Carlos E. Crespo-HernándezDepartment of Chemistry

Email: carlos.crespo@case.edu

Ohio Supercomputer CenterColumbus, Ohio

April 4, 2008

Excess Energy Flow in DNA: Bench and Computer Experiments

Working in Unison

Acknowledgement

Prof. Bern Kohler and Group Members

National Institute of Health (R01-GM64563)

Prof. Terry Gustafson and the Center for Chemical and Biophysical Dynamics, The Ohio State University

Ohio Supercomputer Center

Case Western Reserve University

NSF-ACES Program and NSF-MRI Grant CHE0443570

1. Close, M. D.; Crespo-Hernández, C. E.; Gorb, L.; Leszczynski, J. J. Phys. Chem. A 2005, 109, 9279.

2. Close, M. D.; Crespo-Hernández, C. E.; Gorb, L.; Leszczynski, J. J. Phys. Chem. A 2006, 110, 7485.

3. Crespo-Hernández, C. E.; Close, M. D.; Gorb, L.; Leszczynski, J. J. Phys. Chem. B 2007, 111, 5386.

4. Crespo-Hernández, C. E.; Marai, C. N. J. AIP Conference Proceedings 2007, 963, 607.5. Law, Y. K.; Azadi, J.; Crespo-Hernández, C. E.; Olmon, E.; Kohler, B. Biophysical J. 2008,

in press.6. Close, M. D.; Crespo-Hernández, C. E.; Gorb, L.; Leszczynski, J. J. Phys. Chem. A 2008,

in press.7. Crespo-Hernández, C. E.; Burdzinski, G.; Arce, R. J. Phys. Chem. A 2008, submitted.

Ohio Supercomputer Center Allocations(since 2005)

Software• Gaussian 03: 2CPUs in parallel, 10-12 hrs, ~ 150-200 RUs

• GROMACS: 4 CPUs in parallel (scaling: 99%), 150 ns trajectories @ 0.767 hrs/ns,~ 50 RUs + ~ 100 RUs for free energy simulations: ~100 RUs

Storage Needs• For the systems and trajectories we are currently running we use ~ 200MB/ns or ~100GB of storage space (before compressed) + scratch space.• Future larger model systems would necessitate larger scale simulations: 8CPus in parallel (scaling: ~81%) at 2.4 hrs/ns.

Publications

Ultrafast Excited State Dynamics of Nucleic Acids

…

…

…

S1 Lifetimes for Nucleosides

Pecourt, J.-M.L.; Peon, J.; Kohler, B. J. Am. Chem. Soc. 2001, 123, 10370. Crespo-Hernández, C.E.; Cohen, B.; Hare, P.; Kohler, B. Chem. Rev., 2004, 104, 1977.Cohen, B.; Crespo-Hernández, C.E.; Kohler, B. J. Chem. Soc., Faraday Discuss. 2004, 127, 137.

1086420

AS /

10

4

2.01.00.0

Time / ps

Urd: = 230 ± 30 fs

6

4

2

0

AS /

104

5.02.50.0

Time / ps

Cyd: = 1.00 ± 0.04 ps

6

4

2

0A

S /

104

5.02.50.0

Time / ps

Thd: = 540 ± 40 fs6

4

2

0

A /

104

5.02.50.0

Time / ps

Ado: = 290 ± 40 fs

6

4

2

0

A /

104

5.02.50.0

Time / ps

Guo: = 460 ± 40 fs

DNA

RNA

Role of Conical Intersections in the Radiationless Decay of DNA Monomers:

Cytosine

Pecourt, J.-M.L.; Peon, J.; Kohler, B. J. Am. Chem. Soc. 2001, 123, 10370.Merchán, M.; Serrano-Andrés, L. J. Am. Chem. Soc., 2003, 125, 8108.

Conical intersections are a likely mechanism for the

ultrafast lifetimes of cytosine and the other DNA bases.

Nucleic Acid Multimers Photophysics:The Role of Base Stacking and Base

Pairing

Effect of Base Stacking Interactions

275.6 nm,0.0266H -> L 78%

H-1 -> L+1 22%

263.6 nm,0.0298H -> L+1 60%H-1 -> L 40%

S0

S1

S2

H

L L+1

H-1

TD-DFT/B3LYP/6-311G(d,p)

1.0

0.8

0.6

0.4

0.2

0.0

As /

10

3

420-2

Time / ps

6 810

2 4 6 8100

2

ApC AMP + CMP

1.5

1.0

0.5

0.0

As /

10

3

420-2

Time / ps

6 810

2 4 6 8100

TpdA AMP + TMP

1.2

1.0

0.8

0.6

0.4

0.2

0.0

As /

10

3

420-2

Time / ps

610

2 4 6100

2 4

ApA AMP

Dinucleotides: stack ↔ unstackNucleotides: unstack

AdeA-AA R = 3 Å R = 4 Å R = 5 Å R = 6 Å

HOMO

A-AA6

LUMO

TD-DFT/B3LYP/6-311G(d,p) Calculations of A-Form ApA

Electronic Coupling versus Interchromophoric Distance

5.2

5.0

4.8

4.6

Exc

itatio

n E

ne

rgy

/ eV

6.05.04.03.0Distance / Å

S1

S2

E= 0.2 eV

AA AMP

R

3000

2500

2000

1500

1000

500

Exc

ition

Spl

ittin

g /

cm-1

-80 -40 0 40 80

P-O Torsion Angle / degrees

Crespo-Hernández, C.E.; Marai, C.N.J. AIP Conference Proceedings 2007, 963, 607.

