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Probing the Conical Intersection Dynamics of the RNA Base Uracil by UV-Pump Stimulated-Raman-Probe Signals; Ab Initio Simulations.

Fingerhut BP, Dorfman KE, Mukamel S - J Chem Theory Comput (2014)

Bottom Line: The simulations rely on a microscopically derived expression that takes into account the path integral of the excited state evolution and the pulse shapes.Analysis of the joint time/frequency resolution of the technique reveals a matter chirp contribution that limits the inherent temporal resolution.Characteristic signatures of relaxation dynamics mediated in the vicinity of conical intersection are predicted.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, University of California , Irvine, California 92697-2025, United States.

ABSTRACT
Nonadiabatic electron and nuclear dynamics of photoexcited molecules involving conical intersections is of fundamental importance in many reactions such as the self-protection mechanism of DNA and RNA bases against UV irradiation. Nonlinear vibrational spectroscopy can provide an ultrafast sensitive probe for these processes. We employ a simulation protocol that combines nonadiabatic on-the-fly molecular dynamics with a mode-tracking algorithm for the simulation of femtosecond stimulated Raman spectroscopy (SRS) signals of the high frequency C-H- and N-H-stretch vibrations of the photoexcited RNA base uracil. The simulations rely on a microscopically derived expression that takes into account the path integral of the excited state evolution and the pulse shapes. Analysis of the joint time/frequency resolution of the technique reveals a matter chirp contribution that limits the inherent temporal resolution. Characteristic signatures of relaxation dynamics mediated in the vicinity of conical intersection are predicted. The C-H and N-H spectator modes provide high sensitivity to their local environment and act as local probes with submolecular and high temporal resolution.

No MeSH data available.


Related in: MedlinePlus

(a) Instantaneous frequencies of C–Hstretch vibrationsof a prototype trajectory showing ππ* → nOπ* relaxation. (b) SRS signal (eq 2) of C–H stretch vibrations (simulated accordingto eq 6). (c) Snapshots of the molecular dynamicsat t = 270 fs (left) and t = 526fs (right). Carbon atoms are colored in black, nitrogen atoms in blue,oxygen atoms in red, and hydrogen atoms in white. (d) Instantaneousfrequencies of N–H stretch vibrations. (e) SRS signal (eq 2) of N–H stretch vibrations.
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fig4: (a) Instantaneous frequencies of C–Hstretch vibrationsof a prototype trajectory showing ππ* → nOπ* relaxation. (b) SRS signal (eq 2) of C–H stretch vibrations (simulated accordingto eq 6). (c) Snapshots of the molecular dynamicsat t = 270 fs (left) and t = 526fs (right). Carbon atoms are colored in black, nitrogen atoms in blue,oxygen atoms in red, and hydrogen atoms in white. (d) Instantaneousfrequencies of N–H stretch vibrations. (e) SRS signal (eq 2) of N–H stretch vibrations.

Mentions: The NA-O-MD simulations yield trajectoriesof the electronic statepotential energies Ei(t) together with the evolving nuclear geometries q(t) as classical objects. We focus onthe time-evolution of the Raman active high frequency C–H-and N–H-stretch vibrations which show spectator character alongthe reaction coordinate. The course of the trajectories is evaluatedwith a δt = 1 fs time step by the mode trackingalgorithm (for details see below). The normal modes are evaluatedalong the trajectory, over the entire normal mode coordinate spaceof the C–H and N–H vibrations, i.e., the inner turningpoint, the equilibrium structure, and the outer turning point. Thisyields a highly oscillating function ω(q(t)) which contains the dependence on the position of thenormal mode coordinate (see dashed lines in Figures 4 and 5)


Probing the Conical Intersection Dynamics of the RNA Base Uracil by UV-Pump Stimulated-Raman-Probe Signals; Ab Initio Simulations.

Fingerhut BP, Dorfman KE, Mukamel S - J Chem Theory Comput (2014)

(a) Instantaneous frequencies of C–Hstretch vibrationsof a prototype trajectory showing ππ* → nOπ* relaxation. (b) SRS signal (eq 2) of C–H stretch vibrations (simulated accordingto eq 6). (c) Snapshots of the molecular dynamicsat t = 270 fs (left) and t = 526fs (right). Carbon atoms are colored in black, nitrogen atoms in blue,oxygen atoms in red, and hydrogen atoms in white. (d) Instantaneousfrequencies of N–H stretch vibrations. (e) SRS signal (eq 2) of N–H stretch vibrations.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3958139&req=5

fig4: (a) Instantaneous frequencies of C–Hstretch vibrationsof a prototype trajectory showing ππ* → nOπ* relaxation. (b) SRS signal (eq 2) of C–H stretch vibrations (simulated accordingto eq 6). (c) Snapshots of the molecular dynamicsat t = 270 fs (left) and t = 526fs (right). Carbon atoms are colored in black, nitrogen atoms in blue,oxygen atoms in red, and hydrogen atoms in white. (d) Instantaneousfrequencies of N–H stretch vibrations. (e) SRS signal (eq 2) of N–H stretch vibrations.
Mentions: The NA-O-MD simulations yield trajectoriesof the electronic statepotential energies Ei(t) together with the evolving nuclear geometries q(t) as classical objects. We focus onthe time-evolution of the Raman active high frequency C–H-and N–H-stretch vibrations which show spectator character alongthe reaction coordinate. The course of the trajectories is evaluatedwith a δt = 1 fs time step by the mode trackingalgorithm (for details see below). The normal modes are evaluatedalong the trajectory, over the entire normal mode coordinate spaceof the C–H and N–H vibrations, i.e., the inner turningpoint, the equilibrium structure, and the outer turning point. Thisyields a highly oscillating function ω(q(t)) which contains the dependence on the position of thenormal mode coordinate (see dashed lines in Figures 4 and 5)

Bottom Line: The simulations rely on a microscopically derived expression that takes into account the path integral of the excited state evolution and the pulse shapes.Analysis of the joint time/frequency resolution of the technique reveals a matter chirp contribution that limits the inherent temporal resolution.Characteristic signatures of relaxation dynamics mediated in the vicinity of conical intersection are predicted.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, University of California , Irvine, California 92697-2025, United States.

ABSTRACT
Nonadiabatic electron and nuclear dynamics of photoexcited molecules involving conical intersections is of fundamental importance in many reactions such as the self-protection mechanism of DNA and RNA bases against UV irradiation. Nonlinear vibrational spectroscopy can provide an ultrafast sensitive probe for these processes. We employ a simulation protocol that combines nonadiabatic on-the-fly molecular dynamics with a mode-tracking algorithm for the simulation of femtosecond stimulated Raman spectroscopy (SRS) signals of the high frequency C-H- and N-H-stretch vibrations of the photoexcited RNA base uracil. The simulations rely on a microscopically derived expression that takes into account the path integral of the excited state evolution and the pulse shapes. Analysis of the joint time/frequency resolution of the technique reveals a matter chirp contribution that limits the inherent temporal resolution. Characteristic signatures of relaxation dynamics mediated in the vicinity of conical intersection are predicted. The C-H and N-H spectator modes provide high sensitivity to their local environment and act as local probes with submolecular and high temporal resolution.

No MeSH data available.


Related in: MedlinePlus