Flavohemoglobins have the particular capability of binding unsaturated and cyclopropanated fatty acids as free acids or phospholipids. Fatty acid binding to the ferric heme results in a weak but direct bonding interaction. Ferrous and ferric protein, in presence or absence of a bound lipid molecule, have been characterized by transient absorption spectroscopy. Measurements have been also carried out both on the ferrous deoxygenated and on the CO bound protein to investigate possible long-range interaction between the lipid acyl chain moiety and the ferrous heme. After excitation of the deoxygenated derivatives the relaxation process reveals a slow dynamics (350 ps) in lipid-bound protein but is not observed in the lipid-free protein. The latter feature and the presence of an extra contribution in the absorption spectrum, indicates that the interaction of iron heme with the acyl chain moiety occurs only in the excited electronic state and not in the ground electronic state. Data analysis highlights the formation of a charge-transfer complex in which the iron ion of the lipid-bound protein in the expanded electronic excited state, possibly represented by a high spin Fe III intermediate, is able to bind to the sixth coordination ligand placed at a distance of at 3.5 angstrom from the iron. A very small nanosecond geminate rebinding is observed for CO adduct in lipid-free but not in the lipid-bound protein. The presence of the lipid thus appears to inhibit the mobility of CO in the heme pocket.

We present the synthesis and spectroscopic characterization of a twisted push-pull biphenyl molecule undergoing photoinduced electron transfer. Steady-state and transient absorption spectra suggest, in this rigid molecular structure, a subtle interplay between locally-excited and charge-transfer states, whose equilibrium and dynamics is only driven by solvation. A theoretical model is presented for the solvation dynamics and, with the support of quantum chemical calculations, we demonstrate the existence of two sets of states, having either local or charge-transfer character, that only "communicate" thanks to solvation, which is the sole driving force for the charge-separation process.

The relationships between the photophysics and structural properties of 4,7-dithien-2-yl-2,1,3-benzothiadiazole as a function of solvent polarity are investigated both experimentally and by computational methods. Stationary fluorescence measurements are consistent with a model envisaging the presence of three types of conformers in equilibrium in the ground state. They are characterized by different relative orientations of the thiophene rings. Due to a low rotational barrier, the sample in solution is characterized by a distribution of relative internal orientations. By applying the Kawski method, we evaluate the average dipole moment of ground and excited states of the three types of conformers. The ground state dipole moments are small and similar for the three types of conformers. On the contrary, dipole moments differ substantially in the excited state. X-ray diffraction of a single crystal confirms the presence of an orientational disorder of thiophene rings. Transient absorption UV-visible spectroscopy experiments allows the identification of the main mechanisms responsible for the large Stokes shift observed in this push-pull molecule. Time dependent spectra provide a picture of the relaxation processes occurring after excitation: the primary step is an internal charge transfer assisted by thiophene ring planarization which occurs on a time scale ranging from 0.88 to 1.3 picoseconds depending on solvent polarity. Moreover, time-resolved fluorescence measurements are consistent with a mechanism involving planarization accompanied by a stabilization of the charge transfer state as observed in polar solvents. In the latter, longer fluorescence lifetimes are observed along with a quantum yield decrease due to the activation of specific non-radiative relaxation channels. The photophysical behavior of 4,7-dithien-2-yl-2,1,3-benzothiadiazole in a solid matrix of polymethyl methacrylate is similar to that observed in solution, but the overall non-radiative process rate is slow with respect to that in the liquid phase. As a consequence, the radiative processes are enhanced giving rise to a fluorescence quantum yield of 90%. Such behavior is consistent with the proposed relaxation model.

The photophysics of 9(19),16(17),23(24)-tri-tert-butyl-2-[ethynyl-(4-carboxymethyl)phenyl] phthalocyaninatozinc(II) (ZnPc) in solution and adsorbed on TiO2 and ZrO2 nanoparticle films is characterized by stationary and time-resolved spectroscopies in the subpicosecond to nanosecond time interval. The comparison between the solution and the solid substrate data allows us to identify different pathways of the energy and electron relaxation. On the solid substrate, the presence of H-aggregates adds a further nonradiative deactivation channel competing with the charge injection into the Ti-2-conducting band, thus providing an explanation of the reduced efficiency of the charge transfer processes. The comparison between the kinetics recorded after excitation of the S-0-S-2 transition and those recorded after excitation of the S-0-S-1 transition provides an estimate of the internal conversion between S-2 and S-1 which occurs very efficiently and on an ultrafast (<50 fs) time scale. The ground-state recovery characterized by the decay of the bleaching band in the transient spectra slows down in TiO2 samples and is taken as evidence of the charge injection in this kind of sample.

