Quantitative x-ray scattering of free molecules

Ma, Lingyu; Goff, Nathan; Carrascosa, Andrés Moreno; Nelson, Silke; Liang, Mengning; Cheng, Xinxin; Yong, Haiwang; Gabalski, Ian; Huang, Lisa; Crane, Stuart W.; Green, Alice E.; Allum, Felix; Lenzen, Philipp; Muvva, Sri Bhavya; Heald, Lauren F.; Liu, Yusong; Bhattacharyya, Surjendu; Larsen, Kirk A.; Graßl, Martin; Forbes, Ruaridh; Centurion, Martin; Wolf, Thomas J. A.; Kirrander, Adam; Minitti, Michael P.; Weber, Peter M.

doi:10.1088/1361-6455/ad78d0

Title: Quantitative x-ray scattering of free molecules

Journal Article · 20 September 2024 · Journal of Physics. B, Atomic, Molecular and Optical Physics

DOI: https://doi.org/10.1088/1361-6455/ad78d0 · OSTI ID:2440455

^[1]; Goff, Nathan ^[2]; Carrascosa, Andrés Moreno ^[3]; Nelson, Silke ^[4]; Liang, Mengning ^[4];

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^[8]; Lenzen, Philipp ^[9]; Muvva, Sri Bhavya ^[10]; Heald, Lauren F. ^[10]; Liu, Yusong ^[4]; Bhattacharyya, Surjendu ^[4]; Larsen, Kirk A. ^[4];

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Brown Univ., Providence, RI (United States); SLAC
Brown Univ., Providence, RI (United States)
Univ. of Oxford (United Kingdom)
SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States). Linac Coherent Light Source (LCLS)
Univ. of California, San Diego, CA (United States)
Stanford Univ., CA (United States); SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States). Photon Ultrafast Laser Science and Engineering Institute (PULSE)
SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States). Photon Ultrafast Laser Science and Engineering Institute (PULSE); European XFEL, Schenefeld (Germany)
SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States). Linac Coherent Light Source (LCLS); SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States). Photon Ultrafast Laser Science and Engineering Institute (PULSE)
SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States). Photon Ultrafast Laser Science and Engineering Institute (PULSE)
Univ. of Nebraska, Lincoln, NE (United States)

Advances in x-ray free electron lasers have made ultrafast scattering a powerful method for investigating molecular reaction kinetics and dynamics. Accurate measurement of the ground-state, static scattering signals of the reacting molecules is pivotal for these pump-probe x-ray scattering experiments as they are the cornerstone for interpreting the observed structural dynamics. Here, this article presents a data calibration procedure, designed for gas-phase x-ray scattering experiments conducted at the Linac Coherent Light Source x-ray Free-Electron Laser at SLAC National Accelerator Laboratory, that makes it possible to derive a quantitative dependence of the scattering signal on the scattering vector. A self-calibration algorithm that optimizes the detector position without reference to a computed pattern is introduced. Angle-of-scattering corrections that account for several small experimental non-idealities are reported. Their implementation leads to near quantitative agreement with theoretical scattering patterns calculated with ab-initio methods as illustrated for two x-ray photon energies and several molecular test systems.

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Research Organization:: SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division (CSGB); USDOE Office of Science (SC), Office of Workforce Development for Teachers & Scientists (WDTS)

Grant/Contract Number:: AC02-76SF00515; SC0017995; SC0020276

OSTI ID:: 2440455

Journal Information:: Journal of Physics. B, Atomic, Molecular and Optical Physics, Journal Name: Journal of Physics. B, Atomic, Molecular and Optical Physics Journal Issue: 20 Vol. 57; ISSN 0953-4075

Publisher:: IOP PublishingCopyright Statement

Country of Publication:: United States

Language:: English

References (56)

