The electronic structure of the flavin cofactor in DNA photolyase.

Density functional theory is used to calculate the electronic structure of the neutral flavin radical, FADH(*), formed in the light-induced electron-transfer reaction of DNA repair in cis,syn-cyclobutane pyrimidine dimer photolyases. Using the hybrid B3LYP functional together with the double-zeta basis set EPR-II, (1)H, (13)C, (15)N, and (17)O isotropic and anisotropic hyperfine couplings are calculated and explained by reference to the electron densities of the highest occupied molecular orbital and of the unpaired spin distribution on the radical. Comparison of calculated and experimental hyperfine couplings obtained from EPR and ENDOR/TRIPLE resonance leads to a refined structure for the FAD cofactor in Escherichia coli DNA photolyase. Hydrogen bonding at N3H, O4, and N5H results in significant changes in the unpaired spin density distribution and hyperfine coupling constants. The calculated electronic structure of FADH(*) provides evidence for a superexchange-mediated electron transfer between the cyclobutane pyrimidine dimer lesion and the 7,8-dimethyl isoalloxazine moiety of the flavin cofactor via the adenine moiety.     

Femtosecond dynamics of flavin cofactor in DNA photolyase: radical reduction, local solvation, and charge recombination

We report here our femtosecond studies of the photoreduction dynamics of the neutral radical flavin (FADH) cofactor in E. coli photolyase, a process converting the inactive form to the biologically active one, a fully reduced deprotonated flavin FADH(-). The observed temporal absorption evolution revealed two initial electron-transfer reactions, occurring in 11 and 42 ps with the neighboring aromatic residues of W382 and F366, respectively. The new transient absorption, observed at 550 nm previously in photolyase, was found from the excited-state neutral radical and is probably caused by strong interactions with the adenine moiety through the flavin U-shaped configuration and the highly polar/charged surrounding residues. The solvation dynamics from the locally ordered water molecules in the active site was observed to occur in approximately 2 ps. These ultrafast ordered-water motions are critical to stabilizing the photoreduction product FADH(-) instantaneously to prevent fast charge recombination. The back electron-transfer reaction was found to occur in approximately 3 ns. This slow process, consistent with ultrafast stabilization of the catalytic cofactor, favors photoreduction in photolyase.     

Ultrafast dynamics of resonance energy transfer in cryptochrome

In this communication, we report the ultrafast dynamics of resonance energy transfer in a blue-light photoreceptor, Vibrio cholerae cryptochrome. The transfer was observed to occur in 60 ps. We also studied the local rigidity and solvation around the binding site of the photoantenna molecule. The results for the first time show energy transfer in cryptochrome suggesting some mechanistic similarities between photolyase that repairs damaged DNA and cryptochrome that mediates blue-light signaling.     

Ultrafast dynamics of flavins in five redox states

We report here our systematic studies of excited-state dynamics of two common flavin molecules, FMN and FAD, in five redox states--oxidized form, neutral and anionic semiquinones, and neutral and anionic fully reduced hydroquinones--in solution and in inert protein environments with femtosecond resolution. Using protein environments, we were able to stabilize two semiquinone radicals and thus observed their weak emission spectra. Significantly, we observed a strong correlation between their excited-state dynamics and the planarity of their flavin isoalloxazine ring. For a bent ring structure, we observed ultrafast dynamics from a few to hundreds of picoseconds and strong excitation-wavelength dependence of emission spectra, indicating deactivation during relaxation. A butterfly bending motion is invoked to get access to conical intersection(s) to facilitate deactivation. These states include the anionic semiquinone radical and fully reduced neutral and anionic hydroquinones in solution. In a planar configuration, flavins have a long lifetime of nanoseconds, except for the stacked conformation of FAD, where intramolecular electron transfer between the ring and the adenine moiety in 5-9 ps as well as subsequent charge recombination in 30-40 ps were observed. These observed distinct dynamics, controlled by the flavin ring flexibility, are fundamental to flavoenzyme's functions, as observed in photolyase with a planar structure to lengthen the lifetime to maximize DNA repair efficiency and in insect type 1 cryptochrome with a flexible structure to vary the excited-state deactivation to modulate the functional channel.     

Ultrafast vibrational spectroscopy of the flavin chromophore

Ultrafast time-resolved infrared (TRIR) spectra of flavin adenine dinucleotide (FAD) and the anion of lumiflavin (Lf-) are described. Ground-state recovery and excited-state decay of FAD reveal a common dominant ultrafast relaxation and a minor slower component. The Lf- transient lacks a fast component. No intermediate species are observed, suggesting that the quenching mechanism is internal conversion promoted by interaction of the adenine and isoalloxazine rings in FAD. Modes are assigned, and the potential for extension of the TRIR method to photoactive proteins is discussed.     

