COST P9 Radiation Damage in Biomolecular Systems Working
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: Applications 1) Excited-state potential-energy surfaces Photochemistry of biomolecules aromatic amino acids (tryptophan and tyrosine) DNA and RNA bases.
Isolated systems and solvated complexes in water or ammonia 2) Photochemical reaction paths 3) Conical intersections Potential energy profiles of the lowest singlet states of (a) phenol, (b) indole, (c) pyrrole Conical intersection between the * 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 * (right) diabatic
states of pyrrole. Circle: position of the S 1-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 S 1-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 (Universit 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 Universit 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 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). 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 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 Lige group related to the
theory of radiation damage Dr. Georges Dive : Centre dingnierie des protines (Universit de Lige, Begium) Catalyticmechanism mechanismof ofserine serineproteases proteasesmachinery machinery Catalytic Transition state model of the cooperative effect between several amino acids H Glu 166 C O O CH2
CH2 H H C O O H N Ser 70 O H CH2 H O CH2 H N
C H H H N CH3 H O Ser 130 CH3 Lys 73 Location Locationof ofthe thetransition transitionstate statestructure structurefor for44types typesof
TS TSCope Cope In Incollaboration collaborationwith withM. M.Desouter Desouterand andB. B.Lasorne LasorneParis ParisXI XI Laboratoire de Chimie Quantique et Photophysique Unit de Chimie Quantique et Physique Atomique Universit Libre de Bruxelles M. Godefroid J. Livin B. Sutcliffe N. Vaeck
G. Verhaegen E. Caut N. Rinskoff Ab initio calculations on biological systems Interactions at the protein-DNA interface cation /H-bond stair motifsH-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 in Reaction path for the electron transfer process Current collaborations : M. Rooman, R. Wintjens and C. Biot (ULB). 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 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: NH
N H NH2 O O O N H O NH2 N N H N NH
A O T O N N N H T N HN H2N 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 S H S 2 H N 8
C 4 HC 5 N 3 HC 6 C 2 N 1 1 0 .0
O 1 7 0 .0 S 1 ( * )m in S ( g s / n O * )C I ( g s / * )C I 5 .3 S 1 ( n O * ) m in -0 .8 0 S 0 ( g s )m in CASSCF description: leading S0/S1 conical (Ground State/n* state). Fluorescing state: n* CASPT2 description: leading S0/S1 conical (Ground State/* state). Fluorescing state: *
M. Merchn y L. Serrano-Andrs, 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 S1
CASPT results at CASSCF-optimized geometry of the S1 potential-energy surface S0 S1 S0 1 ps 1 ps experimental lifetime MIN- local minimum SP- saddle-point CI- conical intersection 1 ns - 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 Spectromtrie Ionique Department of Theoretical Physics and et Molculaire Universit Claude Bernard- Lyon I Gdask University of Technology CNRS (France) (Poland) Dr. Marie-Christine Bacchus-Montabonel Prof. Jozef E. Sienkiewicz Dr. Suzanne Tergiman Marta abuda Katarzyna Piechowska Mathematical Methods
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 - wave packet propagations methods Ion-biomolecule reactions : Uracyl + Cq+ experiment : J. de Vries, R. Hoekstra, R. Morgenstern, T. Schlathlter, J. Phys. B 35, 4373 (2002) Work in progress Cq+ Adiabatic potentials U + C2+ U + C2+; U+ + C+(2D); U+ + C+(2P), Phys. Rev A 64, 042721 (2001) IJQC, 89, 322 (2002); IJQC 97 (2004) Phys. Rev. A 63, 042704 (2001) J. Chem. Phys. 114, 8741 (2001) Photodissociation reactions Wave packet propagation methods for polyatomic systems with constrained Hamiltonian methodology.
Collaboration Michle 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 stat - selective dissociation - non-adiabatic effects Examples : Photodissociation of bromoacetyl chloride at 248 nm 7.5 kcal/ mol ! = 248 nm NONADI ABATI C RECROSSI NG OF THE BARRI ER = DI ABATI C TRAPPI NG 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 Universit 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 C of bromoacethyl chloride Br in excited electronic h states Cl Simulation by quantum dynamics C 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 path model breaks down V2 D Isomerisation of methoxy radical B. Lasorne, G. Dive, D. Lauvergnat and M. DesouterLecomte, 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). Adnine-H 2 O E (kcal/mol)
4 TDHF (3 tats) Adnine+H 2 O E (ua) -0,3 n->pi* interdite Reaction coordinate permise Experimental signals pi->pi* -0,4 H transfer between OH radical 2 2,5
d A-W () 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 Coordonne de raction 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 Universit Louis Pasteur, Strasbourg France Quantum chemistry and excited states dynamics in transition metal complexes Chantal Daniel Nadia Ben Amor Hlne Bolvin
Alain Strich Julien Bossert Ph D Sbastien 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 MLCT 400fs 1 SBLCT 3 Visible
X X CO loss Mn-H homolysis 1 MLCT Mn-COax HM(CO)3(-diimine) M=Mn Mn-H 1 MLCT
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Method of Estimation of Design discharge (Para 4.3 of substructure code ) Contd. Para 4.3.1 where Stream flow records (yearly peak discharges) are available for the desired recurrence interval or more - design discharge shall be : The computed flood...
Enthalpy ΔH. The heat absorbed/released by a reaction is described using the term enthalpy. ... The maximum/minimum temperature is recorded. Water is the most common solvent, therefore the specific heat capacity of the solution is assumed to be the same...
PROMINENT EU project2015-2018PROteinMINing of Cereal side-streams Exploring Novel Technological Concepts. Project introduction. October 2015. This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 668953−PROMINENT.
Reasoning - A baseball player's batting average is calculated by dividing the number of hits by the number of at bats.In Major League Baseball, a .330 career batting average is relatively rare; only 30 players in MLB history have batted...