1
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Hsiao HW, Narendra N, Kubis T. Long range piezoelectricity effects in van der Waals heterobilayer systems beyond 1000 atoms. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2024; 36:265901. [PMID: 38518366 DOI: 10.1088/1361-648x/ad3708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/22/2024] [Indexed: 03/24/2024]
Abstract
Twist angle is a relevant design and control component for the piezoelectric coefficients of van der Waals (vdW) heterostructures. This theoretical work assesses in high detail the impact of the twist angle on the piezoelectricity of two-dimensional (2D) heterobilayer systems. We expand the density-functional based tight-binding method to predict the piezoelectric coefficients of twisted and corrugated 2D heterobilayer structures with more than 1000 atoms. We showcase the method on hexagonal III-V/transition metal dichalcogenide vdW heterosystems. Our calculations yield a periodic relationship between the in-plane piezoelectric coefficients and the corresponding twist angles, indicating the tunability of the in-plane piezoelectricity. In contrast, the out-of-plane piezoelectricity is not twist angle dependent, but nonlinearly changes with the average interlayer distance.
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Affiliation(s)
- Han-Wei Hsiao
- Elmore Family School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN 47907, United States of America
| | - Namita Narendra
- Elmore Family School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN 47907, United States of America
| | - Tillmann Kubis
- Elmore Family School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN 47907, United States of America
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2
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Vuong VQ, Aradi B, Niklasson AMN, Cui Q, Irle S. Multipole Expansion of Atomic Electron Density Fluctuation Interactions in the Density-Functional Tight-Binding Method. J Chem Theory Comput 2023; 19:7592-7605. [PMID: 37890454 PMCID: PMC10821749 DOI: 10.1021/acs.jctc.3c00778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2023]
Abstract
The accuracy of the density-functional tight-binding (DFTB) method in describing noncovalent interactions is limited due to its reliance on monopole-based spherical charge densities. In this study, we present a multipole-extended second-order DFTB (mDFTB2) method that takes into account atomic dipole and quadrupole interactions. Furthermore, we combine the multipole expansion with the monopole-based third-order contribution, resulting in the mDFTB3 method. To assess the accuracy of mDFTB2 and mDFTB3, we evaluate their performance in describing noncovalent interactions, proton transfer barriers, and dipole moments. Our benchmark results show promising improvements even when using the existing electronic parameters optimized for the original DFTB3 model. Both mDFTB2 and mDFTB3 outperform their monopole-based counterparts, DFTB2 and DFTB3, in terms of accuracy. While mDFTB2 and mDFTB3 perform comparably for neutral and positively charged systems, mDFTB3 exhibits superior performance over mDFTB2 when dealing with negatively charged systems and proton transfers. Overall, the incorporation of the multipole expansion significantly enhances the accuracy of the DFTB method in describing noncovalent interactions and proton transfers.
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Affiliation(s)
- Van-Quan Vuong
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Bálint Aradi
- Bremen Center for Computational Materials Science, Universität Bremen, Bremen 28359, Germany
| | - Anders M N Niklasson
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
- Department of Physics, Boston University, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Stephan Irle
- Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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3
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Ruderman A, Oviedo MB, Paz SA, Leiva EPM. Diversity of Behavior after Collisions of Sn and Si Nanoparticles Found Using a New Density Functional Tight-Binding Method. J Phys Chem A 2023; 127:8955-8965. [PMID: 37831543 DOI: 10.1021/acs.jpca.3c05534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
We present a new approach to studying nanoparticle collisions using density functional based tight binding (DFTB). A novel DFTB parametrization has been developed to study the collision process of Sn and Si clusters (NPs) using molecular dynamics (MD). While bulk structures were used as training sets, we show that our model is able to accurately reproduce the cohesive energy of the nanoparticles using density functional theory (DFT) as a reference. A surprising variety of phenomena are revealed for the Si/Sn nanoparticle collisions, depending on the size and velocity of the collision: from core-shell structure formation to bounce-off phenomena.
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Affiliation(s)
- Andrés Ruderman
- Facultad de Matemática, Astronomía Física y Computación, Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina
- Consejo Nacional de Investigaciones Cientıficas y Técnicas (CONICET), Instituto de Física Enrique Gaviola (IFEG), Córdoba X5000HUA, Argentina
| | - María Belén Oviedo
- Facultad de Ciencias Quımicas, Departamento de Quımica Teórica y Computacional, Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina
- Consejo Nacional de Investigaciones Cientıficas y Técnicas (CONICET), Instituto de Fisicoquımica de Córdoba (INFIQC), Córdoba X5000HUA, Argentina
| | - Sergio Alexis Paz
- Facultad de Ciencias Quımicas, Departamento de Quımica Teórica y Computacional, Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina
- Consejo Nacional de Investigaciones Cientıficas y Técnicas (CONICET), Instituto de Fisicoquımica de Córdoba (INFIQC), Córdoba X5000HUA, Argentina
| | - Ezequiel P M Leiva
- Facultad de Ciencias Quımicas, Departamento de Quımica Teórica y Computacional, Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina
- Consejo Nacional de Investigaciones Cientıficas y Técnicas (CONICET), Instituto de Fisicoquımica de Córdoba (INFIQC), Córdoba X5000HUA, Argentina
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4
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Vuong VQ, Lee KH, Savara AA, Fung V, Irle S. Toward Quantum Chemical Free Energy Simulations of Platinum Nanoparticles on Titania Support. J Chem Theory Comput 2023; 19:6471-6483. [PMID: 37647252 DOI: 10.1021/acs.jctc.3c00661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Platinum nanoparticles (Pt-NPs) supported on titania surfaces are costly but indispensable heterogeneous catalysts because of their highly effective and selective catalytic properties. Therefore, it is vital to understand their physicochemical processes during catalysis to optimize their use and to further develop better catalysts. However, simulating these dynamic processes is challenging due to the need for a reliable quantum chemical method to describe chemical bond breaking and bond formation during the processes but, at the same time, fast enough to sample a large number of configurations required to compute the corresponding free energy surfaces. Density functional theory (DFT) is often used to explore Pt-NPs; nonetheless, it is usually limited to some minimum-energy reaction pathways on static potential energy surfaces because of its high computational cost. We report here a combination of the density functional tight binding (DFTB) method as a fast but reliable approximation to DFT, the steered molecular dynamics (SMD) technique, and the Jarzynski equality to construct free energy surfaces of the temperature-dependent diffusion and growth of platinum particles on a titania surface. In particular, we present the parametrization for Pt-X (X = Pt, Ti, or O) interactions in the framework of the second-order DFTB method, using a previous parametrization for titania as a basis. The optimized parameter set was used to simulate the surface diffusion of a single platinum atom (Pt1) and the growth of Pt6 from Pt5 and Pt1 on the rutile (110) surface at three different temperatures (T = 400, 600, 800 K). The free energy profile was constructed by using over a hundred SMD trajectories for each process. We found that increasing the temperature has a minimal effect on the formation free energy; nevertheless, it significantly reduces the free energy barrier of Pt atom migration on the TiO2 surface and the transition state (TS) of its deposition. In a concluding remark, the methodology opens the pathway to quantum chemical free energy simulations of Pt-NPs' temperature-dependent growth and other transformation processes on the titania support.
