Theoretical Developments for Radiation Damage in Biomolecular Systems

1. COST P9 Radiation Damage in Biomolecular Systems Working Group 4 Theoretical developments for radiation damages

2. Research topics of the Domcke group related to the theory of radiation damage Theoretical Chemistry Technical University of Munich Garching, GERMANY

3. Ab initio studies Applications • Photochemistry of biomolecules • aromatic amino acids (tryptophan and tyrosine) • DNA and RNA bases. • Isolated systems and solvated complexes in water or ammonia Multireference ab initio methods to explore: • Excited-state potential-energy surfaces • Photochemical reaction paths • Conical intersections Conical intersection between the πσ* state and the ground state of pyrrole Potential energy profiles of the lowest singlet states of (a) phenol, (b) indole, (c) pyrrole

4. Dynamics at conical intersections: femtochemistry Observables for analysis • electronic population probabilities • coherence and energy transfer of vibrational modes • reaction probabilities for photodissociation. 0 fs 6 fs Methods • Time-dependent wave-packet propagation • Reduced density-matrix propagation 12 fs 18 fs Time-dependent probability density of the tuning mode of the S1-S2 conical intersection of pyrazine Probability density of the S0 (left) and πσ* (right) diabatic states of pyrrole. Circle: position of the S1-S0 conical intersection

5. Theory of femtosecond time-resolved nonlinear spectroscopy Method development for the simulation of • general four-wave mixing spectra • time-gated fluorescence spectra • time-resolved photoelectron spectra Applications organic chromophore Pump-probe spectra for amino acids and DNA bases Resonance Raman (a) and stimulated emission (b) contributions to the integral transient transmittance spectrum of pyrazine Integral transient transmittance spectrum for the S1-S2 conical intersection of pyrazine

6. Research topics of the Siena group related to the theory of radiation damage Prof. Massimo Olivucci, Dipartimento di Chimica (Università di Siena, Italy)

7. PHOTOISOMERIZATION MECHANISM AND EXCITED STATE FORCE FIELD OF BIOLOGICAL CHROMOPHORES DEVELOPMENT OF HYBRID METHODS FOR STUDYING PHOTOISOMERIZATION PROCESSES IN LARGE MOLECULAR SYSTEMS

8. PHOTOISOMERIZATION MECHANISM AND EXCITED STATE FORCE FIELD OF BIOLOGICAL CHROMOPHORES REACTION PATH COMPUTATIONS IN GREEN FLUORESCENT PROTEIN AND ITS MUTANTS

9. COMPUTER DESIGN OF A NOVEL BIO-MIMETIC MOLECULAR MOTOR

10. INTERSECTION SPACE MAPPING OF ORGANIC AND BIO-ORGANIC CHROMOPHORES

11. Maurizio Persico, Benedetta Mennucci, Giovanni Granucci Dipartimento di Chimica e Chimica IndustrialeUniversità di PisaPolarizable Continuum Model • Treatment of solvent effects by a Polarizable Continuum Model (PCM) • The Hamiltonian of the solute includes the reaction field generated by the solvent • The solute cavity is of arbitrary shape and the solvent response is computed in terms of an apparent surface charge spread on the cavity • Geometry optimization of solvated molecules with analytical gradients for many kinds of ab initio wavefunctions • Many static and dynamic properties of solutes (optical, magnetic etc). (Tomasi et al, Phys. Chem. Chem. Phys., 4, 5697, 2002) • Excited state calculations taking into account solvent reorganization (Mennucci et al, J. Am. Chem. Soc., 122, 10621 (2000); J. Phys. Chem. A, 105, 7126 (2001); J. Phys. Chem. A, 105, 4749 (2001). • Excitation energy transfer between solvated chromophores (Iozzi et al, J. Chem. Phys. in press)

12. Photochemistry with semiempirical methods. • Aim: running simulations of nonadiabatic dynamics • Solution: “on the fly” semiempirical calculation of CI wavefunctions and energies, with floating occupation MO’s (Granucci et al, J. Chem. Phys. 114, 10608, 2001). • Optimization of semiempirical parameters, to reproduce ab initio and/or experimental data. • Semiclassical treatment of the dynamics (surface hopping). • Swarms of trajectories with sampling of initial conditions according to Wigner or Boltzmann distributions. • Results: reaction mechanism, quantum yields, decay times, transient spectra, etc • Typical application: photoisomerization of azobenzene (Ciminelli et al, Chem. Eur. J., in press).

13. Photochemistry of complex systems by a QM/MM extension of the semiempirical method. • QM subsystem: the chromophore and/or reactive centre. • MM subsytem: the solvent, a solid surface, a natural or synthetic polymeric matrix…whatever takes part in the dynamics without breaking bonds or getting electronically excited. • The electrostatic interactions between the QM and MM subsystems are introduced into the QM hamiltonian, for a correct treatment of state-specific effects of the environment (Persico et al, THEOCHEM 621, 119, 2003). • Covalent bonding between the QM and MM subsystems is represented by the “connection atom” method (Toniolo et al, Theoret. Chem. Acc., in press) • Typical applications: photodissociation of ClOOCl adsorbed on ice; internal conversion dynamics of the chromophore of the Green Fluorescent Protein, in vacuo, in water and in the biological matrix.

