Mariangela Di Donato | Università degli Studi di Firenze (University of Florence) (original) (raw)
Papers by Mariangela Di Donato
The Journal of Physical Chemistry B, 2004
The mechanism of electron transfer (ET) from the primary to the secondary quinone of bacterial ph... more The mechanism of electron transfer (ET) from the primary to the secondary quinone of bacterial photosynthetic reaction centers is discussed on the basis of theoretical computations of the minimum energy nuclear configurations and ET coupling elements, and quantum dynamic simulations of elementary reaction steps. For ET to occur via tunneling, unreasonably high values of the electronic coupling elements or very stringent energy conditions, i.e., tight degeneracy (within a few cm -1 ) between the initial and final vibronic states, are necessary, both for the direct and through-bridge (superexchange) routes. The assumption of tight degeneracy significantly slows down the process so that other competitive processes, such as proton transfer from the H-bonded HisM219 to the primary quinone, can take place. All these results suggest that the iron-histidine bridge can play an important role in the ET mechanism.
Physical Chemistry Chemical Physics, 2014
In this work we present the synthesis, time-resolved spectroscopic characterization and computati... more In this work we present the synthesis, time-resolved spectroscopic characterization and computational analysis of a bichromophore composed of two very well-known naturally occurring dyes: 7-hydroxycoumarin (umbelliferone) and 1,2-dihydroxyanthraquinone (alizarin). The umbelliferone donor (Dn) and alizarin acceptor (Ac) moieties are linked to a triazole ring viaσ bonds, providing a flexible structure. By measuring the fluorescence quantum yields and the ultrafast transient absorption spectra we demonstrate the high efficiency (∼85%) and the fast nature (∼1.5 ps) of the energy transfer in this compound. Quantum chemical calculations, within the density functional theory (DFT) approach, are used to characterize the electronic structure of the bichromophore (Bi) in the ground and excited states. We simulate the absorption and fluorescence spectra using the TD-DFT methods and the vertical gradient approach (VG), and include the solvent effects by adopting the conductor-like polarizable continuum model (CPCM). The calculated electronic structure suggests the occurrence of weak interactions between the electron densities of Dn and Ac in the excited state, indicating that the Förster-type transfer is the appropriate model for describing the energy transfer in this system. The average distance between Dn and Ac moieties calculated from the conformational analysis (12 Å) is in very good agreement with the value estimated from the Förster equation (∼11 Å). At the same time, the calculated rate constant for energy transfer, averaged over multiple conformations of the system (3.6 ps), is in reasonable agreement with the experimental value (1.6 ps) estimated by transient absorption spectroscopy. The agreement between experimental results and computational data leads us to conclude that the energy transfer in Bi is well described by the Förster mechanism.
Physical Chemistry Chemical Physics, 2014
In this work we present the synthesis, time-resolved spectroscopic characterization and computati... more In this work we present the synthesis, time-resolved spectroscopic characterization and computational analysis of a bichromophore composed of two very well-known naturally occurring dyes: 7-hydroxycoumarin (umbelliferone) and 1,2-dihydroxyanthraquinone (alizarin). The umbelliferone donor (Dn) and alizarin acceptor (Ac) moieties are linked to a triazole ring viaσ bonds, providing a flexible structure. By measuring the fluorescence quantum yields and the ultrafast transient absorption spectra we demonstrate the high efficiency (∼85%) and the fast nature (∼1.5 ps) of the energy transfer in this compound. Quantum chemical calculations, within the density functional theory (DFT) approach, are used to characterize the electronic structure of the bichromophore (Bi) in the ground and excited states. We simulate the absorption and fluorescence spectra using the TD-DFT methods and the vertical gradient approach (VG), and include the solvent effects by adopting the conductor-like polarizable continuum model (CPCM). The calculated electronic structure suggests the occurrence of weak interactions between the electron densities of Dn and Ac in the excited state, indicating that the Förster-type transfer is the appropriate model for describing the energy transfer in this system. The average distance between Dn and Ac moieties calculated from the conformational analysis (12 Å) is in very good agreement with the value estimated from the Förster equation (∼11 Å). At the same time, the calculated rate constant for energy transfer, averaged over multiple conformations of the system (3.6 ps), is in reasonable agreement with the experimental value (1.6 ps) estimated by transient absorption spectroscopy. The agreement between experimental results and computational data leads us to conclude that the energy transfer in Bi is well described by the Förster mechanism.
The Journal of Physical Chemistry B, 2013
In this work, we studied the valence tautomerism process on two different Co-dioxolene complexes ... more In this work, we studied the valence tautomerism process on two different Co-dioxolene complexes by means of transient infrared spectroscopy (TRIR). The molecules investigated are ls-Co(III)(Cat-N-BQ)(Cat-N-SQ) (DQ2) and [ls-Co(III)(tpy)(Cat-N-SQ)]PF6 (tpy), where Cat-NBQ = 2-(2-hydroxy-3,5-ditert-butylphenyl-imino)-4,6-ditert-butylcyclohexa-3,5-dienone, Cat-N-SQ is the dianionic radical analogue, and tpy = 2,2'-6-2″-terpyridine. DFT calculations of the harmonic frequencies for the two complexes allow us to pinpoint the normal modes to be used as markers of the semiquinonate and benzoquinonate isomers. The photoinduced one-electron charge transfer process from the radical semiquinonate ligand to the metal center leads to a ls-Co(II)(x)(Cat-N-BQ) electronic state (where x is the other ligand). Following this first step, an ultrafast ISC process (τ < 200 fs) takes places, yielding the benzoquinonate isomer (hs-Co(II)(x)(Cat-N-BQ)). In the experiments, we employed different excitation wavelengths on resonance with different absorption bands of the two samples. Excitation in the ligand-to-metal charge transfer (LMCT) band at ∼520 nm and in the semiquinonate band at ∼1000 nm induces the valence tautomerism (VT) in both samples. From the time evolution of the TRIR spectra, we determine the time constants of the vibrational cooling in the tautomeric state (7-14 ps) and the ground state recovery times (∼350 ps for tpy and ∼450 ps for DQ2). In contrast, when the pump frequency is set at 712 nm, on resonance with the benzoquinonate absorption band of the second active ligand of the DQ2, no electron transfer takes place: the TRIR spectra basically show only ground state bleaching bands and no marker band of the tautomeric conversion shows up.
