1. Primary Event in Vision

2. Ultrafast Photo-Isomerization Mechanism

3. Technological applications: associative memory devices R.R. Birge et.al. J. Phys. Chem. B 1999,103, 10746

4. Femto-second Spectroscopic Measurements

5. Boundary C -C of Lys296 ONIOM QM/MM B3LYP/631G*:Amber QM Layer (red): 54-atomsMM Layer (red): 5118-atoms E E ONIOM =E MM,full +E QM,red -E MM,red

6. Reaction Path: negative-rotation

7. Energy Storage Reaction Energy Profile: QM/MM ONIOM-EE (B3LYP/6-31G*:Amber) * Exp Value : Dihedral angle 11-cis rhodopsin all-trans bathorhodopsin Intermediate conformation

8. 11-cis rhodopsin all-trans bathorhodopsin Intermediate conformation

9. Isomerization Process C12 C11 N H2O Glu113 C13

10. Superposition of Rhodopsin and Bathorhodopsin in the Binding-Pocket: Storage of Strain-Energy

11. Charge-Separation Mechanism Reorientation of Polarized Bonds H H

12. Energy Storage[QM/MM ONIOM-EE (B3LYP/6-31G*:Amber)] Energy Storage[QM/MM ONIOM-ME(B3LYP/6-31G*:Amber)] - Electrostatic Contribution of Individual Residues Electrostatic Contribution to the Total Energy Storage 62%

13. TD-DFT Electronic Excitations ONIOM-EE (TD-B3LYP/6-31G*:Amber) E rhod. E TD-B3LYP//B3LYP/6-31G*:Amber CASPT2//CASSCF/6-31G*:Amber E batho. Experimental Values in kcal/mol 63.5 64.1 57.4 60.33.2 54.03.4

14. Time-Sliced Simulations of Quantum Processes

15. Wu,Y.; Batista, V.S. J. Chem. Phys. 118, 6720 (2003) Wu,Y.; Batista, V.S. J. Chem. Phys. 119, 7606 (2003) Wu,Y.; Batista, V.S. J. Chem. Phys. 121, 1676 (2004) Chen, X., Wu,Y.; Batista, V.S. J. Chem. Phys. 122, 64102 (2005) Wu,Y.; Herman, M.F.; Batista, V.S. J. Chem. Phys. 122, 114114 (2005) Wu,Y.; Batista, V.S. J. Chem. Phys. (2006) 124, 224305 Chen, X.; Batista, V.S. J. Chem. Phys. (2006) 125, 124313 Chen, X.; Batista, V.S. J. Photochem. Photobiol. 190, 274-282 (2007) MP/SOFT Method Trotter Expansion

16. Bichromatic coherent-control (Weak-field limit)

17. | k > | j > Isomerization coordinate, Quantum interference of molecular wavepackets associated with indistinguishable pathways to the same target state

18. Time dependent wavepacket undergoing nonadiabatic dynamics at the conical intersection of S1/S0 potential energy surfaces Chen X, Batista VS; J. Photochem. Photobiol. 190, 274-282 (2007)

19. Ground vibrational state

20. First Excited Vibrational State

21. Bichromatic coherent-control Pulse Relative Phases Pulse Relative Intensities

22. Bichromatic coherent-control Pulse Relative Phases Pulse Relative Intensities

23. Bichromatic coherent-control Pulse Relative Phases

24. Flores SC and Batista VS, J. Phys. Chem. B (2004) 108: 6745-6749 Gascon JA, Batista VS, Biophys. J. (2004) 87:2931-29411 Gascon JA, Sproviero EM, Batista VS, J. Chem. Theor. Comput. (2005) 1:674-685 Gascon JA, Sproviero EM, Batista VS, Acc. Chem. Res. (2006) 39, 184-193 Chen X and Batista VB, J. Photochem. Photobiol. submitted (2007) 190, 274-282, 2007 The Primary Step in Vision cis/trans isomerization in visual rhodopsin

25. Empirical model (Domcke, Stock)

26. Time dependent reactant population P trans (S 0 ) P cis (S 1 ) Chen X, Batista VS; J. Photochem. Photobiol. submitted (2007) * Flores SC and Batista VS, J. Phys. Chem. B (2004) 108: 6745-6749 MP/SOFT TDSCF * Time, fs 0.67

27. | k > | j > Isomerization coordinate, Quantum interference of molecular wavepackets associated with indistinguishable pathways to the same target state Flores SC; Batista VS, J. Phys. Chem. B 108: 6745-6749 (2004) Batista VS; Brumer P, Phys. Rev. Lett. 89, 143201 (2002)

28. Quantum interference of indistinguishable pathways to the same target state x O. Nairz, M. Arndt and A. Zeilinger Am. J. Phys. 71, 319 (2003) | j > | k > | x i > | x f >

29. CR = Bichirped Coherent Control Scenario Flores SC; Batista VS, J. Phys. Chem. B (2004) 108: 6745-6749 Chirped Pump Pulses (Wigner transformation forms)

30. Energy Reaction coordinate (Stretch. Coord.) S1S1 NC : PC : Impulsive Stimulated Raman Scattering

31. Excited State S1 Ground State S0 cistrans Exact Quantum Dynamics Simulations (t=218 fs, CR=212 fs 2 )

32. Positively Chirped Pulse (PC), strong field

33. Excited State S1 Ground State S0 cistrans Exact Quantum Dynamics Simulations (t=218 fs, CR=-146 fs 2 )

34. Negatively Chirped Pulse (NC), strong field

35. Bichirped Coherent Control Maps (1.2 ps) Pulse Relative Intensities Pulse Relative Phases

36. Conclusions We have shown that the photoisomerization of rhodopsin can be controlled by changing the coherence properties of the initial state in accord with a coherent control scenario that entails two femtosecond chirped pulses. We have shown that the underlying physics involves controlling the dynamics of a subcomponent of the system (the photoinduced rotation along the C11-C12 bond) in the presence of intrinsic decoherence induced by the vibronic activity. Control over 5-10% product yields should be possible, despite the ultrafast intrinsic decoherence phenomena, providing results of broad theoretical and experimental interest.

37. Conclusions We have shown that the ONIOM-EE (B3LYP/6-31G*:Amber) level of theory, in conjunction with high-resolution structural data, predicts the energy storage through isomerization, in agreement with experiments. We have shown that structural distortions account for 40% of the energy stored, while the remaining 60 % is electrostatic energy due to stretching of the salt-bridge between the protonated Schiff-base and the Glu113 counterion. We have shown that the salt-bridge stretching mechanism involves reorientation of polarized bonds due to torsion of the polyene chain at the linkage to Lys296, without displacing the linkage relative to Glu113 or redistributing charges within the chromophore

38. Conclusions (cont.) We have demonstrated that a hydrogen-bonded water molecule, consistently found by X-ray crystallographic studies, can assist the salt- bridge stretching process by stabilizing the reorientation of polarized bonds. We have shown that the absence of Wat2b, however, does not alter the overall structural rearrangements and increases the total energy storage in 1 kcal/mol. We have demonstrated that the predominant electrostatic contributions to the total energy storage result from the interaction of the protonated Schiff-based retinyl chromophore with four surrounding polar residues and a hydrogen bonded water molecule. We have shown that the ONIOM-EE (TD-B3LYP/6- 31G*:Amber//B3LYP/6-31G:Amber) level of theory, predicts vertical excitation energy shifts in quantitative agreement with experiments, while the individual excitations of rhodopsin and bathorhodopsin are overestimated by 10%.