Conical Intersection Passages of Molecules Probed by X-ray Diffraction and Stimulated Raman Spectroscopy

Nam, Yeonsig; Keefer, Daniel; Nenov, Artur; Conti, Irene; Aleotti, Flavia; Segatta, Francesco; Lee, Jin Yong; Garavelli, Marco; Mukamel, Shaul

doi:10.1021/acs.jpclett.1c03814

Title: Conical Intersection Passages of Molecules Probed by X-ray Diffraction and Stimulated Raman Spectroscopy

Journal Article · 20 December 2021 · Journal of Physical Chemistry Letters

DOI: https://doi.org/10.1021/acs.jpclett.1c03814 · OSTI ID:1922851

^[1];

^[2];

^[3];

^[3]; Aleotti, Flavia ^[3];

^[3];

^[4];

^[3];

^[2]

Univ. of California, Irvine, CA (United States); Sungkyunkwan Univ., Suwon (Korea); Regents, University of California, Irvine
Univ. of California, Irvine, CA (United States)
Univ. degli Studi di Bologna (Italy)
Sungkyunkwan Univ., Suwon (Korea)

Conical intersections (CoIns) play an important role in ultrafast relaxation channels. Their monitoring remains a formidable experimental challenge. We theoretically compare the probing of the S₂ → S₁ CoIn passage in 4-thiouracil by monitoring its vibronic coherences, using off-resonant X-ray-stimulated Raman spectroscopy (TRUECARS) and time resolved X-ray diffraction (TRXD). The quantum nuclear wavepacket (WP) dynamics provides an accurate picture of the photoinduced dynamics. Upon photoexcitation, the WP oscillates among the Franck–Condon point, the S2 minimum, and the CoIn with a 70 fs period. A vibronic coherence first emerges at 20 fs and can be observed until the S₂ state is fully depopulated. The distribution of the vibronic frequencies involved in the coherence is recorded by the TRUECARS spectrogram. Here, the TRXD signal provides spatial images of electron densities associated with the CoIn. In combination, the two signals provide a complementary picture of the nonadiabatic passage, which helps in the study of the underlying photophysics in thiobases.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Univ. of California, Irvine, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division

Grant/Contract Number:: FG02-04ER15571; SC0019484

OSTI ID:: 1922851

Journal Information:: Journal of Physical Chemistry Letters, Journal Name: Journal of Physical Chemistry Letters Journal Issue: 51 Vol. 12; ISSN 1948-7185

Publisher:: American Chemical SocietyCopyright Statement

Country of Publication:: United States

Language:: English

References (47)

