1
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Mehmood A, Silfies MC, Durden AS, Allison TK, Levine BG. Simulating ultrafast transient absorption spectra from first principles using a time-dependent configuration interaction probe. J Chem Phys 2024; 161:044107. [PMID: 39041880 DOI: 10.1063/5.0215890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 06/30/2024] [Indexed: 07/24/2024] Open
Abstract
Transient absorption spectroscopy (TAS) is among the most common ultrafast photochemical experiments, but its interpretation remains challenging. In this work, we present an efficient and robust method for simulating TAS signals from first principles. Excited-state absorption and stimulated emission (SE) signals are computed using time-dependent complete active space configuration interaction (TD-CASCI) simulations, leveraging the robustness of time-domain simulation to minimize electronic structure failure. We demonstrate our approach by simulating the TAS signal of 1'-hydroxy-2'-acetonapthone (HAN) from ab initio multiple spawning nonadiabatic molecular dynamics simulations. Our results are compared to gas-phase TAS data recorded from both jet-cooled (T ∼ 40 K) and hot (∼403 K) molecules via cavity-enhanced TAS (CE-TAS). Decomposition of the computed spectrum allows us to assign a rise in the SE signal to excited-state proton transfer and the ultimate decay of the signal to relaxation through a twisted conical intersection. The total cost of computing the observable signal (∼1700 graphics processing unit hours for ∼4 ns of electron dynamics) was markedly less than that of performing the ab initio multiple spawning calculations used to compute the underlying nonadiabatic dynamics.
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Affiliation(s)
- Arshad Mehmood
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
- Institute for Advanced Computational Science, Stony Brook University, Stony Brook, New York 11794, USA
| | - Myles C Silfies
- Department of Physics, Stony Brook University, Stony Brook, New York 11794, USA
| | - Andrew S Durden
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
- Institute for Advanced Computational Science, Stony Brook University, Stony Brook, New York 11794, USA
| | - Thomas K Allison
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
- Department of Physics, Stony Brook University, Stony Brook, New York 11794, USA
| | - Benjamin G Levine
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
- Institute for Advanced Computational Science, Stony Brook University, Stony Brook, New York 11794, USA
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2
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Makhov DV, Hutton L, Kirrander A, Shalashilin DV. Ultrafast electron diffraction of photoexcited gas-phase cyclobutanone predicted by ab initio multiple cloning simulations. J Chem Phys 2024; 160:164310. [PMID: 38661201 DOI: 10.1063/5.0203683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/02/2024] [Indexed: 04/26/2024] Open
Abstract
We present the result of our calculations of ultrafast electron diffraction (UED) for cyclobutanone excited into the S2 electronic state, which is based on the non-adiabatic dynamics simulations with the Ab Initio Multiple Cloning (AIMC) method with the electronic structure calculated at the SA(3)-CASSCF(12,12)/aug-cc-pVDZ level of theory. The key features in the UED pattern were identified, which can be used to distinguish between the reaction pathways observed in the AIMC dynamics, although there is a significant overlap between representative signals due to the structural similarity of the products. The calculated UED pattern can be compared with the experiment.
