Excess energy flow in dna bench and computer experiments working in unison
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Excess Energy Flow in DNA: Bench and Computer Experiments Working in Unison. Carlos E. Crespo-Hernández Department of Chemistry Email: [email protected] Ohio Supercomputer Center Columbus, Ohio April 4, 2008. Acknowledgement. Prof. Bern Kohler and Group Members

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Excess energy flow in dna bench and computer experiments working in unison

Excess Energy Flow in DNA: Bench and Computer Experiments Working in Unison

Carlos E. Crespo-Hernández

Department of Chemistry

Email: [email protected]

Ohio Supercomputer Center

Columbus, Ohio

April 4, 2008


Acknowledgement

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


Excess energy flow in dna bench and computer experiments working in unison

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

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.


Excess energy flow in dna bench and computer experiments working in unison

Ultrafast ExcitedState Dynamics of Nucleic Acids


Excess energy flow in dna bench and computer experiments working in unison

S1 Lifetimes for Nucleosides

DNA

RNA

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.


Excess energy flow in dna bench and computer experiments working in unison

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

Conical intersections are a likely mechanism for the

ultrafast lifetimes of cytosine and the other DNA bases.

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.


Excess energy flow in dna bench and computer experiments working in unison

Nucleic Acid Multimers Photophysics:

The Role of Base Stacking and Base Pairing


Excess energy flow in dna bench and computer experiments working in unison

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

L+1

L

H

H-1

S2

S1

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

H-1 -> L 40%

275.6 nm,0.0266H -> L 78%

H-1 -> L+1 22%

S0

Effect of Base Stacking Interactions

Dinucleotides: stack↔unstack

Nucleotides: unstack


Excess energy flow in dna bench and computer experiments working in unison

A-AA

R = 3 Å

Ade

R = 4 Å

R = 5 Å

R = 6 Å

HOMO

LUMO

A-AA6

Electronic Coupling versus Interchromophoric Distance

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

Crespo-Hernández, C.E.; Marai, C.N.J. AIP Conference Proceedings2007, 963, 607.

R

AA AMP

E= 0.2 eV


Excess energy flow in dna bench and computer experiments working in unison

Reversible Redox Potentials of DNA Nucleosides

Crespo-Hernández, C.E.; Close, M. D.; Gorb, L.; Leszczynski J. Phys. Chem. B2007, 111, 5386.


Excess energy flow in dna bench and computer experiments working in unison

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.

G°  E°ox - E°red  IP - EA

The decay rates of the long-lived states increase with increasing driving force

for charge recombination as expected in the Marcus inverted region.


Excess energy flow in dna bench and computer experiments working in unison

Role of the Driving Force for Charge Separation

  • Crespo-Hernández, C.E.; Cohen, B.; Kohler, B. Nature2005, 436, 1141.

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

d(AT)9•d(AT)9

d(GC)9•d(GC)9

d(IC)9•d(IC)9

ΔG(GC) >ΔG(AT) >ΔG(IC)


Excess energy flow in dna bench and computer experiments working in unison

Singlet or triplet state?

UV

Formation time scale?

T<>T photodimers account

for ~90% of DNA Damage*

Excited State Dynamics and DNA Photochemistry:

Making Connections

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


Excess energy flow in dna bench and computer experiments working in unison

Thymine Dimerization in DNA is an Ultrafast Reaction

  • Crespo-Hernández, C.E.; Cohen, B.; Kohler, B. Nature2005, 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. Science2007, 315, 625.

Steady State IR

fs-Time-Resolved IR

Time / ps

fs-Transient Absorption

 = 740  12 fs


Prediction of t t yields from md simulations

Prediction of T<>T Yields from MD Simulations

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

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.


Excess energy flow in dna bench and computer experiments working in unison

Conclusions

Our combined experimental and computational

studies have shown:

  • 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.


Excess energy flow in dna bench and computer experiments working in unison

Sn

probe

S1

A

Energy

pump

S0

t < 0

t = 0

t = t1

t = tn

probe delay

“initiation”

Sn

6 eV

Time / fs

S1

4.2 eV

kr

knr

S0

0 eV

probe600 nm

pump267 nm

Conceptual Pump-Probe Transient Absorption Experiment

probe

pump

DOD

0-

Delay / fs


Excess energy flow in dna bench and computer experiments working in unison

Femtosecond Pump-Probe Transient Absorption Setup

Mira, Evolution, Legend

OPA; 230-1300 nm

2.9

W

, 800 nm, 35 fs

mm BBO

Delay Stage

400 nm

Water Cell

mm BBO

1cm

Computer Controlled Wave Plate

267 nm

WLC; 350-900 nm

Prism-Compressor

Optical Chopper

Lockin Amplifier

Polarizer

1mm

F

l

o

w

C

el

l

Monochrometer

PD/PMT

Beam Blocker


Excess energy flow in dna bench and computer experiments working in unison

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.


Temperature dependence of the decays of polya and amp

Temperature Dependence of the Decays of PolyA and AMP

Crespo-Hernández, C.E.; Kohler, B. J. Phys. Chem. B2004, 108, 11182.

Excimer State is Localized between two Stacked Bases.

PolyA

AMP


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