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Das M, Gangopadhyay D, Hudecová J, Kessler J, Kapitán J, Bouř P. Monitoring Conformation and Protonation States of Glutathione by Raman Optical Activity and Molecular Dynamics. Chempluschem 2023; 88:e202300219. [PMID: 37283530 DOI: 10.1002/cplu.202300219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/07/2023] [Accepted: 06/07/2023] [Indexed: 06/08/2023]
Abstract
Glutathione (GSH) is a common antioxidant and its biological activity depends on the conformation and protonation state. We used molecular dynamics, Raman and Raman optical activity (ROA) spectroscopies to investigate GSH structural changes in a broad pH range. Factor analysis of the spectra provided protonation constants (2.05, 3.45, 8.62, 9.41) in good agreement with previously published values. Following the analysis, spectra of differently protonated forms were obtained by extrapolation. The complete deprotonation of the thiol group above pH 11 was clearly visible in the spectra; however, many spectral features did not change much with pH. Experimental spectra at various pH values were decomposed into the simulated ones, which allowed us to study the conformer populations and quality of molecular dynamics (MD). According to this combined ROA/MD analysis conformation of the GSH backbone is affected by the pH changes only in a limited way. The combination of ROA with the computations thus has the potential to improve the MD force field and obtain more accurate populations of the conformer species. The methodology can be used for any molecule, but for a more detailed insight better computational techniques are needed in the future.
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Affiliation(s)
- Moumita Das
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
- Department of Analytical Chemistry Faculty of Chemical Engineering, University of Chemistry and Technology, Technická 5, 16628, Prague 6, Czech Republic
| | - Debraj Gangopadhyay
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Jana Hudecová
- Department of Optics, Palacký University, 17. listopadu 12, 77146, Olomouc, Czech Republic
| | - Jiří Kessler
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Josef Kapitán
- Department of Optics, Palacký University, 17. listopadu 12, 77146, Olomouc, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
- Department of Analytical Chemistry Faculty of Chemical Engineering, University of Chemistry and Technology, Technická 5, 16628, Prague 6, Czech Republic
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2
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Novichkov D, Trigub A, Gerber E, Nevolin I, Romanchuk A, Matveev P, Kalmykov S. Laboratory-based X-ray spectrometer for actinide science. JOURNAL OF SYNCHROTRON RADIATION 2023; 30:1114-1126. [PMID: 37738030 PMCID: PMC10624025 DOI: 10.1107/s1600577523006926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/06/2023] [Indexed: 09/23/2023]
Abstract
X-ray absorption and emission spectroscopies nowadays are advanced characterization methods for fundamental and applied actinide research. One of the advantages of these methods is to reveal slight changes in the structural and electronic properties of radionuclides. The experiments are generally carried out at synchrotrons. However, considerable progress has been made to construct laboratory-based X-ray spectrometers for X-ray absorption and emission spectroscopies. Laboratory spectrometers are reliable, effective and accessible alternatives to synchrotrons, especially for actinide research, which allow dispensing with high costs of the radioactive sample transport and synchrotron time. Moreover, data from laboratory spectrometers, obtained within a reasonable time, are comparable with synchrotron results. Thereby, laboratory spectrometers can complement synchrotrons or can be used for preliminary experiments to find perspective samples for synchrotron experiments with better resolution. Here, the construction and implementation of an X-ray spectrometer (LomonosovXAS) in Johann-geometry at a radiochemistry laboratory is reported. Examples are given of the application of LomonosovXAS to actinide systems relevant to the chemistry of f-elements, the physical chemistry of nuclear power engineering and the long-term disposal of spent nuclear fuel.