Ultrafast relaxation dynamics of the excited states of Michler's thione

Ultrafast relaxation dynamics of the S2 and S1 states of 4,4'-bis(N,N-dimethylamino)thiobenzophenone (Michler's thione, MT) have been investigated in different kinds of solvents, using steady-state absorption and emission as well as femtosecond transient absorption and fluorescence up-conversion spectroscopic techniques. Steady-state fluorescence measurements, following photoexcitation to the S2 state of MT, reveal weak fluorescence from the S2 state (phi F approximately 10(-3) in nonpolar and 10(-4) in polar solvents) but much weaker fluorescence from the S1 state. Yield of fluorescence from the S2 state is reduced in polar solvents because of reduced energy gap between the S2 and S1 states, Delta E(S2-S1), as well as interaction with the solvent molecules. Occurrence of S2-fluorescence in polar solvents, despite small energy gap, suggests that symmetry allowed S2(1A1) --> S0 (1A1) radiative and symmetry forbidden S2(1A1) --> S1 (1A2) nonradiative transitions are the factors responsible for the S2 fluorescence in MT. Lifetime of the S2 state is shorter (varying in the range 0.28-3.5 ps in different solvents) than that predicted from the Delta E(S2-S1) value and this can be attributed to its flexible molecular structure, which promotes an efficient intramolecular radiationless deactivation pathways. The lifetime of the S1 state (approximately 1.9-6.5 ps) is also very short because of small energy difference between the S1 and T1 states (Delta E(S1-T1) approximately 300 cm(-1)) in cyclohexane and hydrogen-bonding interaction as well as the presence of the isoenergetic T1(pipi*) state to enhance the rate of the intersystem crossing process from the S1(npi*) state in protic solvents.     

Infrared spectrum and absorption coefficient of the cofactor flavin in water

Flavins play a key role as redox cofactors of enzymes involved in important metabolic processes. Moreover, they undergo photochemical reactions as chromophores in sensors of blue light or magnetic field in many organisms. The reaction mechanisms of flavoproteins have been investigated by infrared spectroscopy and theoretical studies. However, basic information on flavins in the infrared spectral range has been missing, such as absorption spectra in water and absorption coefficients. Here, the cofactors flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) were investigated in aqueous medium by Fourier transform infrared spectroscopy. Transmission and attenuated total reflection (ATR) configuration were employed in direct comparison. Absorption spectra in the range of 920–1800 cm⁻¹ were determined after accurate subtraction of the contributions from the water vibrations. The important carbonyl vibrations were resolved at 1661 and 1712 cm⁻¹. The absorption spectra may serve as a reference for theoretical and experimental studies on the effect of the microenvironment on the flavin cofactor. Furthermore, the molar absorption coefficient of FAD at 1547 cm⁻¹ was determined to 2200 L mol⁻¹ cm⁻¹ with an integral absorption coefficient of ∼50,000 L mol⁻¹ cm⁻². These values are prerequisite for the determination of reaction yields in flavoproteins from reaction-induced difference spectra.     

Ultrafast predissociation dynamics of water molecules excited to the electronic C and D states

Two-photon excitation with femtosecond laser pulses in the spectral range 240-250 nm was used to prepare vapor phase H(2)O and D(2)O in the C (1)B(1) and D (1)A(1) states. Both states are predissociated via the B (1)A(1) state, forming excited OH/OD(A (2)Sigma(+)) as well as ground state OH/OD(X (2)Pi). We used ultrashort infrared probe pulses (1.65-2.42 microm) to control the ratio between these excited and ground state fragments originating from the dissociation process. Time resolved detection of the OH/OD(A (2)Sigma(+)) --> OH/OD(X (2)Pi) fluorescence allows us to monitor the dynamics of the predissociation. For the heterogeneous predissociation out of the C(1)B(1) state life times of (0.5 +/- 0.1) ps and (1.2 +/- 0.1) ps were found for H(2)O and D(2)O, respectively. The purely homogeneous character of the predissociation out of the D (1)A(1) state was monitored.     

