1
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Chen Y, Rana R, Zhang Y, Hoffman AS, Huang Z, Yang B, Vila FD, Perez-Aguilar JE, Hong J, Li X, Zeng J, Chi M, Kronawitter CX, Wang H, Bare SR, Kulkarni AR, Gates BC. Dynamic structural evolution of MgO-supported palladium catalysts: from metal to metal oxide nanoparticles to surface then subsurface atomically dispersed cations. Chem Sci 2024; 15:6454-6464. [PMID: 38699272 PMCID: PMC11062082 DOI: 10.1039/d4sc00035h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 03/21/2024] [Indexed: 05/05/2024] Open
Abstract
Supported noble metal catalysts, ubiquitous in chemical technology, often undergo dynamic transformations between reduced and oxidized states-which influence the metal nuclearities, oxidation states, and catalytic properties. In this investigation, we report the results of in situ X-ray absorption spectroscopy, scanning transmission electron microscopy, and other physical characterization techniques, bolstered by density functional theory, to elucidate the structural transformations of a set of MgO-supported palladium catalysts under oxidative treatment conditions. As the calcination temperature increased, the as-synthesized supported metallic palladium nanoparticles underwent oxidation to form palladium oxides (at approximately 400 °C), which, at approximately 500 °C, were oxidatively fragmented to form mixtures of atomically dispersed palladium cations. The data indicate two distinct types of atomically dispersed species: palladium cations located at MgO steps and those embedded in the first subsurface layer of MgO. The former exhibit significantly higher (>500 times) catalytic activity for ethylene hydrogenation than the latter. The results pave the way for designing highly active and stable supported palladium hydrogenation catalysts with optimized metal utilization.
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Affiliation(s)
- Yizhen Chen
- Department of Chemical Engineering, University of California Davis California 95616 USA
| | - Rachita Rana
- Department of Chemical Engineering, University of California Davis California 95616 USA
| | - Yizhi Zhang
- School of Materials Engineering, Purdue University West Lafayette Indiana 47907 USA
| | - Adam S Hoffman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory Menlo Park California 94025 USA
| | - Zhennan Huang
- Oak Ridge National Laboratory Oak Ridge Tennessee 37830 USA
| | - Bo Yang
- School of Materials Engineering, Purdue University West Lafayette Indiana 47907 USA
| | - Fernando D Vila
- Department of Physics, University of Washington Seattle Washington 98195 USA
| | - Jorge E Perez-Aguilar
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory Menlo Park California 94025 USA
| | - Jiyun Hong
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory Menlo Park California 94025 USA
| | - Xu Li
- National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Strongly-Coupled Quantum Matter Physics, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, Department of Chemical Physics, University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Jie Zeng
- National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Strongly-Coupled Quantum Matter Physics, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, Department of Chemical Physics, University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Miaofang Chi
- Oak Ridge National Laboratory Oak Ridge Tennessee 37830 USA
| | - Coleman X Kronawitter
- Department of Chemical Engineering, University of California Davis California 95616 USA
| | - Haiyan Wang
- School of Materials Engineering, Purdue University West Lafayette Indiana 47907 USA
| | - Simon R Bare
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory Menlo Park California 94025 USA
| | - Ambarish R Kulkarni
- Department of Chemical Engineering, University of California Davis California 95616 USA
| | - Bruce C Gates
- Department of Chemical Engineering, University of California Davis California 95616 USA
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2
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Vila FD, Rehr JJ, Kowalski K, Peng B. RT-EOM-CCSD Calculations of Inner and Outer Valence Ionization Energies and Spectral Functions. J Chem Theory Comput 2024; 20:1796-1801. [PMID: 38422509 DOI: 10.1021/acs.jctc.3c01371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Photoelectron spectroscopy (PES) is a standard experimental method for material characterization, but its interpretation can be hampered by its reliance on standard materials. To facilitate the study of unknown systems, theoretical methods are desirable. Here, we present a real-time equation-of-motion coupled cluster (RT-EOM-CC) approach for valence PES, extending our core-level development. We demonstrate that RT-EOM-CC yields ionization energies and spectral functions in good agreement with experimental and CI-based results, even for some more correlated cases.
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Affiliation(s)
- Fernando D Vila
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - John J Rehr
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Karol Kowalski
- William R. Wiley Environmental Molecular Sciences Laboratory, Battelle, Pacific Northwest National Laboratory, K8-91, P.O. Box 999, Richland, Washington 99352, United States
| | - Bo Peng
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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3
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Filardi LR, Vila FD, Hong J, Hoffman AS, Perez-Aguilar JE, Bare SR, Runnebaum RC, Kronawitter CX. Impact of Local Structure in Supported CaO Catalysts for Soft-Oxidant-Assisted Methane Coupling Assessed through Ca K-Edge X-ray Absorption Spectroscopy. J Phys Chem C Nanomater Interfaces 2024; 128:1165-1176. [PMID: 38293693 PMCID: PMC10823472 DOI: 10.1021/acs.jpcc.3c06527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 02/01/2024]
Abstract
Soft-oxidant-assisted methane coupling has emerged as a promising pathway to upgrade methane from natural gas sources to high-value commodity chemicals, such as ethylene, at selectivities higher than those associated with oxidative (O2) methane coupling (OCM). To date, few studies have reported investigations into the electronic structure and the microscopic physical structure of catalytic active sites present in the binary metal oxide catalyst systems that are known to be effective for this reaction. Correlating the catalyst activity to specific active site structures and electronic properties is an essential aspect of catalyst design. Here, we used X-ray absorption spectroscopy at the Ca K-edge to ascertain the most probable local environment of Ca in the ZnO-supported Ca oxide catalysts. These catalysts are shown here to be active for N2O-assisted methane coupling (N2O-OCM) and have previously been reported to be active for CO2-assisted methane coupling (CO2-OCM). X-ray absorption near edge structure features at multiple Ca loadings are interpreted through simulated spectra derived from ab initio full multiple scattering calculations. These simulations included consideration of CaO structures organized in multiple spatial arrangements-linear, planar, and cubic-with separate analyses of Ca atoms in the surfaces and bulk of the three-dimensional structures. The morphology of the oxide clusters was found to influence the various regions of the X-ray absorption spectrum differently. Experiment and theory show that for low-Ca-loading catalysts (≤1 mol %), which contain sites particularly active for methane coupling, Ca primarily exists in an oxidized state that is consistent with the coordination environment of Ca ions in one- and two-dimensional clusters. In addition to their unique nanoscale structures, the spectra also indicate that these clusters have varying degrees of undercoordinated surface Ca atoms that could further influence their catalytic activities. The local Ca structure was correlated to methane coupling activity from N2O-OCM and previously reported CO2-OCM reactor studies. This study provides a unique perspective on the relationship between the catalyst physical and electronic structure and active sites for soft-oxidant-assisted methane coupling, which can be used to inform future catalyst development.