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Affiliation(s)
- Daniil Novichkov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, Moscow 119991, Russian Federation
| | - Alexander Trigub
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, Moscow 119991, Russian Federation
- National Research Centre Kurchatov Institute, Ploshchad Akademika Kurchatova 1, Moscow 123182, Russian Federation
| | - Evgeny Gerber
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, Moscow 119991, Russian Federation
| | - Iurii Nevolin
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, Moscow 119991, Russian Federation
| | - Anna Romanchuk
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, Moscow 119991, Russian Federation
| | - Petr Matveev
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, Moscow 119991, Russian Federation
| | - Stepan Kalmykov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, Moscow 119991, Russian Federation
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3
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Pollock CJ, Debefve LM. Resonant Excitation Unlocks Chemical Selectivity of Platinum Lβ Valence-to-Core X-ray Emission Spectra. Inorg Chem 2023; 62:13681-13691. [PMID: 37578150 PMCID: PMC10467576 DOI: 10.1021/acs.inorgchem.3c01930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Indexed: 08/15/2023]
Abstract
Valence-to-core X-ray emission spectroscopy (VtC XES) is an emerging technique that uses hard X-rays to probe the valence electronic structure of an absorbing atom. Despite finding varied applications for light elements and first row transition metals, little work has been done on heavier elements such as second and third row transition metals. This lack of application is at least partially due to the relatively low resolution of the data at the high energies required to measure these elements, which obscures the useful chemical information that can be extracted from the lower energy, higher resolution spectra of lighter elements. Herein, we collect data on a set of platinum-containing compounds and demonstrate that the VtC XES resolution can be dramatically enhanced by exciting the platinum atom in resonance with its L3-edge white line absorption. Whereas spectra excited using standard nonresonant absorption well above the Pt L3-edge display broad, unfeatured VtC regions, resonant XES (RXES) spectra have more than twofold improved resolution and are revealed to be rich in chemical information with the ability to distinguish between even closely related species. We further demonstrate that these RXES spectra may be used to selectively probe individual components of a mixture of Pt-containing compounds, establishing this technique as a viable probe for chemically complex samples. Lastly, it is shown that the spectra are interpretable using a molecular orbital framework and may be calculated using density functional theory, thus suggesting resonant excitation as a general strategy for extracting chemically useful information from heavy element VtC spectra.
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Affiliation(s)
- Christopher J. Pollock
- Cornell High Energy Synchrotron Source,
Wilson Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Louise M. Debefve
- Cornell High Energy Synchrotron Source,
Wilson Laboratory, Cornell University, Ithaca, New York 14853, United States
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4
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de Kock S, Skudler K, Matsidik R, Sommer M, Müller M, Walter M. NEXAFS spectra of model sulfide chains: implications for sulfur networks obtained from inverse vulcanization. Phys Chem Chem Phys 2023; 25:20395-20404. [PMID: 37465922 DOI: 10.1039/d3cp02285d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Inverse vulcanization is a promising route to stabilize sulfur in lithium-sulfur batteries, but the resulting sulfur strand lengths in the materials are elusive. We address the strand length by characterization via sulfur near edge X-ray absorption fine structure (NEXAFS) spectroscopy. Theoretical predictions of NEXAFS spectra for model molecules containing strands with up to three sulfur atoms are verified by experiment. The near perfect agreement between simulation and experiment on the absolute energy scale allows for the predictions for larger chain lengths also. Inspection and interpretation of NEXAFS spectra from real battery materials on this basis reveals the appearance of single connecting sulfur atoms for very low sulfur content, and of longer strands when the sulfur fraction increases.
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Affiliation(s)
- Sunel de Kock
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany.
| | - Konstantin Skudler
- Physikalisch-Technische Bundesanstalt, Abbestr. 2-12, 10587 Berlin, Germany
| | - Rukiya Matsidik
- Institute for Chemistry, Polymer Chemistry, Chemnitz University of Technology, 09111 Chemnitz, Germany
- Forschungszentrum MAIN, TU Chemnitz, Rosenbergstraße 6, 09126 Chemnitz, Germany
| | - Michael Sommer
- Institute for Chemistry, Polymer Chemistry, Chemnitz University of Technology, 09111 Chemnitz, Germany
- Forschungszentrum MAIN, TU Chemnitz, Rosenbergstraße 6, 09126 Chemnitz, Germany
| | - Matthias Müller
- Physikalisch-Technische Bundesanstalt, Abbestr. 2-12, 10587 Berlin, Germany
| | - Michael Walter
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany.
