Probing and Driving Molecular Dynamics with Femtosecond Pulses

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1 Miroslav Kloz Probing and Driving Molecular Dynamics with Femtosecond Pulses (wavelengths above 200 nm, energies below mj)

2 Why femtosecond lasers in biology?

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4 Scales of size and time are closely rerated! ms μs ns ps fs as

5 X-ray experiments are practically never at natural conditions (crystals, jets, vacuum, 77K..) Expensive => cannot be done at high throughput (there is just one Higgs boson, but millions of different organisms each with thousands of proteins) Structure does not directly explain function

6 BLUF domain Biological photo sensor Using FAD (Flavin Adenine Dinucleotide) as cofactor (biological APD )

7 Flavin, Cofactor operating in visible Visible near UV fs-ns

8 Amino acids UV fs-ns

9 Bond structure (vibration spectroscopy) Mid IR fs-μs

10 Backbone bulk modes THz ps - ms

11 Protein (cofactor) migration and aggregation (ms s)

12 No need for extreme powers or extreme time resolution BUT: But extremely broad probes (both in time and spectrally) Ideally non-invasive and tissue penetrating

13 Pulse sequences allows to resolve direct relation among processes Δt Detect by weak broadband pulses Excite by strong narrowband pulses Combine (time resolved experiment)

14 High power VIS + near UV/IR VIS + UV + IR MID - IR Ultrashort shaped spectrally narrowed

15 Time window

16 1 fs = s BIOLOGY ~4.3 x s since Big Bang ~2.5 x 10 9 s ~ Life of average men ~0.1 s fastest process we can perceive by our senses Femtosecond Too slow Common life experience Too fast

17 1 khz Regenerative amplifier 1 82 MHz oscillator seed gate 1 fs < Δt < 1 ms 1 khz Regenerative amplifier 2 Modern femtosecond laser technology allows to scan 10 orders of magnitude of dynamic range in a single experiment

18 Rhodopsin photoreceptors

19 fs-mid-ir ps-vis ultrashort ~5fs vis Supercontinum probe Actinic pulse (photo trigger) THz Fs transient absorption vis Fs transient absorption mid IR Mixed 2D IR x Raman Transient THz THz pumped transient absorption

20 Vibrational spectroscopy

21 Every bond has characteristic vibration

22 Direct: (E photon = E transition ) (Mid IR) ΔE E ΔE Raman: ΔE = E transition

23 Mid IR

24 Ground IR I 1 Transient I 0 vibration = log(i 1 /I 0 ) From Scatterhood..(2014)

25 Raman x Stimulated Raman

26 Spontaneous Raman scattering Inelastic light scattering photon splits into photon and phonon k2 photon E 2 E 1 ΔE phonon E E 1 - E 2

27 -k2 + k1 +k2 = k1 2 k1 k2 photon Pump Probe 1 0 parametric amplification phonon

28 In Raman spectroscopy you can chose your radiation based on: What is easiest (cheapest) to produce? What is most sensitive to detect? What is least invasive to the sample? What has the best penetration dept? What delivers shorter pulses?

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30 Signal is collected only in the volume where the pulses overlap with sufficient density Environment of the lab and sample cell can be ignored. No water problems! Distance between the sample and detector is unimportant (within the pointing stability of the laser)

31 femtosecond pulse triggers reaction under study (by heating, excitation, impulsively ) Δt FSRS probe records a snapshot of Raman spectra at given delay

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33 2D spectrocopy

34 At certain size incomputable Too many combinations.

35 Bump key Time domain 2D Lock picking Frequency domain 2D

36 excite one vibration and observe effect on the other Mapping GFP structure evolution during proton transfer with femtosecond Raman spectroscopy Link to 3D structure is much more direct! Nature (12 November 2009) Fang,...Mathies

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38 TOCSY spectra of a peptide NMR Photon echo of Fenna-Matthews-Olson complex (Nature, 2007)

39 Whole series of 2D spectroscopies can be run In some cases even simultaneously. fs-mid- IR ps-vis ultrashort ~5fs vis Conventional 2D IR Mixed 2D IR x Raman Raman in time domain 2D visible X-ray ω 1 -ω 2 X-ray Site specific excitation Dipole approximation no longer valid, any state can be excited regardless of symmetry Smaller spectral dispersion Fewer unwanted signals X-ray Raman resonant with core electrons

40 High power VIS + near UV/IR VIS + UV + IR MID - IR Ultrashort shaped spectrally narrowed

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42 Biology Mathematics (physics)

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45 At certain size incomputable Too many combinations.

46 Bump key Time domain 2D Lock picking Frequency domain 2D

47 excite one vibration and observe effect on the other Mapping GFP structure evolution during proton transfer with femtosecond Raman spectroscopy Link to 3D structure is much more direct! Nature (12 November 2009) Fang,...Mathies

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49 TOCSY spectra of a peptide NMR Photon echo of Fenna-Matthews-Olson complex (Nature, 2007)

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