1 ultrafast processes in molecules mario barbatti [email protected] introduction
TRANSCRIPT
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Ultrafast processes in moleculesUltrafast processes in molecules
Mario [email protected]
Introduction
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settling the bases: photochemistry, excited states, and conical intersections
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Photochemistry & Photophysics
3
Stating the problem:
• What does happen to a molecule when it is electronically excited?
• How does it relax and get rid of the energy excess?
• How long does this process take?• What products are formed?• How does the relaxation affect or is affected by the environment?
• Is it possible to interfere and to control the outputs?
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Why to study it?
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Basic sciences Interaction photon/matterCoeherence/decoherenceNature of transition statesNonadiabatic phenomena
Biology Light and UV detectionPhotosynthesisGenetic code degradationCellular proton pump
Atmospheric sciences
UV induced chemistryGreenhouse effect
Astrophysics Interstellar molecular synthesis
Technology Control of chemical reactionsMolecular photo-switches
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Pump-probe experiments based on ultra-fast laser pulses have increased the resolution of the chemical measurements to the femtosecond (10-15 s) time scale.
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The need for Theory
6
Theory is necessary to map the ground and excited state surfaces and to model the mechanisms taking place upon the photoexcitation.
Theory is indispensable to deconvolute the raw time-resolved experimental information and to reveal the nature of the transition species.
In particular, excited-state dynamics simulations can shed light on time dependent properties such as lifetimes and reaction yields.
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Photochemistry and photophysics
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Basic process I: Radiati ve decay (fl uorescence)
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P ~ |j|m |i|2
t ~ ns
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Basic process II: Non-radiati ve decay
9
P ~ v j| |iN
t ~ fs
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The Static Problem
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1.How are the excited state surfaces?
2. For which geometries does the molecule have conical intersections?
3. Can the molecule reach them?
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Conical intersections
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Antol et al. JCP 127, 234303 (2007)Barbatti et al., Chem. Phys. 349, 278 (2008)
pyridoneformamide
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Conical intersection Structure Examples
Twisted Polar substituted ethylenes (CH2NH2+)
PSB3, PSB4HBT
Twisted-pyramidalized Ethylene6-membered rings (aminopyrimidine)4MCFStilbene
Stretched-bipyramidalized
Polar substituted ethylenesFormamide5-membered rings (pyrrole, imidazole)
H-migration/carbene EthylideneCyclohexene
Out-of-plane O FormamideRings with carbonyl groups (pyridone,cytosine, thymine)
Bond breaking Heteroaromatic rings (pyrrole, adenine, thiophene, furan, imidazole)
Proton transfer Watson-Crick base pairs
X C
R1
R2
R3
R4
X C
R1
R2R3
R4
X C
R1
R2 R3
R4
C
R1R2
R3
H
C O
R1
R2
X Y
R1
R2
X
R1 R2
H
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Conical intersecti ons: Twisted-pyramidalized
13
(b)
3 2
1
65
4(a)
(b)
3 2
1
65
4(a)
(b)(b)
3 2
1
65
4(a)
3 2
1
65
4(a)
Barbatti et al. PCCP 10, 482 (2008)
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0 1 2 3 4 5 60
1
2
3
4
5
6
7
0 1 2 3 4 5 60
1
2
3
4
5
6
7
0 1 2 3 4 5 60
1
2
3
4
5
6
7
0 1 2 3 4 5 60
1
2
3
4
5
6
7
0 1 2 3 4 5 60
1
2
3
4
5
6
7
0 1 2 3 4 5 60
1
2
3
4
5
6
7
0 1 2 3 4 5 60
1
2
3
4
5
6
7
0 1 2 3 4 5 60
1
2
3
4
5
6
7
dMW
(amu1/2Å)
6S1
n*
dMW
(amu1/2Å)
E8
*
4H3
*
dMW
(amu1/2Å)
Ene
rgy
(eV
)
2E
*
B3,6
n*
Ene
rgy
(eV
)
2H3
*E
nerg
y (e
V)
E3
*
4S3
n*
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The Dynamics Problem
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At a certain excitation energy:
1. Which reaction path is the most important for the excited-state
relaxation?