- Cluster of Excellence livMatS @ FIT, Freiburg, Germany
- Fraunhofer IWM, MikroTribologie Centrum μTC, Freiburg, Germany
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5
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Vogt LI, Cotelesage JJH, Dolgova NV, Boyes C, Qureshi M, Sokaras D, Sharifi S, George SJ, Pickering IJ, George GN. Sulfur X-ray Absorption and Emission Spectroscopy of Organic Sulfones. J Phys Chem A 2023; 127:3692-3704. [PMID: 36912654 DOI: 10.1021/acs.jpca.2c08647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
The sulfones are a widespread group of organo-sulfur compounds, which contain the sulfonyl SO2 group attached to two carbons and have a formal sulfur oxidation state of +2. We have examined the sulfur K near-edge X-ray absorption spectroscopy (XAS) of a range of different sulfones and find substantial spectroscopic variability depending upon the nature of the coordination to the sulfonyl group. We have also examined the sulfur Kβ X-ray emission spectroscopy (XES) of selected representative sulfones. Density functional theory simulations show satisfactory reproduction of both absorption and emission spectra while enabling assignment of the various transitions comprising the spectra. The correspondence between observed and simulated spectra shows promise for ab initio prediction of sulfur X-ray absorption and emission spectra of sulfones of any substituent. The absorption spectra and, to a lesser extent, the emission spectra are sensitive to the nature of the organic groups bound to the sulfonyl (SO2) moiety, clearly showing the potential of X-ray spectroscopy as an in situ probe of sulfone chemistry.
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Affiliation(s)
- Linda I Vogt
- Molecular and Environmental Sciences Group, Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E2, Canada
| | - Julien J H Cotelesage
- Molecular and Environmental Sciences Group, Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E2, Canada
| | - Natalia V Dolgova
- Molecular and Environmental Sciences Group, Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E2, Canada
| | - Curtis Boyes
- Molecular and Environmental Sciences Group, Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E2, Canada
| | - Muhammad Qureshi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Dimosthenis Sokaras
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Samin Sharifi
- Chevron Energy Technology Company, Richmond, California 94802, United States
| | - Simon J George
- Simon Scientific, P.O. Box 71024, Richmond, California 94807, United States
| | - Ingrid J Pickering
- Molecular and Environmental Sciences Group, Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E2, Canada.,Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C9, Canada
| | - Graham N George
- Molecular and Environmental Sciences Group, Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E2, Canada.,Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C9, Canada
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6
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Guo Z, Zhang Y, Xu W, Jin S, Gan X, Zhang H, Chen D, Jia Q. A von Hamos full-cylindrical spectrometer based on striped Si/Ge crystal for advanced x-ray spectroscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2023; 94:023102. [PMID: 36859069 DOI: 10.1063/5.0133896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
High-energy resolution core-level spectroscopies, including a group of different techniques to obtain element-specific information of the electronic structure around an absorption site, have become powerful tools for studying the chemical state, local geometric structure, and the nature of chemical bonding. High-resolution x-ray absorption and x-ray emission spectroscopies are well-established experimental techniques but have always been limited by the number of emitted photons and the limited acceptance of solid angles, as well as requiring high energy stability and repeatability for the whole experimental setup. A full-cylindrical x-ray spectrometer based on flexible HAPG (highly annealed pyrolitic graphite) mosaic crystals is an effective solution for the above issues. However, large-area HAPG remains expensive and is often not easy to access. Here, we present an alternative approach by using segmented single crystals (Si and Ge) with different orientations instead of the HAPG as a dispersive element. The proposed method drastically improved the energy resolution up to 0.2-2 eV in the range of 2-10 keV. High-pressure x-ray emission and resonant x-ray emission spectra are presented to demonstrate the capabilities of the instrument. The new design is particularly suitable for high-resolution spectroscopy applications at fourth-generation synchrotron radiation sources or free-electron lasers.
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Affiliation(s)
- Zhiying Guo
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Yujun Zhang
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Xu
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - ShuoXue Jin
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolong Gan
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Han Zhang
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Dongliang Chen
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Quanjie Jia
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
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7
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Samal B, Voora VK. Modeling Nonresonant X-ray Emission of Second- and Third-Period Elements without Core-Hole Reference States and Empirical Parameters. J Chem Theory Comput 2022; 18:7272-7285. [PMID: 36350224 DOI: 10.1021/acs.jctc.2c00647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Nonresonant X-ray emission (XE) energies and oscillator strengths are obtained using the effective potential of the generalized Kohn-Sham semi-canonical projected random phase approximation (GKS-spRPA) method. XE energies are estimated as a difference between the valence and core ionization eigenvalues, while the oscillator strengths are obtained within a frozen orbital approximation. This straightforward approach provides accurate XE energies without any need for core-hole reference states, empirical shifting parameters, or tuning of density functionals. To account for relativistic corrections to the core orbitals, we have formulated a scalar relativistic (sr) GKS-spRPA approach based on the spin-free X2C one-electron Hamiltonian. The sr-GKS-spRPA method provides highly reliable XE energies using uncontracted basis-sets on atoms where the core-hole is created prior to emission. For the largest basis-sets used in our study, using completely uncontracted polarized core-valence Dunning basis-sets, the mean absolute errors (MAEs) are within 0.7 eV compared to experimental reference values for a test-set consisting of 27 valence-to-core XE energies of molecules with second- and third-period elements. Considering a balance of accuracy and computational effort, we recommend the use of s-uncontracted def2-TZVP for second-period and all-uncontracted def2-TZVP for third-period elements. For this recommended basis-set, the MAE is 0.2 eV. The analytically continued sr-GKS-spRPA approach, with an O(N4) computational cost, enables efficient computation of XE spectra of molecules such as S8 and C60 with several core-hole states.
