1
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Tu NTP, Williamson S, Johnson ER, Rowley CN. Modeling Intermolecular Interactions with Exchange-Hole Dipole Moment Dispersion Corrections to Neural Network Potentials. J Phys Chem B 2024; 128:8290-8302. [PMID: 39166778 DOI: 10.1021/acs.jpcb.4c02882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Neural network potentials (NNPs) are an innovative approach for calculating the potential energy and forces of a chemical system. In principle, these methods are capable of modeling large systems with an accuracy approaching that of a high-level ab initio calculation, but with a much smaller computational cost. Due to their training to density-functional theory (DFT) data and neglect of long-range interactions, some classes of NNPs require an additional term to include London dispersion physics. In this Perspective, we discuss the requirements for a dispersion model for use with an NNP, focusing on the MLXDM (Machine Learned eXchange-Hole Dipole Moment) model developed by our groups. This model is based on the DFT-based XDM dispersion correction, which calculates interatomic dispersion coefficients in terms of atomic moments and polarizabilities, both of which can be approximated effectively using neural networks.
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Affiliation(s)
| | - Siri Williamson
- Department of Chemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Erin R Johnson
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4J3, Canada
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2
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Fox R, Klug J, Thompson D, Reilly A. Computational predictions of cocrystal formation: A benchmark study of 28 assemblies comparing five methods from high-throughput to advanced models. J Comput Chem 2024. [PMID: 38958249 DOI: 10.1002/jcc.27454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 07/04/2024]
Abstract
Cocrystals are assemblies of more than one type of molecule stabilized through noncovalent interactions. They are promising materials for improved drug formulation in which the stability, solubility, or biocompatibility of the active pharmaceutical ingredient (API) is improved by including a coformer. In this work, a range of density functional theory (DFT) and density functional tight binding (DFTB) models are systematically compared for their ability to predict the lattice enthalpy of a broad range of existing pharmaceutically relevant cocrystals. These range from cocrystals containing model compounds 4,4'-bipyridine and oxalic acid to those with the well benchmarked APIs of aspirin and paracetamol, all tested with a large set of alternative coformers. For simple cocrystals, there is a general consensus in lattice enthalpy calculated by the different DFT models. For the cocrystals with API coformers the cocrystals, enthalpy predictions depend strongly on the DFT model. The significantly lighter DFTB models predict unrealistic values of lattice enthalpy even for simple cocrystals.
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Affiliation(s)
- Robert Fox
- School of Chemical Sciences, Dublin City University, Dublin, Ireland
| | - Joaquin Klug
- Department of Life Sciences, Faculty of Sciences, Atlantic Technological University, ATU Sligo, Sligo, Ireland
| | - Damien Thompson
- Department of Physics, Bernal Institute, University of Limerick, Limerick, Ireland
| | - Anthony Reilly
- School of Chemical Sciences, Dublin City University, Dublin, Ireland
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3
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Ibrahim A, Roy PN. A neural network-based four-body potential energy surface for parahydrogen. J Chem Phys 2024; 160:244308. [PMID: 38916269 DOI: 10.1063/5.0214495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 06/06/2024] [Indexed: 06/26/2024] Open
Abstract
We present an isotropic ab initio (para-H2)4 four-body interaction potential energy surface (PES). The electronic structure calculations are performed at the correlated coupled-cluster theory level, with single, double, and perturbative triple excitations. They use an atom-centered augmented correlation-consistent double zeta basis set, supplemented by a (3s3p2d) midbond function. We use a multilayer perceptron to construct the PES. We apply a rescaling transformation to the output energies during training to improve the prediction of weaker energies in the sample data. At long distances, the interaction energies are adjusted to match the empirically derived four-body dispersion interaction. The four-body interaction energy at short intermolecular separations is net repulsive. The use of this four-body PES, in combination with a first principles pair potential for para-H2 [J. Chem. Phys. 119, 12551 (2015)] and an isotropic ab initio three-body potential for para-H2 [J. Chem. Phys. 156, 044301 (2022)], is expected to provide closer agreement with experimental results.