Physical Chemistry Chemical Physics, 2014
In this work we present the synthesis, time-resolved spectroscopic characterization and computati... more In this work we present the synthesis, time-resolved spectroscopic characterization and computational analysis of a bichromophore composed of two very well-known naturally occurring dyes: 7-hydroxycoumarin (umbelliferone) and 1,2-dihydroxyanthraquinone (alizarin). The umbelliferone donor (Dn) and alizarin acceptor (Ac) moieties are linked to a triazole ring viaσ bonds, providing a flexible structure. By measuring the fluorescence quantum yields and the ultrafast transient absorption spectra we demonstrate the high efficiency (∼85%) and the fast nature (∼1.5 ps) of the energy transfer in this compound. Quantum chemical calculations, within the density functional theory (DFT) approach, are used to characterize the electronic structure of the bichromophore (Bi) in the ground and excited states. We simulate the absorption and fluorescence spectra using the TD-DFT methods and the vertical gradient approach (VG), and include the solvent effects by adopting the conductor-like polarizable continuum model (CPCM). The calculated electronic structure suggests the occurrence of weak interactions between the electron densities of Dn and Ac in the excited state, indicating that the Förster-type transfer is the appropriate model for describing the energy transfer in this system. The average distance between Dn and Ac moieties calculated from the conformational analysis (12 Å) is in very good agreement with the value estimated from the Förster equation (∼11 Å). At the same time, the calculated rate constant for energy transfer, averaged over multiple conformations of the system (3.6 ps), is in reasonable agreement with the experimental value (1.6 ps) estimated by transient absorption spectroscopy. The agreement between experimental results and computational data leads us to conclude that the energy transfer in Bi is well described by the Förster mechanism.
The Journal of Chemical Physics, 2015
By means of one- and two-dimensional transient infrared spectroscopy and femtosecond stimulated R... more By means of one- and two-dimensional transient infrared spectroscopy and femtosecond stimulated Raman spectroscopy, we investigated the excited state dynamics of peridinin, a carbonyl carotenoid occurring in natural light harvesting complexes. The presence of singly and doubly excited states, as well as of an intramolecular charge transfer (ICT) state, makes the behavior of carbonyl carotenoids in the excited state very complex. In this work, we investigated by time resolved spectroscopy the relaxation of photo-excited peridinin in solvents of different polarities and as a function of the excitation wavelength. Our experimental results show that a characteristic pattern of one- and two-dimensional infrared bands in the C=C stretching region allows monitoring the relaxation pathway. In polar solvents, moderate distortions of the molecular geometry cause a variation of the single/double carbon bond character, so that the partially ionic ICT state is largely stabilized by the solvent reorganization. After vertical photoexcitation at 400 nm of the S2 state, the off-equilibrium population moves to the S1 state with ca. 175 fs time constant; from there, in less than 5 ps, the non-Franck Condon ICT state is reached, and finally, the ground state is recovered in 70 ps. That the relevant excited state dynamics takes place far from the Franck Condon region is demonstrated by its noticeable dependence on the excitation wavelength.
Biochimica et biophysica acta, 2015
In recent years visible pump/mid-infrared (IR) probe spectroscopy has established itself as a key... more In recent years visible pump/mid-infrared (IR) probe spectroscopy has established itself as a key technology to unravel structure-function relationships underlying the photo-dynamics of complex molecular systems. In this contribution we review the most important applications of mid-infrared absorption difference spectroscopy with sub-picosecond time-resolution to photosynthetic complexes. Considering several examples, such as energy transfer in photosynthetic antennas and electron transfer in reaction centers and even more intact structures, we show that the acquisition of ultrafast time resolved mid-IR spectra has led to new insights into the photo-dynamics of the considered systems and allows establishing a direct link between dynamics and structure, further strengthened by the possibility of investigating the protein response signal to the energy or electron transfer processes. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
The journal of physical chemistry. B, Jan 28, 2007
Excitation energy transfer in the Photosystem II core antenna complex CP43 has been investigated ... more Excitation energy transfer in the Photosystem II core antenna complex CP43 has been investigated by vis/vis and vis/mid-IR pump-probe spectroscopy with the aim of understanding the relation between the dynamics of energy transfer and the structural arrangement of individual chlorophyll molecules within the protein. Energy transfer was found to occur on time scales of 250 fs, 2-4 ps, and 10-12 ps. The vis/mid-IR difference spectra show that the excitation is initially distributed over chlorophylls located in environments with different polarity, since two 9-keto C=O stretching bleachings, at 1691 and 1677 cm-1, are observable at early delay times. Positive signals in the initial difference spectra around 1750 and 1720 cm-1 indicate the presence of a charge transfer state between strongly interacting chlorophylls. We conclude, both from the spectral behavior in the visible when the annihilation processes are increased and from the vis/mid-IR data, that there are two pigments (one abso...