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Affiliation(s)
- Bibek Samal
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai400005, India
| | - Vamsee K Voora
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai400005, India
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8
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Smith N, Wilson MA. Understanding Cysteine Chemistry Using Conventional and Serial X-Ray Protein Crystallography. CRYSTALS 2022; 12:1671. [PMID: 36685087 PMCID: PMC9850494 DOI: 10.3390/cryst12111671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Proteins that use cysteine residues for catalysis or regulation are widely distributed and intensively studied, with many biomedically important examples. Enzymes where cysteine is a catalytic nucleophile typically generate covalent catalytic intermediates whose structures are important for understanding mechanism and for designing targeted inhibitors. The formation of catalytic intermediates can change enzyme conformational dynamics, sometimes activating protein motions that are important for catalytic turnover. However, these transiently populated intermediate species have been challenging to structurally characterize using traditional crystallographic approaches. This review describes the use and promise of new time-resolved serial crystallographic methods to study cysteine-dependent enzymes, with a focus on the main (Mpro) and papain-like (PLpro) cysteine proteases of SARS-CoV-2 as well as other examples. We review features of cysteine chemistry that are relevant for the design and execution of time-resolved serial crystallography experiments. In addition, we discuss emerging X-ray techniques such as time-resolved sulfur X-ray spectroscopy that may be able to detect changes in sulfur charge state and covalency during catalysis or regulatory modification. In summary, cysteine-dependent enzymes have features that make them especially attractive targets for new time-resolved serial crystallography approaches, which can reveal both changes to enzyme structure and dynamics during catalysis in crystalline samples.
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9
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Tetef S, Kashyap V, Holden WM, Velian A, Govind N, Seidler GT. Informed Chemical Classification of Organophosphorus Compounds via Unsupervised Machine Learning of X-ray Absorption Spectroscopy and X-ray Emission Spectroscopy. J Phys Chem A 2022; 126:4862-4872. [PMID: 35839329 DOI: 10.1021/acs.jpca.2c03635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We analyze an ensemble of organophosphorus compounds to form an unbiased characterization of the information encoded in their X-ray absorption near-edge structure (XANES) and valence-to-core X-ray emission spectra (VtC-XES). Data-driven emergence of chemical classes via unsupervised machine learning, specifically cluster analysis in the Uniform Manifold Approximation and Projection (UMAP) embedding, finds spectral sensitivity to coordination, oxidation, aromaticity, intramolecular hydrogen bonding, and ligand identity. Subsequently, we implement supervised machine learning via Gaussian process classifiers to identify confidence in predictions that match our initial qualitative assessments of clustering. The results further support the benefit of utilizing unsupervised machine learning as a precursor to supervised machine learning, which we term Unsupervised Validation of Classes (UVC), a result that goes beyond the present case of X-ray spectroscopies.