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Affiliation(s)
- Alexander Ibrahim
- Department of Physics and Astronomy, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Pierre-Nicholas Roy
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
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4
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Nicolle A, Deng S, Ihme M, Kuzhagaliyeva N, Ibrahim EA, Farooq A. Mixtures Recomposition by Neural Nets: A Multidisciplinary Overview. J Chem Inf Model 2024; 64:597-620. [PMID: 38284618 DOI: 10.1021/acs.jcim.3c01633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Artificial Neural Networks (ANNs) are transforming how we understand chemical mixtures, providing an expressive view of the chemical space and multiscale processes. Their hybridization with physical knowledge can bridge the gap between predictivity and understanding of the underlying processes. This overview explores recent progress in ANNs, particularly their potential in the 'recomposition' of chemical mixtures. Graph-based representations reveal patterns among mixture components, and deep learning models excel in capturing complexity and symmetries when compared to traditional Quantitative Structure-Property Relationship models. Key components, such as Hamiltonian networks and convolution operations, play a central role in representing multiscale mixtures. The integration of ANNs with Chemical Reaction Networks and Physics-Informed Neural Networks for inverse chemical kinetic problems is also examined. The combination of sensors with ANNs shows promise in optical and biomimetic applications. A common ground is identified in the context of statistical physics, where ANN-based methods iteratively adapt their models by blending their initial states with training data. The concept of mixture recomposition unveils a reciprocal inspiration between ANNs and reactive mixtures, highlighting learning behaviors influenced by the training environment.
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Affiliation(s)
- Andre Nicolle
- Aramco Fuel Research Center, Rueil-Malmaison 92852, France
| | - Sili Deng
- Massachusetts Institute of Technology, Cambridge 02139, Massachusetts, United States
| | - Matthias Ihme
- Stanford University, Stanford 94305, California, United States
| | | | - Emad Al Ibrahim
- King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Aamir Farooq
- King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
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5
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Nickerson CJ, Bryenton KR, Price AJA, Johnson ER. Comparison of Density-Functional Theory Dispersion Corrections for the DES15K Database. J Phys Chem A 2023; 127:8712-8722. [PMID: 37793049 DOI: 10.1021/acs.jpca.3c04332] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
While density-functional theory (DFT) remains one of the most widely used tools in computational chemistry, most functionals fail to properly account for the effects of London dispersion. Hence, there are many popular post-self-consistent methods to add a dispersion correction to the DFT energy. Until now, the most popular methods have never been compared on equal footing due to not being implemented in the same electronic structure packages. In this work, we performed a large-scale benchmarking study, directly comparing the accuracy of the exchange-hole dipole moment (XDM), D3BJ, D4, TS, MBD, and MBD-NL dispersion models when applied to the recent DES15K database of nearly 15,000 molecular complexes at both expanded and compressed geometries. Our study showed similarly good performance for all dispersion methods (except TS) when applied to neutral complexes. However, they all performed worse for ionic complexes, particularly those involving dications of alkaline earth metals, due to systematic overbinding by the base PBE0 density functional. Investigation of the largest outliers also revealed that only the MBD and MBD-NL methods demonstrate surprising errors for complexes involving alkali metal cations at compressed geometries where they tended to significantly overbind. As we would expect minimal dispersion binding for such complexes, we further investigated the origins of these errors for the potential energy curve of a model cation-π complex. Overall, there is little choice between the XDM, D3BJ, D4, MBD, and MBD-NL dispersion methods for most systems. However, the MBD-based methods are not recommended for complexes involving organic species and alkali or alkaline earth metal cations, for example when modeling Li+ intercalation into graphite.
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Affiliation(s)
- Cameron J Nickerson
- Department of Physics and Atmospheric Science, Dalhousie University, 6310 Coburg Rd, Halifax, Nova Scotia B3H 4R2, Canada
| | - Kyle R Bryenton
- Department of Physics and Atmospheric Science, Dalhousie University, 6310 Coburg Rd, Halifax, Nova Scotia B3H 4R2, Canada
| | - Alastair J A Price
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd, Halifax, Nova Scotia B3H 4R2, Canada
| | - Erin R Johnson
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd, Halifax, Nova Scotia B3H 4R2, Canada
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6
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Bandyopadhyay P, Sadhukhan M. Modeling coarse-grained van der Waals interactions using dipole-coupled anisotropic quantum Drude oscillators. J Comput Chem 2023; 44:1164-1173. [PMID: 36645104 DOI: 10.1002/jcc.27073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 01/17/2023]
Abstract
The Quantum Drude Oscillator (QDO) model is a promising candidate for accurately calculating the van der Waals (vdW) interaction. Anisotropic QDO models have recently been used to represent quantum fluctuations of molecular fragments rather than that of single atoms. While this model promises accurate calculation of vdW energy, there is significant room for improvements, such as incorporating a proper fragmentation method, higher-order dispersion corrections, and so forth. The present work attempts to gauge dipole-dipole interactions' ability without fragmentation. A suitable anisotropic damping function is also introduced to work with anisotropic QDO. This revised model accurately predicts the binding energies of vdW complexes for most of the systems considered. This work indicates the limit of dipole approximation for an anisotropic QDO-based model.
