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Ultrafast processes in molecules
Introduction
Mario Barbatti
[email protected]
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settling the bases:
photochemistry, excited states, and
conical intersections
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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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Basic sciences
Biology
Atmospheric sciences
Astrophysics
Technology
Interaction photon/matter
Coeherence/decoherence
Nature of transition states
Nonadiabatic phenomena
Light and UV detection
Photosynthesis
Genetic code degradation
Cellular proton pump
UV induced chemistry
Greenhouse effect
Interstellar molecular synthesis
Control of chemical reactions
Molecular 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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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 timeresolved 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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P ~ |j|m |i|2
t ~ ns
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P ~ vN  j| |i
t ~ fs
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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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formamide
pyridone
Antol et al. JCP 127, 234303 (2007)
Barbatti et al., Chem. Phys. 349, 278 (2008)
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Conical intersection
Twisted
Structure
Examples
R1
X
R4
C
R3
R2
Twisted-pyramidalized
R1
X
C
R2
Stretchedbipyramidalized
R4
R3
R4
R1
X
C
R3
R2
H-migration/carbene
Out-of-plane O
H
C
R3
R2
R1
R1
C
O
R1
X
Ethylene
6-membered rings (aminopyrimidine)
4MCF
Stilbene
Polar substituted ethylenes
Formamide
5-membered rings (pyrrole, imidazole)
Ethylidene
Cyclohexene
Formamide
Rings with carbonyl groups (pyridone,
cytosine, thymine)
R2
Bond breaking
Polar substituted ethylenes (CH2NH2+)
PSB3, PSB4
HBT
Heteroaromatic rings (pyrrole, adenine,
thiophene, furan, imidazole)
Y
R2
X
Proton transfer
R1
H
Watson-Crick base pairs
R2
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1

