? is removed from the solution. Steady‐state fluorescence and excited‐state lifetime measurements show that this reversible machine‐like motion modulates several technically useful optical properties, including a three‐fold increase in deep‐red fluorescence emission that is observable to the naked eye. The excited states were characterized quantitatively by time‐correlated single photon counting, femtosecond transient absorption spectroscopy, and nanosecond laser flash photolysis. Cl^? binding to the rotaxane increases the squaraine excited singlet state lifetime from 1.5 to 3.1 ns, and decreases the excited triplet state lifetime from >200 to 44 μs. Apparently, the surrounding macrocycle quenches the excited singlet state of the encapsulated squaraine dye and stabilizes the excited triplet state. Prototype dipsticks were prepared by adsorbing the lipophilic rotaxane onto the ends of narrow, C18‐coated, reverse‐phase silica gel plates. The fluorescence intensity of a dipstick increased eighteen‐fold upon dipping in an aqueous solution of tetrabutylammonium chloride (300 mM ) and was subsequently reversed by washing with pure water. It is possible to develop the dipsticks for colorimetric determination of Cl^? levels by the naked eye. After dipping into aqueous tetrabutylammonium chloride, a dipstick’s color slowly fades at a rate that depends on the amount of Cl^? in the aqueous solution. The fading process is due primarily to hydrolytic bleaching of the squaraine chromophore within the rotaxane. That is, association of Cl^? to immobilized rotaxane induces macrocycle translocation and exposure of the electrophilic C₄O₂ core of the squaraine station, which is in turn attacked by the ambient moisture to produce a bleached product.     

The Femtochemistry of a Ferracyclobutadiene

The eminent role of metallacyclobutadienes as catalytic intermediates in organic synthesis and polymer chemistry is widely acknowledged. In contrast, their photochemistry is as yet entirely unexplored. Herein, the photo‐induced primary processes of a ferracyclobutadiene tricarbonyl complex in solution are revealed by femtosecond mid‐infrared spectroscopy. The time‐resolved vibrational spectra expose an ultrafast substitution of a basal CO ligand by a solvent molecule in a consecutive dissociation–association mechanism. Following optical excitation, the system relaxes non‐radiatively to the triplet ground state from which a CO is expelled. Since the triplet state is bound with respect to Fe−CO cleavage, the dissociation can only occur from vibrationally excited states. The excitation energy, vibrational relaxation, and intersystem crossing to the singlet ground state control the primary quantum yield for formation of the ferracyclic dicarbonyl–solvent product complex.