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Guibourg P, Dontot L, Anglade PM, Gervais B. DFTB Simulation of Charged Clusters Using Machine Learning Charge Inference. J Chem Theory Comput 2024; 20:4007-4018. [PMID: 38690586 DOI: 10.1021/acs.jctc.4c00107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
We present a modification to self-consistent charge density functional-based tight binding (SCC-DFTB), which allows computation based on approximate atomic charges. We obtain these charges by means of a machine learning (ML) process that combines a Coulomb model with a neural network. This allows us to avoid the SCC cycles in the SCC-DFTB calculation while maintaining its accuracy. The main input of the model is the atomic positions characterized by a set of atom-centered symmetry functions. The charge inference from our ML algorithm is as close as 10-2 units of charge from the exact SCC solution. Our ML-DFTB approach provides a good approximation of the density matrix and of the energy and forces with only a single diagonalization. This is a significant computational saving with respect to the complete SCC algorithm, which allows us to investigate a bigger ensemble of atoms. We show the quality of our approach in the case of charged silicon carbide (SiC) clusters. The ML-DFTB potential energy surface (PES) mimics the SCC-DFTB PES rather well, despite its simplicity. This allows us to obtain the same geometric structure ordering with respect to energy for small clusters. The dissociation barriers for ion emission are well-reproduced, which opens the way to investigating ion field emission and charged cluster stability. The ML-DFTB approach is obviously not limited to charged clusters or SiC materials. It opens a new route to investigate larger clusters than those investigated by standard SCC-DFTB, as well as surface and solid-state chemistry at the atomic level.
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Affiliation(s)
- Paul Guibourg
- Laboratoire Cimap, UMR6252─Université de Caen Normandie, École Nationale Supérieure d'Ingénieures de Caen, Commissariat à l'Énergie Atomique, Centre National de la Recherche Scientifique, 6 Boulevard Du Maréchal Juin, 14050 Caen Cedex, France
| | - Léo Dontot
- Laboratoire Cimap, UMR6252─Université de Caen Normandie, École Nationale Supérieure d'Ingénieures de Caen, Commissariat à l'Énergie Atomique, Centre National de la Recherche Scientifique, 6 Boulevard Du Maréchal Juin, 14050 Caen Cedex, France
| | - Pierre-Matthieu Anglade
- Laboratoire Cimap, UMR6252─Université de Caen Normandie, École Nationale Supérieure d'Ingénieures de Caen, Commissariat à l'Énergie Atomique, Centre National de la Recherche Scientifique, 6 Boulevard Du Maréchal Juin, 14050 Caen Cedex, France
| | - Benoit Gervais
- Laboratoire Cimap, UMR6252─Université de Caen Normandie, École Nationale Supérieure d'Ingénieures de Caen, Commissariat à l'Énergie Atomique, Centre National de la Recherche Scientifique, 6 Boulevard Du Maréchal Juin, 14050 Caen Cedex, France
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Lutz JJ, Byrd JN, Lotrich VF, Jensen DS, Zádor J, Hubbard JA. A theoretical investigation of the hydrolysis of uranium hexafluoride: the initiation mechanism and vibrational spectroscopy. Phys Chem Chem Phys 2022; 24:9634-9647. [PMID: 35404371 DOI: 10.1039/d1cp05268c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Depleted uranium hexafluoride (UF6), a stockpiled byproduct of the nuclear fuel cycle, reacts readily with atmospheric humidity, but the mechanism is poorly understood. We compare several potential initiation steps at a consistent level of theory, generating underlying structures and vibrational modes using hybrid density functional theory (DFT) and computing relative energies of stationary points with double-hybrid (DH) DFT. A benchmark comparison is performed to assess the quality of DH-DFT data using reference energy differences obtained using a complete-basis-limit coupled-cluster (CC) composite method. The associated large-basis CC computations were enabled by a new general-purpose pseudopotential capability implemented as part of this work. Dispersion-corrected parameter-free DH-DFT methods, namely PBE0-DH-D3(BJ) and PBE-QIDH-D3(BJ), provided mean unsigned errors within chemical accuracy (1 kcal mol-1) for a set of barrier heights corresponding to the most energetically favorable initiation steps. The hydrolysis mechanism is found to proceed via intermolecular hydrogen transfer within van der Waals complexes involving UF6, UF5OH, and UOF4, in agreement with previous studies, followed by the formation of a previously unappreciated dihydroxide intermediate, UF4(OH)2. The dihydroxide is predicted to form under both kinetic and thermodynamic control, and, unlike the alternate pathway leading to the UO2F2 monomer, its reaction energy is exothermic, in agreement with observation. Finally, harmonic and anharmonic vibrational simulations are performed to reinterpret literature infrared spectroscopy in light of this newly identified species.