Femtochemistry: Atomic-Scale Dynamics of the Chemical Bond Using Ultrafast Lasers (Nobel Lecture) Zewail, Ahmed H. Angewandte Chemie International Edition, Vol. 39, Issue 15, p. 2586-2631 https://doi.org/10.1002/1521-3773(20000804)39:15<2586::AID-ANIE2586>3.0.CO;2-O	journal	August 2000
Simplicity Beneath Complexity: Counting Molecular Electrons Reveals Transients and Kinetics of Photodissociation Reactions Ruddock, Jennifer M.; Zotev, Nikola; Stankus, Brian Angewandte Chemie, Vol. 131, Issue 19 https://doi.org/10.1002/ange.201902228	journal	February 2019
Electron and X-Ray Methods of Ultrafast Structural Dynamics: Advances and Applications Chergui, Majed; Zewail, Ahmed H. ChemPhysChem, Vol. 10, Issue 1 https://doi.org/10.1002/cphc.200800667	journal	January 2009
Putting the Disulfide Bridge at Risk: How UV‐C Radiation Leads to Ultrafast Rupture of the S‐S Bond Larsen, Martin A. B.; Skov, Anders B.; Clausen, Christian M. ChemPhysChem, Vol. 19, Issue 21, p. 2829-2834 https://doi.org/10.1002/cphc.201800610	journal	August 2018
Molpro: a general-purpose quantum chemistry program package: Molpro Werner, Hans-Joachim; Knowles, Peter J.; Knizia, Gerald Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 2, Issue 2 https://doi.org/10.1002/wcms.82	journal	July 2011
X-Ray Interactions: Photoabsorption, Scattering, Transmission, and Reflection at E = 50-30,000 eV, Z = 1-92 Henke, B. L.; Gullikson, E. M.; Davis, J. C. Atomic Data and Nuclear Data Tables, Vol. 54, Issue 2, p. 181-342 https://doi.org/10.1006/adnd.1993.1013	journal	July 1993
Centering of ultrafast time-resolved pump–probe electron diffraction patterns Cardoza, Job D.; Dudek, Raymond C.; Mawhorter, Richard J. Chemical Physics, Vol. 299, Issue 2-3 https://doi.org/10.1016/j.chemphys.2003.12.018	journal	April 2004
Structure sensitive photoionization via Rydberg levels Kuthirummal, Narayanan; Weber, Peter M. Journal of Molecular Structure, Vol. 787, Issue 1-3 https://doi.org/10.1016/j.molstruc.2005.10.043	journal	April 2006
The potential and limitations of neutrons, electrons and X-rays for atomic resolution microscopy of unstained biological molecules Henderson, Richard Quarterly Reviews of Biophysics, Vol. 28, Issue 2 https://doi.org/10.1017/S003358350000305X	journal	May 1995
Capturing Chemistry in Action with Electrons: Realization of Atomically Resolved Reaction Dynamics Ischenko, Anatoly A.; Weber, Peter M.; Miller, R. J. Dwayne Chemical Reviews, Vol. 117, Issue 16 https://doi.org/10.1021/acs.chemrev.6b00770	journal	May 2017
From the (1B) Spectroscopic State to the Photochemical Product of the Ultrafast Ring-Opening of 1,3-Cyclohexadiene: A Spectral Observation of the Complete Reaction Path Pemberton, Christine C.; Zhang, Yao; Saita, Kenichiro The Journal of Physical Chemistry A, Vol. 119, Issue 33 https://doi.org/10.1021/acs.jpca.5b05672	journal	August 2015
Determining Orientations of Optical Transition Dipole Moments Using Ultrafast X-ray Scattering Yong, Haiwang; Zotev, Nikola; Stankus, Brian The Journal of Physical Chemistry Letters, Vol. 9, Issue 22 https://doi.org/10.1021/acs.jpclett.8b02773	journal	October 2018
Ab Initio Calculation of Molecular Diffraction Northey, Thomas; Zotev, Nikola; Kirrander, Adam Journal of Chemical Theory and Computation, Vol. 10, Issue 11 https://doi.org/10.1021/ct500096r	journal	October 2014
Effects of Electron Correlation in X-Ray and Electron Diffraction Bartell, L. S.; Gavin, R. M. Journal of the American Chemical Society, Vol. 86, Issue 17 https://doi.org/10.1021/ja01071a019	journal	September 1964
Ultrafast Diffraction Imaging of the Electrocyclic Ring-Opening Reaction of 1,3-Cyclohexadiene Dudek, Ray C.; Weber, Peter M. The Journal of Physical Chemistry A, Vol. 105, Issue 17 https://doi.org/10.1021/jp010122t	journal	May 2001
Rydberg Fingerprint Spectroscopy: A New Spectroscopic Tool with Local and Global Structural Sensitivity Gosselin, Jaimie L.; Weber, Peter M. The Journal of Physical Chemistry A, Vol. 109, Issue 22 https://doi.org/10.1021/jp0503866	journal	June 2005
Structural Dynamics in Floppy Systems: Ultrafast Conformeric Motions in Rydberg-Excited Triethylamine Deb, Sanghamitra; Bayes, Brian A.; Minitti, Michael P. The Journal of Physical Chemistry A, Vol. 115, Issue 10 https://doi.org/10.1021/jp110905h	journal	March 2011
