Precipitaciones

Understanding how biological molecules balance excitation energy from multiple photons while maintaining high oxidation states can play an important role in photosynthesis mimicking solar devices. Excited state PCET plays a role in photosynthetic oxygen production by PS II and the oxygen evolving complex (OEC).39 In order to oxidize two water molecules to produce oxygen, four photons must be absorbed.39, 40

In the photosynthetic apparatus excited state energy is converted into transiently stored redox equivalents that drive PCET reactions for water oxidation and NADP reduction. Photochemically driven PCET in DNA base pairs is utilized to avoid photo-damage.41 The mechanisms by which coupled proton transfer events assist in excited state energy dissipation and photostability in DNA molecule base pairs has been explored by ultrafast transient laser techniques.4241 Proton transfer events in photoexcited Watson-Crick DNA base pairs occur on extremely rapid time scales. Calculations on guanine-cytosine (GC) base pairs predict

conical intersections that connect the * excited state to the ground state.41 The net proton transfer event is illustrated in Figure 2.17.

Figure 2.17. Watson-Crick ground state guanine-cytosine base pair, shown following excitation and resultant excited state proton transfer. Figure from Markwick, 2007.41

These charge transfer pathways connect excited states with ground states and avoid photodamage through rapid relaxation directly to the ground state through conical intersections.41, 43 Similar ultrafast deactivation through a conical intersection is also observed in Watson-Crick adenine-thymine (AT) base pairs.10

Hydrogen bonding is an integral feature of most biological structures, and may play a general role in excited state dynamics and reactivity following charge transfer excitation of peptides. 43 Green Fluorescent Proteins (GFP) offer an example where hydrogen bonding and proton transfer play important roles in excited state dynamics based on recent

experimental and theoretical studies.44-49 Prior hydrogen bonding ensures that proton transfer events triggered by photoexcitation can occur following light absorption. This conclusion is supported by computational studies.45, 49

Ultrafast time-resolved fluorescence studies show that the neutral transition state (I*) is formed very rapidly (< 1 ps) following excitation to the initial neutral excited state (A*).48 The rapid (sub-picosecond) time scale means the A*  I* transition occurs more rapidly “than excess energy can be dissipated, and the initial I* state is formed vibrationally hot.”48 “Pre-existence of a low-barrier or barrierless H-bond between the phenol group of the chromophore and a side chain of aspartate” ensures facile proton transfer.48 Figure 2.18, shows the initial configuration of the GFP protein, A. Following excitation and the sequence, A  A*  I*, the intermediate state, I*, either relaxes to the ground state and returns to A, or follows an alternate path to B* which decays to a long lived B state.47-49 This structure helps create a series of hydrogen bonding protons throughout the molecule or a proton wire effect that facilitates proton shifts through this bonded system. An example of the proton wire effect is illustrated in Figure 2.19 which is observed following excitation in wild type GFP.46

Figure 2.18. Illustration of interconversion between A and B forms of the green fluorescent protein (GFP) chromophore through I*. Figure from Stoner-Ma, 2008 (adapted from Brejc et al).48

Figure 2.19. Proton wire effect leading to excited state proton transfer (ESPT) following excitation in wild-type GFP. Excitation at 370-400 nm, leads to stepwise proton transfer through the structure to Glu222. Figure from Remington, 2006.46

2.7 References

1.  DiLabio, G. A.; Johnson, E. R., Journal of the American Chemical Society 2007, 129 (19), 6199‐

6203.   

2.  Ding, F. Z.; Smith, J. M.; Wang, H. B., Journal of Organic Chemistry 2009, 74 (7), 2679‐2691.   

3.  Edwards, S. J.; Soudackov, A. V.; Hammes‐Schiffer, S., Journal of Physical Chemistry A 2009, 

113 (10), 2117‐2126.   

4.  Hammes‐Schiffer, S.; Soudackov, A. V., J. Phys. Chem. B 2008, 112 (45), 14108‐14123.   

5.  Gagliardi, C. J.; Westlake, B. C.; Kent, C. A.; Paul, J. J.; Papanikolas, J. M.; Meyer, T. J., 

Coordination Chemistry Reviews In Press, Corrected Proof.   

6.  Venkataraman, C.; Soudackov, A. V.; Hammes‐Schiffer, S., Journal of Chemical Physics 2009, 

131 (15), 11.   

