Nonadiabatic Car-Parrinello Molecular Dynamics Studies of Photochemical Processes
Final Report Abstract
We have applied our recently developed nonadiabatic ab initio molecular dynamics (na-AIMD) technique to the study of photoexcited DNA and RNA building blocks. In addition to the canonical tautomers, a number of rare tautomers have been investigated. Moreover, effects of substitution and solvation have been studied in detail. The simulations of nonradiative decay in aqueous solution, in particular, demonstrate the strength of the na-AIMD technique employed here as it permits the treatment of solute and solvent on an equal footing. Condensed phase calculations can be directly compared with those in the gas phase because the same computational setup can be used. The excited state lifetimes determined from the na-AIMD simulations are generally in good agreement with experimental data. In addition, the na-AIMD simulations provide detailed insights into the dynamical mechanism of radiationless decay. The time evolution of the nonadiabatic transition probability could be correlated with certain vibrational motions. In this way, the simulations yield the driving modes of internal conversion. In an oversimplified picture, nonradiative decay in U and C is controlled by a torsional motion about the C(5)C(6) double bond, while in the canonical G tautomer out-of-plane deformations of the six-membered ring are chiefly responsible for internal conversion. In the case of G, the canonical, biologically relevant, 9H-keto form indeed exhibits photophysical properties which are distinctly different from other tautomers. Its excited state lifetime, for example, is the shortest of all tautomers. This is a consequence of its pronounced out-of-plane distortions absent in other tautomers. Methylation has been found to prolong the lifetime of both the 9H-keto and the 7H-keto form of G. In the case of C, methylation stabilizes a dark n?? state which decays rapidly. In aqueous solution, nonradiative decay of 9H-keto G is slowed down considerably due to the fact that the crucial out-of-plane motions are damped and the excited state structure of G remains largely planar. For U, on the other hand, the decay mechanisms in solution and in the gas phase are qualitatively the same. In the canonical GC base pair, radiationless decay is governed by a rather different scenario. Photoexcitation first induces a coupled proton–electron transfer from G to C. The resulting charge transfer state is close to a conical intersection providing an efficient route for internal conversion. Back in the ground state the original Watson-Crick structure is restored rapidly. This ultrafast photocycle may indeed protect nucleic acids from suffering radiation induced damage. We have performed multiscale simulations of the phototriggered unfolding of a tetrapeptide combining (na-)AIMD and classical MD. Photocleavage of the disulphide bridge is seen to occur on the femtosecond timescale, while recombination takes place in the sub-nanosecond regime contrary to recent experimental interpretations. We have implemented both an analyical and a finite difference scheme to calculate ROKS/KS S1/S0 nonadiabatic coupling vectors. A comparison to CASSCF results for a number of test molecules reveals excellent agreement.
Publications
- H. Langer, N. L. Doltsinis, and D. Marx: Excited state dynamics and coupled proton-electron transfer of guanine: from the gas phase via microsolvation to aqueous solution, ChemPhysChem, 6 (2005) 1734-1737.
- N. L. Doltsinis and D. S. Kosov: Plane wave/pseudopotential implementation of excited state gradients in density functional linear response theory: a new route via implicit differentiation , J. Chem. Phys., 122 (2005) 144101-1 - 144101-7.
- H. Langer: Nonadiabatic ab initio molecular dynamics simulations of photoexcited nucleobases, PhD Thesis, Ruhr-Universität Bochum, 2006.
- N. L. Doltsinis: Molecular dynamics beyond the Born-Oppenheimer approximation: mixed quantum-classical approaches, in Computational Nanoscience: Do it yourself !, edited by S. Blügel, J. Grotendorst and D. Marx (NIC, FZ Jülich, 2006), pp. 389-409. ISBN: 3-00-017350-1.
- H. Nieber and N. L. Doltsinis: Elucidating ultrafast nonradiative decay of photoexcited uracil in aqueous solution by ab initio molecular dynamics, Chem. Phys., 347 (2008) 405-412.
- H. Nieber: Nonadiabatic ab initio and QM/MM molecular dynamics simulations of photoexcited biosystems, PhD Thesis, King's College London, 2008.
- N. L. Doltsinis, P. R. L. Markwick, H. Nieber, and H. Langer: Ultrafast radiationless decay in Nucleic Acids: Insights From Nonadiabatic Ab Initio Molecular Dynamics, in Radiation Induced Molecular Phenomena in Nucleic Acid, edited by M. K. Shukla and J. Leszczynski under the book series Challenges and Advances in Computational Chemistry and Physics edited by J. Leszczynski (Springer, Netherlands, 2008), pp. 265-299. ISBN: 978-1-4020-8181-5.
- M. B¨ockmann, N. L. Doltsinis, and D. Marx: On the Workings of Azobenzene Photoswitches in Bulk Materials, Phys. Rev. E, 78 (2008) 036101.
- N. A. Besley and N. L. Doltsinis: Ab Initio Finite Temperature Electronic Absorption Spectrum of Formamide, J. Chem. Theory Comput., 2 (2006) 1598.
- N. L. Doltsinis and K. Fink: Comment on "Excitations in photoactive molecules from quantum Monte Carlo" [J. Chem. Phys. 121 (2004) 5836], J. Chem. Phys., 122 (2005) 087101.
- P. R. L. Markwick and N. L. Doltsinis: Ultrafast repair of irradiated DNA: Nonadiabatic ab initio simulations of the GC photocycle, J. Chem. Phys., 126 (2007) 175102.
- P. R. L. Markwick, N. L. Doltsinis, and J. Schlitter: Probing Irradiation Induced DNA Damage Mechanisms using Excited State Car-Parrinello Molecular Dynamics, J. Chem. Phys., 126 (2007) 045104.