2. How long does this relaxation take?
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about methods & programs
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Subject Approach Methods
Vertical excitation spectra
Conventional adiabatic quantum chemistry
MRCI, CC2, TDDFT
Stationary points in excited states
Conventional adiabatic quantum chemistry
MRCI, CC2, TDDFT
Conical intersections Nonadiabatic quantum chemistry
MRCI, MCSCF
Reaction paths Convent. adiabatic quantum chemistry (multireference)
MRCI, CASPT2, MCSCF
Lifetime and yields Mixed quantum-classical dynamics methods
MRCI, MCSCF(+ MM)
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Ene
rgy
Reaction coordinate
From quantum to (semi)classical
Wave packet propagation
Surface hopping propagation
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Cremer-Pople parameters
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Q
q
f
Boat
Chair
Envelope
Twisted-chair
Screw-boat
Ex.: 1S6 = Screw-boat with atoms 1 above the
plane and 6 below
Cremer and Pople, JACS 97, 1358 (1975)
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dynamics: adenine
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Photochemical process
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Photophysical process
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UV absorption of nucleobases
• PCCP 12, 4959 (2010)
4 5 6
0.2
0.4
0.6
0.8
1S
olar
irra
dian
ce (
W.m
-2nm
-1)
Photon energy (eV)
Surface
Extraterrestrial
0.0
0.2
0.4
0.6
Cro
ss s
ectio
n (Å
2 )
AdeGua
Thy
Cyt
Ura
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Excited-state lifetimes (vapor)
Base t1 (ps) t2 (ps)
Ade 1.00
Gua 0.36
Thy 0.49 6.4
Ura 0.53 2.4
Cyt 0.82 3.2
• Ullrich, Schultz, Zgierski, Stolow, PCCP 6, 2796 (2004)
Short lifetimes together with the low fluorescence quantum yields indicate internal
conversion through conical intersections
Purines: single stepPyrimidines: multiple steps
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Lifetime & photostability
A short lifetime can enhance the photostability because the molecule does not stay too long in reactive excited states
This effect might have constituted an evolutionary advantage for the five nucleobases forming DNA and RNA
Indeed, there are experimental evidences that purine precursors in the prebiotic world were photostable
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1 ps 30 ps
9H-Adenine 2-aminopurine
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Adenine: conical intersections
N9 H
N1
C2
H
pp*/cs
pp*/cs
psNH*/cs
9
6
2
Many conical intersections available. Which of them
are used for internal conversion? Why? On
which time scale?
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Adenine: photodynamics
E (eV)
DR (Å.amu1/2)
-4 0 43
5
-6 0 63
5
-3 0 33
5
-6 0 63
5
Ade Gua
Cyt Thy / Ura
cs
pp*
np*
cs
pp*
np*
cs
pp*
np*
cs
np*
A1A2
G1
C2
C1c
P1b
pp* P1
P1a
P1cP2
C1
A2aA1a G1a
P2aP1d
C1d
C1b
C1a
G2
G2a
N9 H
N1
C2
H
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Adenine: deactivation mechanismsE (eV)
DR (Å.amu1/2)
cs
pp*
np*
cs
pp*
np*
cs
pp*
np*
cs
np*
pp*
-4 0 43
5
-6 0 63
5
-3 0 33
5
-6 0 63
5
Ade Gua
Cyt Thy / Ura
A2
A2a
A1
A1a
• JACS 130, 6831 (2008)
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GuanineE (eV)
DR (Å.amu1/2)
-4 0 43
5
-6 0 63
5
-3 0 33
5
-6 0 63
5
Ade Gua
Cyt Thy / Ura
cs
pp*
np*
cs
pp*
np*
cs
pp*
np*
cs
np*
A1A2
pp*
A2aA1a
G1
G1a
G2
G2a
• J Chem Phys 134, 014304 (2011)
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G2
G2a
Thymine and uracilE (eV)