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Affiliation(s)
- Van-Quan Vuong
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Ka Hung Lee
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Aditya A Savara
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Victor Fung
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Stephan Irle
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996, United States
- Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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5
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Garrity KF, Choudhary K. Fast and accurate prediction of material properties with three-body tight-binding model for the periodic table. PHYSICAL REVIEW MATERIALS 2023; 7:10.1103/physrevmaterials.7.044603. [PMID: 37274125 PMCID: PMC10236923 DOI: 10.1103/physrevmaterials.7.044603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Parametrized tight-binding models fit to first-principles calculations can provide an efficient and accurate quantum mechanical method for predicting properties of molecules and solids. However, well-tested parameter sets are generally only available for a limited number of atom combinations, making routine use of this method difficult. Furthermore, many previous models consider only simple two-body interactions, which limits accuracy. To tackle these challenges, we develop a density functional theory database of nearly 1 000 000 materials, which we use to fit a universal set of tight-binding parameters for 65 elements and their binary combinations. We include both two-body and three-body effective interaction terms in our model, plus self-consistent charge transfer, enabling our model to work for metallic, covalent, and ionic bonds with the same parameter set. To ensure predictive power, we adopt a learning framework where we repeatedly test the model on new low-energy crystal structures and then add them to the fitting data set, iterating until predictions improve. We distribute the materials database and tools developed in this paper publicly.
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6
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Gao R, Hu Z, Mao J, Chen S, Yam C, Chen G. Self-Consistent-Charge Density-Functional Tight-Binding Parameters for Modeling an All-Solid-State Lithium Battery. J Chem Theory Comput 2023; 19:1381-1387. [PMID: 36812059 DOI: 10.1021/acs.jctc.2c01115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
All-solid-state lithium-ion batteries have been a promising solution for next-generation energy storage due to their safety and potentially high energy density. In this work, we developed a density-functional tight-binding (DFTB) parameter set for modeling solid-state lithium batteries, focusing on the band alignment at electrolyte/electrode interfaces. Despite DFTB being widely applied in the simulation of large-scale systems, parametrization is usually done for single materials, and less attention is paid to band alignment among multiple materials. Band offsets at the electrolyte/electrode interfaces are key quantities determining the performance. Here, an automated global optimization method based on DFTB confinement potentials of all elements is developed, while the band offsets between electrodes and electrolytes are introduced as constraints during the optimization. The parameter set is applied to model an all-solid-state Li/Li2PO2N/LiCoO2 battery, and its electronic structure shows a good agreement with that from density-functional theory (DFT) calculations.
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Affiliation(s)
- Rongzhi Gao
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
| | - Ziyang Hu
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China.,Hong Kong Quantum AI Lab Limited, Hong Kong SAR 999077, China
| | - Jianjun Mao
- Hong Kong Quantum AI Lab Limited, Hong Kong SAR 999077, China
| | - Shuguang Chen
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China.,Hong Kong Quantum AI Lab Limited, Hong Kong SAR 999077, China
| | - ChiYung Yam
- Hong Kong Quantum AI Lab Limited, Hong Kong SAR 999077, China.,Shenzhen Institute for Advanced Study, University of Electronic Science and Technology of China, Shenzhen 518000, China
| | - GuanHua Chen
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China.,Hong Kong Quantum AI Lab Limited, Hong Kong SAR 999077, China
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7
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Kumar A, Arantes PR, Saha A, Palermo G, Wong BM. GPU-Enhanced DFTB Metadynamics for Efficiently Predicting Free Energies of Biochemical Systems. Molecules 2023; 28:molecules28031277. [PMID: 36770943 PMCID: PMC9920250 DOI: 10.3390/molecules28031277] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/17/2023] [Accepted: 01/24/2023] [Indexed: 01/31/2023] Open
Abstract
Metadynamics calculations of large chemical systems with ab initio methods are computationally prohibitive due to the extensive sampling required to simulate the large degrees of freedom in these systems. To address this computational bottleneck, we utilized a GPU-enhanced density functional tight binding (DFTB) approach on a massively parallelized cloud computing platform to efficiently calculate the thermodynamics and metadynamics of biochemical systems. To first validate our approach, we calculated the free-energy surfaces of alanine dipeptide and showed that our GPU-enhanced DFTB calculations qualitatively agree with computationally-intensive hybrid DFT benchmarks, whereas classical force fields give significant errors. Most importantly, we show that our GPU-accelerated DFTB calculations are significantly faster than previous approaches by up to two orders of magnitude. To further extend our GPU-enhanced DFTB approach, we also carried out a 10 ns metadynamics simulation of remdesivir, which is prohibitively out of reach for routine DFT-based metadynamics calculations. We find that the free-energy surfaces of remdesivir obtained from DFTB and classical force fields differ significantly, where the latter overestimates the internal energy contribution of high free-energy states. Taken together, our benchmark tests, analyses, and extensions to large biochemical systems highlight the use of GPU-enhanced DFTB simulations for efficiently predicting the free-energy surfaces/thermodynamics of large biochemical systems.
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Affiliation(s)
- Anshuman Kumar
- Materials Science & Engineering Program, University of California-Riverside, Riverside, CA 92521, USA
| | - Pablo R. Arantes
- Department of Bioengineering, University of California-Riverside, Riverside, CA 92521, USA
| | - Aakash Saha
- Department of Bioengineering, University of California-Riverside, Riverside, CA 92521, USA
| | - Giulia Palermo
- Department of Bioengineering, University of California-Riverside, Riverside, CA 92521, USA
| | - Bryan M. Wong
- Materials Science & Engineering Program, University of California-Riverside, Riverside, CA 92521, USA
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, USA
- Department of Physics & Astronomy, University of California-Riverside, Riverside, CA 92521, USA
- Correspondence:
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8
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Nakai H, Kobayashi M, Yoshikawa T, Seino J, Ikabata Y, Nishimura Y. Divide-and-Conquer Linear-Scaling Quantum Chemical Computations. J Phys Chem A 2023; 127:589-618. [PMID: 36630608 DOI: 10.1021/acs.jpca.2c06965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Fragmentation and embedding schemes are of great importance when applying quantum-chemical calculations to more complex and attractive targets. The divide-and-conquer (DC)-based quantum-chemical model is a fragmentation scheme that can be connected to embedding schemes. This feature article explains several DC-based schemes developed by the authors over the last two decades, which was inspired by the pioneering study of DC self-consistent field (SCF) method by Yang and Lee (J. Chem. Phys. 1995, 103, 5674-5678). First, the theoretical aspects of the DC-based SCF, electron correlation, excited-state, and nuclear orbital methods are described, followed by the two-component relativistic theory, quantum-mechanical molecular dynamics simulation, and the introduction of three programs, including DC-based schemes. Illustrative applications confirmed the accuracy and feasibility of the DC-based schemes.