Using heterodyne-detected optical Kerr effect (HD-OKE) measurements, we investigate the vibrational dynamics and the structural relaxation of water nanoconfined in Vycor porous silica samples (pore size ≃ 4 nm) at different levels of hydration and temperatures. At low levels of hydration corresponding to two complete superficial water layers, no freezing occurs and the water remains mobile at all the investigated temperatures with dynamic features similar, but not equal to, the bulk water. The fully hydrated sample shows the formation of ice at about 248 K. This process does not involve all the contained water; a part of it remains in a supercooled phase. The structural relaxation times measured from the decay of the time-dependent HD-OKE signal shows the temperature dependence largely affected by the hydration level; the low frequency (ν < 500 cm−1) vibrational spectra obtained by the Fourier transforms of the HD-OKE signal appear less affected by confinement.

Carbon monoxide recombination dynamics in a mutant of the truncated hemoglobin from Thermobida fusca (3F-Tf-trHb) has been analyzed by means of ultrafast Visible-pump/MidIR-probe spectroscopy and compared with that of the wild-type 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.

Internal water molecules play an active role in ligand uptake regulation, since displacement of retained water molecules from protein surfaces or cavities by incoming ligands can promote favorable or disfavorable effects over the global binding process. Detection of these water molecules by X-ray crystallography is difficult given their positional disorder and low occupancy. In this work, we employ a combination of molecular dynamics simulations and ligand rebinding over a broad time range to shed light into the role of water molecules in ligand migration and binding. Computational studies on the unliganded structure of the thermostable truncated hemoglobin from Thermobifida fusca (Tf-trHbO) show that a water molecule is in the vicinity of the iron heme, stabilized by WG8 with the assistance of YCD1, exerting a steric hindrance for binding of an exogenous ligand. Mutation of WG8 to F results in a significantly lower stabilization of this water molecule and in subtle dynamical structural changes that favor ligand binding, as observed experimentally. Water is absent from the fully hydrophobic distal cavity of the triple mutant YB10F-YCD1F-WG8F (3F), due to the lack of residues capable of stabilizing it nearby the heme. In agreement with these effects on the barriers for ligand rebinding, over 97% of the photodissociated ligands are rebound within a few nanoseconds in the 3F mutant case. Our results demonstrate the specific involvement of water molecules in shaping the energetic barriers for ligand migration and binding.

The exciton generation and recombination dynamics in semiconductor nanocrystals are very sensitive to small variations in dimensions, shape and surface capping. In the present work CdTe quantum dots are synthesized in water using 3-mercaptopropionic acid and 1-thioglycerol as stabilizers. Nanocrystals with an average dimension of 4.0 ± 1.0 and 3.7 ± 0.9 nm were obtained, when 3-mercaptopropionic acid or 1-thioglycerol, respectively, was used as a capping agent. The steady-state characterization shows that the two types of colloids have different luminescence behavior. In order to investigate the electronic structure and the dynamics of the exciton state, a combined study in the time domain has been carried out by using fluorescence time-correlated single photon counting and femtosecond transient absorption techniques. The electron-hole radiative recombination follows the non-exponential decay law for both colloids, which results in different average decay time values (of the order of tens of nanoseconds) for the two samples. The data demonstrate that the process is slower for 1-thioglycerol-stabilized colloids. The ultrafast transient absorption measurements are performed at two different excitation wavelengths (at the band gap and at higher energies). The spectra are dominated in both types of samples by the negative band-gap bleaching signals although transient positive absorption bands due to the electrons in the conduction band are observable. The analysis of the signals is affected by the different interactions with the defect states, due to ligand capping capacities. In particular, the data indicate that in 1-thioglycerol-stabilized colloids the non-radiative recombination processes are kinetically more competitive than the radiative recombination. Therefore the comparison of the data obtained from the two samples is interpreted in terms of the effects of the capping agents on the electronic relaxation of the colloids.