The Journal of Physical Chemistry B, 2014
Carbon monoxide recombination dynamics in a mutant of the truncated hemoglobin from Thermobida f ... more Carbon monoxide recombination dynamics in a mutant of the truncated hemoglobin from Thermobida f usca (3F-Tf-trHb) has been analyzed by means of ultrafast Visible-pump/MidIR-probe spectroscopy and compared with that of the wildtype protein. In 3F-Tf-trHb, three topologically relevant amino acids, responsible for the ligand stabilization through the formation of a H-bond network (TyrB10 TyrCD1 and TrpG8), have been replaced by Phe residues. X-ray diffraction data show that Phe residues in positions B10 and G8 maintain the same rotameric arrangements as Tyr and Trp in the wild-type protein, while Phe in position CD1 displays significant rotameric heterogeneity. Photodissociation of the ligand has been induced by exciting the sample with 550 nm pump pulses and the CO rebinding has been monitored in two mid-IR regions respectively corresponding to the ν(CO) stretching vibration of the iron-bound CO (1880−1980 cm −1 ) and of the dissociated free CO (2050−2200 cm −1 ). In both the mutant and wild-type protein, a significant amount of geminate CO rebinding is observed on a subnanosecond time scale. Despite the absence of the distal pocket hydrogen-bonding network, the kinetics of geminate rebinding in 3F-Tf-trHb is very similar to the wild-type, showing how the reactivity of dissociated CO toward the heme is primarily regulated by the effective volume and flexibility of the distal pocket and by caging effects exerted on the free CO on the analyzed time scale.
The Journal of Chemical Physics, 2014
We have studied the effect of transient vibrational inversion of population in trans-β-apo-8(&... more We have studied the effect of transient vibrational inversion of population in trans-β-apo-8(')-carotenal on the time-resolved femtosecond stimulated Raman scattering (TR-FSRS) signal. The experimental data are interpreted by applying a quantum mechanical approach, using the formalism of projection operators for constructing the theoretical model of TR-FSRS. Within this theoretical frame we explain the presence of transient Raman losses on the Stokes side of the TR-FSRS spectrum as the effect of vibrational inversion of population. In view of the obtained experimental and theoretical results, we conclude that the excited S2 electronic level of trans-β-apo-8(')-carotenal relaxes towards the S0 ground state through a set of four vibrational sublevels of S1 state.
The Journal of Physical Chemistry B, 2012
Carbon monoxide recombination dynamics upon photodissociation with visible light has been charact... more Carbon monoxide recombination dynamics upon photodissociation with visible light has been characterized by means of ultrafast visible-pump/MidIR probe spectroscopy for the truncated hemoglobins from Thermobif ida f usca and Bacillus subtilis. Photodissociation has been induced by exciting the sample at two different wavelengths: 400 nm, corresponding to the heme absorption in the B-band, and 550 nm, in the Q-bands. The bleached iron−CO coordination band located at 1850−1950 cm −1 and the free CO absorption band in the region 2050−2200 cm −1 have been observed by probe pulses tuned in the appropriate infrared region. The kinetic traces measured at 1850−1950 cm −1 reveal multiexponential subnanosecond dynamics that have been interpreted as arising from fast geminate recombination of the photolyzed CO. A compared analysis of the crystal structure of the two proteins reveals a similar structure of their distal heme pocket, which contains conserved polar and aromatic amino acid residues closely interacting with the iron ligand. Although fast geminate recombination is observed in both proteins, several kinetic differences can be evidenced, which can be interpreted in terms of a different structural flexibility of the corresponding heme distal pockets. The analysis of the free CO band-shape and of its dynamic evolution brings out novel features about the nature of the docking site inside the protein cavity.
The Journal of Physical Chemistry B, 2004
ABSTRACT The mechanism of electron transfer (ET) from the primary to the secondary quinone of bac... more ABSTRACT The mechanism of electron transfer (ET) from the primary to the secondary quinone of bacterial photosynthetic reaction centers is discussed on the basis of theoretical computations of the minimum energy nuclear configurations and ET coupling elements, and quantum dynamic simulations of elementary reaction steps. For ET to occur via tunneling, unreasonably high values of the electronic coupling elements or very stringent energy conditions, i.e., tight degeneracy (within a few cm-1) between the initial and final vibronic states, are necessary, both for the direct and through-bridge (superexchange) routes. The assumption of tight degeneracy significantly slows down the process so that other competitive processes, such as proton transfer from the H-bonded HisM219 to the primary quinone, can take place. All these results suggest that the iron−histidine bridge can play an important role in the ET mechanism.
Journal of Theoretical Biology, 2000
The mechanism of long-range electron transfer between the primary and the secondary quinone of ph... more The mechanism of long-range electron transfer between the primary and the secondary quinone of photosynthetic reaction centers has been investigated, with particular attention on the role of the iron-histidine bridge. Computations suggest that in such a system, where the molecular subunits are packed together by H-bonds, a mobile electron, injected on one end of the chain, can be carried to the other end by switching the positions of the H-bonded hydrogens. Energy estimates would suggest that the proposed mechanism is plausible and worthy of further experimental investigations.