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Affiliation(s)
- Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo169-8555, Japan.,Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo169-8555, Japan
| | - Masato Kobayashi
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido060-0810, Japan.,Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, Hokkaido001-0021, Japan
| | - Takeshi Yoshikawa
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba274-8510, Japan
| | - Junji Seino
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo169-8555, Japan.,Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo169-8555, Japan
| | - Yasuhiro Ikabata
- Information and Media Center, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi441-8580, Japan.,Department of Computer Science and Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi441-8580, Japan
| | - Yoshifumi Nishimura
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo169-8555, Japan
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9
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Gorges J, Bädorf B, Hansen A, Grimme S. Efficient Computation of the Interaction Energies of Very Large Non-covalently Bound Complexes. Synlett 2022. [DOI: 10.1055/s-0042-1753141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
AbstractWe present a new benchmark set consisting of 16 large non-covalently bound systems (LNCI16) ranging from 380 up to 1988 atoms and featuring diverse interaction motives. Gas-phase interaction energies are calculated with various composite DFT, semi-empirical quantum mechanical (SQM), and force field (FF) methods and are evaluated using accurate DFT reference values. Of the employed QM methods, PBEh-3c proves to be the most robust for large systems with a relative mean absolute deviation (relMAD) of 8.5% with respect to the reference interaction energies. r2SCAN-3c yields an even smaller relMAD, at least for the subset of complexes for which the calculation could be converged, but is less robust for systems with smaller HOMO–LUMO gaps. The inclusion of Fock-exchange is therefore important for the description of very large non-covalent interaction (NCI) complexes in the gas phase. GFN2-xTB was found to be the best performer of the SQM methods with an excellent result of only 11.1% deviation. From the assessed force fields, GFN-FF and GAFF achieve the best accuracy. Considering their low computational costs, both can be recommended for routine calculations of very large NCI complexes, with GFN-FF being clearly superior in terms of general applicability. Hence, GFN-FF may be routinely applied in supramolecular synthesis planning.1 Introduction2 The LNCI16 Benchmark Set3 Computational Details4 Generation of Reference Values5 Results and Discussion6 Conclusions
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10
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Jha G, Heine T. DFTB Parameters for the Periodic Table: Part III, Spin-Orbit Coupling. J Chem Theory Comput 2022; 18:4472-4481. [PMID: 35737969 DOI: 10.1021/acs.jctc.2c00376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Spin-orbit coupling (SOC) is crucially important for the correct description of the electronic structure and transport properties of inorganic semiconductors, and for assessing topological properties as in topological insulators. We present a consistent set of SOC parameters for the density-functional based tight-binding (DFTB) method covering the elements throughout the periodic table. The parameters are based on atomic SOC data calculated at the level of density-functional theory (DFT). We tested these parameters for representative systems with significant SOC, including transition metal dichalcogenide two-dimensional crystals, III-V bulk semiconductors, and topological insulators. Our parameterization opens the door for DFTB-based electronic structure and transport calculations of very large systems, such as twisted van der Waals heterostructures.
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Affiliation(s)
- Gautam Jha
- Helmholtz-Zentrum Dresden-Rossendorf, Institut für Ressourcenökologie, Bautzner Landstraße 400, 01328 Dresden, Germany.,TU Dresden, Fakultät für Chemie und Lebensmittelchemie, Bergstraße 66c, 01062 Dresden, Germany
| | - Thomas Heine
- Helmholtz-Zentrum Dresden-Rossendorf, Institut für Ressourcenökologie, Bautzner Landstraße 400, 01328 Dresden, Germany.,TU Dresden, Fakultät für Chemie und Lebensmittelchemie, Bergstraße 66c, 01062 Dresden, Germany.,Department of Chemistry, Yonsei University, Seodaemun-gu, Seoul120-749, Republic of Korea
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11
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Celik FA, Koksal K, Yilmaz E. The effect of molecular decoration on formation of curved and twisted graphene. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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12
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Chen B, Crespi VH, Hoffmann R. Theoretical Studies of Furan and Thiophene Nanothreads: Structures, Cycloaddition Barriers, and Activation Volumes. J Am Chem Soc 2022; 144:9044-9056. [PMID: 35549167 DOI: 10.1021/jacs.2c01720] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This theoretical study examines the formation, structure, and stability of two of the most ordered nanothreads produced yet, those derived from furan and thiophene. The energetic consequences and activation barriers of the first two steps of oligomerization via a Diels-Alder mechanism were examined. The ca. 20 GPa difference in the synthetic pressures (lower for furan) is explainable in terms of the greater loss of aromaticity by the thiophene. The effects of pressure on the reaction profiles, operating through a volume decrease along the reaction coordinate, are illustrated. The interesting option of polymerization proceeding in one or two directions opens up the possibility of polymers with opposing, cumulative dipole moments. The computed activation volumes are consistently more negative for furan, in accordance with the lower onset pressure of furan polymerization. The energetics of three ordered polymer structures were examined. The syn polymer, with all O/S atoms on the same side, if not allowed to distort, is at a high energy relative to the other two due to the O/S lone pair repulsion, understandably greater for S than for O at the 2.8/2.6 Å separation. Set free, the syn isomers curve or arch in two- or three-dimensional (helical) ways, whose energetics are traced in detail. The syn polymer can also stabilize itself by twisting into zig-zag or helical energy minima. The release of strain in a linear thread as the pressure is relaxed to 1 atm, with consequent thread curving, is a likely mechanism for the observed loss of the crystalline order in the polymer as it is returned to ambient pressure.
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Affiliation(s)
- Bo Chen
- Donostia International Physics Center, Paseo Manuel de Lardizabal, 4, Donostia-San Sebastian 20018, Spain.,Ikerbasque, Basque Foundation for Science, Plaza Euskadi 5, Bilbao 48009, Spain
| | - Vincent H Crespi
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Department of Physics, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Materials Research Institute, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Department of Materials Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Roald Hoffmann
- Baker Laboratory, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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13
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Yusef Buey M, Mineva T, Rapacioli M. Coupling density functional based tight binding with class 1 force fields in a hybrid QM/MM scheme. Theor Chem Acc 2022. [DOI: 10.1007/s00214-022-02878-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Kitheka M, Redington M, Zhang J, Yao Y, Goyal P. BENCHMARKS OF THE DENSITY FUNCTIONAL TIGHT-BINDING METHOD FOR REDOX, PROTONATION AND ELECTRONIC PROPERTIES OF QUINONES. Phys Chem Chem Phys 2022; 24:6742-6756. [DOI: 10.1039/d1cp05333g] [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
Organic materials with controllable molecular design and sustainable resources are promising electrode materials. Crystalline quinones have been investigated in a variety of rechargeable battery chemistries due to their ubiquitous nature,...
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15
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Nurhuda M, Perry CC, Addicoat MA. Performance of GFN1-xTB for periodic optimization of Metal Organic Frameworks. Phys Chem Chem Phys 2022; 24:10906-10914. [DOI: 10.1039/d2cp00184e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Tight-binding approaches bridge the gap between force field methods and Density Functional Theory (DFT). Density Functional Tight Binding (DFTB) has been employed for a wide range of systems containing up...
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16
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Ma X, Rohdenburg M, Knorke H, Kawa S, Liu JKY, Aprà E, Asmis KR, Azov VA, Laskin J, Jenne C, Kenttamaa HI, Warneke J. Binding of Saturated and Unsaturated C6-Hydrocarbons to the Electrophilic Anion [B12Br11]−: A Systematic Mechanistic Study. Phys Chem Chem Phys 2022; 24:21759-21772. [DOI: 10.1039/d2cp01042a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The highly reactive gaseous ion [B12Br11]– is a metal-free closed-shell anion which spontaneously forms covalent bonds with hydrocarbon molecules, including alkanes. Herein, we systematically investigate the reaction mechanism for binding...
