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

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

Ab initio studies Multireference ab initio methods to explore: 1) Excited-state potential-energy surfaces 2) Photochemical reaction paths 3) Conical intersections Applications  Photochemistry of biomolecules aromatic amino acids (tryptophan and tyrosine) DNA and RNA bases.  Isolated systems and solvated complexes in water or ammonia 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

Dynamics at conical intersections: femtochemistry Methods  Time-dependent wave-packet propagation  Reduced density-matrix propagation Observables for analysis  electronic population probabilities  coherence and energy transfer of vibrational modes  reaction probabilities for photodissociation. Time-dependent probability density of the tuning mode of the S 1 -S 2 conical intersection of pyrazine Probability density of the S 0 (left) and πσ* (right) diabatic states of pyrrole. Circle: position of the S 1 -S 0 conical intersection 0 fs 6 fs 12 fs 18 fs

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 Integral transient transmittance spectrum for the S 1 -S 2 conical intersection of pyrazine Resonance Raman (a) and stimulated emission (b) contributions to the integral transient transmittance spectrum of pyrazine

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

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

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

COMPUTER DESIGN OF A NOVEL BIO-MIMETIC MOLECULAR MOTOR

INTERSECTION SPACE MAPPING OF ORGANIC AND BIO- ORGANIC CHROMOPHORES

Maurizio Persico, Benedetta Mennucci, Giovanni Granucci Dipartimento di Chimica e Chimica Industriale Università di Pisa Polarizable 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, (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)

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).

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.

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)

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

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

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

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

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

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

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

Research Group QCEXVAL Quantum Chemistry of the Excited State University of Valencia, Spain Main Research Lines 1. Quantum-Chemical Photobiology in the Excited State: Photophysics and Photochemistry of Biomolecules (BIOQCEX) 2. Theoretical Ab Initio Spectroscopy (THEOSPEC) 3. Molecular Direct Ab Initio Reaction Dynamics for the Excited State (RADEX) Permanent and research staffPh. D. Students Dr. Manuela Merchán Teresa Climent Dr. Luis Serrano-Andrés (Local COST coordinator) Daniel Roca Sanjuán Dr. Remedios González-Luque Juan José Serrano Pérez Dr. Mercedes Rubio

Radiation Damage in Biological Systems: Quantum-Chemical Photochemistry in the Excited State 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 basesPairs of DNA bases AT A T Phototherapeutic molecules: psoralen

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 Example: ultrafast radiationless relaxation of singlet excited cytosine M. Merchán y L. Serrano-Andrés, J. Am. Chem. Soc. 125, 8108 (2003) CASSCF description: leading S 0 /S 1 conical (Ground State/n  * state). Fluorescing state: n  * CASPT2 description: leading S 0 /S 1 conical (Ground State/  * state). Fluorescing state:  *

Research topics of the Sobolewski group related to the theory of radiation damage UV excitation radiationless decay 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 Warsaw

Large-amplitude out-of-plane vibrational motion MIN- local minimum SP- saddle-point CI- conical intersection CASPT results at CASSCF-optimized geometry of the S 1 potential-energy surface  1 ps  1 ps  1 ns -experimental lifetime S1S1 S1S1 S0S0 S0S0

Guanine-Cytosine base pair CASPT results at CIS-optimized geometry of the S 1 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

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

Charge transfer processes 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, (2001) IJQC, 89, 322 (2002); IJQC 97 (2004) - wave packet propagations methods Phys. Rev. A 63, (2001) J. Chem. Phys. 114, 8741 (2001) Ion-biomolecule reactions : Uracyl + C q+ experiment : Adiabatic potentials U + C 2+ J. de Vries, R. Hoekstra, R. Morgenstern, T. Schlathölter, U + C 2+ ; U + + C +(2 D); U + + C +(2 P), J. Phys. B 35, 4373 (2002) Work in progress C q+

Photodissociation reactions Wave packet propagation methods for polyatomic systems with constrained Hamiltonian methodology. Collaboration Michèle Desouter-Lecomte-lcp Orsay and Nathalie Vaeck-ULB 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) Problems : - mechanism involving excited states - selective dissociation - non-adiabatic effects

Laboratoire de Chimie Physique Université de Paris-Sud Orsay France M. 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

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

Some recent applications Tunneling splitting in CH 3 OH by HADA in D S. Blasco and D. Lauvergnat, Chem. Phys. Lett, 373, 344 (2003) Diabatic trapping in the competitive dissociation of bromoacethyl chloride in excited electronic states B. Lasorne, M.-C. Bacchus-Montabonel, N. Vaeck and M. Desouter-Lecomte J. Chem. Phys. 120, 1271, 2004 C C H H O h Cl Br = 248nm Simulation by quantum dynamics Experimental branching ratio Cl:Br = 1.0:0.4   V2DV2D B. Lasorne, G. Dive, D. Lauvergnat and M. Desouter-Lecomte, J. Chem. Phys., 118, 5831 (2003). Analysis of wave packet behavior when the reaction path model breaks down Isomerisation of methoxy radical Dimerisation of cyclopentadiene Tunneling splitting around 9 cm - 1

Some applications on the COST P9 theme Simulation of pump-probe experiences on clusters adenine-(H 2 O) n H. 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 Reaction coordinate IRC OH° on C1

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

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

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