Journal of Chemical Theory and Computation, 2007
Chemical Physics Letters, 2005
Intramolecular reorganization energies and Franck-Condon integrals of two redox cofactors of bact... more Intramolecular reorganization energies and Franck-Condon integrals of two redox cofactors of bacterial photosynthetic reaction centers have been evaluated by DFT computations of the optimum geometries and vibrational frequencies of the normal and reduced forms. The intramolecular modes which play a major role in electron transfer dynamics have been identified by Duschin-skyÕs analysis and the Franck-Condon integrals have been computed by using the whole set of normal coordinates of the acceptor and donor groups, in order to reliably account both for shifts, mix, and frequency change of the normal coordinates.
Chemical Physics Letters, 2003
The role of the iron-histidine bridge in bacterial photosynthetic reaction centres has been inves... more The role of the iron-histidine bridge in bacterial photosynthetic reaction centres has been investigated by means of ab initio computations and quantum dynamics of elementary reaction steps. Full geometry optimization and wave packet dynamics show that, upon the arrival of a photo-electron, the primary quinone takes up a proton from the H-bonded histidine in a very fast process, which occurs in a few tens of femtoseconds. The proton transfer step significantly stabilizes the charge separated state, inhibiting the backward charge recombination process. Electron transfer to the secondary quinone can then take place by switching the positions of both the H-bonded hydrogens, in a Bjerrium type mechanism involving whole hydrogen atoms rather than protons.
Biophysical Journal, 2008
It is now quite well accepted that charge separation in PS2 reaction centers starts predominantly... more It is now quite well accepted that charge separation in PS2 reaction centers starts predominantly from the accessory chlorophyll B A and not from the special pair P 680 . To identify spectral signatures of B A, and to further clarify the process of primary charge separation, we compared the femtosecond-infrared pump-probe spectra of the wild-type (WT) PS2 core complex from the cyanobacterium Synechocystis sp. PCC 6803 with those of two mutants in which the histidine residue axially coordinated to P B (D2-His 197 ) has been changed to Ala or Gln. By analogy with the structure of purple bacterial reaction centers, the mutated histidine is proposed to be indirectly H-bonded to the C 9 ¼O carbonyl of the putative primary donor B A through a water molecule. The constructed mutations are thus expected to perturb the vibrational properties of B A by modifying the hydrogen bond strength, possibly by displacing the H-bonded water molecule, and to modify the electronic properties and the charge localization of the oxidized donor P 1 680 : Analysis of steady-state light-induced Fourier transform infrared difference spectra of the WT and the D2-His 197 Ala mutant indeed shows that a modification of the axially coordinating ligand to P B induces a charge redistribution of P 1 680 : In addition, a comparison of the time-resolved visible/midinfrared spectra of the WT and mutants has allowed us to investigate the changes in the kinetics of primary charge separation induced by the mutations and to propose a band assignment identifying the characteristic vibrations of B A.
Biophysical Journal, 2009
Light harvesting complex II (LHCII) is the most abundant protein in the thylakoid membrane of hig... more Light harvesting complex II (LHCII) is the most abundant protein in the thylakoid membrane of higher plants and green algae. LHCII acts to collect solar radiation, transferring this energy mainly toward photosystem II, with a smaller amount going to photosystem I; it is then converted into a chemical, storable form. We performed time-resolved femtosecond visible pump/mid-infrared probe and visible pump/visible probe absorption difference spectroscopy on purified LHCII to gain insight into the energy transfer in this complex occurring in the femto-picosecond time regime. We find that information derived from mid-infrared spectra, together with structural and modeling information, provides a unique visualization of the flow of energy via the bottleneck pigment chlorophyll a604.
Phys. Chem. Chem. Phys., 2015
We have analyzed the excited state dynamics of the heteroleptic [(NCS)2Ru(bpy-(COOH)2)(bpy-(C6H13... more We have analyzed the excited state dynamics of the heteroleptic [(NCS)2Ru(bpy-(COOH)2)(bpy-(C6H13)2)] Z907 solar cell sensitizer in solution and when adsorbed onto thin TiO2 films, by combining transient visible and infrared (IR) spectroscopies with ab initio Density Functional Theory (DFT) and Time-Dependent DFT (TDDFT) calculations. Upon excitation with ultra-short pulses in ethanol and dimethyl-sulphoxide solutions, the visible spectra show the appearance of a positive signal around 650 nm, within the instrumental time resolution (<100 fs), which in ethanol undergoes a red-shift in about 20 ps. Measurements in the IR indicate that, upon excitation, both the CN and CO marker bands, associated with the NCS and COOH groups, downshift in frequency, in response to intramolecular ligand + metal (Ru-NCS) to ligand' (bpy-COOH2) charge transfer (LML'CT). Vibrational cooling is observed in both solvents; in ethanol it is overtaken by the hydrogen bond dynamics. On the basis of DFT/TDDFT calculations, explicitly modeling the interaction of the NCS and COOH groups with solvent (ethanol) molecules, we rationalize the observed IR and visible spectral evolution as arising from the change in the hydrogen-bond network, which accompanies the transition to the lowest-energy triplet state. This interpretation provides a consistent explanation of what is also observed in the transient visible spectra. Transient IR measurements repeated for molecules adsorbed on TiO2 and ZrO2 films, allow us to identify the structural changes signaling the dye triplet excited state formation and evidence multiexponential electron injection rates into the semiconductor TiO2 film.