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17
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Li Y, Liu Y, Yuan J, Luo Y, Jiang Q, Wang F, Meng J. Molecular Dynamics Simulations of the Thermal Decomposition of 3,4-Bis(3-nitrofurazan-4-yl)furoxan. ACS OMEGA 2021; 6:33470-33481. [PMID: 34926897 PMCID: PMC8674911 DOI: 10.1021/acsomega.1c04166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
When stimulated, for example, by a high temperature, the physical and chemical properties of energetic materials (EMs) may change, and, in turn, their overall performance is affected. Therefore, thermal stability is crucial for EMs, especially the thermal dynamic behavior. In the past decade, significant efforts have been made to study the thermal dynamic behavior of 3,4-bis(3-nitrofurazan-4-yl)furoxan (DNTF), one of the new high-energy-density materials (HEDMs). However, the thermal decomposition mechanism of DNTF is still not specific or comprehensive. In this study, the self-consistent-charge density-functional tight-binding method was combined with molecular dynamics (MD) simulations to reveal the differences in the thermal decomposition of DNTF under four heating conditions. The O-N (O) bond would fracture first during DNTF initial thermal decomposition at medium and low temperatures, thus triggering the cracking of the whole structure. At 2000 and 2500 K, NO2 loss on outer ring I is the fastest initial thermal decomposition pathway, and it determines that the decomposition mechanism is different from that of a medium-low temperature. NO2 is found to be the most active intermediate product; large molecular fragments, such as C2N2O, are found for the first time. Hopefully, these results could provide some insights into the decomposition mechanism of new HEDMs.
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Affiliation(s)
- Yang Li
- School of Environment and Safety Engineering, North University of China, Taiyuan 030051, China
| | - Yucun Liu
- School of Environment and Safety Engineering, North University of China, Taiyuan 030051, China
| | - Junming Yuan
- School of Environment and Safety Engineering, North University of China, Taiyuan 030051, China
| | - Yiming Luo
- Xi'an Modern Chemistry Research Institute, Xi'an, Shaanxi 710065, China
| | - Qiuli Jiang
- Xi'an Modern Chemistry Research Institute, Xi'an, Shaanxi 710065, China
| | - Fanfan Wang
- School of Environment and Safety Engineering, North University of China, Taiyuan 030051, China
- Institute of Chemical Materials, China Academy of Engineering Physics (CAEP), P. O. Box 919-311, Mianyang, Sichuan 621900, China
| | - Jingwei Meng
- School of Environment and Safety Engineering, North University of China, Taiyuan 030051, China
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18
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Oshiki J, Nakano H, Sato H. Controlling potential difference between electrodes based on self-consistent-charge density functional tight binding. J Chem Phys 2021; 154:144107. [PMID: 33858148 DOI: 10.1063/5.0047992] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A proper understanding and description of the electronic response of the electrode surfaces in electrochemical systems are quite important because the interactions between the electrode surface and electrolyte give rise to unique and useful interfacial properties. Atomistic modeling of the electrodes requires not only an accurate description of the electronic response under a constant-potential condition but also computational efficiency in order to deal with systems large enough to investigate the interfacial electrolyte structures. We thus develop a self-consistent-charge density functional tight binding based method to model a pair of electrodes in electrochemical cells under the constant-potential condition. The method is more efficient than the (ab initio) density functional theory calculations so that it can treat systems as large as those studied in classical atomistic simulations. It can also describe the electronic response of electrodes quantum mechanically and more accurately than the classical counterparts. The constant-potential condition is introduced through a Legendre transformation of the electronic energy with respect to the difference in the number of electrons in the two electrodes and their electrochemical potential difference, through which the Kohn-Sham equations for each electrode are variationally derived. The method is applied to platinum electrodes faced parallel to each other under an applied voltage. The electronic response to the voltage and a charged particle is compared with the result of a classical constant-potential method based on the chemical potential equalization principle.
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Affiliation(s)
- Jun Oshiki
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Hiroshi Nakano
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
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19
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Ammothum Kandy AK, Wadbro E, Aradi B, Broqvist P, Kullgren J. Curvature Constrained Splines for DFTB Repulsive Potential Parametrization. J Chem Theory Comput 2021; 17:1771-1781. [PMID: 33606527 PMCID: PMC8023658 DOI: 10.1021/acs.jctc.0c01156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The Curvature Constrained
Splines (CCS) methodology has been used
for fitting repulsive potentials to be used in SCC-DFTB calculations.
The benefit of using CCS is that the actual fitting of the repulsive
potential is performed through quadratic programming on a convex objective
function. This guarantees a unique (for strictly convex) and optimum
two-body repulsive potential in a single shot, thereby making the
parametrization process robust, and with minimal human effort. Furthermore,
the constraints in CCS give the user control to tune the shape of
the repulsive potential based on prior knowledge about the system
in question. Herein, we developed the method further with new constraints
and the capability to handle sparse data. We used the method to generate
accurate repulsive potentials for bulk Si polymorphs and demonstrate
that for a given Slater-Koster table, which reproduces the experimental
band structure for bulk Si in its ground state, we are unable to find
one single two-body repulsive potential that can accurately describe
the various bulk polymorphs of silicon in our training set. We further
demonstrate that to increase transferability, the repulsive potential
needs to be adjusted to account for changes in the chemical environment,
here expressed in the form of a coordination number. By training a
near-sighted Atomistic Neural Network potential, which includes many-body
effects but still essentially within the first-neighbor shell, we
can obtain full transferability for SCC-DFTB in terms of describing
the energetics of different Si polymorphs.
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Affiliation(s)
| | - Eddie Wadbro
- Department of Computing Science, Umeå University, Umeå SE-901 87, Sweden
| | - Bálint Aradi
- Bremen Center for Computational Materials Science, University of Bremen, Am Fallturm 1, 28359 Bremen, Germany
| | - Peter Broqvist
- Department of Chemistry - Ångström Laboratory, Uppsala University, Box 538, 751 21 Uppsala, Sweden
| | - Jolla Kullgren
- Department of Chemistry - Ångström Laboratory, Uppsala University, Box 538, 751 21 Uppsala, Sweden
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20
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Panosetti C, Anniés SB, Grosu C, Seidlmayer S, Scheurer C. DFTB Modeling of Lithium-Intercalated Graphite with Machine-Learned Repulsive Potential. J Phys Chem A 2021; 125:691-699. [PMID: 33426892 DOI: 10.1021/acs.jpca.0c09388] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lithium ion batteries have been a central part of consumer electronics for decades. More recently, they have also become critical components in the quickly arising technological fields of electric mobility and intermittent renewable energy storage. However, many fundamental principles and mechanisms are not yet understood to a sufficient extent to fully realize the potential of the incorporated materials. The vast majority of concurrent lithium ion batteries make use of graphite anodes. Their working principle is based on intercalation, the embedding and ordering of (lithium-) ions in two-dimensional spaces between the graphene sheets. This important process, it yields the upper bound to a battery's charging speed and plays a decisive role in its longevity, is characterized by multiple phase transitions, ordered and disordered domains, as well as nonequilibrium phenomena, and therefore quite complex. In this work, we provide a simulation framework for the purpose of better understanding lithium-intercalated graphite and its behavior during use in a battery. To address large system sizes and long time scales required to investigate said effects, we identify the highly efficient, but semiempirical density functional tight binding (DFTB) as a suitable approach and combine particle swarm optimization (PSO) with the machine learning (ML) procedure Gaussian process regression (GPR) as implemented in the recently developed GPrep package for DFTB repulsion fitting to obtain the necessary parameters. Using the resulting parametrization, we are able to reproduce experimental reference structures at a level of accuracy which is in no way inferior to much more costly ab initio methods. We finally present structural properties and diffusion barriers for some exemplary system states.
