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Fischer M, Brauer J. Studying the adsorption of emerging organic contaminants in zeolites with dispersion-corrected density functional theory calculations: From numbers to recommendations. ChemistryOpen 2024; 13:e202300273. [PMID: 38385822 PMCID: PMC11230941 DOI: 10.1002/open.202300273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/10/2024] [Indexed: 02/23/2024] Open
Abstract
Adsorption energies obtained from dispersion-corrected density functional theory (DFT) calculations show a considerable dependence on the choice of exchange-correlation functional and dispersion correction. A number of investigations have employed different approaches to compute adsorption energies of small molecules in zeolites, using reference values from high-level calculations and/or experiments. Such comparative studies are lacking for larger functional organic molecules such as pharmaceuticals or personal care products, despite their potential relevance for applications, e. g., in contaminant removal or drug delivery. The present study aims to fill this gap by comparing adsorption energies and, for selected cases, equilibrium structures of emerging organic contaminants adsorbed in MOR- and FAU-type all-silica zeolites. A total of 13 dispersion-corrected DFT approaches are compared, including methods using a pairwise dispersion correction as well as non-local van der Waals density functionals. While absolute values of adsorption energies vary widely, qualitative trends across the set of zeolite-guest combinations are not strongly dependent on the choice of functional. For selected cluster models, DFT adsorption energies are compared to reference values from coupled cluster (DLPNO-CCSD(T)) calculations. Although all DFT approaches deliver systematically more negative adsorption energies than the coupled cluster reference, this tendency is least pronounced for the rev-vdW-DF2 functional.
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Affiliation(s)
- Michael Fischer
- Crystallography and GeomaterialsFaculty of GeosciencesUniversity of BremenKlagenfurter Straße 2–428359BremenGermany
- Bremen Center for Computational Materials Science and MAPEX Center for Materials and ProcessesUniversity of Bremen28359BremenGermany
| | - Jakob Brauer
- Crystallography and GeomaterialsFaculty of GeosciencesUniversity of BremenKlagenfurter Straße 2–428359BremenGermany
- Bremen Center for Computational Materials Science and MAPEX Center for Materials and ProcessesUniversity of Bremen28359BremenGermany
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2
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Xi ZK, Ding YH, Tian X. Building a New Platform for Significantly Improving Performance of Hartree-Fock and CCSD(T) Correlation Energy Based on Two-Point Complete Basis Set Extrapolation Schemes. J Phys Chem A 2024. [PMID: 38686765 DOI: 10.1021/acs.jpca.4c01712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
The leading cause of high expense in gold standard coupled cluster theory is that calculations of electronic energies converge exceedingly slowly with an increased basis set size. Extrapolation principally allows for achieving higher-quality outcomes at reduced costs. Numerous extrapolation formulas have been developed, with attempts to predict energies up to the complete basis set limit. Unfortunately, since the intricate shape of the function hinges on the molecular properties with the highest angular momentum of the basis set, the accuracy of the extrapolated energies highly depends on the fitted empirical parameters, which rely on the quality of the data sets for fitting. In this work, to overcome the extrapolation deficiency caused by the very limited data sets and smaller basis sets in the early stages, we constructed a new benchmark platform that includes a broader data set of 183 species (containing open-shell, closed-shell, ionic, and neutral species) and a larger basis set up to aug-cc-pV6Z. The newly optimized parameters can significantly improve the energy-predictive abilities of ten published formulas. Notably, all ten formulas perform quite similarly under the new platform with the reoptimized parameters. Finally, we built an online calculator for researchers to use for these extrapolation schemes. Our work would reignite the interest and applications of the underestimated formulas.
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Affiliation(s)
- Zhao-Kai Xi
- †Key Laboratory of Carbon Materials of Zhejiang Province, Wenzhou Key Lab of Advanced Energy Storage and Conversion, Zhejiang Province Key Lab of Leather Engineering, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, P. R. China
| | - Yi-Hong Ding
- Key Laboratory of Carbon Materials of Zhejiang Province, Wenzhou Key Lab of Advanced Energy Storage and Conversion, Zhejiang Province Key Lab of Leather Engineering, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, P. R. China
- Institute of Theoretical Chemistry, Jilin University, Changchun 130023, P. R. China
| | - Xiao Tian
- School of Mathematics and Science, Hebei GEO University, Shijiazhuang 050031, P. R. China
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Holm S, Unzueta PA, Thompson K, Martínez TJ. Single-Point Extrapolation to the Complete Basis Set Limit through Deep Learning. J Chem Theory Comput 2023. [PMID: 37192428 DOI: 10.1021/acs.jctc.2c01298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Machine learning (ML) offers an attractive method for making predictions about molecular systems while circumventing the need to run expensive electronic structure calculations. Once trained on ab initio data, the promise of ML is to deliver accurate predictions of molecular properties that were previously computationally infeasible. In this work, we develop and train a graph neural network model to correct the basis set incompleteness error (BSIE) between a small and large basis set at the RHF and B3LYP levels of theory. Our results show that, when compared to fitting to the total potential, an ML model fitted to correct the BSIE is better at generalizing to systems not seen during training. We test this ability by training on single molecules while evaluating on molecular complexes. We also show that ensemble models yield better behaved potentials in situations where the training data is insufficient. However, even when only fitting to the BSIE, acceptable performance is only achieved when the training data sufficiently resemble the systems one wants to make predictions on. The test error of the final model trained to predict the difference between the cc-pVDZ and cc-pV5Z potential is 0.184 kcal/mol for the B3LYP density functional, and the ensemble model accurately reproduces the large basis set interaction energy curves on the S66x8 dataset.