Dithionated Nucleobases as Effective Photodynamic Agents against Human Epidermoid Carcinoma Cells Pollum, Marvin; Lam, Minh; Jockusch, Steffen ChemMedChem, Vol. 13, Issue 10 https://doi.org/10.1002/cmdc.201800148	journal	April 2018
Photochemistry of Nucleic Acid Bases and Their Thio- and Aza-Analogues in Solution Pollum, Marvin; Martínez-Fernández, Lara; Crespo-Hernández, Carlos E. Topics in Current Chemistry https://doi.org/10.1007/128_2014_554	book	January 2014
Density matrix averaged atomic natural orbital (ANO) basis sets for correlated molecular wave functions: I. First row atoms Widmark, Per-Olof; Malmqvist, Per-�ke; Roos, Bj�rn O. Theoretica Chimica Acta, Vol. 77, Issue 5 https://doi.org/10.1007/BF01120130	journal	January 1990
4-thiouridine photosensitized RNA-protein crosslinking in mammalian cells Favre, A.; Moreno, G.; Blondel, M. O. Biochemical and Biophysical Research Communications, Vol. 141, Issue 2 https://doi.org/10.1016/S0006-291X(86)80250-9	journal	December 1986
The multi-state CASPT2 method Finley, James; Malmqvist, Per-Åke; Roos, Björn O. Chemical Physics Letters, Vol. 288, Issue 2-4 https://doi.org/10.1016/S0009-2614(98)00252-8	journal	May 1998
Ultrafast Nonlinear Optical Signals Viewed from the Molecule’s Perspective Mukamel, Shaul; Rahav, Saar Advances In Atomic, Molecular, and Optical Physics https://doi.org/10.1016/S1049-250X(10)59006-2	book	January 2010
Linear absorption spectra of solvated thiouracils resolved at the hybrid RASPT2/MM level Nenov, Artur; Conti, Irene; Borrego-Varillas, Rocio Chemical Physics, Vol. 515 https://doi.org/10.1016/j.chemphys.2018.07.025	journal	November 2018
Femtosecond nanocrystallography using X-ray lasers for membrane protein structure determination Fromme, Petra; Spence, John CH Current Opinion in Structural Biology, Vol. 21, Issue 4 https://doi.org/10.1016/j.sbi.2011.06.001	journal	August 2011
Stimulated X-ray Resonant Raman Spectroscopy of Conical Intersections in Thiophenol Cho, Daeheum; Rouxel, Jérémy R.; Mukamel, Shaul The Journal of Physical Chemistry Letters, Vol. 11, Issue 11 https://doi.org/10.1021/acs.jpclett.0c00949	journal	May 2020
Stimulated X-ray Raman Imaging of Conical Intersections Cho, Daeheum; Mukamel, Shaul The Journal of Physical Chemistry Letters, Vol. 11, Issue 1 https://doi.org/10.1021/acs.jpclett.9b03020	journal	November 2019
Diffractive Imaging of Conical Intersections Amplified by Resonant Infrared Fields Keefer, Daniel; Rouxel, Jérémy R.; Aleotti, Flavia Journal of the American Chemical Society, Vol. 143, Issue 34 https://doi.org/10.1021/jacs.1c06068	journal	August 2021
Controlling Photorelaxation in Uracil with Shaped Laser Pulses: A Theoretical Assessment Keefer, Daniel; Thallmair, Sebastian; Matsika, Spiridoula Journal of the American Chemical Society, Vol. 139, Issue 14 https://doi.org/10.1021/jacs.6b12033	journal	February 2017
RNA Environment Is Responsible for Decreased Photostability of Uracil Reiter, Sebastian; Keefer, Daniel; de Vivie-Riedle, Regina Journal of the American Chemical Society, Vol. 140, Issue 28 https://doi.org/10.1021/jacs.8b02962	journal	June 2018
Observation of the Sub-100 Femtosecond Population of a Dark State in a Thiobase Mediating Intersystem Crossing Borrego-Varillas, Rocío; Teles-Ferreira, Danielle C.; Nenov, Artur Journal of the American Chemical Society, Vol. 140, Issue 47 https://doi.org/10.1021/jacs.8b07057	journal	October 2018
Excited-State Dynamics in 6-Thioguanosine from the Femtosecond to Microsecond Time Scale Reichardt, Christian; Guo, Cao; Crespo-Hernández, Carlos E. The Journal of Physical Chemistry B, Vol. 115, Issue 12 https://doi.org/10.1021/jp112018u	journal	March 2011
X-rays inspire electron movies Vrakking, Marc J. J.; Elsaesser, Thomas Nature Photonics, Vol. 6, Issue 10 https://doi.org/10.1038/nphoton.2012.247	journal	October 2012
Conical-intersection dynamics and ground-state chemistry probed by extreme-ultraviolet time-resolved photoelectron spectroscopy von Conta, A.; Tehlar, A.; Schletter, A. Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-05292-4	journal	August 2018
Three-dimensional view of ultrafast dynamics in photoexcited bacteriorhodopsin in the multiphoton regime and biological relevance Miller, R. J. Dwayne; Paré-Labrosse, Olivier; Sarracini, Antoine Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-14971-0	journal	March 2020