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Affiliation(s)
- Dmitry V Makhov
- School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom
- School of Mathematics, University of Bristol, Fry Building, Woodland Road, Bristol BS8 1UG, United Kingdom
| | - Lewis Hutton
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom
| | - Adam Kirrander
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom
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3
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Suchan J, Liang F, Durden AS, Levine BG. Prediction challenge: First principles simulation of the ultrafast electron diffraction spectrum of cyclobutanone. J Chem Phys 2024; 160:134310. [PMID: 38573851 DOI: 10.1063/5.0198333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024] Open
Abstract
Computer simulation has long been an essential partner of ultrafast experiments, allowing the assignment of microscopic mechanistic detail to low-dimensional spectroscopic data. However, the ability of theory to make a priori predictions of ultrafast experimental results is relatively untested. Herein, as a part of a community challenge, we attempt to predict the signal of an upcoming ultrafast photochemical experiment using state-of-the-art theory in the context of preexisting experimental data. Specifically, we employ ab initio Ehrenfest with collapse to a block mixed quantum-classical simulations to describe the real-time evolution of the electrons and nuclei of cyclobutanone following excitation to the 3s Rydberg state. The gas-phase ultrafast electron diffraction (GUED) signal is simulated for direct comparison to an upcoming experiment at the Stanford Linear Accelerator Laboratory. Following initial ring-opening, dissociation via two distinct channels is observed: the C3 dissociation channel, producing cyclopropane and CO, and the C2 channel, producing CH2CO and C2H4. Direct calculations of the GUED signal indicate how the ring-opened intermediate, the C2 products, and the C3 products can be discriminated in the GUED signal. We also report an a priori analysis of anticipated errors in our predictions: without knowledge of the experimental result, which features of the spectrum do we feel confident we have predicted correctly, and which might we have wrong?
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Affiliation(s)
- Jiří Suchan
- Institute of Advanced Computational Science, Stony Brook University, Stony Brook, New York 11794, USA
| | - Fangchun Liang
- Institute of Advanced Computational Science, Stony Brook University, Stony Brook, New York 11794, USA
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
| | - Andrew S Durden
- Institute of Advanced Computational Science, Stony Brook University, Stony Brook, New York 11794, USA
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
| | - Benjamin G Levine
- Institute of Advanced Computational Science, Stony Brook University, Stony Brook, New York 11794, USA
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
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4
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Northey T, Kirrander A, Weber PM. Extracting the electronic structure signal from X-ray and electron scattering in the gas phase. JOURNAL OF SYNCHROTRON RADIATION 2024; 31:303-311. [PMID: 38385277 PMCID: PMC10914165 DOI: 10.1107/s1600577524000067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/03/2024] [Indexed: 02/23/2024]
Abstract
X-ray and electron scattering from free gas-phase molecules is examined using the independent atom model (IAM) and ab initio electronic structure calculations. The IAM describes the effect of the molecular geometry on the scattering, but does not account for the redistribution of valence electrons due to, for instance, chemical bonding. By examining the total, i.e. energy-integrated, scattering from three molecules, fluoroform (CHF3), 1,3-cyclohexadiene (C6H8) and naphthalene (C10H8), the effect of electron redistribution is found to predominantly reside at small-to-medium values of the momentum transfer (q ≤ 8 Å-1) in the scattering signal, with a maximum percent difference contribution at 2 ≤ q ≤ 3 Å-1. A procedure to determine the molecular geometry from the large-q scattering is demonstrated, making it possible to more clearly identify the deviation of the scattering from the IAM approximation at small and intermediate q and to provide a measure of the effect of valence electronic structure on the scattering signal.
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Affiliation(s)
- Thomas Northey
- Department of Chemistry, Brown University, Providence, RI 02912, USA
| | - Adam Kirrander
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Peter M. Weber
- Department of Chemistry, Brown University, Providence, RI 02912, USA
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5
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Acheson K, Kirrander A. Automatic Clustering of Excited-State Trajectories: Application to Photoexcited Dynamics. J Chem Theory Comput 2023; 19:6126-6138. [PMID: 37703098 PMCID: PMC10536988 DOI: 10.1021/acs.jctc.3c00776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Indexed: 09/14/2023]
Abstract
We introduce automatic clustering as a computationally efficient tool for classifying and interpreting trajectories from simulations of photo-excited dynamics. Trajectories are treated as time-series data, with the features for clustering selected by variance mapping of normalized data. The L2-norm and dynamic time warping are proposed as suitable similarity measures for calculating the distance matrices, and these are clustered using the unsupervised density-based DBSCAN algorithm. The silhouette coefficient and the number of trajectories classified as noise are used as quality measures for the clustering. The ability of clustering to provide rapid overview of large and complex trajectory data sets, and its utility for extracting chemical and physical insight, is demonstrated on trajectories corresponding to the photochemical ring-opening reaction of 1,3-cyclohexadiene, noting that the clustering can be used to generate reduced dimensionality representations in an unbiased manner.
