Multireference-Ab Initio Dynamics
Simulations of the Photostability of
DNA Bases
Hans Lischka
Institute for Theoretical Chemistry
COLUMBUS Program
System
• Focus: multireference calculations on ground and
excited states
• Methods: MCSCF, MR-CISD, MR-ACPF/AQCC, Spinorbit CI
• Analytic MR-CI gradients, nonadiabatic couplings,
parallel CI
• Authors: R. Shepard, I. Shavitt, R. M. Pitzer, H.Lischka
–
–
–
–
Vienna: M. Barbatti, M. Ruckenbauer, J. Szymczak, B. Sellner
Budapest: P. G. Szalay
Jülich: Th. Müller
Columbus/Ohio S. Brozell, …
• Web page: http://www. univie.ac.at/columbus
Photodynamics
• Input includes the energy surfaces, energy
•
•
gradients and nonadiabatic coupling vectors
What kind of dynamics – quantum (wavepacket)
or surface-hopping?
Restricted set of internal coordinates vs. onthe-fly approach with full set of internal
coordinates?
Development of the surface-hopping program
NEWTON-X
A TOOL-KIT: FROM POTENTIAL SURFACES TO
PHOTODYNAMICS
Available QC codes
• COLUMBUS (MR-CISD, State-averaged
•
•
•
•
•
CASSCF)
TURBOMOLE (RI-CC2, TDDFT: adiabatic
dynamics)
MOPAC
Coming: ACES II (EOM-CCSD, nonadiabatic
couplings (P. G. Szalay, A. Tajti)
Installation in progress: DFTB (TD-DFTB,
adiabatic dynamics)
In development: QM/MM for solvation based
on COLUMBUS
Ultrafast decay of DNA/RNA bases
NH2
N
NH
NH2
N
N
N
N
NH
O
O
O
NH
NH
NH
N
O
NH2
NH
H3C
O
NH
NH
Canuel et al. JCP 122, 074316 (2005)
Fast deactivation times for the DNA/RNA bases 
Photostability of DNA/RNA under the UV solar radiation?
Relevance for prebiotic evolution?
O
Lifetime:
Between 750 fs [1] and 1.1 ps [2]
Mechanism:
Single-exponential decay [3]
Double-exponential decay [2]
1: 100 fs– relaxation into S1 [4]
2: 1 ps– relaxation into S0
1: 100 fs– relaxation into S0(*)[5]
2: 1 ps– relaxation into S0(n*)
Triple-exponential decay [1]
0
750
1500
delay time / fs
[1] Ullrich et al. JACS 126, 2262 (2004)
[2] Canuel et al. JCP 122, 074316 (2005)
[3] Kang et al. JACS 124, 12958 (2002)
[4] Perun et al. JACS 127, 6257 (2005)
[5] Serrano-Andrés et al. PNAS 103, 8691 (2006)
Photodynamics of DNA bases
Hydrogen detachment
s*/S0 crossing
Adenine: Ring puckering
*/S0 crossing
Marian, JCP 122, 104314 (2005)
9H-adenine, Sobolewski and Domcke,
Eur. Phys. J. D 20, 369 (2002)
Perun, Sobolewski and Domcke, JACS 127, 6257 (2005)
Serrano-Andrés, Merchán and Borin, PNAS 103, 8691 (2006)
Three-state model
1 ps
100 fs
Serrano-Andrés, Merchán and Borin, Chem. Eur. J. 12, 6559 (2006)
Aminopyrimidine  9H Adenine
H
H
H
H
N
N
7
6
10
5
N
6
H
N
1
H
2
5
7
N
8
1
N
3
4
H
6-aminopyrimidine
H
2
N
3
4
H
N9
H
9H-adenine
Ring puckering vs. NH2 out-of-plane motion
CASSCF(8el,7orb), state-averaging over 2 and 3 states
6-31G* basis
Cremer-Pople parameters
• Any puckered N-membered ring is described
by a special subset of N-3 coordinates
• Cremer and Pople [1] gave an useful
prescription using the deviations from the
average ring plane
• For 6-memberd rings, these coordinates are:
Q – degree of puckering
q and f – type of puckering
[1] Cremer and Pople, JACS 97, 1358 (1975)
Chair
Twisted-chair
Envelope
Q
q
Screw-boat
f
Boat
Example: 1S6 = Screw-boat with atoms 1 above the plane and 6 below
Boeyers, J. Cryst. Mol. Struct. 8, 317 (1978)
9-H Adenine MXS Structures
7
7
Energy (eV)
6
6
5
5
5
4
4
4
3
3
3
2
2
H3
1
2
1
2
3
4
5
6
S3
0
1
2
3
4
5
6
0
5
5
4
4
4
3
3
3
2
2
2
E3
0
0
1
2
3
4
5
0
0
7
7
6
6
*
5
B3,6
1
6
1
2
3
4
5
4
3
3
2
E
1
0
1
2
3
4
1/2
dMW (amu Å)
5
6
6
n*
6
S1
1
0
0
3
4
5
6
s*
E8
1
0
0
1
2
3
4
dMW (amu Å)
2
2
2
1/2
5
4
1
6
5
1
H3
0
7
n*
6
*
4
1
6
7
7
s*
2
4
1
0
0
Energy (eV)
n*
6
*
0
Energy (eV)
7
0
1
2
3
4
1/2
dMW (amu Å)
5
6
5
6
Adenine Dynamics
Lifetime
1.0
S3
Occupation
0.8
S1
0.6
0.4
S0
S2
0.2
0.0
0
S1:
f t  
2
1  2
100 200
  t 
  t 