Ultrafast vibrational dynamics observed in higher electronic excited states of iodine using pump-UV DFWM spectroscopy

By using a combination of an initial pump pulse and a degenerate four-wave mixing process, we show that an interrogation of the vibrational dynamics occurring in different electronic states of molecules is possible. The technique is applied to iodine. The initial pump pulse is used to populate the B((3)Pi) state of molecular iodine in the gas phase. Now, by using an internal time delay in the DFWM process, which is resonant with the transition between the B state and a higher lying ion-pair state, the vibrational dynamics of the B state and the ion-pair state could be observed. States of even symmetry are investigated, which are accessed by a one photon transition from the B state. By a proper choice of the wavelengths used for the pump and DFWM beams, the dynamics of ion-pair states belonging to two different tiers are monitored.     

Time-resolved fluorescence analysis of the mobile flavin cofactor in p -hydroxybenzoate hydroxylase

Conformational heterogeneity of the FAD cofactor in p-hydroxybenzoate hydroxylase (PHBH) was investigated with time-resolved polarized flavin fluorescence. For binary enzyme/substrate (analogue) complexes of wild-type PHBH and Tyr222 mutants, crystallographic studies have revealed two distinct flavin conformations; the ‘in’ conformation with the isoalloxazine ring located in the active site, and the ‘out’ conformation with the isoalloxazine ring disposed towards the protein surface. Fluorescence-lifetime analysis of these complexes revealed similar lifetime distributions for the ‘in’ and ‘out’ conformations. The reason for this is twofold. First, the active site of PHBH contains various potential fluorescence-quenching sites close to the flavin. Fluorescence analysis of uncomplexed PHBH Y222V and Y222A showed that Tyr222 is responsible for picosecond fluorescence quenching free enzyme. In addition, other potential quenching sites, including a tryptophan and two tyrosines involved in substrate binding, are located nearby. Since the shortest distance between these quenching sites and the isoalloxazine ring differs only little on average, these aromatic residues are likely to contribute to fluorescence quenching. Second, the effect of flavin conformation on the fluorescence lifetime distribution is blurred by binding of the aromatic substrates: saturation with aromatic substrates induces highly efficient fluorescence quenching. The flavin conformation is therefore only reflected in the small relative contributions of the longer lifetimes.     

Ultrafast coherent dynamics of nonadiabatically coupled quasi-degenerate excited states in molecules: Population and vibrational coherence transfers

Results of a theoretical study of ultrafast coherent dynamics of nonadiabatically coupled quasi-degenerate π-electronic excited states of molecules were presented. Analytical expressions for temporal behaviors of population and vibrational coherence were derived using a simplified model to clarify the quantum mechanical interferences between the two coherently excited electronic states, which appeared in the nuclear wavepacket simulations [M. Kanno, H. Kono, Y. Fujimura, S.H. Lin, Phys. Rev. Lett 104 (2010) 108302]. The photon-polarization direction of the linearly polarized laser, which controls the populations of the two quasi-degenerate electronic states, determines constructive or destructive interference. Features of the vibrational coherence transfer between the two coupled quasi-electronic states through nonadiabatic couplings are also presented. Information on both the transition frequency and nonadiabatic coupling matrix element between the two states can be obtained by analyzing signals of two kinds of quantum beats before and after transfer through nonadiabatic coupling.     

Ultrafast dynamics of UV-excited imidazole

The ultrafast dynamics of UV-excited imidazole in the gas phase is investigated by theoretical nonadiabatic dynamics simulations and experimental time-resolved photoelectron spectroscopy. The results show that different electronic excited-state relaxation mechanisms occur, depending on the pump wavelength. When imidazole is excited at 239.6 nm, deactivation through the NH-dissociation conical intersection is observed on the sub-50 fs timescale. After 200.8 nm excitation, competition between NH-dissociation and NH-puckering conical intersections is observed. The NH-dissociation to NH-puckering branching ratio is predicted to be 21:4, and the total relaxation time is elongated by a factor of eight. A procedure for simulation of photoelectron spectra based on dynamics results is developed and employed to assign different features in the experimental spectra.     

Ultrafast dynamics of isolated fluorenone

The ultrafast dynamics of isolated 9-fluorenone was studied by femtosecond time-resolved photoionization and photoelectron spectroscopy. The molecule was excited around 264-266 nm into the S(6) state. The experimental results indicate that the excitation is followed by a multistep deactivation. A time constant of 50 fs or less corresponds to a fast redistribution of energy within the initially excited manifold of states, i.e., a motion away from the Franck-Condon region. Internal conversion to the S(1) state then proceeds within 0.4 ps. The S(1) state is long-lived, and only a lower bound of 20 ps can be derived. In addition, we computed excited state energies and oscillator strengths by TD-DFT theory, supporting the interpretation of the experimental data.     

