COST%20P9

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COST P9 Radiation Damage in Biomolecular
Systems Working Group 4 Theoretical
developments for radiation damages
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Research topics of the Domcke group related to
the theory of radiation damage

• Theoretical Chemistry
• Technical University of Munich
• Garching, GERMANY

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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 ps state and
the ground state of pyrrole
Potential energy profiles of the lowest singlet
states of (a) phenol, (b) indole, (c) pyrrole
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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.

0 fs
6 fs
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 ps
(right) diabatic states of pyrrole. Circle
position of the S1-S0 conical intersection
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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
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Research topics of the Siena group related to the
theory of radiation damage Prof. Massimo
Olivucci, Dipartimento di Chimica (Università di
Siena, Italy)
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PHOTOISOMERIZATION MECHANISM AND EXCITED STATE
FORCE FIELD OF BIOLOGICAL CHROMOPHORES
DEVELOPMENT OF HYBRID METHODS FOR STUDYING
PHOTOISOMERIZATION PROCESSES IN LARGE MOLECULAR
SYSTEMS
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PHOTOISOMERIZATION MECHANISM AND EXCITED STATE
FORCE FIELD OF BIOLOGICAL CHROMOPHORES REACTION
PATH COMPUTATIONS IN GREEN FLUORESCENT PROTEIN
AND ITS MUTANTS
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COMPUTER DESIGN OF A NOVEL BIO-MIMETIC MOLECULAR
MOTOR
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INTERSECTION SPACE MAPPING OF ORGANIC AND
BIO-ORGANIC CHROMOPHORES
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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)

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Photochemistry with semiempirical methods.

• Aim running simulations of nonadiabatic dynamics
• Solution on the fly semiempirical calculation
  of CI wavefunctions and energies, with floating
  occupation MOs (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).

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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 matrixwhatever
  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.

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Research topics of the Liège group related to the
theory of radiation damage Dr. Georges Dive 
Centre dingénierie des protéines (Université
de Liège, Begium)
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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
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Location of the transition state structure for 4
types of b lactam antibiotic
PenG 2nd conf.
Pen G 1st conf
3-cephem
carbapenem
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With Min1 more stable than Min2
M.N. Ramquet, G. Dive, D. Dehareng J. Chem. Phys.
2000, 112, 4923 - 4934
Energy hypersurface analysis
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TS  7n 
Diels Alder dicyclopentadiene
TS  Cope 
In collaboration with M. Desouter and B. Lasorne
Paris XI
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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
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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).
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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
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Research Group QCEXVAL Quantum Chemistry of the
Excited State University of Valencia, Spain
Permanent and research staff Ph. 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
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)
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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
Pairs of DNA bases
Phototherapeutic molecules psoralen
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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)
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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
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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
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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
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Dynamics and Interactions

• Laboratoire de Spectrométrie Ionique
  Department of Theoretical Physics and et
  Moléculaire Mathematical Methods
• Université Claude Bernard- Lyon I Gdansk
  University of Technology CNRS (France)
  (Poland)
• Dr. Marie-Christine Bacchus-Montabonel Prof.
  Jozef E. Sienkiewicz
• Dr. Suzanne Tergiman
• Marta Labuda
• Katarzyna Piechowska

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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, 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 potentials U
  C2
• J. de Vries, R. Hoekstra, R. Morgenstern, T.
  Schlathölter, U C2 U C(2D) U
  C(2P),
• J. Phys. B 35, 4373 (2002)

Cq
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Photodissociation reactions

• Wave packet propagation methods for polyatomic
  systems with constrained Hamiltonian methodology.
• Collaboration Michèle Desouter-Lecomte-lcp Orsay
  and Nathalie Vaeck-ULB

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)
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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
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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
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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 ClBr 1.00.4
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).
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Some applications on the COST P9 theme
Simulation of pump-probe experiences on clusters
adenine-(H2O)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
IRC OH on C1
Reaction coordinate
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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
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• 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

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• Quantum Chemical calculation of excited states
  properties
• in transition metal complexes
• Wavepacket simulation of excited dynamics and
  ultra-fast photofragmentation processes in
  organometallics

1MLCT
Mn-COax
Mn-H
1MLCT