Ultrafast Visible and Ultraviolet Fluorescence Studies of Molecular and Biological Sytems in Solution

A wide variety of physical and chemical processes at the molecular level, as charge or energy transfer, solvation, electronic as well as vibrational relaxation, is at the origin of the biological functionality of proteins. The work reported in this thesis is devoted to the study of these molecular dynamics in different chromophore systems. More specifically, this study is focused on the role of these dynamics in the ultrafast photophysics and photochemistry of haemoproteins. This important class of proteins has been widely studied through various spectroscopic techniques, in order to understand their functionality. These proteins contain several chromophore moieties, among which one aminoacid residue, Tryptophan, and the haem prosthetic group, which are of particular interest in this work. While Tryptophan is used as a probe of the local environment via intermolecular relaxation dynamics, we investigated the role of haem intramolecular dynamics on the protein functionality. While different kind of ultrafast spectroscopic techniques are indicated to tackle these issues, like pump probe or photon-echo peak shift experiments, we choose a different approach to probe directly the energetic relaxation, which consists in following the ultrafast changes in the photoluminescence spectrum. The dynamics are then extracted from the spectral evolution of the emission. With this purpose, we implemented a fluorescence up-conversion set-up, which allows us resolving temporally and spectrally the photoluminescence of the sample under investigation, excited with an ultrashort light pulse, and with a temporal resolution on the femtosecond timescale. The thesis is structured in 9 chapters. Chapter 1 resumes the theoretical background required for the interpretation of the experimental results. Chapter 2 describes the photophysical properties of the different systems investigated. Chapter 3 presents the experimental technique of fluorescence up-conversion, used to achieve broadband femtosecond detection of photoluminescence. In Chapter 4, we present a study on the role of ultrafast vibrational and structural dynamics on the time-resolved fluorescence spectra from two UV dyes. The measurements allow us exploring the capabilities of the set-up in revealing subtle relaxation dynamics with an unequaled accuracy. In Chapter 5, we move on to the study of the relaxation dynamics of Tryptophan (Trp) in water. This aminoacid served as an in vivo probe of solvation dynamics, owing to its high dipolar moment in its excited state. Our study focuses on water reorganization around the chromophore and on the distinction of this important process from the electronic internal conversion occurring on a similar timescale. In the framework of the study of protein dynamics, Chapter 6 reports the investigation of a family of molecules extensively found in nature, namely porphyrins. In these molecular systems, a quite complex pattern of intramolecular relaxation mechanisms occurs, which needed to be clarified. A systematic study on the free base and on a wide series of metallo-porphyrins definitely clarified the picture of their electronic relaxation pathways. We finally elaborate a comprehensive scheme of this relaxation, including substituent's influence. The mechanisms observed are intrinsically related to the photophysical properties used by nature, as will be illustrated in the next Chapter. Trp and metallo-porphyrin constitute the key natural chromophore molecules for the non-invasive spectroscopic investigation of complex biological systems as haemoproteins. In Chapter 7, we follow relaxation dynamics of photo-excited Tryptophan and Haem (Fe-porphyrin) in ferro- and ferricytochrome c and in Myoglobin in its met form. In the former protein, an ultrafast energy transfer from Tryptophan to Heme is evidenced, the efficiency of which is found to depend on the oxidation state. The energetic relaxation pathway of the haem, also dependent on the oxidation state, is characterized by a porphyrin to metal charge transfer that triggers the ligand dissociation. In metMyoglobin, the fluorescence contribution of the two Tryptophans (W14 and W7), also quenched by resonant energy transfer to the haem, are temporally and spectrally separated, and the solvation dynamics of W7, located in the water-protein interface, is followed. The haem of metMb, which is in the ferric form, shows an electronic relaxation similar to that of ferricytochrome c. In parallel to the biology oriented investigations presented above, we extended our study to the metal-polypiridine complexes. Due to their specific photophysics, mainly characterized by a photo-induced Metal-to-Ligand Charge Transfer (MLCT), they are extensively used in photochemical applications involving charge transfer dynamics. In particular, they are used as sensitizer in the Dye-Sensitized-Solar-Cells (DSSCs). In Chapter 8, we present studies of these dyes, both in solution and adsorbed on a substrate, in order to understand the role of intra- and intermolecular dynamics on the electron injection process occurring upon absorption of light. Finally, Chapter 9 summarizes the conclusions of the investigations of the various systems studied.

