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 S1-S2 conical intersection of pyrazine

3 3.5 4 4.5 5 5.5 6 6.5 70

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

3 3.5 4 4.5 5 5.5 6 6.5 7−2

−1.5

−1

−0.5

0

0.5

1

1.5

2

3 3.5 4 4.5 5 5.5 6 6.5 7−2

−1.5

−1

−0.5

0

0.5

1

1.5

2

3 3.5 4 4.5 5 5.5 6 6.5 7−2

−1.5

−1

−0.5

0

0.5

1

1.5

2

3 3.5 4 4.5 5 5.5 6 6.5 7−2

−1.5

−1

−0.5

0

0.5

1

1.5

2

3 3.5 4 4.5 5 5.5 6 6.5 7−2

−1.5

−1

−0.5

0

0.5

1

1.5

2

3 3.5 4 4.5 5 5.5 6 6.5 7−2

−1.5

−1

−0.5

0

0.5

1

1.5

2

3 3.5 4 4.5 5 5.5 6 6.5 7−2

−1.5

−1

−0.5

0

0.5

1

1.5

2

Probability density of the S0 (left) and πσ* (right) diabatic states of pyrrole. Circle: position of the S1-S0 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 S1-S2 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, 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)

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)

CH2 CH2

C N

O

O

H N H

CH3

H

O

C

H

O

O

H

CH3CH2CH2

NH

C

H

O

H

H

OH

H

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 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 ββββ lactam antibiotic

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

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 π/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

in

out

in

out

in

out

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

C C

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 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

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:

N

NNH

N

N H 2

HN

N NH

N

O

H2N

NH

NH

O

O

NH

NH

O

O

N

NH

NH2

O

Monomers of DNA bases Pairs of DNA bases

A T

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 S0/S1 conical (Ground State/nπ* state). Fluorescing state: nπ*

CASPT2 description: leading S0/S1 conical (Ground State/ππ* state). Fluorescing state: ππ*

S1 (nO m inπ* )S (

1 minππ* )

0.05.3

10.0

-0.8

(gs/ππ* )CI

(gs/ π* )CI

nO

S0

S 1 S2

N3

C2

N1

HC6

HC5

C4

N8

O7

HH

S (gs0 min

)

Research topics of the Sobolewski group related to the theory of radiation

damage U

V e

xcit

ati

on

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-02668 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 S1

potential-energy surface

≤ 1 ps ≥ 1 ps > 1 ns -experimental lifetime

S1

S1

S0

S0

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

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-Montabonel Prof. 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, 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)

Work in progress

Cq+

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

L.J. Butler, Annu. Rev. Phys. Chem. 49, 125 (1998)

NONADIABATIC RECROSSING OF THEBARRIER = DIABATIC TRAPPING

λλλλ = 248 nm7.5 kcal/mol !

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 CH3OH by HADA in 1 + 11 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 hνννν

Cl

Br λλλλ = 248nm

Simulation by quantum dynamics

Experimental branching ratio Cl:Br = 1 .0:0.4

φ θ

V2D

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-(H2O)n H. Kang, K.T. Lee , S.K. Kim, Chem. Phys. Letters 359, 213 (2002).

-2,0

0,0

2,0

4,0

6,0

8,0

10,0

12,0

2 2,5 3 3,5 4

Adénine-H2OE (kcal/mol)

d (Å)

B3LYP/6-31G**MP2/6-31G**

HF/6-31G**

-0,4

-0,3

2 2,5 3 3,5 4

TDHF (3 états)Adénine+H

2OE (ua)

dA-W

(Å)

pi->pi*

n->pi*

interdite

permise

Reaction coordinate

Experimental signals

H transfer between OH radical

and different C of the ribose

-1

-0 .5

0

0 .5

-8 -6 -4 -2 0 2 4 6 8

Coordonnée de réaction

E a.u.

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

2 2.5 3 3.5 4 4.5 5 5.5 61.5

22.5

33.5

44.5

55.5

6

20000

30000

40000

50000

Mn-COaxial (Angs.)

Mn-H (Angs.)

Energy (cm-1)

0 fs

5 10

5

10

15

Mn-H (a.u.)

Mn-C

O (a.u.)

50 fs

5 10

5

10

15

Mn-H (a.u.)

150 fs

5 10

5

10

15

Mn-H (a.u.)

Mn-C

O (a.u.)

250 fs

5 10

5

10

15

Mn-H (a.u.)

•Quantum Chemical calculation of excited states properties in transition metal complexes

•Wavepacket simulation of excited dynamics and ultra-fast photofragmentation

processes in organometallics

1MLCT 400fs

CO loss

Visible

X X

3SBLCT Mn-H

homolysis

HM(CO)3(α-diimine) M=Mn

Mn

-CO

ax

Mn-H

1MLCT

1MLCT