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Affiliation(s)
- Jesse J Lutz
- Center for Computing Research (CCR), Sandia National Laboratories, Albuquerque, New Mexico, USA.
| | - Jason N Byrd
- ENSCO, Inc., 4849 North Wickham Road, Melbourne, Florida, 32940, USA
| | - Victor F Lotrich
- ENSCO, Inc., 4849 North Wickham Road, Melbourne, Florida, 32940, USA
| | - Daniel S Jensen
- Center for Computing Research (CCR), Sandia National Laboratories, Albuquerque, New Mexico, USA.
| | - Judit Zádor
- Combustion Research Facility, Sandia National Laboratories, Livermore, California, USA
| | - Joshua A Hubbard
- Center for Computing Research (CCR), Sandia National Laboratories, Albuquerque, New Mexico, USA.
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Persistent Planar Tetracoordinate Carbon in Global Minima Structures of Silicon-Carbon Clusters. ATOMS 2022. [DOI: 10.3390/atoms10010027] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Recently, we reported a series of global minima whose structures consist of carbon rings decorated with heavier group 14 elements. Interestingly, these structures feature planar tetracoordinate carbons (ptCs) and result from the replacement of five or six protons (H+) from the cyclopentadienyl anion (C5H5−) or the pentalene dianion (C8H62−) by three or four E2+ dications (E = Si–Pb), respectively. The silicon derivatives of these series are the Si3C5 and Si4C8 clusters. Here we show that ptC persists in some clusters with an equivalent number of C and Si atoms, i.e., Si5C5, Si8C8, and Si9C9. In all these species, the ptC is embedded in a pentagonal C5 ring and participates in a three-center, two-electron (3c-2e) Si-ptC-Si σ-bond. Furthermore, these clusters are π-aromatic species according to chemical bonding analysis and magnetic criteria.
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The Lowest-Energy Isomer of C2Si2H4 Is a Bridged Ring: Reinterpretation of the Spectroscopic Data Based on DFT and Coupled-Cluster Calculations. INORGANICS 2019. [DOI: 10.3390/inorganics7040051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The lowest-energy isomer of C 2 Si 2 H 4 is determined by high-accuracy ab initio calculations to be the bridged four-membered ring 1,2-didehydro-1,3-disilabicyclo[1.1.0]butane (1), contrary to prior theoretical and experimental studies favoring the three-member ring silylsilacyclopropenylidene (2). These and eight other low-lying minima on the potential energy surface are characterized and ordered by energy using the CCSD(T) method with complete basis set extrapolation, and the resulting benchmark-quality set of relative isomer energies is used to evaluate the performance of several comparatively inexpensive approaches based on many-body perturbation theory and density functional theory (DFT). Double-hybrid DFT methods are found to provide an exceptional balance of accuracy and efficiency for energy-ordering isomers. Free energy profiles are developed to reason the relatively large abundance of isomer 2 observed in previous measurements. Infrared spectra and photolysis reaction mechanisms are modeled for isomers 1 and 2, providing additional insight about previously reported spectra and photoisomerization channels.