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Affiliation(s)
- Kyle Acheson
- EaStCHEM,
School of Chemistry and Centre for Science at Extreme Conditions, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, U.K.
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
| | - Adam Kirrander
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
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6
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Bertram L, Weber PM, Kirrander A. Mapping the photochemistry of cyclopentadiene: from theory to ultrafast X-ray scattering. Faraday Discuss 2023; 244:269-293. [PMID: 37132432 DOI: 10.1039/d2fd00176d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The photoinduced ring-conversion reaction when cyclopentadiene (CP) is excited at 5.10 eV is simulated using surface-hopping semiclassical trajectories with XMS(3)-CASPT2(4,4)/cc-pVDZ electronic structure theory. In addition, PBE0/def2-SV(P) is employed for ground state propagation of the trajectories. The dynamics is propagated for 10 ps, mapping both the nonadiabatic short-time dynamics (<300 fs) and the increasingly statistical dynamics on the electronic ground state. The short-time dynamics yields a mixture of hot CP and bicyclo[2.1.0]pentene (BP), with the two products reached via different regions of the same conical intersection seam. On the ground state, we observe slow conversion from BP to CP which is modelled by RRKM theory with a transition state determined using PBE0/def2-TZVP. The CP products are furthermore associated with ground state hydrogen shifts and some H-atom dissociation. Finally, the prospects for detailed experimental mapping using novel ultrafast X-ray scattering experiments are discussed and observables for such experiments are predicted. In particular, we assess the possibility of retrieving electronic states and their populations alongside the structural dynamics.
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Affiliation(s)
- Lauren Bertram
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK.
| | - Peter M Weber
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Adam Kirrander
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK.
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7
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Acheson K, Kirrander A. Robust Inversion of Time-Resolved Data via Forward-Optimization in a Trajectory Basis. J Chem Theory Comput 2023; 19:2721-2734. [PMID: 37129988 DOI: 10.1021/acs.jctc.2c01113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
An inversion method for time-resolved data from ultrafast experiments is introduced, based on forward-optimization in a trajectory basis. The method is applied to experimental data from X-ray scattering of the photochemical ring-opening reaction of 1,3-cyclohexadiene and electron diffraction of the photodissociation of CS2. In each case, inversion yields a model that reproduces the experimental data, identifies the main dynamic motifs, and agrees with independent experimental observations. Notably, the method explicitly accounts for continuity constraints and is robust even for noisy data.
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Affiliation(s)
- Kyle Acheson
- EaStCHEM, School of Chemistry and Centre for Science at Extreme Conditions, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, United Kingdom
| | - Adam Kirrander
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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8
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Keefer D, Cavaletto SM, Rouxel JR, Garavelli M, Yong H, Mukamel S. Ultrafast X-Ray Probes of Elementary Molecular Events. Annu Rev Phys Chem 2023; 74:73-97. [PMID: 37093660 DOI: 10.1146/annurev-physchem-062322-051532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Elementary events that determine photochemical outcomes and molecular functionalities happen on the femtosecond and subfemtosecond timescales. Among the most ubiquitous events are the nonadiabatic dynamics taking place at conical intersections. These facilitate ultrafast, nonradiative transitions between electronic states in molecules that can outcompete slower relaxation mechanisms such as fluorescence. The rise of ultrafast X-ray sources, which provide intense light pulses with ever-shorter durations and larger observation bandwidths, has fundamentally revolutionized our spectroscopic capabilities to detect conical intersections. Recent theoretical studies have demonstrated an entirely new signature emerging once a molecule traverses a conical intersection, giving detailed insights into the coupled nuclear and electronic motions that underlie, facilitate, and ultimately determine the ultrafast molecular dynamics. Following a summary of current sources and experiments, we survey these techniques and provide a unified overview of their capabilities. We discuss their potential to dramatically increase our understanding of ultrafast photochemistry.