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Affiliation(s)
- Samantha Tetef
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Vikram Kashyap
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - William M Holden
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Alexandra Velian
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Niranjan Govind
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Gerald T Seidler
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
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10
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Nascimento DR, Govind N. Computational approaches for XANES, VtC-XES, and RIXS using linear-response time-dependent density functional theory based methods. Phys Chem Chem Phys 2022; 24:14680-14691. [PMID: 35699090 DOI: 10.1039/d2cp01132h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The emergence of state-of-the-art X-ray light sources has paved the way for novel spectroscopies that take advantage of their atomic specificity to shed light on fundamental physical, chemical, and biological processes both in the static and time domains. The success of these experiments hinges on the ability to interpret and predict core-level spectra, which has opened avenues for theory to play a key role. Over the last two decades, linear-response time-dependent density functional theory (LR-TDDFT), despite various theoretical challenges, has become a computationally attractive and versatile framework to study excited-state spectra including X-ray spectroscopies. In this context, we focus our discussion on LR-TDDFT approaches for the computation of X-ray Near-Edge Structure (XANES), Valence-to-Core X-ray Emission (VtC-XES), and Resonant Inelastic X-ray Scattering (RIXS) spectroscopies in molecular systems with an emphasis on Gaussian basis set implementations. We illustrate these approaches with applications and provide a brief outlook of possible new directions.
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Affiliation(s)
- Daniel R Nascimento
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA.
| | - Niranjan Govind
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA.
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11
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Cutsail III GE, DeBeer S. Challenges and Opportunities for Applications of Advanced X-ray Spectroscopy in Catalysis Research. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- George E. Cutsail III
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
- Institute of Inorganic Chemistry, University of Duisburg-Essen, Universitätsstr. 5-7, 45117 Essen, Germany
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
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12
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Henthorn JT, DeBeer S. Selenium Valence-to-Core X-ray Emission Spectroscopy and Kβ HERFD X-ray Absorption Spectroscopy as Complementary Probes of Chemical and Electronic Structure. Inorg Chem 2022; 61:2760-2767. [PMID: 35113562 PMCID: PMC8848279 DOI: 10.1021/acs.inorgchem.1c02802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
Selenium X-ray absorption
spectroscopy (XAS) has found widespread
use in investigations of Se-containing materials, geochemical processes,
and biologically active sites. In contrast to sulfur Kβ X-ray
emission spectroscopy (XES), which has been found to contain electronic
and structural information complementary to S XAS, Se Kβ XES
remains comparatively underexplored. Herein, we present the first
Se Valence-to-Core (VtC) XES studies of reduced Se-containing compounds
and FeSe dimers. Se VtC XES is found to be sensitive to changes in
covalent Se bonding interactions (Se–Se/Se–C/Se–H
bonding) while being relatively insensitive to changes in Fe oxidation
states as selenide bridges in FeSe dimers ([Fe2Se2]2+ vs [Fe2Se2]+). In
contrast, Se Kβ HERFD XAS is demonstrated to be quite sensitive
to changes in the Fe oxidation state with Se Kβ HERFD XAS demonstrating
experimental resolution equivalent to Kα HERFD XAS. Additionally,
computational studies reveal both Se VtC XES and XAS to be sensitive
to selenium protonation in FeSe complexes. Selenium is a trace element that plays
vital roles in biological
and geochemical cycles, energy storage, photovoltaics, and nanomaterials.
Herein, selenium Valence-to-Core X-ray emission spectroscopy is explored
as a new method of probing the chemical and electronic structure in
selenium-containing compounds, demonstrating sensitivity to selenium
bonding interactions. When paired with high-resolution Se X-ray absorption
spectroscopy (HERFD XAS), these two methods have the potential to
reveal greater insight into protonation and redox changes of Se-substituted
FeS clusters.
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Affiliation(s)
- Justin T Henthorn
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
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13
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Tetef S, Govind N, Seidler GT. Unsupervised machine learning for unbiased chemical classification in X-ray absorption spectroscopy and X-ray emission spectroscopy. Phys Chem Chem Phys 2021; 23:23586-23601. [PMID: 34651631 DOI: 10.1039/d1cp02903g] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We report a comprehensive computational study of unsupervised machine learning for extraction of chemically relevant information in X-ray absorption near edge structure (XANES) and in valence-to-core X-ray emission spectra (VtC-XES) for classification of a broad ensemble of sulphorganic molecules. By progressively decreasing the constraining assumptions of the unsupervised machine learning algorithm, moving from principal component analysis (PCA) to a variational autoencoder (VAE) to t-distributed stochastic neighbour embedding (t-SNE), we find improved sensitivity to steadily more refined chemical information. Surprisingly, when embedding the ensemble of spectra in merely two dimensions, t-SNE distinguishes not just oxidation state and general sulphur bonding environment but also the aromaticity of the bonding radical group with 87% accuracy as well as identifying even finer details in electronic structure within aromatic or aliphatic sub-classes. We find that the chemical information in XANES and VtC-XES is very similar in character and content, although they unexpectedly have different sensitivity within a given molecular class. We also discuss likely benefits from further effort with unsupervised machine learning and from the interplay between supervised and unsupervised machine learning for X-ray spectroscopies. Our overall results, i.e., the ability to reliably classify without user bias and to discover unexpected chemical signatures for XANES and VtC-XES, likely generalize to other systems as well as to other one-dimensional chemical spectroscopies.
