Haiwang Yong, Jennifer M Ruddock, Brian Stankus, Lingyu Ma, Wenpeng Du, Nathan Goff, Yu Chang, Nikola Zotev, Darren Bellshaw, Sébastien Boutet, Sergio Carbajo, Jason E Koglin, Mengning Liang, Joseph S Robinson, Adam Kirrander, Michael P Minitti, Peter M Weber
Author Information
Haiwang Yong: Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA. ORCID
Jennifer M Ruddock: Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA.
Brian Stankus: Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA.
Lingyu Ma: Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA.
Wenpeng Du: Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA. ORCID
Nathan Goff: Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA.
Yu Chang: Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA. ORCID
Nikola Zotev: School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, United Kingdom.
Darren Bellshaw: School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, United Kingdom.
Sébastien Boutet: Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.
Sergio Carbajo: Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.
Jason E Koglin: Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.
Mengning Liang: Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.
Joseph S Robinson: Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.
Adam Kirrander: School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, United Kingdom. ORCID
Michael P Minitti: Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA. ORCID
Peter M Weber: Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA. ORCID
Pump-probe gas phase X-ray scattering experiments, enabled by the development of X-ray free electron lasers, have advanced to reveal scattering patterns of molecules far from their equilibrium geometry. While dynamic displacements reflecting the motion of wavepackets can probe deeply into the reaction dynamics, in many systems, the thermal excitation embedded in the molecules upon optical excitation and energy randomization can create systems that encompass structures far from the ground state geometry. For polyatomic molecular systems, large amplitude vibrational motions are associated with anharmonicity and shifts of interatomic distances, making analytical solutions using traditional harmonic approximations inapplicable. More generally, the interatomic distances in a polyatomic molecule are not independent and the traditional equations commonly used to interpret the data may give unphysical results. Here, we introduce a novel method based on molecular dynamic trajectories and illustrate it on two examples of hot, vibrating molecules at thermal equilibrium. When excited at 200 nm, 1,3-cyclohexadiene (CHD) relaxes on a subpicosecond time scale back to the reactant molecule, the dominant pathway, and to various forms of 1,3,5-hexatriene (HT). With internal energies of about 6 eV, the energy thermalizes quickly, leading to structure distributions that deviate significantly from their vibrationless equilibrium. The experimental and theoretical results are in excellent agreement and reveal that a significant contribution to the scattering signal arises from transition state structures near the inversion barrier of CHD. In HT, our analysis clarifies that previous inconsistent structural parameters determined by electron diffraction were artifacts that might have resulted from the use of inapplicable analytical equations.
