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 ChemistryTheoretical Chemistry

Technical University of MunichTechnical University of Munich

Garching, GERMANYGarching, GERMANY

Ab initio studiesAb initio studies

Multireference ab initio methods to explore:Multireference ab initio methods to explore:

1)1) Excited-state potential-energy surfacesExcited-state potential-energy surfaces

2)2) Photochemical reaction pathsPhotochemical reaction paths

3)3) Conical intersectionsConical 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: femtochemistryDynamics at conical intersections: femtochemistry

MethodsMethods

Time-dependent wave-packet propagationTime-dependent wave-packet propagation

Reduced density-matrix propagationReduced 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 pyrazineProbability 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 Theory of femtosecond time-resolved nonlinear spectroscopyspectroscopy

Method developmentMethod development for the simulation of for the simulation of

general four-wave mixing spectra general four-wave mixing spectra

time-gated fluorescence spectra time-gated fluorescence spectra

time-resolved photoelectron spectratime-resolved photoelectron spectra

ApplicationsApplications

organic chromophoreorganic chromophore

Pump-probe spectra for amino acids and DNA basesPump-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

OH 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 machineryCatalytic mechanism of serine proteases machinery

Pen G: 1st confPen G: 1st conf

PenG: 2nd conf.PenG: 2nd conf.

3-cephem3-cephem carbapenemcarbapenem

Location of the transition state structure for 4 types of lactam antibiotic Location of the transition state structure for 4 types of lactam antibiotic

With Min1 more stable than Min2M.N. Ramquet, G. Dive, D. Dehareng J. Chem. Phys. 2000, 112, 4923 - 4934M.N. Ramquet, G. Dive, D. Dehareng J. Chem. Phys. 2000, 112, 4923 - 4934

Energy hypersurface analysisEnergy hypersurface analysis

Diels Alder: dicyclopentadieneDiels Alder: dicyclopentadieneTS « 7n »TS « 7n »

TS « Cope »TS « Cope »

In collaboration with M. Desouter and B. Lasorne Paris XIIn collaboration with M. Desouter and B. Lasorne Paris XI

Laboratoire de Chimie Quantique et Photophysique

Université Libre de Bruxelles

M. GodefroidJ. LiévinB. SutcliffeN. VaeckG. Verhaegen

E. CauëtN. 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

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 physicsTowards 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

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). Locationof minima, transition states, reaction paths, and, mainly, conical intersections is the firstinformation 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

NH2

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

AT

A

T

Phototherapeutic molecules: psoralen

Methods: Ab Initio CASSCF/CASPT2Requirements: 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/n* state). Fluorescing state: n* CASPT2 description: leading S0/S1 conical (Ground State/* state). Fluorescing state: *

S 1(n O m in* )S (1 m in* )

0.05.3

10.0

-0.8

(gs/* )CI

(gs/ * )CIn O

S 0

S 1 S 2

N 3

C 2

N 1

HC 6

HC 5

C 4

N 8

O 7

HH

S (gs0 m in)

Research topics of the Sobolewski group

related to the theory of radiation damage

UV

exc

itat

ion

radiationlessdecay

Ab initio explorations of the potentialenergy surfaces of bioaromatic systemsalong intramolecular coordinates relevantfor fast radiationless decay of electronicexcitation

Institute of Physics, Polish Academy of Science PL-02668 Warsaw

Large-amplitude out-of-plane vibrational motion

MIN- local minimumSP- saddle-pointCI- conical intersection

CASPT resultsat CASSCF-optimizedgeometry of the S1

potential-energy surface

1 ps 1 ps 1 ns -experimental lifetime

S1

S1

S0

S0

Guanine-Cytosine base pair

CASPT resultsat CIS-optimizedgeometry of the S1

potential-energy surface

LE-locally excited stateCT- charge-transfer stateNOM-nominal formSPT-single-proton transferred formETH- 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 processesThe 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 reactionsWave 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 intersectionexperiment: 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

= 248 nm7.5 kcal/mol !

Laboratoire de Chimie PhysiqueUniversité de Paris-Sud

Orsay 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

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

HH

Oh

Cl

Br

= 248nm

Simulation by quantum dynamics

Experimental branching ratio Cl:Br = 1.0:0.4

V2

D

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 CNRSUniversité Louis Pasteur, Strasbourg France

Quantum chemistry and excited states dynamics in transition metal complexes

Chantal DanielNadia Ben AmorHélène Bolvin

Alain StrichJulien 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

1MLCT 400fs

CO loss

Visible

XX3SBLCT Mn-H

homolysis

HM(CO)3(-diimine) M=Mn

Mn

-CO

ax

Mn-H

1MLCT

1MLCT