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Affiliation(s)
- Samantha Tetef
- Department of Physics, University of Washington, Seattle, WA 98195, USA.
| | - Niranjan Govind
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Gerald T Seidler
- Department of Physics, University of Washington, Seattle, WA 98195, USA.
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14
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Fehse M, Iadecola A, Simonelli L, Longo A, Stievano L. The rise of X-ray spectroscopies for unveiling the functional mechanisms in batteries. Phys Chem Chem Phys 2021; 23:23445-23465. [PMID: 34664565 DOI: 10.1039/d1cp03263a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Synchrotron-based techniques have been key tools in the discovery, understanding, and development of battery materials. In this review, some of the most suitable X-ray spectroscopy related techniques employed for addressing diverse scientific cases connected to battery science are highlighted. Furthermore, current shortcomings, intrinsic limitations, and ongoing challenges of individual techniques are pointed out, providing an outlook of future trends that are relevant to the battery research community. In particular, the ongoing development of next generation synchrotrons, machine learning algorithms for data analysis and combined theoretical/experimental approaches will enhance the already powerful assets of these advanced spectroscopic methods.
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Affiliation(s)
| | - Antonella Iadecola
- Rééseau sur le Stockage Electrochimique de l'Energie (RS2E), CNRS, Amiens, France
| | | | - Alessandro Longo
- European Synchrotron Radiation Facility, Grenoble, France.,Istituto per lo Studio dei Materiali Nanostrutturati, ISMN-CNR UOS di Palermo, Palermo, Italy
| | - Lorenzo Stievano
- Rééseau sur le Stockage Electrochimique de l'Energie (RS2E), CNRS, Amiens, France.,ICGM, Univ. Montpellier, CNRS, ENSCM, Montpellier, France.
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15
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Weinhardt L, Hauschild D, Steininger R, Jiang N, Blum M, Yang W, Heske C. Sulfate Speciation Analysis Using Soft X-ray Emission Spectroscopy. Anal Chem 2021; 93:8300-8308. [PMID: 34076421 DOI: 10.1021/acs.analchem.1c01187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The chemical and electronic structures of 15 different sulfates are studied using S L2,3 soft X-ray emission spectroscopy (XES). Sulfur L2,3 XES spectra of sulfates are distinctively different from those of other sulfur compounds, which makes XES a powerful technique for sulfate detection. Furthermore, subtle but distinct differences between the spectra of sulfates with different cations are observed, which allow a further differentiation of the specific compound. Most prominently, the position and width of the emission from "S 3s" derived bands systematically vary for different compounds, which can be understood with electronic structure and spectral calculations based on density functional theory.