Ultrafast dynamics of water in cationic micelles

The effect of confinement on the dynamical properties of liquid water is investigated for water enclosed in cationic reverse micelles. The authors performed mid-infrared ultrafast pump-probe spectroscopy on the OH-stretch vibration of isotopically diluted HDO in D(2)O in cetyltrimethylammonium bromide (CTAB) reverse micelles of various sizes. The authors observe that the surfactant counterions are inhomogeneously distributed throughout the reverse micelle, and that regions of extreme salinity occur near the interfacial Stern layer. The authors find that the water molecules in the core of the micelles show similar orientational dynamics as bulk water, and that water molecules in the counterion-rich interfacial region are much less mobile. An explicit comparison is made with the dynamics of water confined in anionic sodium bis(2-ethythexyl) sulfosuccinate (AOT) reverse micelles. The authors find that interfacial water in cationic CTAB reverse micelles has a higher orientational mobility than water in anionic AOT reverse micelles.     

Ultrafast dynamics of a spiropyran in water

The reversible switching of a water-soluble spiropyran compound is recorded over 1 ns by means of femtosecond vis-pump/vis- and IR-probe spectroscopy under aqueous conditions. Our investigations reveal that the photochemical conversion from the closed spiropyran to the open merocyanine takes 1.6 ps whereas the reversed photoreaction is accomplished within 25 ps. The combination of time-resolved and steady-state observations allows us to reveal central parts of the reaction pathway leading to either form. The enhanced water solubility, its fast and efficient switching behavior, and its stability against hydrolysis over a time range of several weeks make this compound an attractive and versatile tool for biological applications.     

Ultrafast twisting dynamics in the excited state of auramine

Relaxation dynamics of the excited state of bis-[4-(dimethylamino)-phenyl] methaniminium chloride (Auramine) has been investigated using subpicosecond time-resolved absorption spectroscopic technique in both aprotic and alcoholic solvents. The locally excited (LE) state, formed following photoexcitation of Auramine using 400 nm light, undergoes intramolecular charge transfer (ICT) process, which is accompanied by the twisting of the dimethylanilino groups. Time evolution of the transient absorption-stimulated emission spectra as well as the wavelength dependence of the temporal dynamics investigated in each kind of solvents suggest that the relaxation process proceeds via the formation of at least two transient states (TS I and TS II), which are geometrical conformers and consecutively formed following the decay of the LE state. Twisting of the dimethylaniline groups are nearly barrierless processes, the rates of which show linear correlation both with the macroscopic or shear viscosities as well as the solvation times of the solvents. Time-dependent and fractional viscosity dependence of the relaxation rates of the LE and the TS I states in aprotic solvents suggest the multidimensionality of the reaction coordinate as well as reveal the viscoelastic property of the solvents. However, in normal alcohols, in addition to these two factors, activation energy of the solvent viscosity may be another important factor for the slower twisting dynamics of Auramine in alcohols. To explain the viscosity dependence of the decay time of the TS II state, which undergoes an efficient internal conversion process to the ground state, the possibility of occurrence of different mechanisms, such as, energy gap law, involvement of intramolecular high frequency modes, as well as the phenyl group twisting motion on a potential energy surface having a photochemical funnel, have been discussed. TDDFT method has been applied to obtain the optimized electronic structures of the transient states but it has been possible to obtain only that for the TS II state.     

Ultrafast dynamics in excited ammonia dimers and trimers

Ammonia dimers and trimers are studied in a femtosecond pump probe experiment. The pump laser (6.2 eV) excites the cluster into the à state which is ionized either by 4.6 eV or by 3.1 eV probe photons. Characteristic differences are explained in terms of a kinetic model involving an internal protonated neutral excited state as an intermediate.     

Ultrafast energy transfer and structural dynamics in DNA

Ultrafast structural dynamics concomitant to excitation energy transfer in DNA has been studied using a pair of pyrene-labeled DNA bases. The temporal evolution of the femtosecond pump-probe spectra reveals the existence of two electronic coupling pathways, through-base stack and through-space, which lead to excitation energy transfer and excimer formation even when the labeled DNA bases are separated by one AT base pair. The electronic coupling which mediates through-base stack energy transfer is so strong that a new absorption band arises in the excited-state absorption spectrum within 300 fs. From the analysis of time-dependent spectral shifts due to through-space excimer formation, the local structural dynamics and flexibility of DNA are characterized on the picosecond and nanosecond time scale.