• Ultrafast Science
  • Vol. 3, Issue 1, 0015 (2023)
Xiangxu Mu1,†, Ming Zhang1,†, Jiechao Feng1, Hanwei Yang1..., Nikita Medvedev2, Xinyang Liu1, Leyi Yang1, Zhenxiang Wu1, Haitan Xu3,4,5,* and Zheng Li1,6,7,*|Show fewer author(s)
Author Affiliations
  • 1State Key Laboratory for Mesoscopic Physics and Collaborative Innovation Center of Quantum Matter, School of Physics, Peking University, Beijing 100871, China.
  • 2Institute of Physics Czech Academy of Science, Na Slovance 2, 182 21 Prague 8, Czech Republic.
  • 3School of Materials Science and Intelligent Engineering, Nanjing University, Suzhou 215163, China.
  • 4Shenzhen Institute for Quantum Science and Engineering, Southern University of Science and Technology, Shenzhen, China.
  • 5School of Physical Sciences, University of Science and Technology of China, Hefei 230026, China.
  • 6Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China.
  • 7Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu 226010, China.
  • show less
    DOI: 10.34133/ultrafastscience.0015 Cite this Article
    Xiangxu Mu, Ming Zhang, Jiechao Feng, Hanwei Yang, Nikita Medvedev, Xinyang Liu, Leyi Yang, Zhenxiang Wu, Haitan Xu, Zheng Li. Identification of the Decay Pathway of Photoexcited Nucleobases[J]. Ultrafast Science, 2023, 3(1): 0015 Copy Citation Text show less
    References

    [1] Smith DMA, Smets J, Elkadi Y, Adamowicz L. Methylation reduces electron affinity of uracil. Ab Initio theoretical study. Chem A Eur J. 1997;101(43):8123.

    [2] Steenken S, Telo JP, Novais HM, Candeias LP. One-electron-reduction potentials of pyrimidine bases, nucleosides, and nucleotides in aqueous solution. consequences for DNA redox chemistry. J Am Chem Soc. 1992;114(12):4701.

    [3] Wolf TJA, Parrish RM, Myhre RH, Martínez TJ, Koch H, Gühr M. Observation of ultrafast intersystem crossing in thymine by extreme ultraviolet time-resolved photoelectron spectroscopy. Chem A Eur J. 2019;123(32):6897–6903.

    [4] Prokhorenko VI, Picchiotti A, Pola M, Dijkstra AG, Miller RJD. New insights into the photophysics of DNA nucleobases. J Phys Chem Lett. 2016;7(22):4445–4450.

    [5] Hudock HR, Levine BG, Thompson AL, Satzger H, Townsend D, Gador N, Ullrich S, Stolow A, Martínez TJ. Ab initio molecular dynamics and time-resolved photoelectron spectroscopy of electronically excited uracil and thymine. J Phys Chem A. 2007;111(34):8500.

    [6] Yarkony DR. Diabolical conical intersections. Rev Mod Phys. 1996;68(4):985–1013.

    [7] Boggio-Pasqua M, Bearpark MJ, Hunt PA, Robb MA. Dihydroazulene/vinylheptafulvene photochromism: A model for one-way photochemistry via a conical intersection. J Am Chem Soc. 2002;124(7):1456.

    [8] Worth GA, Cederbaum LS. Beyond born-oppenheimer: Molecular dynamics through a conical ntersection. Annu Rev Phys Chem. 2004;55(1):127.

    [9] Domcke W, Yarkony DR. Role of conical intersections in molecular spectroscopy and photoinduced chemical dynamics. Annu Rev Phys Chem. 2012;63(1):325.

    [10] Nachtigallová D, Aquino AJA, Szymczak JJ, Barbatti M, Hobza P, Lischka H. Nonadiabatic dynamics of uracil: Population split among different decay mechanisms. Chem A Eur J. 2011;115(21):5247–5255.

    [11] Lan Z, Fabiano E, Thiel W. Photoinduced nonadiabatic dynamics of pyrimidine nucleobases: On-the-fly surface-hopping study with semiempirical methods. J Phys Chem B. 2009;113(11):3548–3555.

    [12] Chakraborty P, Liu Y, McClung S, Weinacht T, Matsika S. Time resolved photoelectron spectroscopy as a test of electronic structure and nonadiabatic dynamics. J Phys Chem Lett. 2021;12(21):5099–5104.

    [13] Fingerhut BP, Dorfman KE, Mukamel S. Monitoring nonadiabatic dynamics of the RNA base uracil by UV pump–IR probe spectroscopy. J Phys Chem Lett. 2013;4(11):1933–1942.

    [14] Hua W, Mukamel S, Luo Y. Transient X-ray absorption spectral fingerprints of the S1 dark state in uracil. J Phys Chem Lett. 2019;10:7172–7178.