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Affiliation(s)
- Chiara Panosetti
- Department of Chemistry, Technische Universität München, Lichtenbergstr. 4, 85748 Garching b. München, Germany
| | - Simon B Anniés
- Department of Chemistry, Technische Universität München, Lichtenbergstr. 4, 85748 Garching b. München, Germany
| | - Cristina Grosu
- Department of Chemistry, Technische Universität München, Lichtenbergstr. 4, 85748 Garching b. München, Germany.,Institute of Energy and Climate Research (IEK-9), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Stefan Seidlmayer
- Heinz Maier-Leibnitz Zentrum (MLZ), Technische Universität München, Lichtenbergstr. 1, 85748 Garching b. München, Germany
| | - Christoph Scheurer
- Department of Chemistry, Technische Universität München, Lichtenbergstr. 4, 85748 Garching b. München, Germany
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21
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Bačić V, Heine T, Kuc A. Analytical approach to phonon calculations in the SCC-DFTB framework. J Chem Phys 2020; 153:144109. [PMID: 33086809 DOI: 10.1063/5.0023666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Detailed derivation of the analytical, reciprocal-space approach of Hessian calculation within the self-consistent-charge density-functional based tight-binding framework (SCC-DFTB) is presented. This approach provides an accurate and efficient way for obtaining the SCC-DFTB Hessian of periodic systems. Its superiority with respect to the traditional numerical force differentiation method is demonstrated for doped graphene, graphene nanoribbons, boron-nitride nanotubes, bulk zinc-oxide, and other systems.
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Affiliation(s)
- Vladimir Bačić
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Thomas Heine
- Helmholtz-Zentrum Dresden-Rossendorf, Abteilung Ressourcenökologie, Forschungsstelle Leipzig, Permoserstr. 15, 04318 Leipzig, Germany
| | - Agnieszka Kuc
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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22
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Pérez‐Jiménez ÁJ, Sancho‐García JC. Theoretical Insights for Materials Properties of Cyclic Organic Nanorings. ADVANCED THEORY AND SIMULATIONS 2020. [DOI: 10.1002/adts.202000110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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23
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Peels M, Knizia G. Fast Evaluation of Two-Center Integrals over Gaussian Charge Distributions and Gaussian Orbitals with General Interaction Kernels. J Chem Theory Comput 2020; 16:2570-2583. [PMID: 32040326 DOI: 10.1021/acs.jctc.9b01296] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We present efficient algorithms for computing two-center integrals and integral derivatives, with general interaction kernels K(r12), over Gaussian charge distributions of general angular momenta l. While formulated in terms of traditional ab initio integration techniques, full derivations and required secondary information, as well as a reference implementation, are provided to make the content accessible to other fields. Concretely, the presented algorithms are based on an adaption of the McMurchie-Davidson Recurrence Relation (MDRR) combined with analytical properties of the solid harmonic transformation; this obviates all intermediate recurrences except the adapted MDRR itself, and allows it to be applied to fully contracted auxiliary kernel integrals. The technique is particularly well-suited for semiempirical molecular orbital methods, where it can serve as a more general and efficient replacement of Slater-Koster tables, and for first-principles quantum chemistry methods employing density fitting. But the formalism's high efficiency and ability of handling general interaction kernels K(r12) and multipolar Gaussian charge distributions may also be of interest for modeling electrostatic interactions and short-range exchange and charge penetration effects in classical force fields and model potentials. With the presented technique, a 4894 × 4894 univ-JKFIT Coulomb matrix JAB = (A|1/r12|B) (183 MiB) can be computed in 50 ms on a Q2'2018 notebook CPU, without any screening or approximations.
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Affiliation(s)
- Mieke Peels
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Gerald Knizia
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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24
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Panosetti C, Engelmann A, Nemec L, Reuter K, Margraf JT. Learning to Use the Force: Fitting Repulsive Potentials in Density-Functional Tight-Binding with Gaussian Process Regression. J Chem Theory Comput 2020; 16:2181-2191. [DOI: 10.1021/acs.jctc.9b00975] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Chiara Panosetti
- Chair for Theoretical Chemistry, Technical University of Munich, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Artur Engelmann
- Chair for Theoretical Chemistry, Technical University of Munich, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Lydia Nemec
- Chair for Theoretical Chemistry, Technical University of Munich, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Karsten Reuter
- Chair for Theoretical Chemistry, Technical University of Munich, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Johannes T. Margraf
- Chair for Theoretical Chemistry, Technical University of Munich, Lichtenbergstr. 4, D-85747 Garching, Germany
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25
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Aguirre NF, Morgenstern A, Cawkwell MJ, Batista ER, Yang P. Development of Density Functional Tight-Binding Parameters Using Relative Energy Fitting and Particle Swarm Optimization. J Chem Theory Comput 2020; 16:1469-1481. [DOI: 10.1021/acs.jctc.9b00880] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Néstor F. Aguirre
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Amanda Morgenstern
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - M. J. Cawkwell
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Enrique R. Batista
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Ping Yang
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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26
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Spiegelman F, Tarrat N, Cuny J, Dontot L, Posenitskiy E, Martí C, Simon A, Rapacioli M. Density-functional tight-binding: basic concepts and applications to molecules and clusters. ADVANCES IN PHYSICS: X 2020; 5:1710252. [PMID: 33154977 PMCID: PMC7116320 DOI: 10.1080/23746149.2019.1710252] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/19/2019] [Indexed: 06/10/2023] Open
Abstract
The scope of this article is to present an overview of the Density Functional based Tight Binding (DFTB) method and its applications. The paper introduces the basics of DFTB and its standard formulation up to second order. It also addresses methodological developments such as third order expansion, inclusion of non-covalent interactions, schemes to solve the self-interaction error, implementation of long-range short-range separation, treatment of excited states via the time-dependent DFTB scheme, inclusion of DFTB in hybrid high-level/low level schemes (DFT/DFTB or DFTB/MM), fragment decomposition of large systems, large scale potential energy landscape exploration with molecular dynamics in ground or excited states, non-adiabatic dynamics. A number of applications are reviewed, focusing on -(i)- the variety of systems that have been studied such as small molecules, large molecules and biomolecules, bare orfunctionalized clusters, supported or embedded systems, and -(ii)- properties and processes, such as vibrational spectroscopy, collisions, fragmentation, thermodynamics or non-adiabatic dynamics. Finally outlines and perspectives are given.
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Affiliation(s)
- Fernand Spiegelman
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
| | - Nathalie Tarrat
- CEMES, Université de Toulouse (UPS), CNRS, UPR8011, Toulouse, Toulouse, France
| | - Jérôme Cuny
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
| | - Leo Dontot
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
| | - Evgeny Posenitskiy
- Laboratoire Collisions Agrégats et Réactivité LCAR/IRSAMC, UMR5589, Université de Toulouse (UPS) and CNRS, Toulouse, France
| | - Carles Martí
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
- Laboratoire de Chimie, UMR5182, Ecole Normale Supérieure de Lyon, Université de Lyon and CNRS, Lyon, France
| | - Aude Simon
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
| | - Mathias Rapacioli
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
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27
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Uratani H, Chou CP, Nakai H. Quantum mechanical molecular dynamics simulations of polaron formation in methylammonium lead iodide perovskite. Phys Chem Chem Phys 2020; 22:97-106. [DOI: 10.1039/c9cp04739e] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Polaron formation in a halide perovskite is analyzed via nanometre-scale quantum mechanical molecular dynamics simulations.