7.  Cox, M. J.; Siwick, B. J.; Bakker, H. J., ChemPhysChem 2009, 10 (1), 236‐244.   

8.  Nunes, R. M. D.; Pineiro, M.; Arnaut, L. G., J. Am. Chem. Soc. 2009, 131 (26), 9456‐9462.   

9.  Frutos, L. M.; Markmann, A.; Sobolewski, A. L.; Domcke, W., J. Phys. Chem. B 2007, 111 (22), 

6110‐6112.   

10.  Perun, S.; Sobolewski, A. L.; Domcke, W., Journal of Physical Chemistry A 2006, 110 (29), 

9031‐9038.   

11.  Samoylova, E.; Radloff, W.; Ritze, H.‐H.; Schultz, T., J. Phys. Chem. A 2009, 113 (29), 8195‐

8201. 

12.  Balzani, V.; Bergamini, G.; Ceroni, P., Coordination Chemistry Reviews 2008, 252 (23‐24), 

2456‐2469.   

13.  Lan, Z. G.; Frutos, L. M.; Sobolewski, A. L.; Domcke, W., Proceedings of the National 

Academy of Sciences of the United States of America 2008, 105 (35), 12707‐12712.   

14.  Prashanthi, S.; Bangal, P. R., Chemical Communications 2009,  (13), 1757‐1759.   

15.  Freys, J. C.; Bernardinelli, G.; Wenger, O. S., Chemical Communications 2008,  (36), 4267‐

4269.   

16.  Kinoshita, I.; Hashimoto, H.; Nishioka, T.; Miyamoto, R.; Kuwamura, N.; Yoshida, Y., 

Photosynthesis Research 2008, 95 (2‐3), 363‐371.   

17.  Rosenthal, J.; Young Elizabeth, R.; Nocera Daniel, G., Inorg Chem 2007, 46 (21), 8668‐75.   

18.  Hodgkiss, J. M.; Krivokapic, A.; Nocera, D. G., J. Phys. Chem. B 2007, 111 (28), 8258‐8268.   

19.  Hodgkiss, J. M.; Damrauer, N. H.; Presse, S.; Rosenthal, J.; Nocera, D. G., Journal of Physical 

Chemistry B 2006, 110 (38), 18853‐18858.   

20.  Irebo, T.; Reece, S. Y.; Sjodin, M.; Nocera, D. G.; Hammarstrom, L., Journal of the American 

Chemical Society 2007, 129 (50), 15462.   

21.  Tishchenko, O.; Truhlar Donald, G.; Ceulemans, A.; Nguyen Minh, T., J Am Chem Soc 2008, 

130 (22), 7000‐10.   

22.  Skone, J. H.; Soudackov, A. V.; Hammes‐Schiffer, S., Journal of the American Chemical Society 

2006, 128 (51), 16655‐16663.   

23.  Sobolewski, A. L.; Domcke, W., J. Phys. Chem. A 2007, 111 (46), 11725‐11735.   

24.  Silverman, L. N.; Spry, D. B.; Boxer, S. G.; Fayer, M. D., J. Phys. Chem. A 2008, 112 (41), 

10244‐10249.   

25.  Gepshtein, R.; Leiderman, P.; Huppert, D.; Project, E.; Nachliel, E.; Gutman, M., J Phys Chem 

B 2006, 110 (51), 26354‐64.   

26.  Spry, D. B.; Fayer, M. D., J Chem Phys 2007, 127 (20), 204501.   

27.  Spry, D. B.; Fayer, M. D., J Chem Phys 2008, 128 (8), 084508.   

28.  Chen, X. H.; Turecek, F., Journal of the American Chemical Society 2006, 128 (38), 12520‐

12530.   

29.  Catalan, J.; Diaz, C.; de Paz, J. L. G., Chemical Physics Letters 2006, 419 (1‐3), 164‐167.   

30.  Sekiya, H.; Sakota, K., Journal of Photochemistry and Photobiology C‐Photochemistry 

Reviews 2008, 9 (2), 81‐91.   

31.  Takeuchi, S.; Tahara, T., Proceedings of the National Academy of Sciences of the United 

States of America 2007, 104 (13), 5285‐5290.   

32.  Yamada, H.; Tanabe, K.; Ito, T.; Nishimoto, S., Chemistry‐a European Journal 2008, 14 (33), 

10453‐10461.   