Time-resolved atomic inner-shell spectroscopy Drescher, M.; Hentschel, M.; Kienberger, R. Nature, Vol. 419, Issue 6909 https://doi.org/10.1038/nature01143	journal	October 2002
Charge localization in a diamine cation provides a test of energy functionals and self-interaction correction Cheng, Xinxin; Zhang, Yao; Jónsson, Elvar Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms11013	journal	March 2016
First lasing and operation of an ångstrom-wavelength free-electron laser Emma, P.; Akre, R.; Arthur, J. Nature Photonics, Vol. 4, Issue 9 https://doi.org/10.1038/nphoton.2010.176	journal	August 2010
A compact X-ray free-electron laser emitting in the sub-ångström region Ishikawa, Tetsuya; Aoyagi, Hideki; Asaka, Takao Nature Photonics, Vol. 6, Issue 8 https://doi.org/10.1038/nphoton.2012.141	journal	June 2012
Reply to: “The diamine cation is not a chemical example where density functional theory fails” Cheng, Xinxin; Jónsson, Elvar; Jónsson, Hannes Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-07683-z	journal	December 2018
Direct observation of nuclear reorganization driven by ultrafast spin transitions Jiang, Yifeng; Liu, Lai Chung; Sarracini, Antoine Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-15187-y	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
The photochemical ring-opening of 1,3-cyclohexadiene imaged by ultrafast electron diffraction Wolf, T. J. A.; Sanchez, D. M.; Yang, J. Nature Chemistry, Vol. 11, Issue 6 https://doi.org/10.1038/s41557-019-0252-7	journal	April 2019
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
Imaging rotations and vibrations in polyatomic molecules with X-ray scattering Moreno Carrascosa, Andrés; Northey, Thomas; Kirrander, Adam Physical Chemistry Chemical Physics, Vol. 19, Issue 11 https://doi.org/10.1039/C6CP06793J	journal	January 2017
Ab initio calculation of inelastic scattering Moreno Carrascosa, Andrés; Kirrander, Adam Physical Chemistry Chemical Physics, Vol. 19, Issue 30 https://doi.org/10.1039/C7CP02054F	journal	January 2017
Effects of probe energy and competing pathways on time-resolved photoelectron spectroscopy: the ring-opening of 1,3-cyclohexadiene Tudorovskaya, Maria; Minns, Russell S.; Kirrander, Adam Physical Chemistry Chemical Physics, Vol. 20, Issue 26 https://doi.org/10.1039/C8CP02397B	journal	January 2018
Ultrafast electron microscopy in materials science, biology, and chemistry King, Wayne E.; Campbell, Geoffrey H.; Frank, Alan Journal of Applied Physics, Vol. 97, Issue 11 https://doi.org/10.1063/1.1927699	journal	June 2005
Ultrafast time-resolved electron diffraction with megavolt electron beams Hastings, J. B.; Rudakov, F. M.; Dowell, D. H. Applied Physics Letters, Vol. 89, Issue 18 https://doi.org/10.1063/1.2372697	journal	October 2006
Ultrafast structural and isomerization dynamics in the Rydberg-exited Quadricyclane: Norbornadiene system Rudakov, Fedor; Weber, Peter M. The Journal of Chemical Physics, Vol. 136, Issue 13 https://doi.org/10.1063/1.3697472	journal	April 2012
Mega-electron-volt ultrafast electron diffraction at SLAC National Accelerator Laboratory Weathersby, S. P.; Brown, G.; Centurion, M. Review of Scientific Instruments, Vol. 86, Issue 7 https://doi.org/10.1063/1.4926994	journal	July 2015
Elastic X-ray scattering from state-selected molecules Northey, Thomas; Moreno Carrascosa, Andrés; Schäfer, Steffen The Journal of Chemical Physics, Vol. 145, Issue 15 https://doi.org/10.1063/1.4962256	journal	October 2016
High current table-top setup for femtosecond gas electron diffraction Zandi, Omid; Wilkin, Kyle J.; Xiong, Yanwei Structural Dynamics, Vol. 4, Issue 4 https://doi.org/10.1063/1.4983225	journal	July 2017
Ultrafast diffraction and structural dynamics: The nature of complex molecules far from equilibrium Ruan, C. -Y.; Lobastov, V. A.; Srinivasan, R. Proceedings of the National Academy of Sciences, Vol. 98, Issue 13 https://doi.org/10.1073/pnas.131192898	journal	June 2001
Brighter, faster, stronger: ultrafast scattering of free molecules Odate, Asami; Kirrander, Adam; Weber, Peter M. Advances in Physics: X, Vol. 8, Issue 1 https://doi.org/10.1080/23746149.2022.2126796	journal	December 2022
