Agnese Marcelli

Excited-state absorption and ultrafast relaxation dynamics of porphyrin, diprotonated porphyrin, and tetraoxaporphyrin dication.

The relaxation dynamics of unsubstituted porphyrin (H2P), diprotonated porphyrin (H4P2+), and tetraoxaporphyrin dication (TOxP2+) has been investigated in the femtosecond-nanosecond time domain upon photoexcitation in the Soret band with pulses of femtosecond duration. By probing with spectrally broad femtosecond pulses, we have observed transient absorption spectra at delay times up to 1.5 ns. The kinetic profiles corresponding with the band maxima due to excited-state absorption have been determined for the three species. Four components of the relaxation process are distinguished for H2P: the unresolvably short B --> Qy internal conversion is followed by the Qy --> Qx process, vibrational relaxation, and thermalization in the Qx state with time constant approximately 150 fs, 1.8 ps, and 24.9 ps, respectively. Going from H2P to TOxP2+, two processes are resolved, i.e., B --> Q internal conversion and thermal equilibration in the Q state. The B --> Q time constant has been determined to be 25 ps. The large difference with respect to the B --> Qy time constant of H2P has been related to the increased energy gap between the coupled states, 9370 cm-1 in TOxP2+ vs 6100 cm-1 in H2P. The relaxation dynamics of H4P2+ has a first ultrafast component of approximately 300 fs assigned as internal conversion between the B (or Soret) state and charge-transfer (CT) states of the H4P2+ complex with two trifluoroacetate counterions. This process is followed by internal CT --> Q conversion (time constant 9 ps) and thermalization in the Q state (time constant 22 ps).

Pyrene-Excimers-Based Antenna 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.

Following Ligand Migration Pathways from Picoseconds to Milliseconds in Type II Truncated Hemoglobin from Thermobifida fusca

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.

Excited States of Porphyrin Macrocycles

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.

Ligand uptake modulation by internal water molecules and hydrophobic cavities in hemoglobins

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.

Chirality driven self-assembly in a fluorescent organogel†

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.

Supercooling and freezing processes in nanoconfined water by time-resolved optical Kerr effect spectroscopy.

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 Truncated Hemoglobins Studied with Visible-Pump MidIR-Probe Spectroscopy

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.

Role of Local Structure and Dynamics of Small Ligand Migration in Proteins: A Study of a Mutated Truncated Hemoprotein from Thermobifida fusca by Time Resolved MIR Spectroscopy

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.