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Affiliation(s)
- Leah R. Filardi
- Department
of Chemical Engineering, University of California,
Davis, Davis, California 95616, United States
| | - Fernando D. Vila
- Department
of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Jiyun Hong
- SSRL,
SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Adam S. Hoffman
- SSRL,
SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | | | - Simon R. Bare
- SSRL,
SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Ron C. Runnebaum
- Department
of Chemical Engineering, University of California,
Davis, Davis, California 95616, United States
- Department
of Viticulture & Enology, University
of California, Davis, Davis, California 95616, United States
| | - Coleman X. Kronawitter
- Department
of Chemical Engineering, University of California,
Davis, Davis, California 95616, United States
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4
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Mejia-Rodriguez D, Aprà E, Autschbach J, Bauman NP, Bylaska EJ, Govind N, Hammond JR, Kowalski K, Kunitsa A, Panyala A, Peng B, Rehr JJ, Song H, Tretiak S, Valiev M, Vila FD. NWChem: Recent and Ongoing Developments. J Chem Theory Comput 2023; 19:7077-7096. [PMID: 37458314 DOI: 10.1021/acs.jctc.3c00421] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
This paper summarizes developments in the NWChem computational chemistry suite since the last major release (NWChem 7.0.0). Specifically, we focus on functionality, along with input blocks, that is accessible in the current stable release (NWChem 7.2.0) and in the "master" development branch, interfaces to quantum computing simulators, interfaces to external libraries, the NWChem github repository, and containerization of NWChem executable images. Some ongoing developments that will be available in the near future are also discussed.
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Affiliation(s)
- Daniel Mejia-Rodriguez
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Edoardo Aprà
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
| | - Nicholas P Bauman
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Eric J Bylaska
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Niranjan Govind
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jeff R Hammond
- Accelerated Computing, NVIDIA Helsinki Oy, Porkkalankatu 1, 00180 Helsinki, Finland
| | - Karol Kowalski
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Alexander Kunitsa
- Zapata Computing, Inc., 100 Federal Street, Boston, Massachusetts 02110, United States
| | - Ajay Panyala
- Advanced Computing, Mathematics, and Data Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Bo Peng
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - John J Rehr
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Huajing Song
- Physics and Chemistry of Materials, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Sergei Tretiak
- Physics and Chemistry of Materials, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Marat Valiev
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Fernando D Vila
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
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5
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Ostervold L, Smerigan A, Liu MJ, Filardi LR, Vila FD, Perez-Aguilar JE, Hong J, Tarpeh WA, Hoffman AS, Greenlee LF, Clark EL, Janik MJ, Bare SR. Cation Incorporation into Copper Oxide Lattice at Highly Oxidizing Potentials. ACS Appl Mater Interfaces 2023; 15:47025-47036. [PMID: 37756387 DOI: 10.1021/acsami.3c10296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
Electrolyte cations can have significant effects on the kinetics and selectivity of electrocatalytic reactions. We show an atypical mechanism through which electrolyte cations can impact electrocatalyst performance─direct incorporation of the cation into the oxide electrocatalyst lattice. We investigate the transformations of copper electrodes in alkaline electrochemistry through operando X-ray absorption spectroscopy in KOH and Ba(OH)2 electrolytes. In KOH electrolytes, both the near-edge structure and extended fine-structure agree with previous studies; however, the X-ray absorption spectra vary greatly in Ba(OH)2 electrolytes. Through a combination of electronic structure modeling, near-edge simulation, and postreaction characterization, we propose that Ba2+ cations are directly incorporated into the lattice and form an ordered BaCuO2 phase at potentials more oxidizing than 200 mV vs the normal hydrogen electrode (NHE). BaCuO2 formation is followed by further oxidation to a bulk Cu3+-like BaxCuyOz phase at 900 mV vs NHE. Additionally, during reduction in Ba(OH)2 electrolyte, we find both Cu-O bonds and Cu-Ba scattering persist at potentials as low as -400 mV vs NHE. To our knowledge, this is the first evidence for direct oxidative incorporation of an electrolyte cation into the bulk lattice to form a mixed oxide electrode. The oxidative incorporation of electrolyte cations to form mixed oxides could open a new route for the in situ formation of active and selective oxidation electrocatalysts.
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Affiliation(s)
- Lars Ostervold
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Adam Smerigan
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Matthew J Liu
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Leah R Filardi
- Department of Chemical Engineering, University of California, Davis, Davis, California 95616, United States
| | - Fernando D Vila
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Jorge E Perez-Aguilar
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Jiyun Hong
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - William A Tarpeh
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Adam S Hoffman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Lauren F Greenlee
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Ezra Lee Clark
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Michael J Janik
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Simon R Bare
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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6
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Smerigan A, Biswas S, Vila FD, Hong J, Perez-Aguilar J, Hoffman AS, Greenlee L, Getman RB, Bare SR. Aqueous Structure of Lanthanide-EDTA Coordination Complexes Determined by a Combined DFT/EXAFS Approach. Inorg Chem 2023; 62:14523-14532. [PMID: 37624729 DOI: 10.1021/acs.inorgchem.3c01334] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2023]
Abstract
Sustainable production of rare earth elements (REEs) is critical for technologies needed for climate change mitigation, including wind turbines and electric vehicles. However, separation technologies currently used in REE production have large environmental footprints, necessitating more sustainable strategies. Aqueous, affinity-based separations are examples of such strategies. To make these technologies feasible, it is imperative to connect aqueous ligand structure to ligand selectivity for individual REEs. As a step toward this goal, we analyzed the extended X-ray absorption fine structure (EXAFS) of four lanthanides (La, Ce, Pr, and Nd) complexed by a common REE chelator, ethylenediaminetetraacetic acid (EDTA) to determine the aqueous-phase structure. Reference structures from density functional theory (DFT) were used to help fit the EXAFS spectra. We found that all four Ln-EDTA coordination complexes formed 9-coordinate structures with 6 coordinating atoms from EDTA (4 carboxyl oxygen atoms and 2 nitrogen atoms) and 3 oxygen atoms from water molecules. All EXAFS fits were of high quality (R-factor < 0.02) and showed decreasing average first-shell coordination distance across the series (2.62-2.57 Å from La-Nd), in agreement with DFT (2.65-2.56 Å from La-Nd). The insights determined herein will be useful in the development of ligands for sustainable rare earth elements (REE) separation technologies.