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Affiliation(s)
- Daniel Keefer
- Department of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California, USA; ,
| | - Stefano M Cavaletto
- Department of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California, USA; ,
- Current affiliation: Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | - Jérémy R Rouxel
- Université de Lyon, UJM-Saint-Etienne, IOGS, Laboratoire Hubert Curien, UMR CNRS 5516, Saint-Etienne, France
| | - Marco Garavelli
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Bologna, Italy
| | - Haiwang Yong
- Department of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California, USA; ,
| | - Shaul Mukamel
- Department of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California, USA; ,
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9
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Gabalski I, Sere M, Acheson K, Allum F, Boutet S, Dixit G, Forbes R, Glownia JM, Goff N, Hegazy K, Howard AJ, Liang M, Minitti MP, Minns RS, Natan A, Peard N, Rasmus WO, Sension RJ, Ware MR, Weber PM, Werby N, Wolf TJA, Kirrander A, Bucksbaum PH. Transient vibration and product formation of photoexcited CS 2 measured by time-resolved x-ray scattering. J Chem Phys 2022; 157:164305. [PMID: 36319419 PMCID: PMC9625835 DOI: 10.1063/5.0113079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/03/2022] [Indexed: 11/14/2022] Open
Abstract
We have observed details of the internal motion and dissociation channels in photoexcited carbon disulfide (CS2) using time-resolved x-ray scattering (TRXS). Photoexcitation of gas-phase CS2 with a 200 nm laser pulse launches oscillatory bending and stretching motion, leading to dissociation of atomic sulfur in under a picosecond. During the first 300 fs following excitation, we observe significant changes in the vibrational frequency as well as some dissociation of the C-S bond, leading to atomic sulfur in the both 1D and 3P states. Beyond 1400 fs, the dissociation is consistent with primarily 3P atomic sulfur dissociation. This channel-resolved measurement of the dissociation time is based on our analysis of the time-windowed dissociation radial velocity distribution, which is measured using the temporal Fourier transform of the TRXS data aided by a Hough transform that extracts the slopes of linear features in an image. The relative strength of the two dissociation channels reflects both their branching ratio and differences in the spread of their dissociation times. Measuring the time-resolved dissociation radial velocity distribution aids the resolution of discrepancies between models for dissociation proposed by prior photoelectron spectroscopy work.
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Affiliation(s)
- Ian Gabalski
- Author to whom correspondence should be addressed:
| | | | - Kyle Acheson
- School of Chemistry, University of Edinburgh, Edinburgh EH8 9YL, United Kingdom
| | | | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Gopal Dixit
- Department of Physics, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | | | - James M. Glownia
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Nathan Goff
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA
| | | | | | - Mengning Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Michael P. Minitti
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Russell S. Minns
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Adi Natan
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Nolan Peard
- Department of Applied Physics, Stanford University, Stanford, California 94305, USA
| | - Weronika O. Rasmus
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Roseanne J. Sension
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Matthew R. Ware
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Peter M. Weber
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA
| | | | | | - Adam Kirrander
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, OX1 3QX Oxford, United Kingdom
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10
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Yong H, Keefer D, Mukamel S. Imaging Purely Nuclear Quantum Dynamics in Molecules by Combined X-ray and Electron Diffraction. J Am Chem Soc 2022; 144:7796-7804. [DOI: 10.1021/jacs.2c01311] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Haiwang Yong
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
- Department of Physics and Astronomy, University of California, Irvine, Irvine, California 92697, United States
| | - Daniel Keefer
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
- Department of Physics and Astronomy, University of California, Irvine, Irvine, California 92697, United States
| | - Shaul Mukamel
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
- Department of Physics and Astronomy, University of California, Irvine, Irvine, California 92697, United States
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11
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Donovan RJ, Kirrander A, Lawley KP. Heavy Rydberg and ion-pair states: chemistry, spectroscopy and theory. INT REV PHYS CHEM 2022. [DOI: 10.1080/0144235x.2022.2077024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Robert J. Donovan
- School of Chemistry, University of Edinburgh, Edinburgh, United Kingdom
| | - Adam Kirrander
- School of Chemistry, University of Edinburgh, Edinburgh, United Kingdom
| | - Kenneth P. Lawley
- School of Chemistry, University of Edinburgh, Edinburgh, United Kingdom
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12
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Moreno Carrascosa A, Coe JP, Simmermacher M, Paterson MJ, Kirrander A. Towards high-resolution X-ray scattering as a probe of electron correlation. Phys Chem Chem Phys 2022; 24:24542-24552. [DOI: 10.1039/d2cp02933b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We demonstrate that X-ray scattering can be used as a probe of electron–electron correlation.