33.  Concepcion, J. J.; Brennaman, M. K.; Deyton, J. R.; Lebedeva, N. V.; Forbes, M. D. E.; 

Papanikolas, J. M.; Meyer, T. J., Journal of the American Chemical Society 2007, 129 (22), 

6968.   

34.  Ludlow Michelle, K.; Soudackov Alexander, V.; Hammes‐Schiffer, S., J Am Chem Soc 2009, 

131 (20), 7094‐102.   

35.  Zhang, H.; Rajesh, C. S.; Dutta, P. K., J. Phys. Chem. A 2008, 112 (5), 808‐817.   

36.  Irebo, T.; Reece, S. Y.; Sjoedin, M.; Nocera, D. G.; Hammarstroem, L., J. Am. Chem. Soc. 2007, 

129 (50), 15462‐15464.   

37.  Irebo, T.; Johansson, O.; Hammarstrom, L., Journal of the American Chemical Society 2008, 

130 (29), 9194.   

38.  Gavrilyuk, A.; Tritthart, U.; Gey, W., Philosophical Magazine 2007, 87 (29), 4519‐4553.   

39.  Barry, B. A.; Cooper, I. B.; De Riso, A.; Brewer, S. H.; Vu, D. M.; Dyer, R. B., Proceedings of the 

National Academy of Sciences of the United States of America 2006, 103 (19), 7288‐7291.   

40.  Cooper, I. B.; Barry, B. A., Biophysical Journal 2008, 95 (12), 5843‐5850.   

41.  Markwick, P. R. L.; Doltsinis, N. L., J Chem Phys 2007, 126 (17), 175102.   

42.  de La Harpe, K.; Crespo‐Hernandez, C. E.; Kohler, B., J. Am. Chem. Soc. 2009, 131 (48), 

17557‐17559.   

43.  Sobolewski, A. L.; Domcke, W., ChemPhysChem 2006, 7 (3), 561‐564.   

44.  Leiderman, P.; Huppert, D.; Agmon, N., Biophysical Journal 2006, 90 (3), 1009‐1018.   

45.  Manca, C., Chemical Physics Letters 2007, 443 (4‐6), 173‐177.   

46.  Remington, S. J., Current Opinion in Structural Biology 2006, 16 (6), 714‐721.   

47.  Stoner‐Ma, D.; Melief, E. H.; Nappa, J.; Ronayne, K. L.; Tonge, P. J.; Meech, S. R., Journal of 

Physical Chemistry B 2006, 110 (43), 22009‐22018.   

48.  Stoner‐Ma, D.; Jaye, A. A.; Ronayne, K. L.; Nappa, J.; Meech, S. R.; Tonge, P. J., Journal of the 

American Chemical Society 2008, 130 (4), 1227‐1235.   

49.  Vendrell, O.; Gelabert, R.; Moreno, M.; Lluch, J. M., Journal of the American Chemical Society 

2006, 128 (11), 3564‐3574.   

Chapter 3

3.1 Introduction

Experiments to probe Electron-Proton Transfer (EPT) dynamics presented in this dissertation were done using ultrafast techniques. The primary technique used to investigate excited state absorptions was femtosecond Transient Absorption (fsTA). When necessary, additional spectroscopic techniques such as nanosecond Transient Absorption (nsTA), Time Correlated Single Photon Counting (TCSPC), and Coherent Raman were performed.

FsTA is an ultrafast pump-probe technique. Our experimental setup allows us to probe excited state absorption or in some cases stimulated emission from 250 fs to 900 ps, providing transient spectra at early times. In the case of nitrophenyl-phenol where additional excited state dynamics continue beyond the fsTA experimental capabilities, additional nsTA experiments were done to probe from 10 ns to microseconds. Alternatively in the case of hydroxycoumarin, TCSPC was used to supplement the fsTA data. TCSPC is a sensitive emission technique with an instrument response of 200 ps, capable of measuring emission out to 56 ns. Finally, Coherent Raman techniques were used to obtain spectra at 20 fs of the excited molecules.

The first section of this chapter discusses the fsTA pump-probe technique in detail. Including a description of the laser source, pump pulse generation, probe pulse generation, experimental setup, and data collection methods. The second section of this chapter briefly describes the ultrafast techniques used to take additional measurements: nsTA, TCSPC, and Coherent Raman. The final section describes sample preparation and characterization.