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Affiliation(s)
- Adam Smerigan
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Sayani Biswas
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Fernando D Vila
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Jiyun Hong
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Jorge Perez-Aguilar
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Adam S Hoffman
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Lauren Greenlee
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Rachel B Getman
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Simon R Bare
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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7
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Pathak H, Panyala A, Peng B, Bauman NP, Mutlu E, Rehr JJ, Vila FD, Kowalski K. Real-Time Equation-of-Motion Coupled-Cluster Cumulant Green's Function Method: Heterogeneous Parallel Implementation Based on the Tensor Algebra for Many-Body Methods Infrastructure. J Chem Theory Comput 2023; 19:2248-2257. [PMID: 37096369 DOI: 10.1021/acs.jctc.3c00045] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
We report the implementation of the real-time equation-of-motion coupled-cluster (RT-EOM-CC) cumulant Green's function method [ J. Chem. Phys. 2020, 152, 174113] within the Tensor Algebra for Many-body Methods (TAMM) infrastructure. TAMM is a massively parallel heterogeneous tensor library designed for utilizing forthcoming exascale computing resources. The two-body electron repulsion matrix elements are Cholesky-decomposed, and we imposed spin-explicit forms of the various operators when evaluating the tensor contractions. Unlike our previous real algebra Tensor Contraction Engine (TCE) implementation, the TAMM implementation supports fully complex algebra. The RT-EOM-CC singles (S) and doubles (D) time-dependent amplitudes are propagated using a first-order Adams-Moulton method. This new implementation shows excellent scalability tested up to 500 GPUs using the Zn-porphyrin molecule with 655 basis functions, with parallel efficiencies above 90% up to 400 GPUs. The TAMM RT-EOM-CCSD was used to study core photoemission spectra in the formaldehyde and ethyl trifluoroacetate (ESCA) molecules. Simulations of the latter involve as many as 71 occupied and 649 virtual orbitals. The relative quasiparticle ionization energies and overall spectral functions agree well with available experimental results.
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Affiliation(s)
- Himadri Pathak
- Advanced Computing, Mathematics, and Data Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ajay Panyala
- Advanced Computing, Mathematics, and Data Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Bo Peng
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Nicholas P Bauman
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Erdal Mutlu
- Advanced Computing, Mathematics, and Data Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - John J Rehr
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Fernando D Vila
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Karol Kowalski
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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8
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Rana R, Vila FD, Kulkarni AR, Bare SR. Bridging the Gap between the X-ray Absorption Spectroscopy and the Computational Catalysis Communities in Heterogeneous Catalysis: A Perspective on the Current and Future Research Directions. ACS Catal 2022. [DOI: 10.1021/acscatal.2c03863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rachita Rana
- Department of Chemical Engineering, University of California, Davis, California95616, United States
| | - Fernando D. Vila
- Department of Physics, University of Washington, Seattle, Washington98195, United States
| | - Ambarish R. Kulkarni
- Department of Chemical Engineering, University of California, Davis, California95616, United States
| | - Simon R. Bare
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California94025, United States
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9
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Nathan SS, Asundi AS, Hoffman AS, Hong J, Zhou C, Vila FD, Cargnello M, Bare SR, Bent SF. Surface Fe Clusters Promote Syngas Reaction to Oxygenates on Rh Catalysts Modified by Atomic Layer Deposition. J Catal 2022. [DOI: 10.1016/j.jcat.2022.08.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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10
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Kas JJ, Vila FD, Tan TS, Rehr JJ. Ab initio calculation of X-ray and related core-level spectroscopies: Green's function approaches. Phys Chem Chem Phys 2022; 24:13461-13473. [PMID: 35616020 DOI: 10.1039/d2cp01167k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
X-Ray and related spectroscopies are powerful probes of atomic, vibrational, and electronic structure. In order to unlock the full potential of such experimental techniques, accurate and efficient theoretical and computational approaches are essential. Here we review the status of a variety of first-principles and nearly first principles techniques for X-ray spectroscopies such as X-ray absorption, X-ray emission, and X-ray photoemission, with a focus on Green's function based methods. In particular, we describe the current state of multiple scattering Green's function techniques available in the FEFF10 code and cumulant Green's function techniques for including the effects of many-body electronic excitations. Illustrative examples are shown for a variety of materials and compared with other theoretical and experimental results.
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Affiliation(s)
| | | | - Tun S Tan
- University of Washington, Seattle, USA.
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11
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Chen Y, Rana R, Huang Z, Vila FD, Sours T, Perez-Aguilar JE, Zhao X, Hong J, Hoffman AS, Li X, Shang C, Blum T, Zeng J, Chi M, Salmeron M, Kronawitter CX, Bare SR, Kulkarni AR, Gates BC. Atomically Dispersed Platinum in Surface and Subsurface Sites on MgO Have Contrasting Catalytic Properties for CO Oxidation. J Phys Chem Lett 2022; 13:3896-3903. [PMID: 35471032 DOI: 10.1021/acs.jpclett.2c00667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Atomically dispersed metals on metal oxide supports are a rapidly growing class of catalysts. Developing an understanding of where and how the metals are bonded to the supports is challenging because support surfaces are heterogeneous, and most reports lack a detailed consideration of these points. Herein, we report two atomically dispersed CO oxidation catalysts having markedly different metal-support interactions: platinum in the first layer of crystalline MgO powder and platinum in the second layer of this support. Structural models have been determined on the basis of data and computations, including those determined by extended X-ray absorption fine structure and X-ray absorption near edge structure spectroscopies, infrared spectroscopy of adsorbed CO, and scanning transmission electron microscopy. The data demonstrate the transformation of surface to subsurface platinum as the temperature of sample calcination increased. Catalyst performance data demonstrate the lower activity but greater stability of the subsurface platinum than of the surface platinum.
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Affiliation(s)
- Yizhen Chen
- Department of Chemical Engineering, University of California, Davis, California 95616, United States
| | - Rachita Rana
- Department of Chemical Engineering, University of California, Davis, California 95616, United States
| | - Zhennan Huang
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Fernando D Vila
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Tyler Sours
- Department of Chemical Engineering, University of California, Davis, California 95616, United States
| | - Jorge E Perez-Aguilar
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | | | - Jiyun Hong
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Adam S Hoffman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Xu Li
- Hefei National Laboratory for Physical Sciences at the Microscale, National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Chunyan Shang
- Hefei National Laboratory for Physical Sciences at the Microscale, National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Thomas Blum
- University of California Irvine, Irvine, California 92697, United States
| | - Jie Zeng
- Hefei National Laboratory for Physical Sciences at the Microscale, National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Miaofang Chi
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | | | - Coleman X Kronawitter
- Department of Chemical Engineering, University of California, Davis, California 95616, United States
| | - Simon R Bare
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Ambarish R Kulkarni
- Department of Chemical Engineering, University of California, Davis, California 95616, United States
| | - Bruce C Gates
- Department of Chemical Engineering, University of California, Davis, California 95616, United States
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12
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Abstract
Many-body excitations in X-ray photoemission spectra have been difficult to simulate from first principles. We have recently developed a cumulant-based one-electron Green's function method using the real-time coupled-cluster-singles equation-of-motion approach (RT-EOM-CCS) that provides a general framework for treating these problems. Here we extend this approach to include double excitations in the ground-state energy and in the coupled cluster amplitudes, which have been implemented using subroutines generated by the Tensor Contraction Engine (TCE). As in the case of the singles approximation, RT-EOM-CCSD yields a nonperturbative cumulant form of the Green's function in terms of the time-dependent cluster amplitudes, adding nonlinear corrections to the traditional cumulant forms. The extended approach is applied to the core-hole spectral function for small molecular systems. We find that, when core-optimized basis sets are used, the doubles contributions reduce the mean absolute errors in the core binding energies of the 10e systems from 0.8 to 0.3 eV. They also significantly improve the quasiparticle-satellite gap by reducing its overestimation from about 3-5 to about 0-1 eV in CH4, NH3, and H2O, and also improving the overall shape of the satellite features. Finally, we demonstrate the application of the new implementation to the larger, classical XPS ESCA series of molecules and show that the singles approximation can be paired with a modest basis set to study carbon speciation.