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Affiliation(s)
| | - Mainak Sadhukhan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
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7
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Price AJA, Otero-de-la-Roza A, Johnson ER. XDM-corrected hybrid DFT with numerical atomic orbitals predicts molecular crystal lattice energies with unprecedented accuracy. Chem Sci 2023; 14:1252-1262. [PMID: 36756332 PMCID: PMC9891363 DOI: 10.1039/d2sc05997e] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Molecular crystals are important for many applications, including energetic materials, organic semiconductors, and the development and commercialization of pharmaceuticals. The exchange-hole dipole moment (XDM) dispersion model has shown good performance in the calculation of relative and absolute lattice energies of molecular crystals, although it has traditionally been applied in combination with plane-wave/pseudopotential approaches. This has limited XDM to use with semilocal functional approximations, which suffer from delocalization error and poor quality conformational energies, and to systems with a few hundreds of atoms at most due to unfavorable scaling. In this work, we combine XDM with numerical atomic orbitals, which enable the efficient use of XDM-corrected hybrid functionals for molecular crystals. We test the new XDM-corrected functionals for their ability to predict the lattice energies of molecular crystals for the X23 set and 13 ice phases, the latter being a particularly stringent test. A composite approach using a XDM-corrected, 25% hybrid functional based on B86bPBE achieves a mean absolute error of 0.48 kcal mol-1 per molecule for the X23 set and 0.19 kcal mol-1 for the total lattice energies of the ice phases, compared to recent diffusion Monte-Carlo data. These results make the new XDM-corrected hybrids not only far more computationally efficient than previous XDM implementations, but also the most accurate density-functional methods for molecular crystal lattice energies to date.
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Affiliation(s)
- Alastair J. A. Price
- Department of Chemistry, Dalhousie University6274 Coburg RdHalifaxB3H 4R2Nova ScotiaCanada
| | - Alberto Otero-de-la-Roza
- Departamento de Química Física y Analítica and MALTA-Consolider Team, Facultad de Química, Universidad de Oviedo Oviedo 33006 Spain
| | - Erin R. Johnson
- Department of Chemistry, Dalhousie University6274 Coburg RdHalifaxB3H 4R2Nova ScotiaCanada
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8
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Missana A, Hauser A, Lawson Daku LM. Environmental Control of the Magnetic Behavior of Transition Metal Complexes: Density Functional Theory Study of Zeolite Y Embedded Complexes [M(bpy) 3] 2+@Y (M = Fe 2+, Co 2+). J Phys Chem A 2022; 126:6221-6235. [PMID: 36067495 DOI: 10.1021/acs.jpca.2c05070] [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
Using the supramolecular approach developed for the study of the guest-host interactions in the zeolite Y encapsulated [Fe(bpy)3]2+ compound: [Fe(bpy)3]2+@Y (bpy = 2,2'-bipyridine) [Vargas et al., J. Chem. Theory Comput. 2009, 5, 97-115], we apply density functional theory (DFT) to the study of the influence of zeolite Y encapsulation on the structural and energetic properties of [Co(bpy)3]2+ in the low-spin (LS) and high-spin (HS) states, while revisiting [Fe(bpy)3]2+@Y. Although the accurate prediction of the HS-LS energy difference ΔEHLel remains challenging for current DFT methods, they give accurate estimates of its variation Δ(ΔEHLel) in a series of complexes of a given transition metal ion. Therefore, denoting [M(bpy)3]2+@YSM as the supramolecular model of the inclusion compounds, the values of ΔEHLel for the bpy complexes in the gas phase and in the supercage of zeolite Y were determined by combining the DFT estimates of Δ(ΔEHLel) in the series {[M(NCH)6]2+, [M(bpy)3]2+, and [M(bpy)3]2+@YSM}, with accurate CCSD(T) estimates of ΔEHLel in the benchmark complexes [M(NCH)6]2+ (M = Fe, Co) [Lawson Daku et al., J. Chem. Theory Comput., 2012, 8, 4216-4231]. Generalized gradient approximations as well as global and range-separated hybrids were employed. In order to better account for the key role of dispersion, they were also augmented with the semiempirical D2, D3BJ, and D3BJM dispersion corrections when available. The use of the D3BJ and D3BJM corrections led to similar results, and this is only with the use of the D2 scheme that (i) the free and encapsulated [Fe(bpy)3]2+ are correctly predicted as LS species and that (ii) the encapsulation of both complexes translates into a destabilization of their HS state with respect to their LS state. The increase of the HS-LS energy difference is smaller for [Co(bpy)3]2+ than [Fe(bpy)3]2+ because the HS-LS molecular volume difference ΔVHL in [Co(bpy)3]2+ is ∼50% smaller than in [Fe(bpy)3]2+. Periodic DFT calculations performed on crystalline [M(bpy)3]2+@Y show that the employed [M(bpy)3]2+@YSM supramolecular model allows the influence of encapsulation on the geometry and the spin-state energetics of [M(bpy)3]2+ (M = Fe, Co) to be quantitatively captured.