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Affiliation(s)
- Andrés Moreno Carrascosa
- EaStCHEM, School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, UK
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Jeremy P. Coe
- Institute of Chemical Sciences, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Mats Simmermacher
- EaStCHEM, School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, UK
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Martin J. Paterson
- Institute of Chemical Sciences, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Adam Kirrander
- EaStCHEM, School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, UK
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
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13
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Matsuda I, Kubota Y. Recent Progress in Spectroscopies Using Soft X-ray Free-electron Lasers. CHEM LETT 2021. [DOI: 10.1246/cl.200881] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Iwao Matsuda
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
- Trans-scale Quantum Science Institute, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuya Kubota
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
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14
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Moreno Carrascosa A, Yang M, Yong H, Ma L, Kirrander A, Weber PM, Lopata K. Mapping static core-holes and ring-currents with X-ray scattering. Faraday Discuss 2021; 228:60-81. [PMID: 33605956 DOI: 10.1039/d0fd00124d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Measuring the attosecond movement of electrons in molecules is challenging due to the high temporal and spatial resolutions required. X-ray scattering-based methods are promising, but many questions remain concerning the sensitivity of the scattering signals to changes in density, as well as the means of reconstructing the dynamics from these signals. In this paper, we present simulations of stationary core-holes and electron dynamics following inner-shell ionization of the oxazole molecule. Using a combination of time-dependent density functional theory simulations along with X-ray scattering theory, we demonstrate that the sudden core-hole ionization produces a significant change in the X-ray scattering response and how the electron currents across the molecule should manifest as measurable modulations to the time dependent X-ray scattering signal. This suggests that X-ray scattering is a viable probe for measuring electronic processes at time scales faster than nuclear motion.
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Affiliation(s)
| | - Mengqi Yang
- Department of Chemistry, 232 Choppin Hall, Baton Rouge, Louisiana 70803, USA
| | - Haiwang Yong
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Lingyu Ma
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Adam Kirrander
- EaStCHEM, School of Chemistry, University of Edinburgh, David Brewster Road, EH9 3FJ Edinburgh, UK
| | - Peter M Weber
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Kenneth Lopata
- Department of Chemistry, 232 Choppin Hall, Baton Rouge, Louisiana 70803, USA and Center for Computation and Technology, Louisiana State University, Baton Roug, Louisiana 70803, USA.
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15
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Ma L, Yong H, Geiser JD, Moreno Carrascosa A, Goff N, Weber PM. Ultrafast x-ray and electron scattering of free molecules: A comparative evaluation. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2020; 7:034102. [PMID: 32637459 PMCID: PMC7316516 DOI: 10.1063/4.0000010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 06/08/2020] [Indexed: 05/09/2023]
Abstract
Resolving gas phase molecular motions with simultaneous spatial and temporal resolution is rapidly coming within the reach of x-ray Free Electron Lasers (XFELs) and Mega-electron-Volt (MeV) electron beams. These two methods enable scattering experiments that have yielded fascinating new results, and while both are important methods for determining transient molecular structures in photochemical reactions, it is important to understand their relative merits. In the present study, we evaluate the respective scattering cross sections of the two methods and simulate their ability to determine excited state molecular structures in light of currently existing XFEL and MeV source parameters. Using the example of optically excited N-methyl morpholine and simulating the scattering patterns with shot noise, we find that the currently achievable signals are superior with x-ray scattering for equal samples and on a per-shot basis and that x-ray scattering requires fewer detected signal counts for an equal fidelity structure determination. Importantly, within the independent atom model, excellent structure determinations can be achieved for scattering vectors only to about 5 Å-1, leaving larger scattering vector ranges for investigating vibrational motions and wavepackets. Electron scattering has a comparatively higher sensitivity toward hydrogen atoms, which may point to applications where electron scattering is inherently the preferred choice, provided that excellent signals can be achieved at large scattering angles that are currently difficult to access.