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Affiliation(s)
- Hiroki Uratani
- Department of Chemistry and Biochemistry
- School of Advanced Science and Engineering
- Waseda University
- Shinjuku-ku
- Japan
| | - Chien-Pin Chou
- Waseda Research Institute for Science and Engineering (WISE)
- Tokyo 169-8555
- Japan
| | - Hiromi Nakai
- Department of Chemistry and Biochemistry
- School of Advanced Science and Engineering
- Waseda University
- Shinjuku-ku
- Japan
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28
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Lü XL, Zhang CX, Wang WJ, Cheng X, Xie H. Excitation and phase transitions of spin density waves in graphene nanoribbons. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:455501. [PMID: 31315099 DOI: 10.1088/1361-648x/ab32ff] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Anti-ferromagnetic states widely exist on graphene zigzag edges. Our previous work (Xie et al 2018 New J. Phys. 20 013035) shows there are also various spin density wave (SDW) states in the graphene nanoribbons (GNR). In this paper, we propose some excitation mechanism of these SDW by the absorbed magnetic atoms with the mean-field Hubbard model and the first-principles calculations. With the Floquet theory, we also find that by regulating the temperature or the light intensity, there are a lot of phase transitions for these SDW. The temperature or light can dramatically modify the inter-edge coupling or the spin stiffness of GNR. The artificial magnetization technique is employed to explore the establishment process of these SDW states. Some interesting intermedia phase transitions and the corresponding spin orders are discovered. This research may be helpful in the understandings and technique controls of magnetic orders in future nano magnetic devices.
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Affiliation(s)
- Xiao-Long Lü
- Department of Physics, Chongqing University, Chongqing 401331, People's Republic of China
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29
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Examination of the performance of semiempirical methods in QM/MM studies of the SN2-like reaction of an adenylyl group transfer catalysed by ANT4′. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2507-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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30
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Gregory KP, Webber GB, Wanless EJ, Page AJ. Lewis Strength Determines Specific-Ion Effects in Aqueous and Nonaqueous Solvents. J Phys Chem A 2019; 123:6420-6429. [DOI: 10.1021/acs.jpca.9b04004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kasimir P. Gregory
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Grant B. Webber
- School of Engineering, The University of Newcastle, Callaghan, New South Wales 2308, Australia
- Priority Research Centre for Advanced Particle Processing and Transport, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Erica J. Wanless
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales 2308, Australia
- Priority Research Centre for Advanced Particle Processing and Transport, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Alister J. Page
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales 2308, Australia
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31
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Podeszwa R, Jankiewicz W, Krzuś M, Witek HA. Correcting long-range electrostatics in DFTB. J Chem Phys 2019; 150:234110. [DOI: 10.1063/1.5099694] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Rafał Podeszwa
- Institute of Chemistry, University of Silesia, Szkolna 9, 41-006 Katowice, Poland
| | - Wojciech Jankiewicz
- Institute of Chemistry, University of Silesia, Szkolna 9, 41-006 Katowice, Poland
| | - Magdalena Krzuś
- Institute of Chemistry, University of Silesia, Szkolna 9, 41-006 Katowice, Poland
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Henryk A. Witek
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, 1001 University Rd., Hsinchu 30010, Taiwan
- Center for Emergent Functional Matter Science, National Chiao Tung University, 1001 University Rd., Hsinchu 30010, Taiwan
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32
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Lee J, Ganguli S, Roy AK, Badescu SC. Density functional tight binding study of β-Ga 2O 3: Electronic structure, surface energy, and native point defects. J Chem Phys 2019; 150:174706. [PMID: 31067881 DOI: 10.1063/1.5088941] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A new parameter set to model monoclinic gallium oxide, β-Ga2O3, with the density functional tight binding (DFTB) method is developed. Using this new parameter set, DFTB calculations of bulk electronic band structure, surface energy of low-index surfaces, and formation energy of native point vacancy defects are performed and compared with the state-of-the-art density functional theory (DFT) calculations using the advanced hybrid exchange correlation functional. DFTB calculates the bandgap energy of 4.87 eV around the Fermi energy with the conduction band approximately following the DFT study by Peelaers and Van de Walle [Phys. Status Solidi B 252, 828 (2015)]. The surface energies calculated feature the correct order of stability among low index surfaces with surface energies in semiquantitative agreement with Bermudez' report [Chem. Phys. 323, 193 (2006)]. Oxygen and gallium vacancy defect formation energies and respective transition levels calculated using DFTB with a new parameter set are in semiquantitative agreement with the previous DFT reports by Varley et al. and Zacherle et al. [Appl. Phys. Lett. 97, 142106 (2010); Phys. Rev. B 87, 235206 (2013)]. This new semiempirical parameter set for β-Ga2O3, validated in bulk, surface, and point properties, would be useful for large spatiotemporal quantum chemical calculations regarding β-Ga2O3.
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Affiliation(s)
- Jonghoon Lee
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, USA
| | - Sabyasachi Ganguli
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, USA
| | - Ajit K Roy
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, USA
| | - Stefan C Badescu
- Sensors Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, USA
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33
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Yeo BC, Kim D, Kim C, Han SS. Pattern Learning Electronic Density of States. Sci Rep 2019; 9:5879. [PMID: 30971723 PMCID: PMC6458116 DOI: 10.1038/s41598-019-42277-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 03/28/2019] [Indexed: 11/25/2022] Open
Abstract
Electronic density of states (DOS) is a key factor in condensed matter physics and material science that determines the properties of metals. First-principles density-functional theory (DFT) calculations have typically been used to obtain the DOS despite the considerable computation cost. Herein, we report a fast machine learning method for predicting the DOS patterns of not only bulk structures but also surface structures in multi-component alloy systems by a principal component analysis. Within this framework, we use only four features to define the composition, atomic structure, and surfaces of alloys, which are the d-orbital occupation ratio, coordination number, mixing factor, and the inverse of miller indices. While the DFT method scales as O(N3) in which N is the number of electrons in the system size, our pattern learning method can be independent on the number of electrons. Furthermore, our method provides a pattern similarity of 91 ~ 98% compared to DFT calculations. This reveals that our learning method will be an alternative that can break the trade-off relationship between accuracy and speed that is well known in the field of electronic structure calculations.
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Affiliation(s)
- Byung Chul Yeo
- Computational Science Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Donghun Kim
- Computational Science Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Chansoo Kim
- Computational Science Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Sang Soo Han
- Computational Science Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea.
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Constantin LA, Fabiano E, Della Sala F. Performance of Semilocal Kinetic Energy Functionals for Orbital-Free Density Functional Theory. J Chem Theory Comput 2019; 15:3044-3055. [DOI: 10.1021/acs.jctc.9b00183] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lucian A. Constantin
- Center for Biomolecular Nanotechnologies @UNILE, Istituto Italiano di Tecnologia, Via Barsanti, I-73010 Arnesano, Italy
| | - Eduardo Fabiano
- Center for Biomolecular Nanotechnologies @UNILE, Istituto Italiano di Tecnologia, Via Barsanti, I-73010 Arnesano, Italy
- Institute for Microelectronics and Microsystems (CNR-IMM), Campus Unisalento, Via Monteroni, 73100 Lecce, Italy
| | - Fabio Della Sala
- Center for Biomolecular Nanotechnologies @UNILE, Istituto Italiano di Tecnologia, Via Barsanti, I-73010 Arnesano, Italy
- Institute for Microelectronics and Microsystems (CNR-IMM), Campus Unisalento, Via Monteroni, 73100 Lecce, Italy
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35
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Leal W, Restrepo G. Formal structure of periodic system of elements. Proc Math Phys Eng Sci 2019; 475:20180581. [PMID: 31105446 DOI: 10.1098/rspa.2018.0581] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 02/25/2019] [Indexed: 02/05/2023] Open
Abstract
For more than 150 years, the structure of the periodic system of the chemical elements has intensively motivated research in different areas of chemistry and physics. However, there is still no unified picture of what a periodic system is. Herein, based on the relations of order and similarity, we report a formal mathematical structure for the periodic system, which corresponds to an ordered hypergraph. It is shown that the current periodic system of chemical elements is an instance of the general structure. The definition is used to devise a tailored periodic system of polarizability of single covalent bonds, where order relationships are quantified within subsets of similar bonds and among these classes. The generalized periodic system allows envisioning periodic systems in other disciplines of science and humanities.