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Affiliation(s)
- F D Vila
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - K Kowalski
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - B Peng
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - J J Kas
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - J J Rehr
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
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13
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Chen Y, Rana R, Sours T, Vila FD, Cao S, Blum T, Hong J, Hoffman AS, Fang CY, Huang Z, Shang C, Wang C, Zeng J, Chi M, Kronawitter CX, Bare SR, Gates BC, Kulkarni AR. A Theory-Guided X-ray Absorption Spectroscopy Approach for Identifying Active Sites in Atomically Dispersed Transition-Metal Catalysts. J Am Chem Soc 2021; 143:20144-20156. [PMID: 34806881 DOI: 10.1021/jacs.1c07116] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Atomically dispersed supported metal catalysts offer new properties and the benefits of maximized metal accessibility and utilization. The characterization of these materials, however, remains challenging. Using atomically dispersed platinum supported on crystalline MgO (chosen for its well-defined bonding sites) as a prototypical example, we demonstrate how systematic density functional theory calculations for assessing all the potentially stable platinum sites, combined with automated analysis of extended X-ray absorption fine structure (EXAFS) spectra, leads to unbiased identification of isolated, surface-enveloped platinum cations as the catalytic species for CO oxidation. The catalyst has been characterized by atomic-resolution imaging and EXAFS and high-energy resolution fluorescence detection X-ray absorption near edge spectroscopy. The proposed platinum sites are in agreement with experiment. This theory-guided workflow leads to rigorously determined structural models and provides a more detailed picture of the structure of the catalytically active site than what is currently possible with conventional EXAFS analyses. As this approach is efficient and agnostic to the metal, support, and catalytic reaction, we posit that it will be of broad interest to the materials characterization and catalysis communities.
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Affiliation(s)
- Yizhen Chen
- Department of Chemical Engineering, University of California, Davis, California 95616, United States
| | - Rachita Rana
- Department of Chemical Engineering, University of California, Davis, California 95616, United States
| | - Tyler Sours
- Department of Chemical Engineering, University of California, Davis, California 95616, United States
| | - Fernando D Vila
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Shaohong Cao
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Thomas Blum
- University of California Irvine, Irvine, California 92697, United States
| | - Jiyun Hong
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Adam S Hoffman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Chia-Yu Fang
- Department of Materials Science and Engineering, University of California, Davis, California 95616, United States
| | - Zhennan Huang
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Chunyan Shang
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, P.R. China
| | - Chuanhao Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, P.R. China
| | - Jie Zeng
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, P.R. China
| | - Miaofang Chi
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Coleman X Kronawitter
- Department of Chemical Engineering, University of California, Davis, California 95616, United States
| | - Simon R Bare
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Bruce C Gates
- Department of Chemical Engineering, University of California, Davis, California 95616, United States
| | - Ambarish R Kulkarni
- Department of Chemical Engineering, University of California, Davis, California 95616, United States
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14
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Kas JJ, Vila FD, Pemmaraju CD, Tan TS, Rehr JJ. Advanced calculations of X-ray spectroscopies with FEFF10 and Corvus. J Synchrotron Radiat 2021; 28:1801-1810. [PMID: 34738933 DOI: 10.1107/s1600577521008614] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
The real-space Green's function code FEFF has been extensively developed and used for calculations of X-ray and related spectra, including X-ray absorption (XAS), X-ray emission (XES), inelastic X-ray scattering, and electron energy-loss spectra. The code is particularly useful for the analysis and interpretation of the XAS fine-structure (EXAFS) and the near-edge structure (XANES) in materials throughout the periodic table. Nevertheless, many applications, such as non-equilibrium systems, and the analysis of ultra-fast pump-probe experiments, require extensions of the code including finite-temperature and auxiliary calculations of structure and vibrational properties. To enable these extensions, we have developed in tandem a new version FEFF10 and new FEFF-based workflows for the Corvus workflow manager, which allow users to easily augment the capabilities of FEFF10 via auxiliary codes. This coupling facilitates simplified input and automated calculations of spectra based on advanced theoretical techniques. The approach is illustrated with examples of high-temperature behavior, vibrational properties, many-body excitations in XAS, super-heavy materials, and fits of calculated spectra to experiment.
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Affiliation(s)
- J J Kas
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - F D Vila
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - C D Pemmaraju
- Theory Institute for Materials and Energy Spectroscopies, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - T S Tan
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - J J Rehr
- Department of Physics, University of Washington, Seattle, WA 98195, USA
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15
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Vila FD, Kas JJ, Rehr JJ, Kowalski K, Peng B. Equation-of-Motion Coupled-Cluster Cumulant Green's Function for Excited States and X-Ray Spectra. Front Chem 2021; 9:734945. [PMID: 34631660 PMCID: PMC8493088 DOI: 10.3389/fchem.2021.734945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/06/2021] [Indexed: 11/13/2022] Open
Abstract
Green’s function methods provide a robust, general framework within many-body theory for treating electron correlation in both excited states and x-ray spectra. Conventional methods using the Dyson equation or the cumulant expansion are typically based on the GW self-energy approximation. In order to extend this approximation in molecular systems, a non-perturbative real-time coupled-cluster cumulant Green’s function approach has been introduced, where the cumulant is obtained as the solution to a system of coupled first order, non-linear differential equations. This approach naturally includes non-linear corrections to conventional cumulant Green’s function techniques where the cumulant is linear in the GW self-energy. The method yields the spectral function for the core Green’s function, which is directly related to the x-ray photoemission spectra (XPS) of molecular systems. The approach also yields very good results for binding energies and satellite excitations. The x-ray absorption spectrum (XAS) is then calculated using a convolution of the core spectral function and an effective, one-body XAS. Here this approach is extended to include the full coupled-cluster-singles (CCS) core Green’s function by including the complete form of the non-linear contributions to the cumulant as well as all single, double, and triple cluster excitations in the CC amplitude equations. This approach naturally builds in orthogonality and shake-up effects analogous to those in the Mahan-Noizeres-de Dominicis edge singularity corrections that enhance the XAS near the edge. The method is illustrated for the XPS and XAS of NH3.