Observation of the molecular response to light upon photoexcitation Yong, Haiwang; Zotev, Nikola; Ruddock, Jennifer M. Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-15680-4	journal	May 2020
Ultrafast X-ray scattering reveals vibrational coherence following Rydberg excitation Stankus, Brian; Yong, Haiwang; Zotev, Nikola Nature Chemistry, Vol. 11, Issue 8 https://doi.org/10.1038/s41557-019-0291-0	journal	July 2019
Increase in the photoreactivity of uracil derivatives by doubling thionation Pollum, M.; Jockusch, S.; Crespo-Hernández, C. E. Phys. Chem. Chem. Phys., Vol. 17, Issue 41 https://doi.org/10.1039/C5CP04822B	journal	January 2015
Monitoring molecular vibronic coherences in a bichromophoric molecule by ultrafast X-ray spectroscopy Keefer, Daniel; Freixas, Victor M.; Song, Huajing Chemical Science, Vol. 12, Issue 14 https://doi.org/10.1039/D0SC06328B	journal	January 2021
Measuring ultrashort laser pulses in the time-frequency domain using frequency-resolved optical gating Trebino, Rick; DeLong, Kenneth W.; Fittinghoff, David N. Review of Scientific Instruments, Vol. 68, Issue 9, p. 3277-3295 https://doi.org/10.1063/1.1148286	journal	September 1997
An accurate and efficient scheme for propagating the time dependent Schrödinger equation Tal‐Ezer, H.; Kosloff, R. The Journal of Chemical Physics, Vol. 81, Issue 9 https://doi.org/10.1063/1.448136	journal	November 1984
Molecular dynamics of pyrazine after excitation to the S2 electronic state using a realistic 24-mode model Hamiltonian Raab, A.; Worth, G. A.; Meyer, H. -D. The Journal of Chemical Physics, Vol. 110, Issue 2 https://doi.org/10.1063/1.478061	journal	January 1999
Quantum dynamics of photoexcited cyclohexadiene introducing reactive coordinates Hofmann, Angelika; de Vivie-Riedle, Regina The Journal of Chemical Physics, Vol. 112, Issue 11 https://doi.org/10.1063/1.481059	journal	March 2000
Stimulated Raman signals at conical intersections: Ab initio surface hopping simulation protocol with direct propagation of the nuclear wave function Kowalewski, Markus; Mukamel, Shaul The Journal of Chemical Physics, Vol. 143, Issue 4 https://doi.org/10.1063/1.4927475	journal	July 2015
Signatures of electronic and nuclear coherences in ultrafast molecular x-ray and electron diffraction Rouxel, Jérémy R.; Keefer, Daniel; Mukamel, Shaul Structural Dynamics, Vol. 8, Issue 1 https://doi.org/10.1063/4.0000043	journal	January 2021
Correlating the motion of electrons and nuclei with two-dimensional electronic-vibrational spectroscopy Oliver, T. A. A.; Lewis, N. H. C.; Fleming, G. R. Proceedings of the National Academy of Sciences, Vol. 111, Issue 28 https://doi.org/10.1073/pnas.1409207111	journal	June 2014
Monitoring molecular nonadiabatic dynamics with femtosecond X-ray diffraction Bennett, Kochise; Kowalewski, Markus; Rouxel, Jérémy R. Proceedings of the National Academy of Sciences, Vol. 115, Issue 26 https://doi.org/10.1073/pnas.1805335115	journal	June 2018
Visualizing conical intersection passages via vibronic coherence maps generated by stimulated ultrafast X-ray Raman signals Keefer, Daniel; Schnappinger, Thomas; de Vivie-Riedle, Regina Proceedings of the National Academy of Sciences, Vol. 117, Issue 39 https://doi.org/10.1073/pnas.2015988117	journal	September 2020
Imaging conical intersection dynamics during azobenzene photoisomerization by ultrafast X-ray diffraction Keefer, Daniel; Aleotti, Flavia; Rouxel, Jérémy R. Proceedings of the National Academy of Sciences, Vol. 118, Issue 3 https://doi.org/10.1073/pnas.2022037118	journal	January 2021
Unveiling the spatial distribution of molecular coherences at conical intersections by covariance X-ray diffraction signals Cavaletto, Stefano M.; Keefer, Daniel; Rouxel, Jérémy R. Proceedings of the National Academy of Sciences, Vol. 118, Issue 22 https://doi.org/10.1073/pnas.2105046118	journal	May 2021
Roadmap of ultrafast x-ray atomic and molecular physics Young, Linda; Ueda, Kiyoshi; Gühr, Markus Journal of Physics B: Atomic, Molecular and Optical Physics, Vol. 51, Issue 3 https://doi.org/10.1088/1361-6455/aa9735	journal	January 2018