Reversible Redox Potentials of DNA NucleosidesCrespo-Hernández, C.E.; Close, M. D.; Gorb, L.; Leszczynski J. Phys. Chem. B 2007, 111, 5386.

Charge Transfer Character of the Excimer/Exciplex

Tomohisa, T.; Su, C.; de la Harpe, K; Crespo-Hernández, C.E.; Kohler, B. Proc. Natl. Acad. Sci. USA 2008, accepted.

The decay rates of the long-lived states increase with increasing driving force for charge recombination as expected in the Marcus inverted region.

G° E°ox - E°red IP - EA

Role of the Driving Force for Charge Separation

-25

-20

-15

-10

-5

0

5

A /

103

604020

Time / ps100

2 3 4 5 61000

buffer D2O

d(GC)9•d(GC)9

-12

-8

-4

0

A /

103

5040302010

Time / ps100

2 3 4 5 61000

buffer D2O

d(IC)9•d(IC)9

ΔG(GC) > ΔG(AT) > ΔG(IC)

-20

-15

-10

-5

0

A /

10

-3

1050 100 1000Time / ps

250 nm

H2O D2O

d(AT)9•d(AT)9

Crespo-Hernández, C.E.; Cohen, B.; Kohler, B. Nature 2005, 436, 1141.

Crespo-Hernández, C. E.; de la Harpe, K.; Kohler, B. J. Am. Chem. Soc. 2008, submitted.

Excited State Dynamics and DNA Photochemistry:Making Connections

T<>T photodimers account

for ~90% of DNA Damage*

UV

Singlet or triplet state?

Formation time scale?

* Cadet, J.; Vigny, P. In Bioorganic Photochemistry; Morrison, H., Ed.; Wiley: New York, 1990; Vol.1, p 1.

Crespo-Hernández, C.E.; Cohen, B.; Kohler, B. Nature 2005, 436, 1141.

Schreier, W.J.; Schrader, T.E.; Koller, F.O.; Gilch, P.; Crespo-Hernández, C.E.; Swaminathan, V.N.; Carell, T.; Zinth, W.; Kohler, B. Science 2007, 315, 625.

Thymine Dimerization in DNA is an Ultrafast Reaction

Steady State IR fs-Time-Resolved IR

0.50

0.25

0.00As /

10

-3

420-2 100 1000

570 nm

5'-TTTTTTTTTTTTTTTTTT-3' TMP

Time / ps

fs-Transient Absorption

= 740 12 fs

Law, Y.K.; Azadi, J.; Crespo-Hernández, C.E.; Cohen, B.; Kohler, B. Biophysical J. 2008, in press.

Prediction of T<>T Yields from MD Simulations

Water/EtOH YieldExp. YieldMD (x 102)----------------------------------------------------------- 0% 1.6 ± 0.3 1.7 40% 1.1 ± 0.1 1.3 50% 0.7 ± 0.2 0.6

Hypothesis: ground-state conformation at the instant when dTpT absorbs light controls the photodimer yield.

• Base stacking controls the excited state dynamics on single and double stranded DNA, forming new long-lived singlet excited states not observed in the monomers.

• The driving force for charge separation and charge recombination in the DNA base stacks modulates the dynamics of the long-lived singlet state.

• The major DNA photoproduct, the thymine photodimer, is formed in less than 1ps in thymine-thymine base stacks and the ground state conformation controls whether the photodimer reaction takes place or not.

• Theoretical calculations have been essential for the visualization of the molecular processes and the elucidation of specific mechanisms of nonradiative deactivation of the excited states in DNA.

Conclusions

Our combined experimental and computational studies have shown:

Conceptual Pump-Probe Transient Absorption Experiment

S0

S1

kr knr

Sn

Energy

4.2 eV

0 eV

6 eV

Delay / fs

OD

Time / fs

A

Sn

S1

S0

t < 0 t = 0 t = t1 t = tn

…

……

…

“initiation”

pump

probe

probe delay

pump

probe

0-

probe600 nm

pump267 nm

PD/PMT

Lockin Amplifier

Monochrometer

Femtosecond Pump-Probe Transient Absorption Setup

OPA; 230-1300 nm

Beam Blocker

1cm

Water Cell

WLC; 350-900 nm

Mira, Evolution, Legend

2.9W, 800 nm, 35 fs

1mm Flow Cell

267 nm

mm BBO

Prism-Compressor

Computer Controlled Wave Plate

Optical Chopper

Polarizer

mm BBODelay Stage

400 nm

Ultrafast Deactivation Channel for Thymine

Dimerization

Boggio-Pasqua, M.; Groenhof, G.; Schäfer, L.V.; Grubmüller, H.; Robb, M.A. J. Am. Chem. Soc. 2007, 129, 10996.

1.0

0.8

0.6

0.4

0.2

0.0

As (

nor

mal

ize

d)

5004003002001000

Time / ps

T = 26 °C T = 34 °C T = 52 °C

6

4

2

0

As /

104

1086420-2

Time / ps

26 °C 34 °C 52 °C

Temperature Dependence of the Decays of PolyA and AMP

PolyA

AMP

Crespo-Hernández, C.E.; Kohler, B. J. Phys. Chem. B 2004, 108, 11182.

0

A (

No

rma

lize

d)

2 4 6100

2 4 61000

0

A (

No

rma

lize

d)

100

Time delay / ps

(a)

poly(A)n

(A)4

ApA

(b)

? poly(A)n

? (A)4

? ApA

Excimer State is Localized between two Stacked Bases.