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Affiliation(s)
- Wilmer Leal
- Bioinformatics Group, Department of Computer Science, Leipzig University, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
| | - Guillermo Restrepo
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
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36
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Chou CP, Sakti AW, Nishimura Y, Nakai H. Development of Divide-and-Conquer Density-Functional Tight-Binding Method for Theoretical Research on Li-Ion Battery. CHEM REC 2019; 19:746-757. [PMID: 30462370 DOI: 10.1002/tcr.201800141] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/25/2018] [Accepted: 10/26/2018] [Indexed: 01/24/2023]
Abstract
The density-functional tight-binding (DFTB) method is one of the useful quantum chemical methods, which provides a good balance between accuracy and computational efficiency. In this account, we reviewed the basis of the DFTB method, the linear-scaling divide-and-conquer (DC) technique, as well as the parameterization process. We also provide some refinement, modifications, and extension of the existing parameters that can be applicable for lithium-ion battery systems. The diffusion constants of common electrolyte molecules and LiTFSA salt in solution have been estimated using DC-DFTB molecular dynamics simulation with our new parameters. The resulting diffusion constants have good agreement to the experimental diffusion constants.
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Affiliation(s)
- Chien-Pin Chou
- Waseda Research Institute for Science and Engineering (WISE), Waseda University, Tokyo, 169-8555, Japan
| | - Aditya Wibawa Sakti
- Element Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Kyotodaigaku-Katsura, Kyoto, 615-8520, Japan
| | - Yoshifumi Nishimura
- Waseda Research Institute for Science and Engineering (WISE), Waseda University, Tokyo, 169-8555, Japan
| | - Hiromi Nakai
- Waseda Research Institute for Science and Engineering (WISE), Waseda University, Tokyo, 169-8555, Japan.,Element Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Kyotodaigaku-Katsura, Kyoto, 615-8520, Japan.,Department of Chemistry and Biochemistry, School of Advanced Science and Enigineering, Waseda University, Tokyo, 169-8555, Japan
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37
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Cawkwell MJ, Perriot R. Transferable density functional tight binding for carbon, hydrogen, nitrogen, and oxygen: Application to shock compression. J Chem Phys 2019; 150:024107. [DOI: 10.1063/1.5063385] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- M. J. Cawkwell
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - R. Perriot
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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38
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Pisarev SA, Shulga DA, Palyulin VA, Zefirov NS. Lone pairs vs. covalent bonds: conformational effects in bicyclo[3.3.1]nonane derivatives. Struct Chem 2018. [DOI: 10.1007/s11224-018-1240-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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39
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Li H, Collins C, Tanha M, Gordon GJ, Yaron DJ. A Density Functional Tight Binding Layer for Deep Learning of Chemical Hamiltonians. J Chem Theory Comput 2018; 14:5764-5776. [PMID: 30351008 DOI: 10.1021/acs.jctc.8b00873] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Current neural networks for predictions of molecular properties use quantum chemistry only as a source of training data. This paper explores models that use quantum chemistry as an integral part of the prediction process. This is done by implementing self-consistent-charge Density-Functional-Tight-Binding (DFTB) theory as a layer for use in deep learning models. The DFTB layer takes, as input, Hamiltonian matrix elements generated from earlier layers and produces, as output, electronic properties from self-consistent field solutions of the corresponding DFTB Hamiltonian. Backpropagation enables efficient training of the model to target electronic properties. Two types of input to the DFTB layer are explored, splines and feed-forward neural networks. Because overfitting can cause models trained on smaller molecules to perform poorly on larger molecules, regularizations are applied that penalize nonmonotonic behavior and deviation of the Hamiltonian matrix elements from those of the published DFTB model used to initialize the model. The approach is evaluated on 15 700 hydrocarbons by comparing the root-mean-square error in energy and dipole moment, on test molecules with eight heavy atoms, to the error from the initial DFTB model. When trained on molecules with up to seven heavy atoms, the spline model reduces the test error in energy by 60% and in dipole moments by 42%. The neural network model performs somewhat better, with error reductions of 67% and 59%, respectively. Training on molecules with up to four heavy atoms reduces performance, with both the spline and neural net models reducing the test error in energy by about 53% and in dipole by about 25%.
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40
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Sorkin V, Zhang YW. Mechanical properties of pristine and defective carbon-phosphide monolayers: a density functional tight-binding study. NANOTECHNOLOGY 2018; 29:435707. [PMID: 30102243 DOI: 10.1088/1361-6528/aad9e8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Using density functional tight-binding theory, we investigated the elastic properties and deformation and failure behaviors of pristine and defective carbon-phosphide (CP) monolayers subjected to uniform uniaxial tensile strain along arm-chair (AC) and zig-zag (ZZ) directions. Two variants of CP (α-CP and β-CP) were studied and two types of carbon and phosphorous vacancies (single and double) were considered. It was found that carbon monovacancies have the lowest formation energy, while phosphorous divacancies have the highest one in both CP allotropes. A strong mechanical anisotropy for CP was found with the Young's modulus and the failure stress along ZZ direction being an order of magnitude larger than those along AC direction. In both allotropes, the Young's modulus, failure stress and strain are considerably affected by vacancies, especially along AC direction. Fracture of pristine CP monolayer occurred via the rupture of phosphorous-phosphorous bonds when CP monolayer is stretched along AC direction, while via the rupture of carbon-phosphorous bonds when stretched along ZZ direction. Defective α-CP and β-CP monolayers both undergo a brittle-like failure initiated around the hosted vacancies at a lower critical strain. The failure strain and stress along the AC direction are affected only by phosphorous vacancies, while along the ZZ direction, they are almost equally affected by both phosphorous and carbon vacancies. These understandings may provide useful guidelines for potential applications of CP monolayers in nanoelectromechanical systems.
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41
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Seibert J, Pisarek J, Schmitz S, Bannwarth C, Grimme S. Extension of the element parameter set for ultra-fast excitation spectra calculation (sTDA-xTB). Mol Phys 2018. [DOI: 10.1080/00268976.2018.1510141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Jakob Seibert
- Mulliken Center for Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Jana Pisarek
- Mulliken Center for Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Sarah Schmitz
- Mulliken Center for Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Christoph Bannwarth
- Mulliken Center for Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, University of Bonn, Bonn, Germany
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42
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Cuny J, Tarrat N, Spiegelman F, Huguenot A, Rapacioli M. Density-functional tight-binding approach for metal clusters, nanoparticles, surfaces and bulk: application to silver and gold. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:303001. [PMID: 29916820 DOI: 10.1088/1361-648x/aacd6c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Density-functional based tight-binding (DFTB) is an efficient quantum mechanical method that can describe a variety of systems, going from organic and inorganic compounds to metallic and hybrid materials. The present topical review addresses the ability and performance of DFTB to investigate energetic, structural, spectroscopic and dynamical properties of gold and silver materials. After a brief overview of the theoretical basis of DFTB, its parametrization and its transferability, we report its past and recent applications to gold and silver systems, including small clusters, nanoparticles, bulk and surfaces, bare and interacting with various organic and inorganic compounds. The range of applications covered by those studies goes from plasmonics and molecular electronics, to energy conversion and surface chemistry. Finally, perspectives of DFTB in the field of gold and silver surfaces and NPs are outlined.