    [15] Richter M, Mai S, Marquetand P, González L. Ultrafast intersystem crossing dynamics in uracil unravelled by ab initio molecular dynamics. Phys Chem Chem Phys. 2014;16(44):24423–24436.

    [16] Brister MM, Crespo-Hernández CE. Direct observation of triplet-state population dynamics in the RNA uracil derivative 1-cyclohexyluracil. J Phys Chem Lett. 2015;6(21):4404–4409.

    [17] Nam Y, Keefer D, Nenov A, Conti I, Aleotti F, Segatta F, Lee JY, Garavelli M, Mukamel S. Conical intersection passages of molecules probed by X-ray diffraction and stimulated raman spectroscopy. J Phys Chem Lett. 2021;12(51):12300–12309.

    [18] Berne BJ, Ciccotti G, Coker DF, Classical and quantum dynamics in condensed phase simulations. Singapore: World Scientific; 1998. p. 385.

    [19] Yang J, Zhu X, F. Nunes JP, Yu JK, Parrish RM, Wolf TJA, Centurion M, Gühr M, Li R, Liu Y, et al. Simultaneous observation of nuclear and electronic dynamics by ultrafast electron diffraction. Science. 2020;368:885.

    [20] Yang J, Zhu X, Wolf TJA, Li Z, Nunes JPF, Coffee R, Cryan JP, Gühr M, Hegazy K, Heinz TF, et al. Imaging CF3I conical intersection and photodissociation dynamics with ultrafast electron diffraction. Science. 2018;361(6397):64–67.

    [21] Wolf TJA, Sanchez DM, Yang J, Parrish RM, Nunes JPF, Centurion M, Coffee R, Cryan JP, Gühr M, Hegazy K, et al. The photochemical ring-opening of 1,3-cyclohexadiene imaged by ultrafast electron diffraction. Nat Chem. 2019;11(6):504–509.

    [22] Duris J, Li S, Driver T, Champenois EG, MacArthur JP, Lutman AA, Zhang Z, Rosenberger P, Aldrich JW, Coffee R, et al. Tunable isolated attosecond X-ray pulses with gigawatt peak power from a free-electron laser. Nat Photonics. 2020;14(1):30–36.

    [23] Duris JP, MacArthur JP, Glownia JM, Li S, Vetter S, Miahnahri A, Coffee R, Hering P, Fry A, Welch ME, et al. Controllable x-ray pulse trains from enhanced self-amplified spontaneous emission. Phys Rev Lett. 2021;126(10):104802.

    [24] Tully JC. Molecular dynamics with electronic transitions. J Chem Phys. 1990;93(2):1061–1071.

    [25] Richter M, Marquetand P, González-Vázquez J, Sola I, González L. SHARC: Ab initio molecular dynamics with surface hopping in the adiabatic representation including arbitrary couplings. J Chem Theory Comput. 2011;7(5):1253–1258.

    [26] Werner HJ, Knowles PJ, Knizia G, Lindh R, Manby FR, Schütz M, Celani P, Györffy W, Kats D, Korona T, et al. Molpro, version 2012.1, a package of ab initio programs (2012).

    [27] Martinez TJ, Ufimtsev IS. Terachem, a package of GPU accelerated ab initio quantum chemistry programs.

    [28] Yang J, Nunes JPF, Ledbetter K, Biasin E, Centurion M, Chen Z, Cordones AA, Crissman C, Deponte DP, Glenzer SH, et al. Structure retrieval in liquid-phase electron scattering. Phys Chem Chem Phys. 2021;23(2):1308–1316.

    [29] Siegbahn K, Nordling C, Fahlman A, Nordberg R, Hamrin K, Hedman J, Johansson G, Bergmark T, Karlsson S-E; Lindgren, Ingvar and Lindberg. ESCA: Atomic, molecular and solid state structure studied by means of electron spectroscopy. Uppsala (Sweden): Almqvist & Wiksells; 1967.

    [30] McFarland BK, Farrell JP, Miyabe S, Tarantelli F, Aguilar A, Berrah N, Bostedt C, Bozek JD, Bucksbaum PH, Castagna JC, et al. Ultrafast X-ray Auger probing of photoexcited molecular dynamics. Nat Commun. 2014;5(1):4235.

    [31] Gao M, Lu C, Jean-Ruel H, Liu LC, Marx A, Onda K, Koshihara S-y, Nakano Y, Shao X, Hiramatsu T, et al. Mapping molecular motions leading to charge delocalization with ultrabright electrons. Nature. 2013;496:343–346.

    Xiangxu Mu, Ming Zhang, Jiechao Feng, Hanwei Yang, Nikita Medvedev, Xinyang Liu, Leyi Yang, Zhenxiang Wu, Haitan Xu, Zheng Li. Identification of the Decay Pathway of Photoexcited Nucleobases[J]. Ultrafast Science, 2023, 3(1): 0015
    Download Citation