14. Research topics of the Liège group related to the theory of radiation damage Dr. Georges Dive : Centre d’ingénierie des protéines (Université de Liège, Begium)

15. Catalytic mechanism of serine proteases machinery Transition state model of the cooperative effect between several amino acids Glu 166 Ser 130 Ser 70 Lys 73

16. Location of the transition state structure for 4 types of b lactam antibiotic PenG: 2nd conf. Pen G: 1st conf 3-cephem carbapenem

17. With Min1 more stable than Min2 M.N. Ramquet, G. Dive, D. Dehareng J. Chem. Phys. 2000, 112, 4923 - 4934 Energy hypersurface analysis

18. TS « 7n » Diels Alder: dicyclopentadiene TS « Cope » In collaboration with M. Desouter and B. Lasorne Paris XI

19. Laboratoire de Chimie Quantique et Photophysique Unité de Chimie Quantique et Physique Atomique Université Libre de Bruxelles M. Godefroid J. Liévin B. Sutcliffe N. Vaeck G. Verhaegen E. Cauët N. Rinskoff

20. Ab initio calculations on biological systems Interactions at the protein-DNA interface Electron transfer in DNA • Ionization potentials of isolated and stacked DNA bases • Excited states of the cations • cation p/H-bond stair motifs Ade+ / Thy+ Cyt+ Gua+ • Histidine - adenine complexes • Reaction path for the electron transfer process Current collaborations : M. Rooman, R. Wintjens and C. Biot (ULB).

21. Nonadiabatic molecular dynamics • Electron transfers processes • of astrophysical interest • for plasma physics • Towards intra or inter biomolecular processes Photodissociations Cl H C C O Br • Towards dissociation by electronic impact Towards optical control of nonadiabatic dynamics Current collaborations : M. Desouter-Lecomte, Orsay and M-C Bacchus-Montabonel, Lyon I

22. Radiation Damage in Biological Systems: Quantum-Chemical Photochemistry in the Excited State T A T A After radiative excitation, relaxation of the energy on the excited state of biological systems may lead to: Ultrafast radiationless deactivation: avoids damage Productive photochemistry: isomerizations, mutations,... The process takes place dynamically on potential energy hypersurfaces (PES). Location of minima, transition states, reaction paths, and, mainly, conical intersections is the first information that quantum chemistry should provide. Goal: to locate conical intersections (CI) and compute reaction paths for relevant biological systems using ab initio methods: Monomers of DNA bases Phototherapeutic molecules: psoralen Pairs of DNA bases

23. Example: ultrafast radiationless relaxation of singlet excited cytosine Methods: Ab Initio CASSCF/CASPT2 Requirements: Location of Conical Intersections and computation of reaction paths with methods that include dynamic correlation (CASPT2, MRCI...). Warning: CASSCF and CASPT2 descriptions differ in many cases CASSCF description: leading S0/S1 conical (Ground State/np* state). Fluorescing state: np* CASPT2 description: leading S0/S1 conical (Ground State/pp* state). Fluorescing state: pp* M. Merchán y L. Serrano-Andrés,J. Am. Chem. Soc. 125, 8108 (2003)

24. radiationless decay UV excitation Research topics of the Sobolewski group related to the theory of radiation damage Ab initio explorations of the potential energy surfaces of bioaromatic systems along intramolecular coordinates relevant for fast radiationless decay of electronic excitation Institute of Physics, Polish Academy of Science PL-02668 Warsaw

25. Large-amplitude out-of-plane vibrational motion CASPT results at CASSCF-optimized geometry of the S1 potential-energy surface S1 S0 S1 MIN- local minimum SP- saddle-point CI- conical intersection S0  1 ps  1 ps  1 ns -experimental lifetime

26. Guanine-Cytosine base pair CASPT results at CIS-optimized geometry of the S1 potential-energy surface LE-locally excited state CT- charge-transfer state NOM-nominal form SPT-single-proton transferred form ETH- out-of-plane deformed cytosine ring

27. Dynamics and Interactions Laboratoire de Spectrométrie Ionique Department of Theoretical Physics andet MoléculaireMathematical Methods Université Claude Bernard- Lyon I Gdańsk University of Technology CNRS (France)(Poland) Dr. Marie-Christine Bacchus-Montabonel Prof. Jozef E. Sienkiewicz Dr. Suzanne Tergiman Marta Łabuda Katarzyna Piechowska