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Affiliation(s)
- Lothar Weinhardt
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen 76344, Germany.,Institute for Chemical Technology and Polymer Chemistry (ITCP), Karlsruhe Institute of Technology (KIT), Karlsruhe 76128, Germany.,Department of Chemistry and Biochemistry, University of Nevada, Las Vegas (UNLV), Las Vegas, Nevada 89154, United States
| | - Dirk Hauschild
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen 76344, Germany.,Institute for Chemical Technology and Polymer Chemistry (ITCP), Karlsruhe Institute of Technology (KIT), Karlsruhe 76128, Germany.,Department of Chemistry and Biochemistry, University of Nevada, Las Vegas (UNLV), Las Vegas, Nevada 89154, United States
| | - Ralph Steininger
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen 76344, Germany
| | - Nan Jiang
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas (UNLV), Las Vegas, Nevada 89154, United States
| | - Monika Blum
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas (UNLV), Las Vegas, Nevada 89154, United States.,Advanced Light Source (ALS), Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Wanli Yang
- Advanced Light Source (ALS), Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Clemens Heske
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen 76344, Germany.,Institute for Chemical Technology and Polymer Chemistry (ITCP), Karlsruhe Institute of Technology (KIT), Karlsruhe 76128, Germany.,Department of Chemistry and Biochemistry, University of Nevada, Las Vegas (UNLV), Las Vegas, Nevada 89154, United States
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16
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Mathe Z, McCubbin Stepanic O, Peredkov S, DeBeer S. Phosphorus Kβ X-ray emission spectroscopy detects non-covalent interactions of phosphate biomolecules in situ. Chem Sci 2021; 12:7888-7901. [PMID: 34168842 PMCID: PMC8188515 DOI: 10.1039/d1sc01266e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Phosphorus is ubiquitous in biochemistry, being found in the phosphate groups of nucleic acids and the energy-transferring system of adenine nucleotides (e.g. ATP). Kβ X-ray emission spectroscopy (XES) of phosphorus has been largely unexplored, with no previous applications to biomolecules. Here, the potential of P Kβ XES to study phosphate-containing biomolecules, including ATP and NADPH, is evaluated, as is the application of the technique to aqueous solution samples. P Kβ spectra offer a detailed picture of phosphate valence electronic structure, reporting on subtle non-covalent effects, such as hydrogen bonding and ionic interactions, that are key to enzymatic catalysis. Spectral features are interpreted using density functional theory (DFT) calculations, and potential applications to the study of biological energy conversion are highlighted. Phosphorus X-ray emission spectroscopy probes non-covalent interactions and electronic structure of phosphate biomolecules in both solid and solution samples.![]()
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Affiliation(s)
- Zachary Mathe
- Max Planck Institute for Chemical Energy Conversion Stiftstr. 34-36 D-45470 Mülheim an der Ruhr Germany
| | - Olivia McCubbin Stepanic
- Max Planck Institute for Chemical Energy Conversion Stiftstr. 34-36 D-45470 Mülheim an der Ruhr Germany
| | - Sergey Peredkov
- Max Planck Institute for Chemical Energy Conversion Stiftstr. 34-36 D-45470 Mülheim an der Ruhr Germany
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion Stiftstr. 34-36 D-45470 Mülheim an der Ruhr Germany
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17
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Biasin E, Nascimento DR, Poulter BI, Abraham B, Kunnus K, Garcia-Esparza AT, Nowak SH, Kroll T, Schoenlein RW, Alonso-Mori R, Khalil M, Govind N, Sokaras D. Revealing the bonding of solvated Ru complexes with valence-to-core resonant inelastic X-ray scattering. Chem Sci 2021; 12:3713-3725. [PMID: 34163645 PMCID: PMC8179428 DOI: 10.1039/d0sc06227h] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/21/2021] [Indexed: 12/27/2022] Open
Abstract
Ru-complexes are widely studied because of their use in biological applications and photoconversion technologies. We reveal novel insights into the chemical bonding of a series of Ru(ii)- and Ru(iii)-complexes by leveraging recent advances in high-energy-resolution tender X-ray spectroscopy and theoretical calculations. We perform Ru 2p4d resonant inelastic X-ray scattering (RIXS) to probe the valence excitations in dilute solvated Ru-complexes. Combining these experiments with a newly developed theoretical approach based on time-dependent density functional theory, we assign the spectral features and quantify the metal-ligand bonding interactions. The valence-to-core RIXS features uniquely identify the metal-centered and charge transfer states and allow extracting the ligand-field splitting for all the complexes. The combined experimental and theoretical approach described here is shown to reliably characterize the ground and excited valence states of Ru complexes, and serve as a basis for future investigations of ruthenium, or other 4d metals active sites, in biological and chemical applications.