The transient evolution of protoporphyrin IX (PPIX) and hemin following the Soret band excitation was measured in the 410–600 nm spectral region with sub-picosecond time resolution. In PPIX the relaxation pathway was characterized in the femto- and picosecond time scale by two processes with time constants of 350 fs and ∼6 ps, describing the evolution of the system through internal Q_y → Q_x conversion and vibrational relaxation and cooling in the Q_x state. The lifetime of the Q_x state was found to be 10.4 ns by time resolved fluorescence measurements. In hemin, the ground state is completely recovered in tens of picoseconds through pathways involving CT and (d,d) states. The experimentally observed vibrational dynamics is mainly due to “hot” ground state transitions.

The low frequency (nu < 500 cm(-1)) vibrational spectra of hydrated porous silica are specifically sensitive to the hydrogen bond interactions and provide a wealth of information on the structural and dynamical properties of the water contained in the pores of the matrix. We investigate systematically this spectral region for a series of Vycor porous silica samples (pore size approximately equal 4 nm) at different levels of hydration, from the dry matrix to completely filled pores. The spectra are obtained as the Fourier transforms of time-resolved heterodyne detected optical Kerr effect (HD-OKE) measurements. The comparison of these spectra with that of bulk water enables us to separately extract and analyze the spectral contributions of the first and second hydration layers, as well as that of bulk-like inner water. We conclude that the extra water entering the pores above approximately equal 10% water/silica weight ratio behaves very similarly to bulk water. At lower levels of hydration, corresponding to two complete superficial water layers or less, the H-bond bending and stretching bands, characteristic of the tetrahedral coordination of water in the bulk phase, progressively disappear: clearly in these conditions the H-bond connectivity is very different from that of liquid water. A similar behavior is observed for the structural relaxation times measured from the decay of the time-dependent HD-OKE signal. The value for the inner water is very similar to that of the bulk liquid; that of the first two water layers is definitely longer by a factor approximately equal 4. These findings should be carefully taken into account when employing pore confinement to extend towards lower temperatures the accessible temperature range of supercooled water.

CO recombination kinetics has been investigated in the type II truncated hemoglobin from Thermobifida fusca (Tf-trHb) over more than 10 time decades (from 1 ps to ∼100 ms) by combining femtosecond transient absorption, nanosecond laser flash photolysis and optoacoustic spectroscopy. Photolysis is followed by a rapid geminate recombination with a time constant of ∼2 ns representing almost 60% of the overall reaction. An additional, small amplitude geminate recombination was identified at ∼100 ns. Finally, CO pressure dependent measurements brought out the presence of two transient species in the second order rebinding phase, with time constants ranging from ∼3 to ∼100 ms. The available experimental evidence suggests that the two transients are due to the presence of two conformations which do not interconvert within the time frame of the experiment. Computational studies revealed that the plasticity of protein structure is able to define a branched pathway connecting the ligand binding site and the solvent. This allowed to build a kinetic model capable of describing the complete time course of the CO rebinding kinetics to Tf-trHb.

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 Thermobifida fusca 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.

We report on a study of the excited state dynamics of a heteroaromatic 4,4′-π-conjugated 2,2′-bipyridine dye, bearing conjugated π-excessive and π-deficient heteroaromatic rings as donor and acceptor substituents, by means of steady state and transient absorption spectroscopy in EtOH solutions and a room temperature. The ground state absorption shows an intense intramolecular charge transfer band in the visible region with a maximum at 515nm. Excited state dynamics is measured by pumping at 480nm at shorter wavelengths from the absorption maximum and probing at specific wavelengths corresponding to bleaching, stimulated emission and at the maximum of excited state absorption. The spectral evolution is also evaluated in the frequency domain as a function of the delay between pump and probe pulses. By means of SVD analysis two components with time constants around 2ps and 150ps are identified. In addition a relevant dynamical Stokes shift of the stimulated emission occurs in the first 60ps which is attributed to solvent dynamics. Ab initio calculations allows to assign the ground spectral features and the excited state conformation. The geometry of the ground and of the first excited state are optimized both in the cisoid and in the transoid forms. The latter results more stable of about 0.4eV.

In this work, we present the characterization of an enantiomeric pair of fluorescent dye organogelators and the properties of their stable gel at low concentration in organic solvents. The gels of both enantiomers and of their mixtures were analyzed by differential scanning calorimetry, circular dichroism (CD), atomic force microscopy, UV-vis absorption, and fluorescence. The acquired data were supported by molecular modeling of the helical assembly of the gelators and by the simulation of their CD spectra by means of DeVoe method, and suggested the occurrence of an enantiomeric discrimination process during the formation of the gels.