DR (Å.amu1/2)
-4 0 43
5
-6 0 63
5
-3 0 33
5
-6 0 63
5
Ade Gua
Cyt Thy / Ura
cs
pp*
np*
cs
pp*
np*
cs
pp*
np*
cs
np*
A1A2
G1
P1b
pp* P1
P1a
P1c
A2aA1a G1a
P2
P2a
• J Phys Chem A 113, 12686 (2009)• J Phys Chem A 115, 5247 (2011)
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G2
G2a
CytosineE (eV)
DR (Å.amu1/2)
-4 0 43
5
-6 0 63
5
-3 0 33
5
-6 0 63
5
Ade Gua
Cyt Thy / Ura
cs
pp*
np*
cs
pp*
np*
cs
pp*
np*
cs
np*
A1A2
G1
P1b
pp* P1
P1a
P1cP2
A2aA1a G1a
P2aP1d
C1c
C1d
C2 C1b
C1C1a
• PCCP 13, 6145 (2011)
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33• PNAS 107, 21453 (2010)
E (eV)
DR (Å.amu1/2)
-4 0 43
5
-6 0 63
5
-3 0 33
5
-6 0 63
5
Ade Gua
Cyt Thy / Ura
cs
pp*
np*
cs
pp*
np*
cs
pp*
np*
cs
np*
A1A2
G1
C2
C1c
P1b
pp* P1
P1a
P1cP2
C1
A2aA1a G1a
P2aP1d
C1d
C1b
C1a
Single step
Multiple steps
G2
G2a
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PHOTOINDUCED PHENOMENA IN NUCLEIC ACIDS
1. Photoinduced processes in nucleic acidsMario Barbatti, Antonio Borin, Susanne Ullrich
2. UV-excitation I: frequency resolvedMattanjah S. de Vries
3. UV-excitation II: time resolvedThomas Schultz
4. Excitation of nucleobases I: reaction pathsManuela Merchán
5. Excitation of nucleobases II: dynamicsLetícia Gonzalez
6. Excitation of paired and stacked nucleobasesDana Nachtigallova, Hans Lischka
7. Modified nucleobasesSpiridoula Matsika
8. UV-excitation of solvated nucleobases ICarlos E. Crespo-Hernandez
Mario Barbatti, Antonio C. Borin, Susanne Ullrich (Eds.)Coming soon
9. UV-excitation of solvated nucleobases IIRoberto Improta
10. Excitation of single and double strands IBern Kohler
11. Excitation of single and double strands IIZhenggang Lan, Walter Thiel
12. Synchrotron irradiation of DNA fragmentsMartin Schwell
13. Physiological aspects of excitation of DNADonat-P. Häder
14. Photoynthesis in prebiotic environmentsScott Sandford
15. Photoinduced charge-transfer in DNA and applications in nano-electronics
Kiyohiko Kawai, Tetsuro Majima16. Electronic energy transfer in nucleic acids
Dimitra Markovitsi
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Excited state dynamics: what have we learned?
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0 90 180 270 3600
90
180
(°)
(°
)
0 90 180 270 3600
90
180
(°)
(°
)
0 fs
120 fs
170 fs
200 fs
9H-adenine
0 90 180 270 3600
90
180
(°)
(°)
2-pyridone
• Chem. Phys. 349, 278 (2008)
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Adenine is trapped close to 2E conformation and because of
this it has time enough to tune the coordinates of the conical intersection. Adenine is a non-
fluorescent species.
Pyridone does not stay close to any specific conformation long enough in order to have time to tune the coordinates of the conical intersections.
Pyridone is a fluorescent species.
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conclusions
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Simple picture
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Beyond the simple picture
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• MQCD simulations are not a substitute for the conventional quantum-chemistry calculations, but a complementary tool to be used carefully given their high computational costs
• They can be specially useful to test specific hypothesis raised either by experimental analysis or conventional calculations
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41Zewail, J. Phys. Chem. A 104, 5660 (2000)
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Next lecture
• Transient spectrum• Excited state surfaces