View
6
Download
0
Category
Preview:
Citation preview
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
Recommended