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Affiliation(s)
- F D Vila
- Department of Physics, University of Washington, Seattle, WA, United States
| | - J J Kas
- Department of Physics, University of Washington, Seattle, WA, United States
| | - J J Rehr
- Department of Physics, University of Washington, Seattle, WA, United States
| | - K Kowalski
- Physical and Computational Science Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - B Peng
- Physical and Computational Science Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
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16
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Abstract
Green's function methods within many-body perturbation theory provide a general framework for treating electronic correlations in excited states and spectra. Here, we develop the cumulant form of the one-electron Green's function using a real-time coupled-cluster equation-of-motion approach, in an extension of our previous study (Rehr J.; et al. J. Chem. Phys. 2020, 152, 174113). The approach yields a nonperturbative expression for the cumulant in terms of the solution to a set of coupled first-order, nonlinear differential equations. The method thereby adds nonlinear corrections to traditional cumulant methods, which are linear in the self-energy. The approach is applied to the core-hole Green's function and is illustrated for a number of small molecular systems. For these systems, we find that the nonlinear contributions yield significant improvements, both for quasiparticle properties such as core-level binding energies and for inelastic losses that correspond to satellites observed in photoemission spectra.
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Affiliation(s)
- F D Vila
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - J J Rehr
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - J J Kas
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - K Kowalski
- William R. Wiley Environmental Molecular Sciences Laboratory, Battelle, Pacific Northwest National Laboratory, K8-91, P.O. Box 999, Richland, Washington 99352, United States
| | - B Peng
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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17
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Rehr JJ, Vila FD, Kas JJ, Hirshberg NY, Kowalski K, Peng B. Equation of motion coupled-cluster cumulant approach for intrinsic losses in x-ray spectra. J Chem Phys 2020; 152:174113. [PMID: 32384843 DOI: 10.1063/5.0004865] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a combined equation of motion coupled-cluster cumulant Green's function approach for calculating and understanding intrinsic inelastic losses in core level x-ray absorption spectra (XAS) and x-ray photoemission spectra. The method is based on a factorization of the transition amplitude in the time domain, which leads to a convolution of an effective one-body absorption spectrum and the core-hole spectral function. The spectral function characterizes intrinsic losses in terms of shake-up excitations and satellites using a cumulant representation of the core-hole Green's function that simplifies the interpretation. The one-body spectrum also includes orthogonality corrections that enhance the XAS at the edge.
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Affiliation(s)
- J J Rehr
- Department of Physics, University of Washington Seattle, Seattle, Washington 98195, USA
| | - F D Vila
- Department of Physics, University of Washington Seattle, Seattle, Washington 98195, USA
| | - J J Kas
- Department of Physics, University of Washington Seattle, Seattle, Washington 98195, USA
| | - N Y Hirshberg
- Department of Physics, University of Washington Seattle, Seattle, Washington 98195, USA
| | - K Kowalski
- Physical Sciences Division, Battelle, Pacific Northwest National Laboratory, K8-91, PO Box 999, Richland, Washington 99352, USA
| | - B Peng
- Physical Sciences Division, Battelle, Pacific Northwest National Laboratory, K8-91, PO Box 999, Richland, Washington 99352, USA
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18
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Asundi AS, Hoffman AS, Bothra P, Boubnov A, Vila FD, Yang N, Singh JA, Zeng L, Raiford JA, Abild-Pedersen F, Bare SR, Bent SF. Understanding Structure-Property Relationships of MoO 3-Promoted Rh Catalysts for Syngas Conversion to Alcohols. J Am Chem Soc 2019; 141:19655-19668. [PMID: 31724857 DOI: 10.1021/jacs.9b07460] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rh-based catalysts have shown promise for the direct conversion of syngas to higher oxygenates. Although improvements in higher oxygenate yield have been achieved by combining Rh with metal oxide promoters, details of the structure of the promoted catalyst and the role of the promoter in enhancing catalytic performance are not well understood. In this work, we show that MoO3-promoted Rh nanoparticles form a novel catalyst structure in which Mo substitutes into the Rh surface, leading to both a 66-fold increase in turnover frequency and an enhancement in oxygenate yield. By applying a combination of atomically controlled synthesis, in situ characterization, and theoretical calculations, we gain an understanding of the promoter-Rh interactions that govern catalytic performance for MoO3-promoted Rh. We use atomic layer deposition to modify Rh nanoparticles with monolayer-precise amounts of MoO3, with a high degree of control over the structure of the catalyst. Through in situ X-ray absorption spectroscopy, we find that the atomic structure of the catalytic surface under reaction conditions consists of Mo-OH species substituted into the surface of the Rh nanoparticles. Using density functional theory calculations, we identify two roles of MoO3: first, the presence of Mo-OH in the catalyst surface enhances CO dissociation and also stabilizes a methanol synthesis pathway not present in the unpromoted catalyst; and second, hydrogen spillover from Mo-OH sites to adsorbed species on the Rh surface enhances hydrogenation rates of reaction intermediates.
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Affiliation(s)
- Arun S Asundi
- Department of Chemical Engineering , Stanford University , Stanford , California 94305 , United States
| | - Adam S Hoffman
- SSRL , SLAC National Accelerator Laboratory , Menlo Park , California 94205 , United States
| | - Pallavi Bothra
- Department of Chemical Engineering , Stanford University , Stanford , California 94305 , United States.,SUNCAT Center for Interface Science and Catalysis , SLAC National Accelerator Laboratory , Menlo Park , California 94205 , United States
| | - Alexey Boubnov
- SSRL , SLAC National Accelerator Laboratory , Menlo Park , California 94205 , United States
| | - Fernando D Vila
- Department of Physics , University of Washington , Seattle , Washington 98195 , United States
| | - Nuoya Yang
- Department of Materials Science and Engineering , Stanford University , Stanford , California 94305 , United States
| | - Joseph A Singh
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Li Zeng
- Department of Chemical Engineering , Stanford University , Stanford , California 94305 , United States
| | - James A Raiford
- Department of Chemical Engineering , Stanford University , Stanford , California 94305 , United States
| | - Frank Abild-Pedersen
- Department of Chemical Engineering , Stanford University , Stanford , California 94305 , United States.,SUNCAT Center for Interface Science and Catalysis , SLAC National Accelerator Laboratory , Menlo Park , California 94205 , United States
| | - Simon R Bare
- SSRL , SLAC National Accelerator Laboratory , Menlo Park , California 94205 , United States
| | - Stacey F Bent
- Department of Chemical Engineering , Stanford University , Stanford , California 94305 , United States
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19
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Travnikova O, Patanen M, Söderström J, Lindblad A, Kas JJ, Vila FD, Céolin D, Marchenko T, Goldsztejn G, Guillemin R, Journel L, Carroll TX, Børve KJ, Decleva P, Rehr JJ, Mårtensson N, Simon M, Svensson S, Sæthre LJ. Energy-Dependent Relative Cross Sections in Carbon 1s Photoionization: Separation of Direct Shake and Inelastic Scattering Effects in Single Molecules. J Phys Chem A 2019; 123:7619-7636. [PMID: 31386367 DOI: 10.1021/acs.jpca.9b05063] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We demonstrate that the possibility of monitoring relative photoionization cross sections over a large photon energy range allows us to study and disentangle shake processes and intramolecular inelastic scattering effects. In this gas-phase study, relative intensities of the carbon 1s photoelectron lines from chemically inequivalent carbon atoms in the same molecule have been measured as a function of the incident photon energy in the range of 300-6000 eV. We present relative cross sections for the chemically shifted carbon 1s lines in the photoelectron spectra of ethyl trifluoroacetate (the "ESCA" molecule). The results are compared with those of methyl trifluoroacetate and S-ethyl trifluorothioacetate as well as a series of chloro-substituted ethanes and 2-butyne. In the soft X-ray energy range, the cross sections show an extended X-ray absorption fine structure type of wiggles, as was previously observed for a series of chloroethanes. The oscillations are damped in the hard X-ray energy range, but deviations of cross-section ratios from stoichiometry persist, even at high energies. The current findings are supported by theoretical calculations based on a multiple scattering model. The use of soft and tender X-rays provides a more complete picture of the dominant processes accompanying photoionization. Such processes reduce the main photoelectron line intensities by 20-60%. Using both energy ranges enabled us to discern the process of intramolecular inelastic scattering of the outgoing electron, whose significance is otherwise difficult to assess for isolated molecules. This effect relates to the notion of the inelastic mean free path commonly used in photoemission studies of clusters and condensed matter.