Ultrafast molecular frame electronic coherences from lab frame scattering anisotropies Makhija, Varun; Veyrinas, Kevin; Boguslavskiy, Andrey E. Journal of Physics B: Atomic, Molecular and Optical Physics, Vol. 53, Issue 11 https://doi.org/10.1088/1361-6455/ab7a84	journal	May 2020
Short-wavelength free-electron laser sources and science: a review Seddon, E. A.; Clarke, J. A.; Dunning, D. J. Reports on Progress in Physics, Vol. 80, Issue 11 https://doi.org/10.1088/1361-6633/aa7cca	journal	October 2017
Multiwavelength Anomalous Diffraction at High X-Ray Intensity Son, Sang-Kil; Chapman, Henry N.; Santra, Robin Physical Review Letters, Vol. 107, Issue 21 https://doi.org/10.1103/PhysRevLett.107.218102	journal	November 2011
X-Ray Diffraction from Isolated and Strongly Aligned Gas-Phase Molecules with a Free-Electron Laser Küpper, Jochen; Stern, Stephan; Holmegaard, Lotte Physical Review Letters, Vol. 112, Issue 8 https://doi.org/10.1103/PhysRevLett.112.083002	journal	February 2014
Coherent Electron Hole Dynamics Near a Conical Intersection Timmers, Henry; Li, Zheng; Shivaram, Niranjan Physical Review Letters, Vol. 113, Issue 11 https://doi.org/10.1103/PhysRevLett.113.113003	journal	September 2014
Catching Conical Intersections in the Act: Monitoring Transient Electronic Coherences by Attosecond Stimulated X-Ray Raman Signals Kowalewski, Markus; Bennett, Kochise; Dorfman, Konstantin E. Physical Review Letters, Vol. 115, Issue 19 https://doi.org/10.1103/PhysRevLett.115.193003	journal	November 2015
Self-Referenced Coherent Diffraction X-Ray Movie of Ångstrom- and Femtosecond-Scale Atomic Motion Glownia, J. M.; Natan, A.; Cryan, J. P. Physical Review Letters, Vol. 117, Issue 15 https://doi.org/10.1103/PhysRevLett.117.153003	journal	October 2016
Generating Single-Spike Hard X-Ray Pulses with Nonlinear Bunch Compression in Free-Electron Lasers Huang, S.; Ding, Y.; Feng, Y. Physical Review Letters, Vol. 119, Issue 15 https://doi.org/10.1103/PhysRevLett.119.154801	journal	October 2017
Ultrafast X-Ray Spectroscopy of Conical Intersections Neville, Simon P.; Chergui, Majed; Stolow, Albert Physical Review Letters, Vol. 120, Issue 24 https://doi.org/10.1103/PhysRevLett.120.243001	journal	June 2018
High Temporal and Spectral Resolution of Stimulated X-Ray Raman Signals with Stochastic Free-Electron-Laser Pulses Cavaletto, Stefano M.; Keefer, Daniel; Mukamel, Shaul Physical Review X, Vol. 11, Issue 1 https://doi.org/10.1103/PhysRevX.11.011029	journal	February 2021
Sub-7-femtosecond conical-intersection dynamics probed at the carbon K-edge Zinchenko, Kristina S.; Ardana-Lamas, Fernando; Seidu, Issaka Science, Vol. 371, Issue 6528 https://doi.org/10.1126/science.abf1656	journal	January 2021
Photocross-Linking of Nucleic Acids to Associated Proteins Meisenheimer, Kristen M.; Koch, Tad H. Critical Reviews in Biochemistry and Molecular Biology, Vol. 32, Issue 2 https://doi.org/10.3109/10409239709108550	journal	January 1997
Ultraviolet Transient Absorption Spectrometer with Sub-20-fs Time Resolution Borrego-Varillas, Rocío; Ganzer, Lucia; Cerullo, Giulio Applied Sciences, Vol. 8, Issue 6 https://doi.org/10.3390/app8060989	journal	June 2018

Similar Records

Visualizing conical intersection passages via vibronic coherence maps generated by stimulated ultrafast X-ray Raman signals

Journal Article · 2020 · Proceedings of the National Academy of Sciences of the United States of America · OSTI ID:1660474

Keefer, Daniel; Schnappinger, Thomas; de Vivie-Riedle, Regina; +1 more

Two-dimensional Fourier transform electronic spectroscopy at a conical intersection

Journal Article · 2014 · Journal of Chemical Physics · OSTI ID:22253370

Kitney-Hayes, Katherine A.; Ferro, Allison A.; Tiwari, Vivek

Nonadiabatic excited-state intramolecular proton transfer in 3-hydroxyflavone: S2 state involvement via multi-mode effect

Journal Article · 2019 · Journal of Chemical Physics · OSTI ID:1761742

Anand, Neethu; Welke, Kai; Irle, Stephan; +1 more

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
Diffraction
Molecules
Probes
Quantum mechanics
Scattering

Title: Conical Intersection Passages of Molecules Probed by X-ray Diffraction and Stimulated Raman Spectroscopy

Citation Formats

References (47)

Similar Records

Related Subjects