3
(a)
4
2


5

6
(b)
Barbatti et al. PCCP 10, 482 (2008)
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7
7
Energy (eV)
6
6
5
5
4
4
4
3
3
3
5
2
2
2
1
H3
1
2
3
4
5
1
6
S3
6
1
2
3
4
5
0
6
n*
4
4
4
3
3
3
2
2
2
B3,6
1
E3
0
1
2
3
4
5
0
6
7
7
6
6
*
5
1
2
3
4
5
4
3
3
2
4
5
6
*
E8
6
0
0
1
2
3
4
5
6
1/2
dMW (amu Å)
n*
5
4
3
1
0
0
2
6
5
1
1
7
5
5
H3
0
0
6
*
4
1
7
7
*
2
4
0
0
Energy (eV)
n*
6
*
0
Energy (eV)
7
2
2
1
E
6
1
0
S1
0
0
1
2
3
4
1/2
dMW (amu Å)
5
6
0
1
2
3
4
5
6
1/2
dMW (amu Å)
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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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Energy
Wave packet propagation
Surface hopping propagation
Reaction coordinate
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Chair
Twisted-chair
Envelope
Q
q
Screw-boat
f
Boat
Cremer and Pople, JACS 97, 1358 (1975)
Ex.: 1S6 = Screw-boat
with atoms 1 above the
plane and 6 below
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dynamics: adenine
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21
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1
0.6
Extraterrestrial
-2
Gua
0.4
0.4
Thy
Surface
Ura
0.2
0.2
Cyt
2
Ade
0.6
Cross section (Å )
-1
Solar irradiance (W.m nm )
0.8
0.0
4
5
6
Photon energy (eV)
• PCCP 12, 4959 (2010)
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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
Short lifetimes
together with the
low fluorescence
quantum yields
indicate internal
conversion through
conical intersections
Purines: single step
Pyrimidines: multiple steps
• Ullrich, Schultz, Zgierski, Stolow, PCCP 6, 2796 (2004)
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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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9H-Adenine
2-aminopurine
1 ps
30 ps
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N9
H
NH*/cs
9
*/cs
6
N1
Many conical intersections
available. Which of them
are used for internal
conversion? Why? On
which time scale?
C2
2
*/cs
H
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E (eV)
n*
A2
A1
*
5
G1
G2
5
*
G2a
n*
A2a
cs
Ade
3
-4
0
cs
-6
C1a C1
5
C1c
C1d
P1
P2
6
P1c
5
P1a
P1b n*
n*
C2 C1b
cs
P2a
P1d
N1
cs
Cyt
3
-3
0
*
*
0
3
H
Gua
3
4
N9
G1a
A1a
Thy / Ura
3
-6
0
6
DR (Å.amu1/2)
C2
H
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E (eV)
n*
A2
A1
*
5
5
*
n*
A2a
A1a
cs
cs
Ade
3
-4
0
Gua
3
4
-6
0
6
*
*
5
5
n*
n*
cs
cs
Cyt
3
-3
0
3
Thy / Ura
3
-6
0
6
DR (Å.amu1/2)
• JACS 130, 6831 (2008)
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E (eV)
n*
A2
A1
*
5
G1
G2
5
*
G2a
n*
A2a
G1a
A1a
cs
cs
Ade
3
-4
0
Gua
3
4
-6
0
6
*
*
5
5
n*
n*
cs
cs
Cyt
3
-3
0
3
Thy / Ura
3
-6
0
6
DR (Å.amu1/2)
• J Chem Phys 134, 014304 (2011)
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E (eV)
n*
A2
A1
*
5
G1
G2
5
*
G2a
n*
A2a
G1a
A1a
cs
cs
Ade
3
-4
0
Gua
3
4
-6
0
*
*
5
P1
P2
6
P1c
5
P1a
P1b n*
n*
cs
cs
Cyt
3
-3
P2a
0
3
• J Phys Chem A 113, 12686 (2009)
• J Phys Chem A 115, 5247 (2011)
Thy / Ura
3
-6
0
6
DR (Å.amu1/2)
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E (eV)
n*
A2
A1
*
5
G1
G2
5
*
G2a
n*
A2a
cs
cs
Ade
3
-4
0
Gua
3
4
-6
5
C1
C1c
P1
P2
6
P1c
5
C1d
P1a
P1b n*
n*
C2 C1b
cs
P2a
P1d
cs
Cyt
3
-3
0
*
*
C1a
G1a
A1a
0
3
Thy / Ura
3
-6
0
6
DR (Å.amu1/2)
• PCCP 13, 6145 (2011)
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E (eV)
n*
A2
A1
*
5
G1
G2
5
*
G2a
n*
A2a
cs
cs
Ade
3
-4
0
Gua
3
4
-6
5
C1
C1c
P1
P2
6
P1c
5
C1d
P1a
P1b n*
n*
C2 C1b
cs
P2a
P1d
cs
Cyt
3
-3
0
*
*
C1a
Single
step
G1a
A1a
0
3
Thy / Ura
3
-6
0
Multiple
steps
6
DR (Å.amu1/2)
• PNAS 107, 21453 (2010)
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PHOTOINDUCED PHENOMENA IN NUCLEIC ACIDS
Mario Barbatti, Antonio C. Borin, Susanne Ullrich (Eds.)
Coming soon
1. Photoinduced processes in nucleic acids
Mario Barbatti, Antonio Borin, Susanne Ullrich
2. UV-excitation I: frequency resolved
Mattanjah S. de Vries
3. UV-excitation II: time resolved
Thomas Schultz
4. Excitation of nucleobases I: reaction paths
Manuela Merchán
5. Excitation of nucleobases II: dynamics
Letícia Gonzalez
6. Excitation of paired and stacked nucleobases
Dana Nachtigallova, Hans Lischka
7. Modified nucleobases
Spiridoula Matsika
8. UV-excitation of solvated nucleobases I
Carlos E. Crespo-Hernandez
9. UV-excitation of solvated nucleobases II
Roberto Improta
10. Excitation of single and double strands I
Bern Kohler
11. Excitation of single and double strands II
Zhenggang Lan, Walter Thiel
12. Synchrotron irradiation of DNA fragments
Martin Schwell
13. Physiological aspects of excitation of DNA
Donat-P. Häder
14. Photoynthesis in prebiotic environments
Scott Sandford
15. Photoinduced charge-transfer in DNA and
applications in nano-electronics
Kiyohiko Kawai, Tetsuro Majima
16. Electronic energy transfer in nucleic acids
Dimitra Markovitsi
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9H-adenine
q (°)
180
170 fs
90
200 fs
0 fs
2-pyridone
120 fs
180
0
0
90
180
270
360
q (°)
f (°)
90
• Chem. Phys. 349, 278 (2008)
0
0
90
180
270
360
f (°)
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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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• 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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Zewail, J. Phys. Chem. A 104, 5660 (2000)
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Next lecture
• Transient spectrum
• Excited state surfaces
Contact
[email protected]
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