期刊
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
卷 10, 期 3, 页码 1172-1188出版社
AMER CHEMICAL SOC
DOI: 10.1021/ct401012u
关键词
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资金
- National Science Foundation (NSF) [CHE-1058791]
- Chemical Sciences, Geosciences and Biosciences Division, Office of Basic Energy Sciences, Office of Science
- (U.S.) Department of Energy (DOE), National Institutes of Health (NIH) [GM-59230]
- DOE
- [CHE-0840513]
- Division Of Chemistry
- Direct For Mathematical & Physical Scien [1361516] Funding Source: National Science Foundation
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.
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