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Affiliation(s)
- Andrea Missana
- Université de Genève, 30 quai Ernest-Ansermet, CH-1211Genève 4, Switzerland
| | - Andreas Hauser
- Université de Genève, 30 quai Ernest-Ansermet, CH-1211Genève 4, Switzerland
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9
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O'Connor D, Bier I, Hsieh YT, Marom N. Performance of Dispersion-Inclusive Density Functional Theory Methods for Energetic Materials. J Chem Theory Comput 2022; 18:4456-4471. [PMID: 35759249 DOI: 10.1021/acs.jctc.2c00350] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular crystals of energetic materials (EMs) are denser than typical molecular crystals and are characterized by distinct intermolecular interactions between nitrogen-containing moieties. To assess the performance of dispersion-inclusive density functional theory (DFT) methods, we have compiled a data set of experimental sublimation enthalpies of 31 energetic materials. We evaluate the performance of three methods: the semilocal Perdew-Burke-Ernzerhof (PBE) functional coupled with the pairwise Tkatchenko-Scheffler (TS) dispersion correction, PBE with the many-body dispersion (MBD) method, and the PBE-based hybrid functional (PBE0) with MBD. Zero-point energy contributions and thermal effects are described using the quasi-harmonic approximation (QHA), including explicit treatment of thermal expansion, which we find to be non-negligible for EMs. The lattice energies obtained with PBE0+MBD are the closest to experimental sublimation enthalpies with a mean absolute error of 9.89 kJ/mol. However, the state-of-the-art treatment of vibrational and thermal contributions makes the agreement with experiment worse. Pressure-volume curves are also examined for six representative materials. For pressure-volume curves, all three methods provide reasonable agreement with experimental data with mean absolute relative errors of 3% or less. Most of the intermolecular interactions typical of EMs, namely nitro-amine, nitro-nitro, and nitro-hydrogen interactions, are more sensitive to the choice of the dispersion method than to the choice of the exchange-correlation functional. The exception is π-π stacking interactions, which are also very sensitive to the choice of the functional. Overall, we find that PBE+TS, PBE+MBD, and PBE0+MBD do not perform as well for energetic materials as previously reported for other classes of molecular crystals. This highlights the importance of testing dispersion-inclusive DFT methods for diverse classes of materials and the need for further method development.
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Affiliation(s)
- Dana O'Connor
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Imanuel Bier
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Yun-Ting Hsieh
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Noa Marom
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States.,Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States.,Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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10
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Jones RO. The chemical bond in solids-revisited. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2022; 34:343001. [PMID: 35636399 DOI: 10.1088/1361-648x/ac7494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
This article complements an earlier topical review of the chemical bond (Jones 2018J. Phys.: Condens. Matter30153001), starting in the mid-19th century and seen from the perspective of a condensed matter physicist. The discussion of applications focused on the structure and properties of phase change materials. We review here additional aspects of chemistry, particularly some that have raised interest recently in this context. Concepts such as 'electron-rich', 'electron-deficient (excess orbital)', 'hypervalent', 'three-centre', and 'metavalent' bonds, and 'multicentre hyperbonding' are now found in the condensed matter literature. They are surveyed here, as well as the bond in metals and the 'Peierls' distortion. What are these concepts, are they related, and are they sometimes new labels for established, but unfamiliar ideas? 'Half bonds' and 'fractional valencies' play a central role in this discussion. It is remarkable that they were introduced 100 years ago, but ignored or forgotten, and have needed to be rediscovered more than once.