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Affiliation(s)
- Elisa Biasin
- Stanford PULSE Institute, SLAC National Accelerator Laboratory Menlo Park CA 94025 USA
| | - Daniel R Nascimento
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory Richland Washington 99352 USA
| | - Benjamin I Poulter
- Department of Chemistry, University of Washington Seattle Washington 98195 USA
| | - Baxter Abraham
- SSRL, SLAC National Accelerator Laboratory Menlo Park California 94025 USA
| | - Kristjan Kunnus
- Stanford PULSE Institute, SLAC National Accelerator Laboratory Menlo Park CA 94025 USA
- LCLS, SLAC National Accelerator Laboratory Menlo Park CA 94025 USA
| | | | - Stanislaw H Nowak
- SSRL, SLAC National Accelerator Laboratory Menlo Park California 94025 USA
| | - Thomas Kroll
- SSRL, SLAC National Accelerator Laboratory Menlo Park California 94025 USA
| | - Robert W Schoenlein
- Stanford PULSE Institute, SLAC National Accelerator Laboratory Menlo Park CA 94025 USA
- LCLS, SLAC National Accelerator Laboratory Menlo Park CA 94025 USA
| | | | - Munira Khalil
- Department of Chemistry, University of Washington Seattle Washington 98195 USA
| | - Niranjan Govind
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory Richland Washington 99352 USA
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18
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Petric M, Rajh A, Vizintin A, Talian SD, Dominko R, Kavčič M. Sulfur valence-to-core X-ray emission spectroscopy study of lithium sulfur batteries. Chem Commun (Camb) 2021; 57:7573-7576. [PMID: 34250987 DOI: 10.1039/d1cc03023j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, valence-to-core (VtC) Kβ sulfur X-ray emission spectroscopy (XES) was used to perform quantitative analysis of different sulfur compounds produced in a lithium sulfur (Li-S) battery during discharge. The analysis is based on the theoretical sulfur Kβ XES spectra obtained from ab initio quantum chemical calculations based on density functional theory. The emphasis is given to the Kβ sulfur XES spectra of the polysulfide molecules (Li2Sx, x = 2,,8) produced electrochemically within the Li-S battery. Ab initio molecular dynamics calculations are used further to calculate also the Kβ spectra of Li2Sx dissolved in a model solvent. Calculated spectra were directly compared with the experimental ones collected with a Johansson type tender XES spectrometer on laboratory synthesized Li2Sx reference standards and pre-cycled battery cathodes. These results demonstrate that sulfur VtC XES can be used effectively to quantitatively analyze electrochemical sulfur conversion, also in a smaller laboratory without the need for large scale synchrotron facilities.
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Affiliation(s)
- Marko Petric
- JoŽef Stefan Institute, Jamova cesta 39, Ljubljana SI-1000, Slovenia. and Faculty of Geotechnical Engineering, University of Zagreb, Hallerova aleja 7, VaraŽdin HR-42000, Croatia
| | - Ava Rajh
- JoŽef Stefan Institute, Jamova cesta 39, Ljubljana SI-1000, Slovenia. and Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, Ljubljana 1000, Slovenia
| | - Alen Vizintin
- National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia
| | | | - Robert Dominko
- National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia and Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna pot 113, Ljubljana 1000, Slovenia
| | - MatjaŽ Kavčič
- JoŽef Stefan Institute, Jamova cesta 39, Ljubljana SI-1000, Slovenia. and Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, Ljubljana 1000, Slovenia
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19
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Qureshi M, Nowak SH, Vogt LI, Cotelesage JJH, Dolgova NV, Sharifi S, Kroll T, Nordlund D, Alonso-Mori R, Weng TC, Pickering IJ, George GN, Sokaras D. Sulfur Kβ X-ray emission spectroscopy: comparison with sulfur K-edge X-ray absorption spectroscopy for speciation of organosulfur compounds. Phys Chem Chem Phys 2020; 23:4500-4508. [PMID: 33355326 DOI: 10.1039/d0cp05323f] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Until recently, sulfur was known as a "spectroscopically silent" element because of a paucity of convenient spectroscopic probes suitable for in situ chemical speciation. In recent years the technique of sulfur K-edge X-ray absorption spectroscopy (XAS) has been used extensively in sulfur speciation in a variety of different fields. With an initial focus on reduced forms of organic sulfur, we have explored a complementary X-ray based spectroscopy - sulfur Kβ X-ray emission spectroscopy (XES) - as a potential analytical tool for sulfur speciation in complex samples. We compare and contrast the sensitivity of sulfur Kβ XES with that of sulfur K-edge XAS, and find differing sensitivities for the two techniques. In some cases an approach involving both sulfur K-edge XAS and sulfur Kβ XES may be a powerful combination for deducing sulfur speciation in samples containing complex mixtures.
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Affiliation(s)
- Muhammad Qureshi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, USA.
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20
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Carter-Fenk K, Herbert JM. State-Targeted Energy Projection: A Simple and Robust Approach to Orbital Relaxation of Non-Aufbau Self-Consistent Field Solutions. J Chem Theory Comput 2020; 16:5067-5082. [DOI: 10.1021/acs.jctc.0c00502] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Kevin Carter-Fenk
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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