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Affiliation(s)
- Oksana Travnikova
- LCPMR, CNRS, Sorbonne Université, UMR7614 Paris, France.,Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin, F-91192 Gif-sur-Yvette, France
| | - Minna Patanen
- Nano and Molecular Systems Research Unit, Faculty of Science, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland
| | - Johan Söderström
- Department of Physics and Astronomy, Uppsala University, P.O. Box 516, 75120 Uppsala, Sweden
| | | | - Joshua J Kas
- Department of Physics, University of Washington, Box 351560, Seattle, Washington 98195-1560, United States
| | - Fernando D Vila
- Department of Physics, University of Washington, Box 351560, Seattle, Washington 98195-1560, United States
| | - Denis Céolin
- Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin, F-91192 Gif-sur-Yvette, France
| | - Tatiana Marchenko
- LCPMR, CNRS, Sorbonne Université, UMR7614 Paris, France.,Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin, F-91192 Gif-sur-Yvette, France
| | | | - Renaud Guillemin
- LCPMR, CNRS, Sorbonne Université, UMR7614 Paris, France.,Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin, F-91192 Gif-sur-Yvette, France
| | - Loïc Journel
- LCPMR, CNRS, Sorbonne Université, UMR7614 Paris, France.,Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin, F-91192 Gif-sur-Yvette, France
| | - Thomas X Carroll
- Division of Natural Sciences, Keuka College, Keuka Park, New York 14478, United States
| | - Knut J Børve
- Department of Chemistry, University of Bergen, Allégaten 41, NO-5007 Bergen, Norway
| | - Piero Decleva
- Dipartimento di Scienze Chimiche e Farmaceutiche, Universitá di Trieste and IOM-CNR, 34127 Trieste, Italy
| | - John J Rehr
- Department of Physics, University of Washington, Box 351560, Seattle, Washington 98195-1560, United States
| | - Nils Mårtensson
- Department of Physics and Astronomy, Uppsala University, P.O. Box 516, 75120 Uppsala, Sweden
| | - Marc Simon
- LCPMR, CNRS, Sorbonne Université, UMR7614 Paris, France.,Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin, F-91192 Gif-sur-Yvette, France
| | - Svante Svensson
- Department of Physics and Astronomy, Uppsala University, P.O. Box 516, 75120 Uppsala, Sweden
| | - Leif J Sæthre
- Department of Chemistry, University of Bergen, Allégaten 41, NO-5007 Bergen, Norway
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20
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Story SM, Vila FD, Kas JJ, Raniga KB, Pemmaraju CD, Rehr JJ. Corvus: a framework for interfacing scientific software for spectroscopic and materials science applications. J Synchrotron Radiat 2019; 26:1694-1704. [PMID: 31490161 DOI: 10.1107/s1600577519007495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 05/23/2019] [Indexed: 06/10/2023]
Abstract
Corvus, a Python-based package designed for managing workflows of physical simulations that utilize multiple scientific software packages, is presented. Corvus can be run as an executable script with an input file and automatically generated or custom workflows, or interactively, in order to build custom workflows with a set of Corvus-specific tools. Several prototypical examples are presented that link density functional, vibrational and X-ray spectroscopy software packages and are of interest to the synchrotron community. These examples highlight the simplification of complex spectroscopy calculations that were previously limited to expert users, and demonstrate the flexibility of the Corvus infrastructure to tackle more general problems in other research areas.
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Affiliation(s)
- S M Story
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - F D Vila
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - J J Kas
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - K B Raniga
- School of Humanities and Sciences, Stanford University, Stanford, CA 94305, USA
| | - C D Pemmaraju
- Theory Institute for Materials and Energy Spectroscopies, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - J J Rehr
- Department of Physics, University of Washington, Seattle, WA 98195, USA
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21
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Vila FD, Spencer JW, Kas JJ, Rehr JJ, Bridges F. Extended X-Ray Absorption Fine Structure of ZrW 2O 8: Theory vs. Experiment. Front Chem 2018; 6:356. [PMID: 30191149 PMCID: PMC6115524 DOI: 10.3389/fchem.2018.00356] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 07/30/2018] [Indexed: 11/13/2022] Open
Abstract
Extended x-ray absorption fine structure (EXAFS) is well-suited for investigations of structure and disorder of complex materials. Recently, experimental measurements and analysis of EXAFS have been carried out to elucidate the mechanisms responsible for the negative thermal expansion (NTE) in zirconium tungstate (ZrW2O8). In contrast to previous work suggesting that transverse O-displacements are largely responsible, the EXAFS analysis suggested that correlated rotations and translations of octahedra and tetrahedra within the structure are a major source. In an effort to resolve this controversy, we have carried out ab initio calculations of the structure, lattice vibrations, and EXAFS of ZrW2O8 based on real-space multiple-scattering calculations using the FEFF9 code and auxiliary calculations of structure and Debye-Waller factors. We find that the theoretical simulations are consistent with observed EXAFS, and show that both of the above mechanisms contribute to the dynamical structure of ZrW2O8.