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Affiliation(s)
- R O Jones
- Peter-Grünberg-Institut PGI-1 and JARA/HPC, Forschungszentrum Jülich, D-52425 Jülich, Germany
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11
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Østrøm I, Hossain MA, Burr PA, Hart JN, Hoex B. Designing 3d metal oxides: selecting optimal density functionals for strongly correlated materials. Phys Chem Chem Phys 2022; 24:14119-14139. [PMID: 35593423 DOI: 10.1039/d2cp01303g] [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
Transition metal oxides (TMOs) have remarkable physicochemical properties, are non-toxic, and have low cost and high annual production, thus they are commonly studied for various technological applications. Density functional theory (DFT) can help to optimize TMO materials by providing insights into their electronic, optical and thermodynamic properties, and hence into their structure-performance relationships, over a wide range of solid-state structures and compositions. However, this is underpinned by the choice of the exchange-correlation (XC) functional, which is critical to accurately describe the highly localized and correlated 3d-electrons of the transition metals in TMOs. This tutorial review presents a benchmark study of density functionals (DFs), ranging from generalized gradient approximation (GGA) to range-separated hybrids (RSH), with the all-electron def2-TZVP basis set, comparing magneto-electro-optical properties of 3d TMOs against experimental observations. The performance of the DFs is assessed by analyzing the band structure, density of states, magnetic moment, structural static and dynamic parameters, optical properties, spin contamination and computational cost. The results disclose the strengths and weaknesses of the XC functionals, in terms of accuracy, and computational efficiency, suggesting the unprecedented PBE0-1/5 as the best candidate. The findings of this work contribute to necessary developments of XC functionals for periodic systems, and materials science modelling studies, particularly informing how to select the optimal XC functional to obtain the most trustworthy description of the ground-state electron structure of 3d TMOs.
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Affiliation(s)
- Ina Østrøm
- School of Photovoltaic and Renewable Energy Engineering, UNSW, Kensington, NSW 2052, Australia.
| | - Md Anower Hossain
- School of Photovoltaic and Renewable Energy Engineering, UNSW, Kensington, NSW 2052, Australia.
| | - Patrick A Burr
- School of Mechanical and Manufacturing Engineering, UNSW, Kensington, NSW 2052, Australia
| | - Judy N Hart
- School of Materials Science & Engineering, UNSW, Kensington, NSW 2052, Australia
| | - Bram Hoex
- School of Photovoltaic and Renewable Energy Engineering, UNSW, Kensington, NSW 2052, Australia.
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12
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Dudek MK, Druzbicki K. Along the road to Crystal Structure Prediction (CSP) of pharmaceutical-like molecules. CrystEngComm 2022. [DOI: 10.1039/d1ce01564h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Computational methods used for predicting crystal structures of organic compounds are mature enough to be routinely used with many rigid and semi-rigid organic molecules. The usefulness of Crystal Structure Prediction...
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13
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Bandyopadhyay P, Priya P, Sadhukhan M. A simple fragment-based method for van der Waals corrections over density functional theory. Phys Chem Chem Phys 2022; 24:8508-8518. [DOI: 10.1039/d2cp00744d] [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
Modeling intermolecular noncovalent interactions between large molecules remains a challenge for the electron structure theory community due to the high cost. Fragment-based methods usually fare well in reducing the cost...
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14
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Vázquez-Fernández I, Drużbicki K, Fernandez-Alonso F, Mukhopadhyay S, Nockemann P, Parker SF, Rudić S, Stana SM, Tomkinson J, Yeadon DJ, Seddon KR, Plechkova NV. Spectroscopic Signatures of Hydrogen-Bonding Motifs in Protonic Ionic Liquid Systems: Insights from Diethylammonium Nitrate in the Solid State. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2021; 125:24463-24476. [PMID: 34795809 PMCID: PMC8592064 DOI: 10.1021/acs.jpcc.1c05137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Diethylammonium nitrate, [N0 0 2 2][NO3], and its perdeuterated analogue, [N D D 2 2] [NO3], were structurally characterized and studied by infrared, Raman, and inelastic neutron scattering (INS) spectroscopy. Using these experimental data along with state-of-the-art computational materials modeling, we report unambiguous spectroscopic signatures of hydrogen-bonding interactions between the two counterions. An exhaustive assignment of the spectral features observed with each technique has been provided, and a number of distinct modes related to NH···O dynamics have been identified. We put a particular emphasis on a detailed interpretation of the high-resolution, broadband INS experiments. In particular, the INS data highlight the importance of conformational degrees of freedom within the alkyl chains, a ubiquitous feature of ionic liquid (IL) systems. These findings also enable an in-depth physicochemical understanding of protonic IL systems, a first and necessary step to the tailoring of hydrogen-bonding networks in this important class of materials.
