Download Dynamics at conical intersections

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
Applications

 aromatic amino acids
(tryptophan and tyrosine)
2) Photochemical reaction paths
 DNA and RNA bases.
3) Conical intersections

Potential energy profiles of the lowest singlet
states of (a) phenol, (b) indole, (c) pyrrole
Photochemistry of biomolecules
Isolated systems and solvated complexes
in water or ammonia
Conical intersection
between
the πσ* state and the
ground state of pyrrole
Dynamics at conical intersections: femtochemistry
Methods
Observables for analysis

Time-dependent wave-packet propagation

electronic population probabilities

Reduced density-matrix propagation

coherence and energy transfer of vibrational
modes

reaction probabilities for photodissociation.
0 fs
6 fs
12 fs
18 fs
Probability density of the S0 (left) and πσ* (right) diabatic
states of pyrrole. Circle: position of the S1-S0 conical
intersection
Time-dependent probability density of the tuning mode
of the S1-S2 conical intersection of pyrazine
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 BIOORGANIC 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 statespecific 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)
Catalytic mechanism of serine proteases machinery
Transition state model of the cooperative effect between several
amino acids
H
Glu 166
C
O
O
CH2
CH2
H
H
N
Ser 70
H
CH2
H
H
N
C
O
C
O
O
H
H
O
H
H N
Ser 130
H
O
CH2
CH3
CH3
Lys 73
Location of the transition state structure for 4 types of b lactam antibiotic
PenG: 2nd conf.
Pen G: 1st conf
3-cephem
carbapenem
WithM.N.
Min1
moreG.stable
Min2
Ramquet,
Dive, D. than
Dehareng
J. Chem. Phys. 2000, 112, 4923 - 4934
Energy hypersurface analysis
TS « 7n »
Diels Alder: dicyclopentadiene
TS « Cope »
In collaboration with M. Desouter and B. Lasorne Paris XI
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
Ab initio calculations on biological systems
Interactions at the protein-DNA
interface
• cation p/H-bond stair motifs
Electron transfer in DNA
• Ionization potentials of isolated
and stacked DNA bases
• Excited states of the cations
Ade+ / Thy+
out
in
• Histidine - adenine complexes
Cyt+
out
out
Gua+
in
• Reaction path for the electron transfer
process
Current collaborations : M. Rooman, R. Wintjens and C. Biot (ULB).
in
Nonadiabatic molecular dynamics
Photodissociations
Cl
H
C
C
O
Electron transfers processes
 of astrophysical interest
 for plasma physics
Towards intra or inter biomolecular
processes
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
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:
O
O
NH
N
H
NH2
O
N
H
O
N
N
N
N
H
T
A
O
O
NH2
N
H
N
NH
N
HN
H2N
T
N
A
N
H
Monomers of DNA bases
Phototherapeutic molecules: psoralen
Pairs of DNA bases
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
S1
S2
H
H
N8
C4
HC5
N3
HC6
C2
N1
10.0
O7
(gs/pp* )CI
0.0
S1(pp* )min
(gs/nOp* )CI
5.3
S1(nOp* )min
-0.8
S0
S0(gs)min
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)
UV excitation
radiationless
decay
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
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
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
et Moléculaire
Université Claude Bernard- Lyon I
CNRS (France)
Department of Theoretical Physics and
Mathematical Methods
Gdańsk University of Technology
(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
Ion-biomolecule reactions : Uracyl + Cq+
experiment :
J. de Vries, R. Hoekstra, R. Morgenstern, T. Schlathölter,
J. Phys. B 35, 4373 (2002)
Cq+
Work in progress
Phys. Rev. A 63, 042704 (2001)
J. Chem. Phys. 114, 8741 (2001)
Adiabatic potentials U + C2+
U + C2+; U+ + C+(2D); U+ + C+(2P),
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
Problems:
- mechanism involving excited states
- selective dissociation
- non-adiabatic effects
Examples :
Photodissociation of
bromoacetyl chloride
at 248 nm
 = 248 nm
7.5 kcal/mol !
NONADIABATIC RECROSSING OF THE
BARRIER = DIABATIC TRAPPING
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)
L.J. Butler, Annu. Rev. Phys. Chem. 49, 125 (1998)
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
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
H
H
competitive dissociation of
C
bromoacethyl chloride in
Br
excited electronic states
hn
Cl
C
Simulation by
quantum dynamics
O
 = 248nm
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 V
2
path model breaks down
D
Isomerisation of
methoxy radical
q
f
B. Lasorne, G. Dive, D. Lauvergnat and M. Desouter-Lecomte,
J. Chem. Phys. , 118, 5831 (2003).
Dimerisation of
cyclopentadiene
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).
Adénine-H 2 O
E (kcal/mol)
12,0
10,0
B3LYP/6-31G**
MP2/6-31G**
8,0
6,0
4,0
HF/6-31G**
2,0
0,0
-2,0
2
2,5
3
3,5
4
d (Å)
TDHF (3 états)
Adénine+H 2 O
E (ua)
-0,3
n->pi*
interdite
Reaction coordinate
permis e
Experimental signals
H transfer between OH radical
pi->pi*
-0,4
2
2,5
d A-W (Å)
3
3,5
0.5
and different C of the ribose
IRC OH° on C1
E a.u.
0
-0.5
-1
-8
-6
-4
-2
0
2
Coordonnée de réaction
Reaction coordinate
4
6
8
4
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
400fs
1MLCT
3SBLCT
X
X
CO loss
Mn-H
homolysis
1MLCT
Mn-COax
HM(CO)3(a-diimine) M=Mn
Visible
Mn-H
1MLCT