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Affiliation(s)
- Fernando D Vila
- Department of Physics, University of Washington, Seattle, WA, United States
| | - John W Spencer
- Department of Physics, University of Washington, Seattle, WA, United States
| | - Joshua J Kas
- Department of Physics, University of Washington, Seattle, WA, United States
| | - John J Rehr
- Department of Physics, University of Washington, Seattle, WA, United States
| | - Frank Bridges
- Department of Physics, University of California, Santa Cruz, Santa Cruz, CA, United States
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22
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Abstract
We present a study of the origin of the negative thermal expansion (NTE) on ZrW2O8 by combining an efficient approach for computing the dynamical matrix with the Lanczos algorithm for generating the phonon density of states in the quasi-harmonic approximation. The simulations show that the NTE arises primarily from the motion of the O-sublattice, and in particular, from the transverse motion of the O atoms in the W–O and W–O–Zr bonds. In the low frequency range these combine to keep the WO4 tetrahedra rigid and induce internal distortions in the ZrO6 octahedra. The force constants associated with these distortions become stronger with expansion, resulting in negative Grüneisen parameters and NTE from the low frequency modes that dominate the positive contributions from the high frequency modes. This leads us to propose an anharmonic, two-frequency Einstein model that quantitatively captures the NTE behavior.
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Affiliation(s)
- Fernando D Vila
- Department of Physics, University of Washington, Seattle, WA, United States
| | - Scott T Hayashi
- Department of Physics, University of Washington, Seattle, WA, United States
| | - John J Rehr
- Department of Physics, University of Washington, Seattle, WA, United States
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23
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Abstract
Supported Pt nanocatalysts generally exhibit anomalous behavior, including negative thermal expansion and large structural disorder. Finite temperature DFT/MD simulations reproduce these properties, showing that they are largely explained by a combination of thermal vibrations and low-frequency disorder. We show here that a full interpretation is more complex and that the DFT/MD mean-square relative displacements (MSRD) can be further separated into vibrational disorder, "dynamic structural disorder" (DSD), and long-time equilibrium fluctuations of the structure dubbed "anomalous structural disorder" (ASD). We find that the vibrational and DSD components behave normally, increasing linearly with temperature while the ASD decreases, reflecting the evolution of mean nanoparticle geometry. As a consequence the usual procedure of fitting the MSRD to normal vibrations plus temperature-independent static disorder results in unphysical bond strengths and Grüneisen parameters.
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Affiliation(s)
- Fernando D Vila
- Department of Physics, University of Washington , Seattle, Washington 98195, United States
| | - John J Rehr
- Department of Physics, University of Washington , Seattle, Washington 98195, United States
| | - Ralph G Nuzzo
- Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
| | - Anatoly I Frenkel
- Department of Materials Science and Chemical Engineering, Stony Brook University , Stony Brook, New York 11794, United States
- Division of Chemistry, Brookhaven National Laboratory , Upton, New York 11973, United States
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24
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Beckwith MA, Ames W, Vila FD, Krewald V, Pantazis DA, Mantel C, Pécaut J, Gennari M, Duboc C, Collomb MN, Yano J, Rehr JJ, Neese F, DeBeer S. How Accurately Can Extended X-ray Absorption Spectra Be Predicted from First Principles? Implications for Modeling the Oxygen-Evolving Complex in Photosystem II. J Am Chem Soc 2015; 137:12815-34. [PMID: 26352328 DOI: 10.1021/jacs.5b00783] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
First principle calculations of extended X-ray absorption fine structure (EXAFS) data have seen widespread use in bioinorganic chemistry, perhaps most notably for modeling the Mn4Ca site in the oxygen evolving complex (OEC) of photosystem II (PSII). The logic implied by the calculations rests on the assumption that it is possible to a priori predict an accurate EXAFS spectrum provided that the underlying geometric structure is correct. The present study investigates the extent to which this is possible using state of the art EXAFS theory. The FEFF program is used to evaluate the ability of a multiple scattering-based approach to directly calculate the EXAFS spectrum of crystallographically defined model complexes. The results of these parameter free predictions are compared with the more traditional approach of fitting FEFF calculated spectra to experimental data. A series of seven crystallographically characterized Mn monomers and dimers is used as a test set. The largest deviations between the FEFF calculated EXAFS spectra and the experimental EXAFS spectra arise from the amplitudes. The amplitude errors result from a combination of errors in calculated S0(2) and Debye-Waller values as well as uncertainties in background subtraction. Additional errors may be attributed to structural parameters, particularly in cases where reliable high-resolution crystal structures are not available. Based on these investigations, the strengths and weaknesses of using first-principle EXAFS calculations as a predictive tool are discussed. We demonstrate that a range of DFT optimized structures of the OEC may all be considered consistent with experimental EXAFS data and that caution must be exercised when using EXAFS data to obtain topological arrangements of complex clusters.
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Affiliation(s)
- Martha A Beckwith
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany.,Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - William Ames
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Fernando D Vila
- Department of Physics, University of Washington , Seattle, Washington 98195, United States
| | - Vera Krewald
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Dimitrios A Pantazis
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Claire Mantel
- Département de Chimie Moléculaire, Université Joseph Fourier Grenoble, CNRS , F-38000 Grenoble, France
| | - Jacques Pécaut
- Laboratoire de Reconnaissance Ionique et Chimie de Coordination, Service de Chimie Inorganique et Biologique, (UMR E-3 CEA/UJF, FRE3200 CNRS), CEA-Grenoble, INAC , 17 rue des Martyrs 38054 Grenoble cedex 9, France
| | - Marcello Gennari
- Département de Chimie Moléculaire, Université Joseph Fourier Grenoble, CNRS , F-38000 Grenoble, France
| | - Carole Duboc
- Département de Chimie Moléculaire, Université Joseph Fourier Grenoble, CNRS , F-38000 Grenoble, France
| | - Marie-Noëlle Collomb
- Département de Chimie Moléculaire, Université Joseph Fourier Grenoble, CNRS , F-38000 Grenoble, France
| | - Junko Yano
- Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - John J Rehr
- Department of Physics, University of Washington , Seattle, Washington 98195, United States
| | - Frank Neese
- 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.,Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
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Carroll TX, Zahl MG, Børve KJ, Sæthre LJ, Decleva P, Ponzi A, Kas JJ, Vila FD, Rehr JJ, Thomas TD. Intensity oscillations in the carbon 1s ionization cross sections of 2-butyne. J Chem Phys 2014; 138:234310. [PMID: 23802963 DOI: 10.1063/1.4810870] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Carbon 1s photoelectron spectra for 2-butyne (CH3C≡CCH3) measured in the photon energy range from threshold to 150 eV above threshold show oscillations in the intensity ratio C2,3/C1,4. Similar oscillations have been seen in chloroethanes, where the effect has been attributed to EXAFS-type scattering from the substituent chlorine atoms. In 2-butyne, however, there is no high-Z atom to provide a scattering center and, hence, oscillations of the magnitude observed are surprising. The results have been analyzed in terms of two different theoretical models: a density-functional model with B-spline atom-centered functions to represent the continuum electrons and a multiple-scattering model using muffin-tin potentials to represent the scattering centers. Both methods give a reasonable description of the energy dependence of the intensity ratios.