28. The group has a wide experience in the field of charge-transfer in ion-atom or molecule processes, in particular with multiply charged ions. Theoretical treatment : - ab-initio molecular calculations - semi-classical or quantal dynamical approaches Phys. Rev A 64, 042721 (2001) IJQC, 89, 322 (2002); IJQC 97 (2004) - wave packet propagations methods Phys. Rev. A 63, 042704 (2001) J. Chem. Phys. 114, 8741 (2001) Ion-biomolecule reactions : Uracyl + Cq+ experiment :Adiabatic potentialsU + C2+ J. de Vries, R. Hoekstra, R. Morgenstern, T. Schlathölter, U + C2+; U+ + C+(2D); U+ + C+(2P), J. Phys. B 35, 4373 (2002) Work in progress Charge transfer processes Cq+

29. Wave packet propagation methods for polyatomic systems with constrained Hamiltonian methodology. Collaboration Michèle Desouter-Lecomte-lcp Orsay and Nathalie Vaeck-ULB Photodissociation reactions Problems: - mechanism involving excited states - selective dissociation - non-adiabatic effects Method: - ab-initio potential energy curves and couplings - hierarchy among coordinates, only active coordinates treated explicitely - wave packet propagation dynamics Examples : Photodissociation of bromoacetyl chloride at 248 nm experiment: L. Butler et al. J. Chem. Phys. 99, 4479 (1993) Photodissociation of vinoxy radical : conical intersection experiment: L.J. Butler et al. J. Chem. Phys. 119, 176 (2003) J. Chem. Phys. 115, 204 (2001)

30. Laboratoire de Chimie PhysiqueUniversité de Paris-SudOrsay FranceM. Desouter-Lecomte and D. Lauvergnat Quantum dynamics in reduced dimensionality in critical region of potential energy surfaces Large amplitude motion in flexible molecules Non adiabatic processes in excited electronic states Wave packets dynamics in bifurcating regions Tunneling during transfer of a light particle Optimum control of wave packet dynamics Dissipative Dynamics

31. Methodology Selection of a group of active coordinates representative of the process Dynamics in the active subspace by Constrained Hamiltonian formalism Coupled adiabatic channels equations or more simply, the Harmonic Adiabatic Approximation (HADA) The Kinetic Energy Operator in Z-matrix coordinates used for the ab initio computation is generated numerically by the Tnum algorithm Extension of the dimension of the quantum active subspace : MCTDH method Analysis of the wave packets Extraction of charge exchange cross section, branching ratio of reactive fluxes, microcanonical or thermal rate constants, vibrational spectrum Discussion of reaction mechanisms

32. Cl H V2D H Br C C l = 248nm f q O hn Some recent applications Tunneling splitting around 9 cm-1 Tunneling splitting in CH3OH by HADA in 1 + 11 D S. Blasco and D. Lauvergnat, Chem. Phys. Lett, 373, 344 (2003) Experimental branching ratio Cl:Br = 1.0:0.4 Diabatic trapping in the competitive dissociation of bromoacethyl chloride in excited electronic states Simulation by quantum dynamics B. Lasorne, M.-C. Bacchus-Montabonel, N. Vaeck and M. Desouter-Lecomte J. Chem. Phys. 120, 1271, 2004 Analysis of wave packet behavior when the reaction path model breaks down Isomerisation of methoxy radical Dimerisation of cyclopentadiene B. Lasorne, G. Dive, D. Lauvergnat and M. Desouter-Lecomte, J. Chem. Phys., 118, 5831 (2003).

33. Some applications on the COST P9 theme Simulation of pump-probe experiences on clusters adenine-(H2O)nH. Kang, K.T. Lee , S.K. Kim, Chem. Phys. Letters 359, 213 (2002). Reaction coordinate Experimental signals H transfer between OH radical and different C of the ribose IRC OH° on C1 Reaction coordinate

34. COST Action P9 Radiation damage in Biomolecular systems Working Group 4: Theoretical Development Laboratoire de Chimie Quantique UMR 7551 CNRS Université Louis Pasteur, Strasbourg France Quantum chemistry and excited states dynamics in transition metal complexes Chantal Daniel Nadia Ben Amor Hélène Bolvin Alain Strich Julien Bossert Ph D Sébastien Villaume Ph D

35. Low-lying absorbing states (UV/visible): spectra, structure, dynamics • Quantum Chemical methods: highly correlated electronic methods • Role of the spin-orbit interactions and non-adiabatic effects • Quantum Dynamics: wavepacket propagations on 1 or 2-D PES • Time-dependent evolution of the molecular system within the first 10 ps

36. Quantum Chemical calculation of excited states properties • in transition metal complexes • Wavepacket simulation of excited dynamics and ultra-fast photofragmentation processes in organometallics HM(CO)3(a-diimine) M=Mn 400fs 1MLCT CO loss X 3SBLCT X Mn-H homolysis Visible 1MLCT Mn-COax Mn-H 1MLCT

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