MASTER THESIS IN PHYSICS Ultrafast spectroscopy and coherent control of Tryptophan-based compounds Author: Supervisor: Luana Olivieri Prof. Tullio Scopigno Co-Supervisors: Dr. Giovanni Batignani Dr. Luigi Bonacina Academic year 2016 iii Acknowledgements Prima di tutto vorrei esprimere la mia gratitudine ai miei relatori il Prof. Tullio Scopigno e il Prof. Jean-Pierre Wolf che mi hanno dato la possibilità di partecipare a questo progetto. Un profondo e sincero ringraziamento va al Dott. Luigi Bonacina e al Dott. Julien Gateau che mi hanno guidato durante l’esperienza a Ginevra, insegnandomi molto dal punto di vista sia pratico che teorico sul controllo coerente di sistemi quantistici. Allo stesso modo, un sentito ringraziamento va al Dott. Giovanni Batignani per il suo aiuto e supporto negli esperimenti di pump-probe (e per la sua infinita disponibilità). Vorrei poi ringraziare Elise Schubert, Michel Moret, Denis Mongin, Va- syl Kilin, Nicolas Berti, Gustavo Sousa, Gabriel Campargue, Carino Fer- rante e Alessandra Virga per aver creato una stimolante e confortevole at- mosfera lavorativa. Sono particolarmente debitrice alla mia famiglia e a tutti i miei amici e colleghi. In particolare vorrei ringraziare Giuseppe Bellanti per l’ imperit- uro supporto e il costante incoraggiamento profuso che mi ha sostenuto nei momenti più difficili di questa esperienza. In fine, vorrei ringraziare l’università "La Sapienza" e l’università di Ginevra per avermi finanziato quest’esperienza attraverso la borsa di stu- dio "SEMP". v Contents Acknowledgements iii Introduction ix 1 Tryptophan1 1.0.1 Ultrafast dynamics of Tryptophan...........2 1.0.2 Raman scattering on Tryptophan............4 1.1 Tryptophan contained in proteins................6 1.1.1 Human Serum Albumin.................6 1.1.2 Immunoglobulin G....................7 2 Coherent control9 2.1 Coherent control over a molecular wavepacket........ 12 2.1.1 Examples of molecular discrimination......... 14 2.2 Optimal quantum control.................... 18 2.2.1 Example: three levels system.............. 20 2.3 Multiobjective Genetic Algorithm................ 22 3 Transient Absorption and Stimulated Raman Spectroscopies 25 3.1 Interaction picture and diagram theory............ 28 3.1.1 Double sided Feynman diagrams of a χ3 process.. 32 3.2 Ultrafast Transient Absorption Spectroscopy......... 34 3.2.1 Singular value decomposition............. 39 3.3 Stimulated Raman Scattering.................. 40 4 Experimental setups 45 4.1 Setup employed in GAP Biophotonics lab........... 45 4.1.1 Sample preparation and handling........... 47 4.2 Experimental setup used in Femtoscopy lab.......... 49 4.3 Pulse characterization...................... 52 4.3.1 Cross-Correlation..................... 52 4.3.2 Frequency-Resolved Optical Gating.......... 53 4.3.3 Self-Diffraction FROG (SD FROG)........... 54 4.3.4 Polarization-Gated FROG (PG FROG)......... 57 4.4 Pulse Shaping........................... 59 4.4.1 MEMS mirrors...................... 59 4.4.2 Geometries of pulse shaper............... 60 vi 4.4.3 Spectral resolution.................... 61 4.5 UV compression with a prism pair............... 64 4.5.1 Propagation of ultrashort light pulse.......... 64 4.5.2 Pulse compression with a prism pair.......... 69 5 Time resolved fluorescence depletion of tryptophan and trypto- phan contained in proteins 71 5.1 Preliminary optimization: NSGA-II applied on cross-correlation signal................................ 71 5.2 Time resolved fluorescence depletion spectroscopy...... 73 5.2.1 Preliminary measurements............... 74 5.2.2 Depletion curves acquired with unshaped pulse... 78 5.2.3 Optimal Dynamics Discrimination applied to IgG and HSA............................ 79 6 Pump probe experiments on Tryptophan 85 6.1 Transient Absorption measurement of Tryptophan...... 85 6.1.1 PG FROG measurements................ 85 6.1.2 Pulse compression performed by prism pair..... 87 6.1.3 Evaluation of the white light’s chirp.......... 89 6.1.4 Transient Absorption measurement of Tryptophan. 90 6.1.5 Glotaran software..................... 91 6.1.6 Estimation of the spectral components with Glotaran 94 6.1.7 DAS spectra treated with superposition process... 97 6.1.8 Results........................... 101 6.2 Stimulated Raman Scattering.................. 