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Affiliation(s)
- Isabel Vázquez-Fernández
- The
QUILL Research Centre, School of Chemistry and Chemical Engineering, The Queen’s University of Belfast, Belfast BT9 5AG, Northern Ireland, U.K.
| | - Kacper Drużbicki
- Materials
Physics Center, CSIC-UPV/EHU, Paseo Manuel de Lardizabal 5, Donostia-San
Sebastian 20018, Spain
- Centre
of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, Lodz 90-363, Poland
| | - Felix Fernandez-Alonso
- Materials
Physics Center, CSIC-UPV/EHU, Paseo Manuel de Lardizabal 5, Donostia-San
Sebastian 20018, Spain
- Donostia
International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, Donostia-San
Sebastian 20018, Spain
- Department
of Physics and Astronomy, University College
London, Gower Street, London WC1E 6BT, U.K.
- Ikerbasque,
Basque Foundation for Science, Plaza Euskadi 5, Bilbao 48009, Spain
| | - Sanghamitra Mukhopadhyay
- ISIS
Facility, Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, U.K.
- Department
of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, U.K.
| | - Peter Nockemann
- The
QUILL Research Centre, School of Chemistry and Chemical Engineering, The Queen’s University of Belfast, Belfast BT9 5AG, Northern Ireland, U.K.
| | - Stewart F. Parker
- ISIS
Facility, Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, U.K.
| | - Svemir Rudić
- ISIS
Facility, Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, U.K.
| | - Simona-Maria Stana
- The
QUILL Research Centre, School of Chemistry and Chemical Engineering, The Queen’s University of Belfast, Belfast BT9 5AG, Northern Ireland, U.K.
| | - John Tomkinson
- ISIS
Facility, Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, U.K.
| | - Darius J. Yeadon
- The
QUILL Research Centre, School of Chemistry and Chemical Engineering, The Queen’s University of Belfast, Belfast BT9 5AG, Northern Ireland, U.K.
| | - Kenneth R. Seddon
- The
QUILL Research Centre, School of Chemistry and Chemical Engineering, The Queen’s University of Belfast, Belfast BT9 5AG, Northern Ireland, U.K.
| | - Natalia V. Plechkova
- The
QUILL Research Centre, School of Chemistry and Chemical Engineering, The Queen’s University of Belfast, Belfast BT9 5AG, Northern Ireland, U.K.
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15
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Kabengele T, Johnson ER. Theoretical modeling of structural superlubricity in rotated bilayer graphene, hexagonal boron nitride, molybdenum disulfide, and blue phosphorene. NANOSCALE 2021; 13:14399-14407. [PMID: 34473160 DOI: 10.1039/d1nr03001a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The superior lubrication capabilities of two-dimensional crystalline materials such as graphene, hexagonal boron nitride (h-BN), and molybdenum disulfide (MoS2) have been well known for many years. It is generally accepted that structural superlubricity in these materials is due to misalignment of the surfaces in contact, known as incommensurability. In this work, we present a detailed study of structural superlubricity in bilayer graphene, h-BN, MoS2, and the novel material blue phosphorene (b-P) using dispersion-corrected density-functional theory with periodic boundary conditions. Potential energy surfaces for interlayer sliding were computed for the standard (1 × 1) cell and three rotated, Moiré unit cells for each material. The energy barriers to form the rotated structures remain higher than the minimum-energy sliding barriers for the (1 × 1) cells. However, if the rotational barriers can be overcome, nearly barrierless interlayer sliding is observed in the rotated cells for all four materials. This is the first density-functional investigation of friction using rotated, Moiré cells, and the first prediction of structural superlubricty for b-P.
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Affiliation(s)
- Tilas Kabengele
- Department of Physics and Atmospheric Science, Dalhousie University, 6310 Coburg Road, Halifax, Nova Scotia, Canada B3H 4R2
| | - Erin R Johnson
- Department of Physics and Atmospheric Science, Dalhousie University, 6310 Coburg Road, Halifax, Nova Scotia, Canada B3H 4R2
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia, Canada B3H 4R2.
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16
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Price AJA, Bryenton KR, Johnson ER. Requirements for an accurate dispersion-corrected density functional. J Chem Phys 2021; 154:230902. [PMID: 34241263 DOI: 10.1063/5.0050993] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Post-self-consistent dispersion corrections are now the norm when applying density-functional theory to systems where non-covalent interactions play an important role. However, there is a wide range of base functionals and dispersion corrections available from which to choose. In this work, we opine on the most desirable requirements to ensure that both the base functional and dispersion correction, individually, are as accurate as possible for non-bonded repulsion and dispersion attraction. The base functional should be dispersionless, numerically stable, and involve minimal delocalization error. Simultaneously, the dispersion correction should include finite damping, higher-order pairwise dispersion terms, and electronic many-body effects. These criteria are essential for avoiding reliance on error cancellation and obtaining correct results from correct physics.
