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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] [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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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Tao Y, Zou W, Nanayakkara S, Kraka E. LModeA-nano: A PyMOL Plugin for Calculating Bond Strength in Solids, Surfaces, and Molecules via Local Vibrational Mode Analysis. J Chem Theory Comput 2022; 18:1821-1837. [PMID: 35192350 DOI: 10.1021/acs.jctc.1c01269] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The analysis of chemical bonding in crystal structures and surfaces is an important research topic in theoretical chemistry. In this work, we present a PyMOL plugin, named LModeA-nano, as implementation of the local vibrational mode theory for periodic systems (Tao et al. J. Chem. Theory Comput. 2019, 15, 1761) assessing bond strength in terms of local stretching force constants in extended systems of one, two, and three dimensions. LModeA-nano can also analyze chemical bonds in isolated molecular systems thus enabling a head-to-head comparison of bond strength across systems with different dimensions in periodicity (0-3D). The new code is interfaced to the output generated by various solid-state modeling packages including VASP, CP2K, Quantum ESPRESSO, CASTEP, and CRYSTAL. LModeA-nano is cross-platform, open-source and freely available on GitHub: https://github.com/smutao/LModeA-nano.
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Affiliation(s)
- Yunwen Tao
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Wenli Zou
- Institute of Modern Physics, Northwest University, and Shaanxi Key Laboratory for Theoretical Physics Frontiers, Xi'an, Shaanxi 710127, P. R. China
| | - Sadisha Nanayakkara
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Elfi Kraka
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
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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] [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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Kas JJ, Vila FD, Pemmaraju CD, Tan TS, Rehr JJ. Advanced calculations of X-ray spectroscopies with FEFF10 and Corvus. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:1801-1810. [PMID: 34738933 DOI: 10.1107/s1600577521008614] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [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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Fan J, Su Y, Zheng Z, Zhao J. Thermal properties of energetic materials from quasi-harmonic first-principles calculations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:275702. [PMID: 33906164 DOI: 10.1088/1361-648x/abfc11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/27/2021] [Indexed: 06/12/2023]
Abstract
The structure and properties at a finite temperature are critical to understand the temperature effects on energetic materials (EMs). Combining dispersion-corrected density functional theory with quasi-harmonic approximation, the thermodynamic properties for several representative EMs, including nitromethane, PETN, HMX, and TATB, are calculated. The inclusion of zero-point energy and temperature effect could significantly improve the accuracy of lattice parameters at ambient condition; the deviations of calculated cell volumes and experimental values at room temperature are within 0.62%. The calculated lattice parameters and thermal expansion coefficients with increasing temperature show strong anisotropy. In particular, the expansion rate (2.61%) of inter-layer direction of TATB is higher than intra-layer direction and other EMs. Furthermore, the calculated heat capacities could reproduce the experimental trends and enrich the thermodynamic data set at finite temperatures. The predicted isothermal and adiabatic bulk moduli could reflect the softening behavior of EMs. These results would fundamentally provide a deep understanding and serve as a reference for the experimental measurement of the thermodynamic parameters of EMs.
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Affiliation(s)
- Junyu Fan
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams (Dalian University of Technology), Ministry of Education, Dalian 116024, People's Republic of China
- Department of Physics, Taiyuan Normal University, Jinzhong 030619, People's Republic of China
- Institute of Computational and Applied Physics, Taiyuan Normal University, Jinzhong 030619, People's Republic of China
| | - Yan Su
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams (Dalian University of Technology), Ministry of Education, Dalian 116024, People's Republic of China
| | - Zhaoyang Zheng
- National Key Laboratory of Shock Wave and Detonation Physics, Institute of Fluid Physics, China Academy of Engineering Physics, Mianyang 621900, People's Republic of China
| | - Jijun Zhao
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams (Dalian University of Technology), Ministry of Education, Dalian 116024, People's Republic of China
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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] [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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