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Fantuzzi F, Oliveira RR, Henkes AV, Rubayo-Soneira J, Nascimento MAC. Mechanistic Insights into the Formation of Lithium Fluoride Nanotubes. Chemistry 2019; 25:5269-5279. [PMID: 30868682 DOI: 10.1002/chem.201805991] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/14/2019] [Indexed: 12/07/2022]
Abstract
Born-Oppenheimer molecular dynamics (BOMD) and periodic density functional theory (DFT) calculations have been applied for describing the mechanism of formation of lithium fluoride (LiF) nanotubes with cubic, hexagonal, octagonal, decagonal, dodecagonal, and tetradecagonal cross-sections. It has been shown that high energy structures, such as nanowires, nanorings, nanosheets, and nanopolyhedra are transient species for the formation of stable nanotubes. Unprecedented (LiF)n clusters (n≤12) were also identified, some of them lying less than 10 kcal mol-[1] above their respective global minima. Such findings indicate that stochastic synthetic techniques, such as laser ablation and chemical vapor deposition, should be combined with a template-driven procedure in order to generate the nanotubes with adequate efficiency. Apart from the stepwise growth of LiF units, the formation of nanotubes was also studied by rolling up a planar square sheet monolayer, which could be hypothetically produced from the exfoliation of the FCC crystal structure. It was shown that both pathways could lead to the formation of alkali halide nanotubes, a still unprecedented set of one-dimensional materials.
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Affiliation(s)
- Felipe Fantuzzi
- Instituto de Química, Universidade Federal do Rio de Janeiro (UFRJ), Av. Athos da Silveira Ramos 149, 21941-909, Rio de Janeiro, Brazil.,Current Address: Institute for Inorganic Chemistry, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Ricardo R Oliveira
- Instituto de Química, Universidade Federal do Rio de Janeiro (UFRJ), Av. Athos da Silveira Ramos 149, 21941-909, Rio de Janeiro, Brazil
| | - Aline V Henkes
- Instituto de Química, Universidade Federal do Rio de Janeiro (UFRJ), Av. Athos da Silveira Ramos 149, 21941-909, Rio de Janeiro, Brazil
| | - Jesús Rubayo-Soneira
- Instituto Superior de Tecnologías y Ciencias Aplicadas (InSTEC), Universidad de La Habana, Ave. Salvador Allende No. 1110, Quinta de los Molinos, 10400, La Habana, Cuba
| | - Marco Antonio Chaer Nascimento
- Instituto de Química, Universidade Federal do Rio de Janeiro (UFRJ), Av. Athos da Silveira Ramos 149, 21941-909, Rio de Janeiro, Brazil
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Lutz JJ, Duan XF, Ranasinghe DS, Jin Y, Margraf JT, Perera A, Burggraf LW, Bartlett RJ. Valence and charge-transfer optical properties for some Si nC m( m, n≤ 12) clusters: Comparing TD-DFT, complete-basis-limit EOMCC, and benchmarks from spectroscopy. J Chem Phys 2018; 148:174309. [DOI: 10.1063/1.5022701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Jesse J. Lutz
- Air Force Institute of Technology, Wright-Patterson Air Force Base, Ohio 45433, USA
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
| | - Xiaofeng F. Duan
- Air Force Institute of Technology, Wright-Patterson Air Force Base, Ohio 45433, USA
- Air Force Research Laboratory DoD Supercomputing Resource Center, Wright-Patterson Air Force Base, Ohio 45433, USA
| | | | - Yifan Jin
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
| | - Johannes T. Margraf
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
| | - Ajith Perera
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
| | - Larry W. Burggraf
- Air Force Institute of Technology, Wright-Patterson Air Force Base, Ohio 45433, USA
| | - Rodney J. Bartlett
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
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Margraf JT, Perera A, Lutz JJ, Bartlett RJ. Single-reference coupled cluster theory for multi-reference problems. J Chem Phys 2017; 147:184101. [DOI: 10.1063/1.5003128] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- Johannes T. Margraf
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
| | - Ajith Perera
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
| | - Jesse J. Lutz
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
| | - Rodney J. Bartlett
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
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