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Affiliation(s)
- Thomas X Carroll
- Division of Natural Sciences, Keuka College, Keuka Park, New York 14478, USA
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Mårtensson N, Söderstrom J, Svensson S, Travnikova O, Patanen M, Miron C, Sæthre LJ, Børve KJ, Thomas TD, Kas JJ, Vila FD, Rehr JJ. On the relation between X-ray Photoelectron Spectroscopy and XAFS. ACTA ACUST UNITED AC 2013. [DOI: 10.1088/1742-6596/430/1/012131] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Goldberg IG, Vila FD, Jach T. Surface Effects on the Crystallization of Cyclo-1,3,5-trimethylene-2,4,6-trinitramine (RDX) and the Consequences for its N K X-ray Emission Spectrum. J Phys Chem A 2012; 116:9897-9. [DOI: 10.1021/jp306978x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ilana G. Goldberg
- Transportation Security Laboratory, Atlantic City, New Jersey 08405, United
States
| | - Fernando D. Vila
- Department
of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Terrence Jach
- Material Measurement Laboratory, National Institute of Standards & Technology, Gaithersburg, Maryland 20899-8371, United States
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Söderström J, Mårtensson N, Travnikova O, Patanen M, Miron C, Sæthre LJ, Børve KJ, Rehr JJ, Kas JJ, Vila FD, Thomas TD, Svensson S. Nonstoichiometric intensities in core photoelectron spectroscopy. Phys Rev Lett 2012; 108:193005. [PMID: 23003034 DOI: 10.1103/physrevlett.108.193005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Indexed: 06/01/2023]
Abstract
X-ray photoemission spectroscopy is used in a great variety of research fields; one observable is the sample's stoichiometry. The stoichiometry can be deduced based on the expectation that the ionization cross sections for innershell orbitals are independent of the molecular composition. Here we used chlorine-substituted ethanes in the gas phase to investigate the apparent carbon stoichiometry. We observe a nonstoichiometric ratio for a wide range of photon energies, the ratio exhibits x-ray-absorption fine structure spectroscopy (EXAFS)-like oscillations and hundreds of eV above the C1s ionization approaches a value far from 1. These effects can be accounted for by considering the scattering of the outgoing photoelectron, which we model by multiple-scattering EXAFS calculations, and by considering the effects of losses due to monopole shakeup and shakeoff and to intramolecular inelastic scattering processes.
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Affiliation(s)
- J Söderström
- Department of Physics and Astronomy, Uppsala University, Box 516, 751 20 Uppsala, Sweden
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Affiliation(s)
- Fernando D. Vila
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Terrence Jach
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - W. T. Elam
- Applied Physics Laboratory, University of Washington, Seattle, Washington 98195, United States
| | - John J. Rehr
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - J. D. Denlinger
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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Vila FD, Strubbe DA, Takimoto Y, Andrade X, Rubio A, Louie SG, Rehr JJ. Basis set effects on the hyperpolarizability of CHCl3: Gaussian-type orbitals, numerical basis sets and real-space grids. J Chem Phys 2010; 133:034111. [DOI: 10.1063/1.3457362] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Abstract
New theoretical and experimental investigations of the occupied and unoccupied local electronic densities of states (DOS) are reported for alpha-Li(3)N. Band-structure and density-functional theory calculations confirm the absence of covalent bonding character. However, real-space full-multiple-scattering (RSFMS) calculations of the occupied local DOS find less extreme nominal valences than have previously been proposed. Nonresonant inelastic x-ray scattering, RSFMS calculations, and calculations based on the Bethe-Salpeter equation are used to characterize the unoccupied electronic final states local to both the Li and N sites. There is a good agreement between experiment and theory. Throughout the Li 1s near-edge region, both experiment and theory find strong similarities in the s-and p-type components of the unoccupied local final DOS projected onto an orbital angular momentum basis (l-DOS). An unexpected, significant correspondence exists between the near-edge spectra for the Li 1s and N 1s initial states. We argue that both spectra are sampling essentially the same final DOS due to the combination of long core-hole lifetimes, long photoelectron lifetimes, and the fact that orbital angular momentum is the same for all relevant initial states. Such considerations may be generally applicable for low atomic number compounds.
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Affiliation(s)
- T T Fister
- Physics Department, University of Washington, Seattle, Washington 98195, USA
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Fister TT, Vila FD, Seidler GT, Svec L, Linehan JC, Cross JO. Local Electronic Structure of Dicarba-closo-dodecarboranes C2B10H12. J Am Chem Soc 2007; 130:925-32. [DOI: 10.1021/ja074794u] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Timothy T. Fister
- Physics Department, University of Washington, Seattle, Washington 98105, Pacific Northwest National Laboratory, Richland, Washington 99352, and Argonne National Laboratory, Argonne, Illinois 60439
| | - Fernando D. Vila
- Physics Department, University of Washington, Seattle, Washington 98105, Pacific Northwest National Laboratory, Richland, Washington 99352, and Argonne National Laboratory, Argonne, Illinois 60439
| | - Gerald T. Seidler
- Physics Department, University of Washington, Seattle, Washington 98105, Pacific Northwest National Laboratory, Richland, Washington 99352, and Argonne National Laboratory, Argonne, Illinois 60439
| | - Lukas Svec
- Physics Department, University of Washington, Seattle, Washington 98105, Pacific Northwest National Laboratory, Richland, Washington 99352, and Argonne National Laboratory, Argonne, Illinois 60439
| | - John C. Linehan
- Physics Department, University of Washington, Seattle, Washington 98105, Pacific Northwest National Laboratory, Richland, Washington 99352, and Argonne National Laboratory, Argonne, Illinois 60439
| | - Julie O. Cross
- Physics Department, University of Washington, Seattle, Washington 98105, Pacific Northwest National Laboratory, Richland, Washington 99352, and Argonne National Laboratory, Argonne, Illinois 60439
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Isborn CM, Leclercq A, Vila FD, Dalton LR, Brédas JL, Eichinger BE, Robinson BH. Comparison of Static First Hyperpolarizabilities Calculated with Various Quantum Mechanical Methods. J Phys Chem A 2007; 111:1319-27. [PMID: 17256825 DOI: 10.1021/jp064096g] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The prediction of nonlinear electro-optic (EO) behavior of molecules with quantum methods is the first step in the development of organic-based electro-optic devices. Typical EO molecules may require calculations with several hundred electrons, which prevents all but the fastest methods (semiempirical and density functional theory (DFT)) from being used for EO estimation. To test the reliability of these methods, we compare dipole moments, polarizabilities, and first-order hyperpolarizabilities for a wide range of structures of experimental interest with Hartree-Fock (HF), intermediate neglect of differential overlap (INDO), and DFT methods. The relative merits of molecules are consistently predictable with every method.
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Affiliation(s)
- C M Isborn
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
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Affiliation(s)
- Fernando D. Vila
- Department of Chemistry and Center for Molecular and Materials Simulations, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Kenneth D. Jordan
- Department of Chemistry and Center for Molecular and Materials Simulations, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
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