The Journal of Physical Chemistry B, 2004
The mechanism of electron transfer (ET) from the primary to the secondary quinone of bacterial ph... more The mechanism of electron transfer (ET) from the primary to the secondary quinone of bacterial photosynthetic reaction centers is discussed on the basis of theoretical computations of the minimum energy nuclear configurations and ET coupling elements, and quantum dynamic simulations of elementary reaction steps. For ET to occur via tunneling, unreasonably high values of the electronic coupling elements or very stringent energy conditions, i.e., tight degeneracy (within a few cm -1 ) between the initial and final vibronic states, are necessary, both for the direct and through-bridge (superexchange) routes. The assumption of tight degeneracy significantly slows down the process so that other competitive processes, such as proton transfer from the H-bonded HisM219 to the primary quinone, can take place. All these results suggest that the iron-histidine bridge can play an important role in the ET mechanism.
Physical Chemistry Chemical Physics, 2014
In this work we present the synthesis, time-resolved spectroscopic characterization and computati... more In this work we present the synthesis, time-resolved spectroscopic characterization and computational analysis of a bichromophore composed of two very well-known naturally occurring dyes: 7-hydroxycoumarin (umbelliferone) and 1,2-dihydroxyanthraquinone (alizarin). The umbelliferone donor (Dn) and alizarin acceptor (Ac) moieties are linked to a triazole ring viaσ bonds, providing a flexible structure. By measuring the fluorescence quantum yields and the ultrafast transient absorption spectra we demonstrate the high efficiency (∼85%) and the fast nature (∼1.5 ps) of the energy transfer in this compound. Quantum chemical calculations, within the density functional theory (DFT) approach, are used to characterize the electronic structure of the bichromophore (Bi) in the ground and excited states. We simulate the absorption and fluorescence spectra using the TD-DFT methods and the vertical gradient approach (VG), and include the solvent effects by adopting the conductor-like polarizable continuum model (CPCM). The calculated electronic structure suggests the occurrence of weak interactions between the electron densities of Dn and Ac in the excited state, indicating that the Förster-type transfer is the appropriate model for describing the energy transfer in this system. The average distance between Dn and Ac moieties calculated from the conformational analysis (12 Å) is in very good agreement with the value estimated from the Förster equation (∼11 Å). At the same time, the calculated rate constant for energy transfer, averaged over multiple conformations of the system (3.6 ps), is in reasonable agreement with the experimental value (1.6 ps) estimated by transient absorption spectroscopy. The agreement between experimental results and computational data leads us to conclude that the energy transfer in Bi is well described by the Förster mechanism.
Physical Chemistry Chemical Physics, 2014
In this work we present the synthesis, time-resolved spectroscopic characterization and computati... more In this work we present the synthesis, time-resolved spectroscopic characterization and computational analysis of a bichromophore composed of two very well-known naturally occurring dyes: 7-hydroxycoumarin (umbelliferone) and 1,2-dihydroxyanthraquinone (alizarin). The umbelliferone donor (Dn) and alizarin acceptor (Ac) moieties are linked to a triazole ring viaσ bonds, providing a flexible structure. By measuring the fluorescence quantum yields and the ultrafast transient absorption spectra we demonstrate the high efficiency (∼85%) and the fast nature (∼1.5 ps) of the energy transfer in this compound. Quantum chemical calculations, within the density functional theory (DFT) approach, are used to characterize the electronic structure of the bichromophore (Bi) in the ground and excited states. We simulate the absorption and fluorescence spectra using the TD-DFT methods and the vertical gradient approach (VG), and include the solvent effects by adopting the conductor-like polarizable continuum model (CPCM). The calculated electronic structure suggests the occurrence of weak interactions between the electron densities of Dn and Ac in the excited state, indicating that the Förster-type transfer is the appropriate model for describing the energy transfer in this system. The average distance between Dn and Ac moieties calculated from the conformational analysis (12 Å) is in very good agreement with the value estimated from the Förster equation (∼11 Å). At the same time, the calculated rate constant for energy transfer, averaged over multiple conformations of the system (3.6 ps), is in reasonable agreement with the experimental value (1.6 ps) estimated by transient absorption spectroscopy. The agreement between experimental results and computational data leads us to conclude that the energy transfer in Bi is well described by the Förster mechanism.
The Journal of Physical Chemistry B, 2013
In this work, we studied the valence tautomerism process on two different Co-dioxolene complexes ... more In this work, we studied the valence tautomerism process on two different Co-dioxolene complexes by means of transient infrared spectroscopy (TRIR). The molecules investigated are ls-Co(III)(Cat-N-BQ)(Cat-N-SQ) (DQ2) and [ls-Co(III)(tpy)(Cat-N-SQ)]PF6 (tpy), where Cat-NBQ = 2-(2-hydroxy-3,5-ditert-butylphenyl-imino)-4,6-ditert-butylcyclohexa-3,5-dienone, Cat-N-SQ is the dianionic radical analogue, and tpy = 2,2'-6-2″-terpyridine. DFT calculations of the harmonic frequencies for the two complexes allow us to pinpoint the normal modes to be used as markers of the semiquinonate and benzoquinonate isomers. The photoinduced one-electron charge transfer process from the radical semiquinonate ligand to the metal center leads to a ls-Co(II)(x)(Cat-N-BQ) electronic state (where x is the other ligand). Following this first step, an ultrafast ISC process (τ < 200 fs) takes places, yielding the benzoquinonate isomer (hs-Co(II)(x)(Cat-N-BQ)). In the experiments, we employed different excitation wavelengths on resonance with different absorption bands of the two samples. Excitation in the ligand-to-metal charge transfer (LMCT) band at ∼520 nm and in the semiquinonate band at ∼1000 nm induces the valence tautomerism (VT) in both samples. From the time evolution of the TRIR spectra, we determine the time constants of the vibrational cooling in the tautomeric state (7-14 ps) and the ground state recovery times (∼350 ps for tpy and ∼450 ps for DQ2). In contrast, when the pump frequency is set at 712 nm, on resonance with the benzoquinonate absorption band of the second active ligand of the DQ2, no electron transfer takes place: the TRIR spectra basically show only ground state bleaching bands and no marker band of the tautomeric conversion shows up.
