1 ultrafast processes in molecules mario barbatti barbatti@kofo.mpg.de introduction

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Ultrafast processes in moleculesUltrafast processes in molecules

Mario Barbattibarbatti@kofo.mpg.de

Introduction

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settling the bases: photochemistry, excited states, and conical intersections

Photochemistry & Photophysics

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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?

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.

The need for Theory

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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 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

Basic process I: Radiati ve decay (fl uorescence)

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P ~ |j|m |i|2

t ~ ns

Basic process II: Non-radiati ve decay

9

P ~ v j| |iN

t ~ fs

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?

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

Conical intersecti ons: Twisted-pyramidalized

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(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*

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

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

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)

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

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

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

41Zewail, J. Phys. Chem. A 104, 5660 (2000)

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Contactbarbatti@kofo.mpg.de

Next lecture

• Transient spectrum• Excited state surfaces