Spectroscopy and dissociation dynamics of cold, biomolecular ions

Monia Guidi

The function of a peptide is intimately connected to its structure, which in solution is the result of the balance between non-covalent interactions within the molecule and the molecule-solvent interactions. Theory has the power to predict the properties of a wide variety of molecules, but the accuracy of the theoretical predictions must be verified by experiments. A way to test, and hopefully improve, theory is to study proteins or peptides in the gas-phase. The combination of mass spectrometry and laser spectroscopy is used to investigate properties of biological ions in the gas-phase. Closed-shell biomolecular ions produced by an electrospray source are cooled down in an RF ion trap to less than 10 K and interrogated spectroscopically. Electronic and conformer-specific vibrational spectra have been measured for small protonated peptides applying photofragment-based detection schemes. These measurements allow us to investigate the role of the charge and the influence of the nature and the position of the chromophore in the peptide chain on its conformational preferences. Highly-resolved conformer-specific vibrational spectra of such species, as well as those of a double-chromophore molecule, help elucidate the mechanism of the IR-UV double-resonance methods and provide benchmarks for testing the accuracy of theoretical calculations. This thesis shows also the experimental developments that allow us to use photofragment-based detection scheme to measure highly-resolved electronic spectra of peptides of up to 17 amino acids, containing one or two chromophores, using infrared laser-assisted photofragment spectroscopy (IRLAPS). The fragmentation yield of UV pre-excited molecules increases by as much as two orders of magnitude when they further interact with the CO2 laser. This approach can be also applied in a IR-UV double resonance scheme, allowing measurements of conformer-specific infrared spectra of protonated peptides. The fragmentation channel, which is always greatly enhanced by IRMPE of UV pre-excited molecules, is the loss of the neutral, aromatic side chain via cleavage of the Cα-Cβ bond, independent of the chromophore excited in the peptide. The possible mechanisms, involving the formation of a long-lived intermediate species, that lead to the formation of the observed photofragment are discussed in this thesis work.

EPFL2010

Ultrafast One- and Two-Dimensional UV Transient Absorption Spectroscopy of Haem Proteins

Cristina Consani

Proteins are dynamic macromolecules, which accomplish biological function driven by long-range interactions and global motions. While their biological function is often clear, little is known about the collective interactions which make these systems real molecular devices. The last decades showed an increased interest in accessing the very early events of protein function and the weak couplings among different sub-units. This implies the capability to observe events which occurs on sub-ps time scales. Ultrafast spectroscopy is a powerful tool to investigate in real time electronic processes and vibrational dynamics in photo-excited systems. The last years showed an increased interest in the UV spectral region, to access spectroscopic features of molecules with electronic excitations located exclusively below 400 nm. Among them, are the high- spin states of metal complexes and the aromatic aminoacids in proteins. Especially, exploring the UV range below 300 nm opened the possibility to employ naturally occurring aminoacids as local probes of protein dynamics and intra-proteins correlations. This allowed to access the dynamical evolution of sites which were previously spectroscopically silent, or whose spectra were too congested, in wild type proteins. In this thesis work, we focus on the study of Fe-based metal complexes, and in partic- ular on wild type haem-proteins in native environment, and we address the questions of the relaxation of the prosthetic group and its interaction with the Trp residues. Despite intensive study, the details of the early haem photocycle in haem proteins is still under debate. With this thesis work, we show the successful combination of our UV- extended broadband transient absorption setup with time gated fluorescence in unraveling the early mechanisms of haem relaxation. In particular, for the first time we found evidence that the electronic relaxation in ferric met-myoglobin is specific for the system and that the widespread analogy among the electronic relaxation in all myoglobin forms should be reconsidered. Despite their capability to access the time scales of Trp de-excitation, these techniques are not the most suitable to investigate the mutual interaction among several residues, nor can they access the dynamics of environmental fluctuations. Two-dimensional spec- troscopies are instead the right tool to solve these issues. To this purpose, we designed an ultra-broadband transient absorption two-dimensional setup in the UV, with a band- width exceeding 60 nm in excitation and 80 nm in detection. The performance of the setup, which is described in details, was successfully demonstrated on UV dyes and bio- logical samples and it represents an excellent complement to Fourier-transform 2D setups, whose biological application in the UV is often compromised by the limited observation bandwidth.