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Affiliation(s)
- Lingyu Ma
- Brown University, Department of Chemistry, Providence, Rhode Island 02912, USA
| | - Haiwang Yong
- Brown University, Department of Chemistry, Providence, Rhode Island 02912, USA
| | - Joseph D. Geiser
- Brown University, Department of Chemistry, Providence, Rhode Island 02912, USA
| | | | - Nathan Goff
- Brown University, Department of Chemistry, Providence, Rhode Island 02912, USA
| | - Peter M. Weber
- Brown University, Department of Chemistry, Providence, Rhode Island 02912, USA
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16
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Zotev N, Moreno Carrascosa A, Simmermacher M, Kirrander A. Excited Electronic States in Total Isotropic Scattering from Molecules. J Chem Theory Comput 2020; 16:2594-2605. [DOI: 10.1021/acs.jctc.9b00670] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nikola Zotev
- EaStCHEM School of Chemistry and Centre for Science at Extreme Conditions, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Andrés Moreno Carrascosa
- EaStCHEM School of Chemistry and Centre for Science at Extreme Conditions, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Mats Simmermacher
- EaStCHEM School of Chemistry and Centre for Science at Extreme Conditions, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Adam Kirrander
- EaStCHEM School of Chemistry and Centre for Science at Extreme Conditions, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, U.K
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Simmermacher M, Moreno Carrascosa A, E. Henriksen N, B. Møller K, Kirrander A. Theory of ultrafast x-ray scattering by molecules in the gas phase. J Chem Phys 2019; 151:174302. [DOI: 10.1063/1.5110040] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Mats Simmermacher
- EaStCHEM, School of Chemistry, University of Edinburgh, EH9 3FJ Edinburgh, United Kingdom
| | | | - Niels E. Henriksen
- Department of Chemistry, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Klaus B. Møller
- Department of Chemistry, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Adam Kirrander
- EaStCHEM, School of Chemistry, University of Edinburgh, EH9 3FJ Edinburgh, United Kingdom
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Moreno Carrascosa A, Yong H, Crittenden DL, Weber PM, Kirrander A. Ab Initio Calculation of Total X-ray Scattering from Molecules. J Chem Theory Comput 2019; 15:2836-2846. [PMID: 30875212 DOI: 10.1021/acs.jctc.9b00056] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a method to calculate total X-ray scattering cross sections directly from ab initio electronic wave functions in atoms and molecules. The approach can be used in conjunction with multiconfigurational wave functions and exploits analytical integrals of Gaussian-type functions over the scattering operator, which leads to accurate and efficient calculations. The results are validated by comparison to experimental results and previous theory for the molecules H2 and CO2. Importantly, we find that the inelastic component of the total scattering varies strongly with molecular geometry. The method is appropriate for use in conjunction with quantum molecular dynamics simulations for the analysis of new ultrafast X-ray scattering experiments and to interpret accurate gas-phase scattering experiments.