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Affiliation(s)
- Alastair J A Price
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd., Halifax, Nova Scotia B3H 4R2, Canada
| | - Kyle R Bryenton
- Department of Physics and Atmospheric Science, Dalhousie University, 6310 Coburg Rd., Halifax, Nova Scotia B3H 4R2, Canada
| | - Erin R Johnson
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd., Halifax, Nova Scotia B3H 4R2, Canada
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17
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Al‐Mahayni H, Wang X, Harvey J, Patience GS, Seifitokaldani A. Experimental methods in chemical engineering: Density functional theory. CAN J CHEM ENG 2021. [DOI: 10.1002/cjce.24127] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Xiao Wang
- Chemical Engineering McGill University Montréal Québec Canada
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18
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Christian MS, Johnson ER, Besmann TM. Interplay between London Dispersion, Hubbard U, and Metastable States for Uranium Compounds. J Phys Chem A 2021; 125:2791-2799. [PMID: 33764761 DOI: 10.1021/acs.jpca.0c10533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
High-throughput computational studies of lanthanide and actinide chemistry with density-functional theory are complicated by the need for Hubbard U corrections, which ensure localization of the f-electrons, but can lead to metastable states. This work presents a systematic investigation of the effects of both Hubbard U value and metastable states on the predicted structural and thermodynamic properties of four uranium compounds central to the field of nuclear fuels: UC, UN, UO2, and UCl3. We also assess the impact of the exchange-hole dipole moment (XDM) dispersion correction on the computed properties. Overall, the choice of Hubbard U value and inclusion of a dispersion correction cause larger variations in the computed geometric properties than result from metastable states. The weak dependence of structure optimization on metastable states should simplify future high-throughput calculations on actinides. Conversely, addition of the dispersion correction is found to offset the repulsion introduced by the Hubbard U term and provides greatly improved agreement with experiment for both cell volumes and heats of formation. The XDM dispersion correction is largely invariant to the chosen U value, making it a robust dispersion correction for actinide systems.
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Affiliation(s)
- Matthew S Christian
- Nuclear Engineering Program, University of South Carolina, Columbia, South Carolina 29208, United States.,Center for Hierarchical Waste Form Materials (CHWM), University of South Carolina, Columbia, South Carolina 29208, United States
| | - Erin R Johnson
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2, Canada
| | - Theodore M Besmann
- Nuclear Engineering Program, University of South Carolina, Columbia, South Carolina 29208, United States.,Center for Hierarchical Waste Form Materials (CHWM), University of South Carolina, Columbia, South Carolina 29208, United States
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19
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Bier I, O'Connor D, Hsieh YT, Wen W, Hiszpanski AM, Han TYJ, Marom N. Crystal structure prediction of energetic materials and a twisted arene with Genarris and GAtor. CrystEngComm 2021. [DOI: 10.1039/d1ce00745a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A molecular crystal structure prediction workflow, based on the random structure generator, Genarris, and the genetic algorithm (GA), GAtor, is successfully applied to two energetic materials and a chiral arene.
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Affiliation(s)
- Imanuel Bier
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Dana O'Connor
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Yun-Ting Hsieh
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Wen Wen
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Anna M. Hiszpanski
- Materials Science Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - T. Yong-Jin Han
- Materials Science Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Noa Marom
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
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20
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Kiely E, Zwane R, Fox R, Reilly AM, Guerin S. Density functional theory predictions of the mechanical properties of crystalline materials. CrystEngComm 2021. [DOI: 10.1039/d1ce00453k] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The DFT-predicted mechanical properties of crystalline materials are crucial knowledge for their screening, design, and exploitation.
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Affiliation(s)
- Evan Kiely
- Department of Physics, Bernal Institute, University of Limerick, V94 T9PX, Ireland
| | - Reabetswe Zwane
- School of Chemical Sciences, Dublin City University (DCU), Glasnevin, D09 C7F8 Dublin, Ireland
- SSPC, Science Foundation Ireland Research Centre for Pharmaceuticals, University of Limerick, V94 T9PX, Ireland
| | - Robert Fox
- School of Chemical Sciences, Dublin City University (DCU), Glasnevin, D09 C7F8 Dublin, Ireland
- SSPC, Science Foundation Ireland Research Centre for Pharmaceuticals, University of Limerick, V94 T9PX, Ireland
| | - Anthony M. Reilly
- School of Chemical Sciences, Dublin City University (DCU), Glasnevin, D09 C7F8 Dublin, Ireland
- SSPC, Science Foundation Ireland Research Centre for Pharmaceuticals, University of Limerick, V94 T9PX, Ireland
| | - Sarah Guerin
- Department of Physics, Bernal Institute, University of Limerick, V94 T9PX, Ireland
- SSPC, Science Foundation Ireland Research Centre for Pharmaceuticals, University of Limerick, V94 T9PX, Ireland
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21
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Abstract
A broad range of approaches to many-body dispersion are discussed, including empirical approaches with multiple fitted parameters, augmented density functional-based approaches, symmetry adapted perturbation theory, and a supermolecule approach based on coupled cluster theory. Differing definitions of "body" are considered, specifically atom-based vs molecule-based approaches.