Thermobifida fusca hemoglobin (TFH) is a prototypical bacterial (class 2) hemoglobin. It has been identified in a thermophilic actinobacterium and overexpressed. The heme cavity properties are mainly related to the polarity and H-bonding capability of the "distal" amino acids: tyrosine (B10 in the myoglobin helix notation), tyrosine (CD1), tryptophan (G8).

The choice of a donor and an acceptor with suitable optical and self-assembly properties is essential in the design of organogel-based light harvesting systems. Organogels can provide supramolecular structures capable of enhancing energy transfer processes. In this work, we present the characterization of N-(naphthalene-1-carboxyamide)-(3S,4S)-pyrrolidin-(3,4)-bisdodecyl-carbamoyldiester (1) and N-(4-nitrobenzofurazan-7-amino)-(3S,4S)-pyrrolidin-(3,4)-bisdodecyl-carbamoyldiester (2) which are used as donor and acceptor moieties, respectively. The donor molecule is hardly capable to form a gelon its own but it can be assembled at reasonable concentrations with the acceptor gelator to form a two-component donor–acceptor organogels in cyclohexane. Stable organogels are formed from cyclohexane for gelator concentrations as low as ≈10−3M. UV–vis and steady-state fluorescence spectroscopies were used to provide a characterization of their molecular interactions. The optical changes observed during the cooling of two-component solutions of these systems are indicative of typical sol–gel transitions. The occurrence of excitation energy transfer processes in the gels is confirmed by comparison of their excitation and absorption spectra.

We investigated a novel bichromophoric antenna system, characterized by energy transfer between a naphthalene group acting as the donor and a benzofurazane group acting as the acceptor. We studied the spectroscopic properties (infrared, Raman, UV–vis and fluorescence) of self-assembled monolayers of this molecular antenna on Ag nanoisland films and the energy-transfer process upon irradiation at 300nm.

We observed Förster resonance energy transfer (FRET) with a covalently linked donor-acceptor pair D-A consisting of two naphthalene groups acting as the donors and a benzofurazan group acting as the acceptor and adsorbed onto Ag or Au nanoisland films. The use of metal nanoisland films, which caused a strong enhancement of the Raman signal, permitted description of the adsorption mechanism onto the two metals. The intense fluorescence response of molecular adsorbates and the different behavior of the antenna on Ag and Au nanoislands are partly explained in terms of the radiating plasmon model.

S1 --> S(n) spectra of porphyrin, diprotonated porphyrin, and tetraoxaporphyrin dication have been measured in the energy range 2-3 eV above S1 at room temperature in solution by means of transient absorption spectroscopy exciting with femtosecond pulses. Highly excited pi pi* states not active in the conventional S0 --> S(n) spectrum have been observed. The experimental data are discussed on the basis of the time dependent density functional theory taking advantage of large scale calculations of configuration interaction between singly excited configurations (DF/SCI). The DF/SCI calculation on porphyrin has allowed to assign g states active in the S1 --> S(n) spectrum. Applying the same calculation method to tetraoxaporphyrin dication the S0 --> S(n) spectrum is reproduced relatively to the Q and B (Soret) bands as well as to the weaker E(u) bands at higher energy. According to our calculation the S1 --> S(n) transient spectrum is related to states of g symmetry mainly arising from excitations between doubly degenerate pi and pi* orbitals such as 2e(g) --> 4e(g). In the case of diprotonated porphyrin it is shown that the complex of the macrocycle with two trifluoroacetate anions plays a significant role for absorption. Charge transfer excitations from the anions to the macrocycle contribute to absorption above the Soret band, justifying the intensity enhancement of the S0 --> S(n) spectrum with respect to the other two macrocyclic systems.

A series of dendrimeric compounds bearing pyrene units were synthesized to afford light-harvesting antennae based on the formation of intramolecular excimers. The synthetic plan profited from the efficiency of the Huisgen reaction, the 1,3-dipolar cycloaddition of azides and terminal alkynes, which allowed ready assembly of the different building blocks. The three molecular antennae obtained, of increasing generation, revealed efficient energy transfer both in solution and in the solid state.