 
exp

exp
  
  2 
  1 
400
600
Time (fs)
1: 22 fs, 2: 538 fs, exp: ~0.1/1 ps
Single trajectory
180
150
6
q (°)
120
170 fs
90
E2
S1
2
E
200 fs
3,6
B
30 120 fs
0
60
3
H2
3
3
3 H4S4
E
120
180
1
S6
0 fs
240
4S3
B
3,6
Hop
60
0
2H3 E3
4H3
300
360
All trajectories
180
150
120
90
60
30
0
0
60
120
180
240
300
360
Aminopyrimidine/Adenine dynamics
• Ring puckering is the main mechanism at
•
•
•
•
•
picosecond level
First step: Fast relaxation S3S2S1 (22 fs)
Second step: S1S0 relaxation (0.5 ps)
After relaxation in to S1: trapping close to 2E
structure
Deactivation almost exclusively at 2E
Deactivation via NH2 out-of-plane motion not
observed
Outlook
• Photodynamics in solution – QM/MM
MRCI, CAS
Force field
• Base pairs – ultrafast deactivation by proton
•
transfer?
Energy trapping due to stacking interaction of
bases
COLUMBUS Photos
OSU May 2000
ANL July 2001
Seattle, July 2001
Acknowledgments
Vienna: Mario Barbatti, Adélia Aquino, Daniel Tunega, Jaroslaw
Szymczak, Matthias Ruckenbauer, B. Sellner, H. Pašalić
Pisa: Maurizio Persico, Giovanni Granucci
Berlin/Prague: V.Bonačić-Koutecký,J. Pittner
Argonne/USA: R. Shepard
Budapest: P. Szalay
Munich: R. de Vivie-Riedle, E. Riedle
Zagreb: Z. Maksić, M. Eckert-Maksić,
M. Vazdar and I. Antol
Sofia: I. Georgieva and N. Trendafilova
Bratislava: V. Lukeš
São Paulo: S. Canuto and K. Coutinho
Rio de Janeiro: M. A. C. Nascimento,
I. Borges, Jr.
Ribeirão Preto: S. E. Galembeck
Prag: P. Hobza
Austrian Science Fund