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Affiliation(s)
- Andrés Moreno Carrascosa
- EaStCHEM, School of Chemistry , University of Edinburgh , David Brewster Road , EH9 3FJ Edinburgh , United Kingdom
| | - Haiwang Yong
- Department of Chemistry , Brown University , Providence , Rhode Island 02912 , United States
| | - Deborah L Crittenden
- Department of Chemistry , University of Canterbury , Private Bag 4800 , Christchurch 8041 , New Zealand
| | - Peter M Weber
- Department of Chemistry , Brown University , Providence , Rhode Island 02912 , United States
| | - Adam Kirrander
- EaStCHEM, School of Chemistry , University of Edinburgh , David Brewster Road , EH9 3FJ Edinburgh , United Kingdom
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19
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Northey T, Kirrander A. Ab Initio Fragment Method for Calculating Molecular X-ray Diffraction. J Phys Chem A 2019; 123:3395-3406. [PMID: 30892904 DOI: 10.1021/acs.jpca.9b00621] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A fragment-based approach for the prediction of elastic X-ray scattering is presented. The total diffraction pattern is assembled from anisotropic form factors calculated for individual molecular fragments, optionally including corrections for pairwise interactions between fragments. The approach is evaluated against full ab initio scattering calculations in the peptide diphenylalanine, and the optimal selection of fragments is examined in the ethanol molecule. The approach is found to improve significantly on the independent atom model while remaining conceptually simple and computationally efficient. It is expected to be particularly useful for macromolecules with repeated subunits, such as peptides, proteins, DNA, or RNA and other polymers, where it is straightforward to define appropriate fragments.
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Affiliation(s)
- Thomas Northey
- EaStCHEM, School of Chemistry , University of Edinburgh , David Brewster Road , Edinburgh EH9 3FJ , United Kingdom
| | - Adam Kirrander
- EaStCHEM, School of Chemistry , University of Edinburgh , David Brewster Road , Edinburgh EH9 3FJ , United Kingdom
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20
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Parrish RM, Martínez TJ. Ab Initio Computation of Rotationally-Averaged Pump-Probe X-ray and Electron Diffraction Signals. J Chem Theory Comput 2019; 15:1523-1537. [PMID: 30702882 DOI: 10.1021/acs.jctc.8b01051] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We develop a new algorithm for the computation of the rotationally averaged elastic molecular diffraction signal for the cases of perpendicular or parallel pump-probe geometries. The algorithm first collocates the charge density from an arbitrary ab initio wave function onto a Becke quadrature grid [A. Becke, J. Chem. Phys. 1988 , 88 , 2457 ], providing a high-fidelity multiresolution representation of the charge density. A double sum is then performed over the Becke grid points, and the interaction between points computed using the scattering kernels of Williamson and Zewail [J. C. Williamson and A. H. Zewail, J. Phys. Chem. 1994 , 98 , 2766 ]. These kernels analytically average over the molecular orientations with the cos2 γ selection factor appropriate for one-photon dipole absorption in a perpendicular pump-probe geometry. We show that the method is converged with small grids containing <500 points/atom. We implement the algorithm on a GPU for increased efficiency and emonstrate the algorithm for molecules with up to a few dozen atoms. We explore the accuracy of the independent atom model (IAM) by comparison with our new and more accurate method. We also investigate the possibility of detecting signatures of electronic transitions in polyatomic pump-probe diffraction experiments.
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Affiliation(s)
- Robert M Parrish
- Department of Chemistry and The PULSE Institute , Stanford University , Stanford , California 94305 , United States.,SLAC National Accelerator Laboratory , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
| | - Todd J Martínez
- Department of Chemistry and The PULSE Institute , Stanford University , Stanford , California 94305 , United States.,SLAC National Accelerator Laboratory , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
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21
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Fundamental Limits on Spatial Resolution in Ultrafast X-ray Diffraction. APPLIED SCIENCES-BASEL 2017. [DOI: 10.3390/app7060534] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Moreno Carrascosa A, Kirrander A. Ab initio calculation of inelastic scattering. Phys Chem Chem Phys 2017; 19:19545-19553. [DOI: 10.1039/c7cp02054f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We calculate nonresonant inelastic electron and X-ray scattering cross sections for bound-to-bound transitions in atoms and molecules from ab initio electronic wavefunctions.
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Affiliation(s)
| | - Adam Kirrander
- EaStCHEM
- School of Chemistry
- University of Edinburgh
- EH9 3FJ Edinburgh
- UK
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