EPFL2012

Influence of the protein environment on spectroscopy and ultrafast dynamics of retinal in bacteriorhodopsin

Selma Schenkl

The environment is important for the exact course of a chemical reaction. As an example of the strong influence of the environment on the reaction, this work studies the isomerization reaction of the chromophore retinal in the binding pocket of the protein bacteriorhodopsin. Three selected distance scales with reference to the chromophore are addressed: The distant protein surface at a length scale of 3-5 nm, the fuzzy environment of the binding pocket (1-2 nm) and the immediate neighborhood represented by the amino acid tryptophan Trp86 (5 Å). First, static absorption and fluorescence spectroscopies are applied to three dimensionally crystallized bacteriorhodopsin. An especially adapted set-up was developed for each task. The analysis of data is carried out in comparison with the measured spectra of the native protein membrane in solution. While the absorption spectrum shows a broadening on the high-energy side, the fluorescence spectrum deviates in the general shape of that measured in solution. The synoptic analysis of all spectra reveals the existence of three spectroscopically distinct species in the crystal: BR490 (absorption maximum at 490 nm) with a relative contribution of 28%, BR570 (native spectrum of solution, 68%), and BR610 ("blue membrane", 4%). BR490 appears particularly in the additional fluorescence band at 550 nm and is assigned to the dehydrated species of bacteriorhodopsin. The presence of that particular species indicates the suppression of rehydration in a partially dehydrated crystal and shows that the three dimensional arrangement hinders water diffusion. A simple model, close domains are assumed to form, eventually suppressing free water diffusion in a crystal. The lack of water on the protein surface modifies the protonation states of the amino acids in the binding pocket and therefore the optical properties of the retinal. The chromophore actually reacts on the alteration of its distant environment upon incorporation in the protein crystal. The second distance scale - the fuzzy environment - is addressed by a time-integrated fluorescence spectroscopy on native bacteriorhodopsin as function of the excitation wavelength (430 nm to 650 nm). The optimized experimental set-up guaranteed that the fluorescence of only the excited state I460 contributed. The measured spectra show maxima at 740 nm, and exhibit a Stokes shift of 5000 cm-1, independent of the excitation wavelength. The similarity of the fluorescence excitation spectrum with the spectrum of absorbed photons excludes energy-dependent loss channels. However, the spectra show a growing asymmetric broadening on the high-energy side with decreasing excitation wavelength. The additional fluorescence originates from vibrational hot states, also supported by the decomposition by Gaussian functions. A comparison with the fluorescence spectrum of blue membranes shows that the low-energy part also arises from vibrational hot states. Consequently, the first fast intramolecular vibrational energy relaxation does not entirely distribute the access-energy to other modes. The remaining energy is found in a quasi-static occupation of vibrational modes. The subsequent second vibrational relaxation — probably not only involving the retinal but also the protein — takes place on a time scale similar to that of the isomerization. The fast isomerization reaction prevents dissipation of energy relaxation of the excited state of the retinal into the protein environment. On a third distance scale, femtosecond spectroscopy in the UV offers a direct view into the electrostatic interaction of the chromophore with its immediate neighborhood. For the first time, the retinal isomerization was studied within the spectral window of the tryptophan absorption from 265 nm to 310 nm. For this, a set-up adapted to UV wavelengths was realized, basing on non-linear optics. The developed single-shot detection system yields a sensitivity of 10-5 in optical density. In the transient absorption measurements, a time resolution of 90 fs was achieved. At short probe wavelengths (265 nm - 294 nm), the measured transients show first a fast reduction of the absorption which subsequently recovers on three time scales (380 fs, 3 ps, > 16 ps). With increasing probe wavelength an induced transient absorption becomes dominant (282 nm - 294 nm). It has a rise time of 280 fs, and decays with a time constant of 4.3 ps. With further increasing probe wavelength the absorption signal decays faster. In response to the complex signature of the transients, an iterative and model-independent transient-decomposition is introduced. A set of three basis elements were identified: one bleach, and two absorption transients. The two induced absorption transients are assigned to retinal. The dynamics of the excited state (I460) in the first retinal-transient is described by two time constants (280 fs and 1 ps). The fast time constant leads to the photoproduct, while the slower one leads back to the ground state, presumably by internal conversion. The 250 fs delayed onset of the second transient (photo-intermediate J) is connected to a wave packet motion in the excited state. This delayed onset of the transient was observed for the first time. It demands a rise time of the J photo-intermediate of only 280 fs. This contrasts common estimates of 500 fs given in literature. For the first time, the temporal behavior of the permanent dipole moment of retinal is observed experimentally. Its evolution is imprinted in the dominant bleach feature (265 nm - 294 nm), originating from tryptophan Trp86. In the excited state, the permanent dipole moment increases strongly within the first 250 fs, and decays exponentially afterwards, following the formation of the photoproduct. However, the related time constant of 380 fs is slightly greater than that of 280 fs of the photoproduct J. This discrepancy may indicate a remaining long-lived polarization of the binding pocket. In brief, by using the intrinsic tryptophan as a probe, the local evolution of the electric field during the isomerization reaction was investigated. Indeed the isomerization reaction is reflected in the immediate environment. The variety of optical spectroscopy provides methods especially adapted for studying the influences of the environment on a chemical reaction. The results achieved here highlight the importance of these influences.

EPFL2004