Observation of femtosecond molecular dynamics via pump–probe gas phase x-ray scattering Budarz, J. M.; Minitti, M. P.; Cofer-Shabica, D. V. Journal of Physics B: Atomic, Molecular and Optical Physics, Vol. 49, Issue 3 https://doi.org/10.1088/0953-4075/49/3/034001	journal	January 2016
Advances in ultrafast gas-phase x-ray scattering Stankus, Brian; Yong, Haiwang; Ruddock, Jennifer Journal of Physics B: Atomic, Molecular and Optical Physics, Vol. 53, Issue 23 https://doi.org/10.1088/1361-6455/abbfea	journal	November 2020
On the Intensity of Total Scattering of X-Rays Waller, I.; Hartree, D. R. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 124, Issue 793 https://doi.org/10.1098/rspa.1929.0101	journal	May 1929
Molecular x-ray- and electron-scattering intensities Thakkar, Ajit J.; Tripathi, A. N.; Smith, Vedene H. Physical Review A, Vol. 29, Issue 3 https://doi.org/10.1103/PhysRevA.29.1108	journal	March 1984
Imaging Molecular Motion: Femtosecond X-Ray Scattering of an Electrocyclic Chemical Reaction Minitti, M. P.; Budarz, J. M.; Kirrander, A. Physical Review Letters, Vol. 114, Issue 25 https://doi.org/10.1103/PhysRevLett.114.255501	journal	June 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
Time-Resolved Conformational Dynamics in Hydrocarbon Chains Minitti, Michael P.; Weber, Peter M. Physical Review Letters, Vol. 98, Issue 25 https://doi.org/10.1103/PhysRevLett.98.253004	journal	June 2007
Characterizing Multiphoton Excitation Using Time-Resolved X-ray Scattering Bucksbaum, Philip H.; Ware, Matthew R.; Natan, Adi Physical Review X, Vol. 10, Issue 1 https://doi.org/10.1103/PhysRevX.10.011065	journal	March 2020
Pump-probe low-energy electron diffraction Thompson, John R.; Weber, Peter M.; Estrup, Peder J. SPIE's 1995 International Symposium on Optical Science, Engineering, and Instrumentation, SPIE Proceedings https://doi.org/10.1117/12.218343	conference	September 1995
High-repetition-rate time-resolved gas phase electron diffraction Geiser, Joseph D.; Weber, Peter M. SPIE's 1995 International Symposium on Optical Science, Engineering, and Instrumentation, SPIE Proceedings https://doi.org/10.1117/12.218345	conference	September 1995
A deep UV trigger for ground-state ring-opening dynamics of 1,3-cyclohexadiene Ruddock, Jennifer M.; Yong, Haiwang; Stankus, Brian Science Advances, Vol. 5, Issue 9 https://doi.org/10.1126/sciadv.aax6625	journal	September 2019
An Atomic-Level View of Melting Using Femtosecond Electron Diffraction Siwick, Bradley J.; Dwyer, Jason R.; Jordan, Robert E. Science, Vol. 302, Issue 5649 https://doi.org/10.1126/science.1090052	journal	November 2003
Femtosecond Crystallography with Ultrabright Electrons and X-rays: Capturing Chemistry in Action Miller, R. J. D. Science, Vol. 343, Issue 6175 https://doi.org/10.1126/science.1248488	journal	March 2014
Femtosecond x-ray spectroscopy of an electrocyclic ring-opening reaction Attar, Andrew R.; Bhattacherjee, Aditi; Pemmaraju, C. D. Science, Vol. 356, Issue 6333 https://doi.org/10.1126/science.aaj2198	journal	April 2017
Imaging CF ₃ I conical intersection and photodissociation dynamics with ultrafast electron diffraction Yang, Jie; Zhu, Xiaolei; Wolf, Thomas J. A. Science, Vol. 361, Issue 6397 https://doi.org/10.1126/science.aat0049	journal	July 2018
Simultaneous observation of nuclear and electronic dynamics by ultrafast electron diffraction Yang, Jie; Zhu, Xiaolei; F. Nunes, J. Pedro Science, Vol. 368, Issue 6493 https://doi.org/10.1126/science.abb2235	journal	May 2020
The Ultrafast Pathway of Photon-Induced Electrocyclic Ring-Opening Reactions: The Case of 1,3-Cyclohexadiene Deb, Sanghamitra; Weber, Peter M. Annual Review of Physical Chemistry, Vol. 62, Issue 1 https://doi.org/10.1146/annurev.physchem.012809.103350	journal	May 2011
Ultrafast Dynamics of 1,3-Cyclohexadiene in Highly Excited States Bühler, Christine C.; Minitti, Michael P.; Deb, Sanghamitra Journal of Atomic, Molecular, and Optical Physics, Vol. 2011 https://doi.org/10.1155/2011/637593	journal	January 2011
Time-Resolved, Laser-Induced Phase Transformation in Aluminum Williamson, S.; Mourou, G.; Li, J. C. M. MRS Proceedings, Vol. 35 https://doi.org/10.1557/PROC-35-87	journal	January 1984

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Title: Quantitative x-ray scattering of free molecules

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