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Affiliation(s)
- Peng Xu
- Department of Chemistry, Iowa State University, Ames, Iowa 50014, United States
| | - Melisa Alkan
- Department of Chemistry, Iowa State University, Ames, Iowa 50014, United States
| | - Mark S Gordon
- Department of Chemistry, Iowa State University, Ames, Iowa 50014, United States
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22
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Konovalov A, Symons BCB, Popelier PLA. On the many-body nature of intramolecular forces in FFLUX and its implications. J Comput Chem 2020; 42:107-116. [PMID: 33107993 DOI: 10.1002/jcc.26438] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 12/24/2022]
Abstract
FFLUX is a biomolecular force field under construction, based on Quantum Chemical Topology (QCT) and machine learning (kriging), with a minimalistic and physically motivated design. A detailed analysis of the forces within the kriging models as treated in FFLUX is presented, taking as a test example a liquid water model. The energies of topological atoms are modeled as 3Natoms -6 dimensional potential energy surfaces, using atomic local frames to represent the internal degrees of freedom. As a result, the forces within the kriging models in FFLUX are inherently N-body in nature where N refers to Natoms . This provides a fuller picture that is closer to a true quantum mechanical representation of interactions between atoms. The presented computational example quantitatively showcases the non-negligible (as much as 9%) three-body nature of bonded forces and angular forces in a water molecule. We discuss the practical impact on the pressure calculation with N-body forces and periodic boundary conditions (PBC) in molecular dynamics, as opposed to classical force fields with two-body forces. The equivalence between the PBC-related correction terms in the general virial equation is shown mathematically.
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Affiliation(s)
- Anton Konovalov
- Manchester Institute of Biotechnology (MIB), Manchester, United Kingdom.,Department of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Benjamin C B Symons
- Manchester Institute of Biotechnology (MIB), Manchester, United Kingdom.,Department of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Paul L A Popelier
- Manchester Institute of Biotechnology (MIB), Manchester, United Kingdom.,Department of Chemistry, University of Manchester, Manchester, United Kingdom
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23
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Otero-de-la-Roza A, Johnson ER. Application of XDM to ionic solids: The importance of dispersion for bulk moduli and crystal geometries. J Chem Phys 2020; 153:054121. [PMID: 32770899 DOI: 10.1063/5.0015133] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Dispersion corrections are essential in the description of intermolecular interactions; however, dispersion-corrected functionals must also be transferrable to hard solids. The exchange-hole dipole moment (XDM) model has demonstrated excellent performance for non-covalent interactions. In this article, we examine its ability to describe the relative stability, geometry, and compressibility of simple ionic solids. For the specific cases of the cesium halides, XDM-corrected functionals correctly predict the energy ranking of the B1 and B2 forms, and a dispersion contribution is required to obtain this result. Furthermore, for the lattice constants of the 20 alkali halides, the performance of XDM-corrected functionals is excellent, provided that the base functional's exchange enhancement factor properly captures non-bonded repulsion. The mean absolute errors in lattice constants obtained with B86bPBE-XDM and B86bPBE-25X-XDM are 0.060 Å and 0.039 Å, respectively, suggesting that delocalization error also plays a minor role in these systems. Finally, we considered the calculation of bulk moduli for alkali halides and alkaline-earth oxides. Previous claims in the literature that simple generalized gradient approximations, such as PBE, can reliably predict experimental bulk moduli have benefited from large error cancellations between neglecting both dispersion and vibrational effects. If vibrational effects are taken into account, dispersion-corrected functionals are quite accurate (4 GPa-5 GPa average error), again, if non-bonded repulsion is correctly represented. Careful comparisons of the calculated bulk moduli with experimental data are needed to avoid systematic biases and misleading conclusions.
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Affiliation(s)
- A Otero-de-la-Roza
- Departamento de Química Física y Analítica and MALTA Consolider Team, Facultad de Química, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Erin R Johnson
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd., Halifax, Nova Scotia B3H 4R2, Canada
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