Physical Chemistry Chemical Physics, 2014
In this work we present the synthesis, time-resolved spectroscopic characterization and computati... more In this work we present the synthesis, time-resolved spectroscopic characterization and computational analysis of a bichromophore composed of two very well-known naturally occurring dyes: 7-hydroxycoumarin (umbelliferone) and 1,2-dihydroxyanthraquinone (alizarin). The umbelliferone donor (Dn) and alizarin acceptor (Ac) moieties are linked to a triazole ring viaσ bonds, providing a flexible structure. By measuring the fluorescence quantum yields and the ultrafast transient absorption spectra we demonstrate the high efficiency (∼85%) and the fast nature (∼1.5 ps) of the energy transfer in this compound. Quantum chemical calculations, within the density functional theory (DFT) approach, are used to characterize the electronic structure of the bichromophore (Bi) in the ground and excited states. We simulate the absorption and fluorescence spectra using the TD-DFT methods and the vertical gradient approach (VG), and include the solvent effects by adopting the conductor-like polarizable continuum model (CPCM). The calculated electronic structure suggests the occurrence of weak interactions between the electron densities of Dn and Ac in the excited state, indicating that the Förster-type transfer is the appropriate model for describing the energy transfer in this system. The average distance between Dn and Ac moieties calculated from the conformational analysis (12 Å) is in very good agreement with the value estimated from the Förster equation (∼11 Å). At the same time, the calculated rate constant for energy transfer, averaged over multiple conformations of the system (3.6 ps), is in reasonable agreement with the experimental value (1.6 ps) estimated by transient absorption spectroscopy. The agreement between experimental results and computational data leads us to conclude that the energy transfer in Bi is well described by the Förster mechanism.
The Journal of Chemical Physics, 2015
By means of one- and two-dimensional transient infrared spectroscopy and femtosecond stimulated R... more By means of one- and two-dimensional transient infrared spectroscopy and femtosecond stimulated Raman spectroscopy, we investigated the excited state dynamics of peridinin, a carbonyl carotenoid occurring in natural light harvesting complexes. The presence of singly and doubly excited states, as well as of an intramolecular charge transfer (ICT) state, makes the behavior of carbonyl carotenoids in the excited state very complex. In this work, we investigated by time resolved spectroscopy the relaxation of photo-excited peridinin in solvents of different polarities and as a function of the excitation wavelength. Our experimental results show that a characteristic pattern of one- and two-dimensional infrared bands in the C=C stretching region allows monitoring the relaxation pathway. In polar solvents, moderate distortions of the molecular geometry cause a variation of the single/double carbon bond character, so that the partially ionic ICT state is largely stabilized by the solvent reorganization. After vertical photoexcitation at 400 nm of the S2 state, the off-equilibrium population moves to the S1 state with ca. 175 fs time constant; from there, in less than 5 ps, the non-Franck Condon ICT state is reached, and finally, the ground state is recovered in 70 ps. That the relevant excited state dynamics takes place far from the Franck Condon region is demonstrated by its noticeable dependence on the excitation wavelength.
Biochimica et biophysica acta, 2015
In recent years visible pump/mid-infrared (IR) probe spectroscopy has established itself as a key... more In recent years visible pump/mid-infrared (IR) probe spectroscopy has established itself as a key technology to unravel structure-function relationships underlying the photo-dynamics of complex molecular systems. In this contribution we review the most important applications of mid-infrared absorption difference spectroscopy with sub-picosecond time-resolution to photosynthetic complexes. Considering several examples, such as energy transfer in photosynthetic antennas and electron transfer in reaction centers and even more intact structures, we show that the acquisition of ultrafast time resolved mid-IR spectra has led to new insights into the photo-dynamics of the considered systems and allows establishing a direct link between dynamics and structure, further strengthened by the possibility of investigating the protein response signal to the energy or electron transfer processes. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
The journal of physical chemistry. B, Jan 28, 2007
Excitation energy transfer in the Photosystem II core antenna complex CP43 has been investigated ... more Excitation energy transfer in the Photosystem II core antenna complex CP43 has been investigated by vis/vis and vis/mid-IR pump-probe spectroscopy with the aim of understanding the relation between the dynamics of energy transfer and the structural arrangement of individual chlorophyll molecules within the protein. Energy transfer was found to occur on time scales of 250 fs, 2-4 ps, and 10-12 ps. The vis/mid-IR difference spectra show that the excitation is initially distributed over chlorophylls located in environments with different polarity, since two 9-keto C=O stretching bleachings, at 1691 and 1677 cm-1, are observable at early delay times. Positive signals in the initial difference spectra around 1750 and 1720 cm-1 indicate the presence of a charge transfer state between strongly interacting chlorophylls. We conclude, both from the spectral behavior in the visible when the annihilation processes are increased and from the vis/mid-IR data, that there are two pigments (one abso...