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Affiliation(s)
- Jérôme Cuny
- Laboratoire de Chimie et Physique Quantiques (LCPQ), Université de Toulouse III [UPS] and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
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43
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Sorkin V, Zhang YW. Effect of vacancies on the mechanical properties of phosphorene nanotubes. NANOTECHNOLOGY 2018; 29:235707. [PMID: 29547132 DOI: 10.1088/1361-6528/aab749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Using density functional tight-binding method, we studied the mechanical properties, deformation and failure of armchair (AC) and zigzag (ZZ) phosphorene nanotubes (PNTs) with monovacancies and divacancies subjected to uniaxial tensile strain. We found that divacancies in AC PNTs and monovacancies in ZZ PNTs possess the lowest vacancy formation energy, which decreases with the tube diameter in AC PNTs and increases in ZZ PNTs. The Young's modulus is reduced, while the radial and thickness Poisson's ratios are increased by hosted vacancies. In defective AC PNTs, deformation involves fracture of the intra-pucker bonds and formation of the new inter-pucker bonds at a critical strain, and the most stretched bonds around the vacancy rupture first, triggering a sequence of the structural transformations terminated by the ultimate failure. The critical strain of AC PNTs is reduced significantly by hosted vacancies, whereas their effect on the critical stress is relatively weaker. Defective ZZ PNTs fail in a brittle-like manner once the most stretched bonds around a vacancy rupture, and vacancies are able to significantly reduce the failure strain but only moderately reduce the failure stress of ZZ PNTs. The understandings revealed here on the mechanical properties and the deformation and failure mechanisms of PNTs provide useful guidelines for their design and fabrication as building blocks in nanodevices.
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44
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Huran AW, Steigemann C, Frauenheim T, Aradi B, Marques MAL. Efficient Automatized Density-Functional Tight-Binding Parametrizations: Application to Group IV Elements. J Chem Theory Comput 2018; 14:2947-2954. [DOI: 10.1021/acs.jctc.7b01269] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ahmad W. Huran
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Conrad Steigemann
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | | | - Bálint Aradi
- BCCMS, University of Bremen, 28359 Bremen, Germany
| | - Miguel A. L. Marques
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
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45
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Van den Bossche M, Grönbeck H, Hammer B. Tight-Binding Approximation-Enhanced Global Optimization. J Chem Theory Comput 2018; 14:2797-2807. [DOI: 10.1021/acs.jctc.8b00039] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Maxime Van den Bossche
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
- Science Institute and Faculty of Physical Sciences, University of Iceland, 107 Reykjavík, Iceland
| | - Henrik Grönbeck
- Department of Physics and Competence Centre for Catalysis, Chalmers University of Technology, 412 58 Göteborg, Sweden
| | - Bjørk Hammer
- Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus, Denmark
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46
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Kowsalya PS, Bhuvanesh NSP, Neelakantan MA. Chemical Reactivity and Quantifying the Intra- and Intermolecular Interactions in Zwitterionic Compounds. ChemistrySelect 2018. [DOI: 10.1002/slct.201702730] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Perumal samy Kowsalya
- Chemistry Research Centre; National Engineering College, K.R. Nagar; Kovilpatti 628 503, Thoothukudi District, Tamil Nadu India
| | | | - Mallanpillai A. Neelakantan
- Chemistry Research Centre; National Engineering College, K.R. Nagar; Kovilpatti 628 503, Thoothukudi District, Tamil Nadu India
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47
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Krishnapriyan A, Yang P, Niklasson AMN, Cawkwell MJ. Numerical Optimization of Density Functional Tight Binding Models: Application to Molecules Containing Carbon, Hydrogen, Nitrogen, and Oxygen. J Chem Theory Comput 2017; 13:6191-6200. [DOI: 10.1021/acs.jctc.7b00762] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- A. Krishnapriyan
- Department
of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
- Theoretical
Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - P. Yang
- Theoretical
Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - A. M. N. Niklasson
- Theoretical
Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - M. J. Cawkwell
- Theoretical
Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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48
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Gruss D, Smolyanitsky A, Zwolak M. Communication: Relaxation-limited electronic currents in extended reservoir simulations. J Chem Phys 2017; 147:141102. [PMID: 29031250 PMCID: PMC5718372 DOI: 10.1063/1.4997022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Open-system approaches are gaining traction in the simulation of charge transport in nanoscale and molecular electronic devices. In particular, "extended reservoir" simulations, where explicit reservoir degrees of freedom are present, allow for the computation of both real-time and steady-state properties but require relaxation of the extended reservoirs. The strength of this relaxation, γ, influences the conductance, giving rise to a "turnover" behavior analogous to Kramers turnover in chemical reaction rates. We derive explicit, general expressions for the weak and strong relaxation limits. For weak relaxation, the conductance increases linearly with γ and every electronic state of the total explicit system contributes to the electronic current according to its "reduced" weight in the two extended reservoir regions. Essentially, this represents two conductors in series-one at each interface with the implicit reservoirs that provide the relaxation. For strong relaxation, a "dual" expression-one with the same functional form-results, except now proportional to 1/γ and dependent on the system of interest's electronic states, reflecting that the strong relaxation is localizing electrons in the extended reservoirs. Higher order behavior (e.g., γ2 or 1/γ2) can occur when there is a gap in the frequency spectrum. Moreover, inhomogeneity in the frequency spacing can give rise to a pseudo-plateau regime. These findings yield a physically motivated approach to diagnosing numerical simulations and understanding the influence of relaxation, and we examine their occurrence in both simple models and a realistic, fluctuating graphene nanoribbon.
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Affiliation(s)
- Daniel Gruss
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
- Maryland Nanocenter, University of Maryland, College Park, MD 20742, USA
| | - Alex Smolyanitsky
- Applied Chemicals and Materials Division, National Institute of Standards and Technology, Boulder, CO 80305, USA
| | - Michael Zwolak
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
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Arshad S, Raveendran Pillai R, Zainuri DA, Khalib NC, Razak IA, Armaković S, Armaković SJ, Renjith R, Panicker CY, Van Alsenoy C. Synthesis, XRD crystal structure, spectroscopic characterization, local reactive properties using DFT and molecular dynamics simulations and molecular docking study of (E)-1-(4-bromophenyl)-3-(4-(trifluoromethoxy)phenyl)prop-2-en-1-one. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.02.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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50
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Nazari F, Whitten JL. Prediction of many-electron wavefunctions using atomic potentials. J Chem Phys 2017; 146:194109. [PMID: 28527434 DOI: 10.1063/1.4983395] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
For a given many-electron molecule, it is possible to define a corresponding one-electron Schrödinger equation, using potentials derived from simple atomic densities, whose solution predicts fairly accurate molecular orbitals for single- and multi-determinant wavefunctions for the molecule. The energy is not predicted and must be evaluated by calculating Coulomb and exchange interactions over the predicted orbitals. Potentials are found by minimizing the energy of predicted wavefunctions. There exist slightly less accurate average potentials for first-row atoms that can be used without modification in different molecules. For a test set of molecules representing different bonding environments, these average potentials give wavefunctions with energies that deviate from exact self-consistent field or configuration interaction energies by less than 0.08 eV and 0.03 eV per bond or valence electron pair, respectively.
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Affiliation(s)
- Fariba Nazari
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Jerry L Whitten
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
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