105 7 Conclusion and Outlook 109 A Labwindows software for FROG measurements 111 B Orhogonalized DAS components 113 Bibliography 117 to Giuseppe Bellanti and my family ix Introduction The chance to observe and manipulate ultrafast dynamics is an intrigu- ing goal in physics and chemistry. The development of femtosecond laser sources in 60’s paved the way to the realization of spectroscopic pump- prove techniques able to track electronic reconfiguration and visualize struc- tural rearrangements in the femtosecond time scale. More recently, a fascinating perspective in the ultrafast community is to ob- tain an active control over complex systems dynamics. Processes like the breaking or the formation of specific chemical bonds are often hampered by the rapid redistribution through all the molecules of the energy locally deposited by mean of a femtosecond laser source, causing a leak of the se- lectivity. Thereby, the field of quantum coherent control emerged from the goal to drive a quantum system from an initial state to a desired final state by exploiting constructive quantum-mechanical interferences: it gives the chance to enhance the transition amplitude of a selected final state and at the same time exploits destructive interference to suppress undesired final states. The initial ideas exploited phase-controlled laser fields to manipu- late quantum-mechanical phases, as proposed by Brumer and Shapiro [1], or precisely timed sequences of ultrashort pulses, as proposed by Tannor and Rice [2,3]. In 1992, H. Rabitz and coworkers introduced the concept of optimal control, in their seminal paper "Teaching laser to control molecules" [4]. They proposed to use a search algorithm to optimize the laser pulse characteristics in a feedback loop configuration to reach most efficiently the desired target. Thus today, a large number of parameters (such as the amplitude and the phase of each spectral component within the laser pulse) has to be con- trolled with new pulse shaping techniques and the help of efficient genetic- type optimization algorithms [5,6]. Within the context of coherent quantum control, quantum manipulation techniques have been applied to unravel microscopic informations on the system and discriminate between different, but very similar, compounds. In this respect, Optimal Dynamic Discrimination (ODD) is a powerful the- ory that is based on the enhancement or reduction of fluorescence of a spe- cific molecule by driving it preferentially into other relaxation pathways. It has been recently demonstrated experimentally achieving the discrimina- tion between small molecules like Riboflavin and Flavin mononucleotide, x Contents Tryptophan and Tyrosine, Tryptophan and Ala-Tryptophan [7,8,9]. Even if the ODD theory allows measuring a target objective, which en- able the identification and discrimination between different compounds, there is not yet a procedure able to combine the informations obtained from the shaped pulse to the dynamics that take place in the excited state. Pump- probe techniques based on ultrafast transient absorption (TA) are able to extract these informations while non-linear Raman spectroscopies can un- veil the structural conformations of the system. Transient absorption spectroscopy in picosecond and femtosecond time do- mains is a sensitive spectroscopic technique for studying the time evolution of excited states and the lifetimes of short-lived intermediates, and it is also useful to follow the energy flow among different chromophores composing the macromolecules. The Stimulated Raman scattering (SRS) was one of the first nonlinear op- tical processes experimentally observed (1962) and its pump-probe version has recently been used to unveil the vibrational and rotational modes of liquids and gases [10]. Moreover, the combination of TA and SRS gives the chance to define a Fem- tosecond stimulated Raman Scattering (FSRS) experiment. FSRS is an ul- trafast nonlinear optical technique able to access the vibrational structural informations of the excited states combining high temporal precision and high spectral resolution within a three-pulse scheme experiment [11]. An actinic pump pulse excites the molecule and initiates the photochemical re- action. The transient structure of the molecule, represented by its Raman spectrum, is then visualized at various time delays by the combination of a narrowband Raman pump pulse and a broadband probe pulse. This thesis addresses the study of the ultrafast dynamics of Tryptophan and Tryptophan-containing proteins within a Swiss NCCR - Molecular Ul- trafast Science Technology (MUST) project, thanks to the collaboration of two physics groups: the Femtoscopy group of Rome led by prof. Tullio Scopigno and GAP Biophotonics group of Geneve guided by prof. Jean- Pierre Wolf that was possible thanks to the Swiss-European Mobility Pro- gram (SEMP) internship. This work aims to study the application of the optimal dynamics discrimi- nation theory to two proteins that contains Tryptophan, human serum albu- min (HSA) and immunoglobulin G (IgG), with the help of coherent control experimental apparatus. In fact, since its great sensitivity to environment, Tryptophan’s fluorescence can be the perfect probe for the detection of dif- ferent proteins