The Journal of Physical Chemistry B, 2014
Carbon monoxide recombination dynamics in a mutant of the truncated hemoglobin from Thermobida f ... more Carbon monoxide recombination dynamics in a mutant of the truncated hemoglobin from Thermobida f usca (3F-Tf-trHb) has been analyzed by means of ultrafast Visible-pump/MidIR-probe spectroscopy and compared with that of the wildtype protein. In 3F-Tf-trHb, three topologically relevant amino acids, responsible for the ligand stabilization through the formation of a H-bond network (TyrB10 TyrCD1 and TrpG8), have been replaced by Phe residues. X-ray diffraction data show that Phe residues in positions B10 and G8 maintain the same rotameric arrangements as Tyr and Trp in the wild-type protein, while Phe in position CD1 displays significant rotameric heterogeneity. Photodissociation of the ligand has been induced by exciting the sample with 550 nm pump pulses and the CO rebinding has been monitored in two mid-IR regions respectively corresponding to the ν(CO) stretching vibration of the iron-bound CO (1880−1980 cm −1 ) and of the dissociated free CO (2050−2200 cm −1 ). In both the mutant and wild-type protein, a significant amount of geminate CO rebinding is observed on a subnanosecond time scale. Despite the absence of the distal pocket hydrogen-bonding network, the kinetics of geminate rebinding in 3F-Tf-trHb is very similar to the wild-type, showing how the reactivity of dissociated CO toward the heme is primarily regulated by the effective volume and flexibility of the distal pocket and by caging effects exerted on the free CO on the analyzed time scale.
The Journal of Chemical Physics, 2014
We have studied the effect of transient vibrational inversion of population in trans-β-apo-8(&... more We have studied the effect of transient vibrational inversion of population in trans-β-apo-8(')-carotenal on the time-resolved femtosecond stimulated Raman scattering (TR-FSRS) signal. The experimental data are interpreted by applying a quantum mechanical approach, using the formalism of projection operators for constructing the theoretical model of TR-FSRS. Within this theoretical frame we explain the presence of transient Raman losses on the Stokes side of the TR-FSRS spectrum as the effect of vibrational inversion of population. In view of the obtained experimental and theoretical results, we conclude that the excited S2 electronic level of trans-β-apo-8(')-carotenal relaxes towards the S0 ground state through a set of four vibrational sublevels of S1 state.
The Journal of Physical Chemistry B, 2012
Carbon monoxide recombination dynamics upon photodissociation with visible light has been charact... more Carbon monoxide recombination dynamics upon photodissociation with visible light has been characterized by means of ultrafast visible-pump/MidIR probe spectroscopy for the truncated hemoglobins from Thermobif ida f usca and Bacillus subtilis. Photodissociation has been induced by exciting the sample at two different wavelengths: 400 nm, corresponding to the heme absorption in the B-band, and 550 nm, in the Q-bands. The bleached iron−CO coordination band located at 1850−1950 cm −1 and the free CO absorption band in the region 2050−2200 cm −1 have been observed by probe pulses tuned in the appropriate infrared region. The kinetic traces measured at 1850−1950 cm −1 reveal multiexponential subnanosecond dynamics that have been interpreted as arising from fast geminate recombination of the photolyzed CO. A compared analysis of the crystal structure of the two proteins reveals a similar structure of their distal heme pocket, which contains conserved polar and aromatic amino acid residues closely interacting with the iron ligand. Although fast geminate recombination is observed in both proteins, several kinetic differences can be evidenced, which can be interpreted in terms of a different structural flexibility of the corresponding heme distal pockets. The analysis of the free CO band-shape and of its dynamic evolution brings out novel features about the nature of the docking site inside the protein cavity.
The Journal of Physical Chemistry B, 2004
ABSTRACT The mechanism of electron transfer (ET) from the primary to the secondary quinone of bac... more ABSTRACT The mechanism of electron transfer (ET) from the primary to the secondary quinone of bacterial photosynthetic reaction centers is discussed on the basis of theoretical computations of the minimum energy nuclear configurations and ET coupling elements, and quantum dynamic simulations of elementary reaction steps. For ET to occur via tunneling, unreasonably high values of the electronic coupling elements or very stringent energy conditions, i.e., tight degeneracy (within a few cm-1) between the initial and final vibronic states, are necessary, both for the direct and through-bridge (superexchange) routes. The assumption of tight degeneracy significantly slows down the process so that other competitive processes, such as proton transfer from the H-bonded HisM219 to the primary quinone, can take place. All these results suggest that the iron−histidine bridge can play an important role in the ET mechanism.
Journal of Theoretical Biology, 2000
The mechanism of long-range electron transfer between the primary and the secondary quinone of ph... more The mechanism of long-range electron transfer between the primary and the secondary quinone of photosynthetic reaction centers has been investigated, with particular attention on the role of the iron-histidine bridge. Computations suggest that in such a system, where the molecular subunits are packed together by H-bonds, a mobile electron, injected on one end of the chain, can be carried to the other end by switching the positions of the H-bonded hydrogens. Energy estimates would suggest that the proposed mechanism is plausible and worthy of further experimental investigations.
