Dna Accumulation Of Base Excitation State Inactivation Of The Semi-classical Dynamics Simulations

Excited electronic states of DNA are the object of intense study both experimentally and theoretically. The dynamics of excited states in monomeric nucleobases can now be routinely observed by ultrafast laser spectroscopy on time scales of hundreds of femtoseconds. Quantum calculation is approaching the coupling between nuclear and electronic motion responsible for nonradiative decay with unprecedented detail. For single bases, a fully microscopic description of nonradiative decay is almost at hand and experiment and quantum dynamics calculations are increasingly congruent about deactivation events. For nucleobase multimers, there is evidence of both slower and faster rates of nonradiative decay than those in single bases, but the underlying mechanisms are poorly understood. Computational efforts combined with new and carefully designed experiments should provide a microscopic explanation of how excited states of DNA oligo- and polynucleotides evolve in time.In this thesis the nonradiative decay of aπ-stacked pair of cytosine, adenine, and thymine molecules, following laser excitation, was studied by semiclassical dynamics simulation technique. Simulation results show that the spatial organization ofπ-stacked bases leads to few new photophysical decay pathways not found in base monomers. These results shed light into the understanding of the deactivation mechanism ofπ-stacked bases.In Chapter 3 we show a systematic study of the deactivation of the excied state ofπstacked cytosines. The study reveals the deactivation of excited states through various channels. The main points from this study are summarized below:1. Simulations find five different decay channels:(1) the deactivation through the formation of a dimmer, (2) the deactivation through an excimer, (3) monomer-like deactivation, (4) the deactivation through the formation of a dimer subsequent to a monomer-like deactivation, and (5) the deactivation through an excimer subsequent to a monomer-like deactivation.2. The excited cytosine in all decay channels above first forms an exciton, an excited state produced by the dipolar coupling of the neutral excited states of individual molecules. An exciton decays within 100 fs.3. Two channels competitively evolve through exciton state. An intensive out-of-plane vibration of the pyrimidine ring at the C5,C6 site disrupts base stacking and leads to a monomer-like decay with a lifetime of 300 fs. When the C5,C6 atomic vibration is weak, base stacking will result in an "excimer", which characterizes a charge transferring, with a lifetime of 800～1000 fs.4. Two competitive channels were found in the conical intersection of monomer-like (CI (monomer-like)).An intensive vibration at H5 or H6 site will lead system towards ground state through a monomer-like decay pathway. A weak vibration at H5 or H6 atom will form excimer.5. An excimer state decays to the ground state before an avoided crossing by charge recombination. Two competitiv channels exist in the avoided crossing due to the vibration amplitude at the C6 atom; a strong vibration results in an excimer and a weak vibration leads to the formation of dimmer.In Chapter 4 we present a semiclassical dynamics simulation study of two stacked adenines irradiated by an ultrashort laser pulses. The simulation found three different decay pathways, of which the timescales are agreement with the multiexponential emission observations in experiment.1. Two different ultrafast laser pulses were used to excite one of the stacked B-DNA adenines. In one case, the excited molecule decays to the ground state by an ultrafast internal conversion in a time scale of～600 fs. The decay is induced by the out-of-plane vibration of H2 atom and the deformation of the pyrimidine ring at the C2 site. In the other case, a covalent bond is formed between two stacked adenine molecules after excitation. The formation of the covalent bond inhibits the deformation of the pyrimidine ring and leads the excimer to decay to the electronic ground state at a longer timescale,～2400 fs after the excitation. The decay in this case is induced by the out-of-plane vibration of H2 atom.2. Semiclassical dynamics simulation of twoπ-stacked B-like adenines shows the formation of a long-lived excimer, with an average C2-C2' distance of 2.2A. The out-of-plane deformations of both C2 and C2' atoms play a significant role in the vibronic coupling between the HOMO and LUMO, which leads to the deactivation of the excimer. This interaction comes from a face-to-face stacked configuration and a very short C2-C2'distance of 1.821A.The simulations also find that interaction between two adenines leads to a new deactivated passway, in which C2 atom and C2'atom close to each other and form a so-called "bonded excimer" intermediate. Lifetime of the "bonded excimer" intermediate is about 500 fs. The deformation of the pyrimidine ring at C2 atom and the displacements of the H2'atom away from pyrimidine ring play a significant role in deactivation process of the "bonded excimer" intermediate. After the deactivation the C2-C2'dissociates and released bond energy converts to molecular kinetic energy. Both adenine molecules decay to a planar geometry.In Chapter 5 we present a semiclassical dynamics simulation of the dimerzation and dissociation of a thymine dimmer by the radiation of an ultrashort laser pulse. The simulation results are summarized below:1. The photophysical decay pathway competes with photochemical decay pathways in dimerzation. Simulation follows two different reaction paths produced by the laser pulses with two different fluences. In one reaction, the stacked thymine molecules form a cyclobutane pyrimidine dimer, which is the main course of photoinduced DNA damage. The formation of two chemical bonds linking two thymines occurs nonsynchronously after the excimer decays to the electronic ground state. In the other reaction, only one bond is formed between the two thymine molecules. In this latter reaction, the bond breaks about 50 fs after formation, and then the two molecules move away from each other. The reaction leads to the DNA damage repair. The simulation finds that the deformation of the pyrimidine ring plays an important role in cleaving this bond.2. The simulation finds that the dissociation follows an asynchronously concerted mechanism where the C5-C5 bond breaks soon after the application of the laser pulse followed by the cleavage of the C6-C6 bond. The dissociation results in two thymine monomers:one is in an electronically excited state and the other is in the ground state. The former decays to the electronic ground state through an avoided crossing induced by the deformation of the pyrimidine ring at the C5 and C6 atom sites.