Journal of Chemical Theory and Computation, 2007
Chemical Physics Letters, 2005
Intramolecular reorganization energies and Franck-Condon integrals of two redox cofactors of bact... more Intramolecular reorganization energies and Franck-Condon integrals of two redox cofactors of bacterial photosynthetic reaction centers have been evaluated by DFT computations of the optimum geometries and vibrational frequencies of the normal and reduced forms. The intramolecular modes which play a major role in electron transfer dynamics have been identified by Duschin-skyÕs analysis and the Franck-Condon integrals have been computed by using the whole set of normal coordinates of the acceptor and donor groups, in order to reliably account both for shifts, mix, and frequency change of the normal coordinates.
Chemical Physics Letters, 2003
The role of the iron-histidine bridge in bacterial photosynthetic reaction centres has been inves... more The role of the iron-histidine bridge in bacterial photosynthetic reaction centres has been investigated by means of ab initio computations and quantum dynamics of elementary reaction steps. Full geometry optimization and wave packet dynamics show that, upon the arrival of a photo-electron, the primary quinone takes up a proton from the H-bonded histidine in a very fast process, which occurs in a few tens of femtoseconds. The proton transfer step significantly stabilizes the charge separated state, inhibiting the backward charge recombination process. Electron transfer to the secondary quinone can then take place by switching the positions of both the H-bonded hydrogens, in a Bjerrium type mechanism involving whole hydrogen atoms rather than protons.
Biophysical Journal, 2008
It is now quite well accepted that charge separation in PS2 reaction centers starts predominantly... more It is now quite well accepted that charge separation in PS2 reaction centers starts predominantly from the accessory chlorophyll B A and not from the special pair P 680 . To identify spectral signatures of B A, and to further clarify the process of primary charge separation, we compared the femtosecond-infrared pump-probe spectra of the wild-type (WT) PS2 core complex from the cyanobacterium Synechocystis sp. PCC 6803 with those of two mutants in which the histidine residue axially coordinated to P B (D2-His 197 ) has been changed to Ala or Gln. By analogy with the structure of purple bacterial reaction centers, the mutated histidine is proposed to be indirectly H-bonded to the C 9 ¼O carbonyl of the putative primary donor B A through a water molecule. The constructed mutations are thus expected to perturb the vibrational properties of B A by modifying the hydrogen bond strength, possibly by displacing the H-bonded water molecule, and to modify the electronic properties and the charge localization of the oxidized donor P 1 680 : Analysis of steady-state light-induced Fourier transform infrared difference spectra of the WT and the D2-His 197 Ala mutant indeed shows that a modification of the axially coordinating ligand to P B induces a charge redistribution of P 1 680 : In addition, a comparison of the time-resolved visible/midinfrared spectra of the WT and mutants has allowed us to investigate the changes in the kinetics of primary charge separation induced by the mutations and to propose a band assignment identifying the characteristic vibrations of B A.
Biophysical Journal, 2009
Light harvesting complex II (LHCII) is the most abundant protein in the thylakoid membrane of hig... more Light harvesting complex II (LHCII) is the most abundant protein in the thylakoid membrane of higher plants and green algae. LHCII acts to collect solar radiation, transferring this energy mainly toward photosystem II, with a smaller amount going to photosystem I; it is then converted into a chemical, storable form. We performed time-resolved femtosecond visible pump/mid-infrared probe and visible pump/visible probe absorption difference spectroscopy on purified LHCII to gain insight into the energy transfer in this complex occurring in the femto-picosecond time regime. We find that information derived from mid-infrared spectra, together with structural and modeling information, provides a unique visualization of the flow of energy via the bottleneck pigment chlorophyll a604.
Phys. Chem. Chem. Phys., 2015
We have analyzed the excited state dynamics of the heteroleptic [(NCS)2Ru(bpy-(COOH)2)(bpy-(C6H13... more We have analyzed the excited state dynamics of the heteroleptic [(NCS)2Ru(bpy-(COOH)2)(bpy-(C6H13)2)] Z907 solar cell sensitizer in solution and when adsorbed onto thin TiO2 films, by combining transient visible and infrared (IR) spectroscopies with ab initio Density Functional Theory (DFT) and Time-Dependent DFT (TDDFT) calculations. Upon excitation with ultra-short pulses in ethanol and dimethyl-sulphoxide solutions, the visible spectra show the appearance of a positive signal around 650 nm, within the instrumental time resolution (<100 fs), which in ethanol undergoes a red-shift in about 20 ps. Measurements in the IR indicate that, upon excitation, both the CN and CO marker bands, associated with the NCS and COOH groups, downshift in frequency, in response to intramolecular ligand + metal (Ru-NCS) to ligand' (bpy-COOH2) charge transfer (LML'CT). Vibrational cooling is observed in both solvents; in ethanol it is overtaken by the hydrogen bond dynamics. On the basis of DFT/TDDFT calculations, explicitly modeling the interaction of the NCS and COOH groups with solvent (ethanol) molecules, we rationalize the observed IR and visible spectral evolution as arising from the change in the hydrogen-bond network, which accompanies the transition to the lowest-energy triplet state. This interpretation provides a consistent explanation of what is also observed in the transient visible spectra. Transient IR measurements repeated for molecules adsorbed on TiO2 and ZrO2 films, allow us to identify the structural changes signaling the dye triplet excited state formation and evidence multiexponential electron injection rates into the semiconductor TiO2 film.