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Affiliation(s)
- Soren Holm
- Department of Chemistry and The PULSE Institute, Stanford University,Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94024, United States
| | - Pablo A Unzueta
- Department of Chemistry and The PULSE Institute, Stanford University,Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94024, United States
| | - Keiran Thompson
- Department of Chemistry and The PULSE Institute, Stanford University,Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94024, United States
| | - Todd J Martínez
- Department of Chemistry and The PULSE Institute, Stanford University,Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94024, United States
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Lehtola S. Meta-GGA Density Functional Calculations on Atoms with Spherically Symmetric Densities in the Finite Element Formalism. J Chem Theory Comput 2023; 19:2502-2517. [PMID: 37084260 PMCID: PMC10173457 DOI: 10.1021/acs.jctc.3c00183] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Indexed: 04/22/2023]
Abstract
Density functional calculations on atoms are often used for determining accurate initial guesses as well as generating various types of pseudopotential approximations and efficient atomic-orbital basis sets for polyatomic calculations. To reach the best accuracy for these purposes, the atomic calculations should employ the same density functional as the polyatomic calculation. Atomic density functional calculations are typically carried out employing spherically symmetric densities, corresponding to the use of fractional orbital occupations. We have described their implementation for density functional approximations (DFAs) belonging to the local density approximation (LDA) and generalized gradient approximation (GGA) levels of theory as well as Hartree-Fock (HF) and range-separated exact exchange [Lehtola, S. Phys. Rev. A 2020, 101, 012516]. In this work, we describe the extension to meta-GGA functionals using the generalized Kohn-Sham scheme, in which the energy is minimized with respect to the orbitals, which in turn are expanded in the finite element formalism with high-order numerical basis functions. Furnished with the new implementation, we continue our recent work on the numerical well-behavedness of recent meta-GGA functionals [Lehtola, S.; Marques, M. A. L. J. Chem. Phys. 2022, 157, 174114]. We pursue complete basis set (CBS) limit energies for recent density functionals and find many to be ill-behaved for the Li and Na atoms. We report basis set truncation errors (BSTEs) of some commonly used Gaussian basis sets for these density functionals and find the BSTEs to be strongly functional dependent. We also discuss the importance of density thresholding in DFAs and find that all of the functionals studied in this work yield total energies converged to 0.1 μEh when densities smaller than 10-11a0-3 are screened out.
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Affiliation(s)
- Susi Lehtola
- Molecular
Sciences Software Institute, Blacksburg, Virginia 24061, United States
- Department
of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
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Watson PD, Corkish TR, Haakansson CT, McKinley AJ, Wild DA. Halide–propene complexes: validated DSD-PBEP86-D3BJ calculations and photoelectron spectroscopy. Phys Chem Chem Phys 2022; 24:25842-25852. [DOI: 10.1039/d2cp03796c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Anion photoelectron spectroscopy has been used to determine the electron binding energies of the X−⋯C3H6 (X = Cl, Br, I) complexes.
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Affiliation(s)
- Peter D. Watson
- School of Molecular Sciences, The University of Western Australia, Crawley, 6009, Western Australia, Australia
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Timothy R. Corkish
- School of Molecular Sciences, The University of Western Australia, Crawley, 6009, Western Australia, Australia
| | - Christian T. Haakansson
- School of Molecular Sciences, The University of Western Australia, Crawley, 6009, Western Australia, Australia
| | - Allan J. McKinley
- School of Molecular Sciences, The University of Western Australia, Crawley, 6009, Western Australia, Australia
| | - Duncan A. Wild
- School of Molecular Sciences, The University of Western Australia, Crawley, 6009, Western Australia, Australia
- School of Science, Edith Cowan University, Joondalup, 6027, Western Australia, Australia
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Tikhonov DS. A simplistic computational procedure for tunneling splittings caused by proton transfer. Struct Chem 2021. [DOI: 10.1007/s11224-021-01845-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AbstractIn this manuscript, we present an approach for computing tunneling splittings for large amplitude motions. The core of the approach is a solution of an effective one-dimensional Schrödinger equation with an effective mass and an effective potential energy surface composed of electronic and harmonic zero-point vibrational energies of small amplitude motions in the molecule. The method has been shown to work in cases of three model motions: nitrogen inversion in ammonia, single proton transfer in malonaldehyde, and double proton transfer in the formic acid dimer. In the current work, we also investigate the performance of different DFT and post-Hartree–Fock methods for prediction of the proton transfer tunneling splittings, quality of the effective Schrödinger equation parameters upon the isotopic substitution, and possibility of a complete basis set (CBS) extrapolation for the resulting tunneling splittings.
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Kraus P. Extrapolating DFT Toward the Complete Basis Set Limit: Lessons from the PBE Family of Functionals. J Chem Theory Comput 2021; 17:5651-5660. [PMID: 34351738 DOI: 10.1021/acs.jctc.1c00542] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Extrapolation of density functional theory results from 2- and 3-ζ calculations is a promising method for extracting higher accuracy data from calculations of systems at the affordability limit. In this work, the author presents formulas for the determination of extrapolation parameters, which account for the makeup of the density functional approximation. The formulas are fitted to reproduce the complete basis set limit energies of PBE and related density functional approximations, using a set of 30 singlet diatomics. Their performance is extensively evaluated using standard benchmark data sets. The current systematically derived expressions are shown to be transferrable outside the PBE family of functional approximations, with the resulting extrapolation parameters outperforming the previous, less-systematic values. A good performance of [2,3]-ζ extrapolations for interaction energies of systems with significant noncovalent character is confirmed and holds even in systems of ∼100 atoms in size.
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Affiliation(s)
- Peter Kraus
- School of Molecular and Life Sciences, Curtin University, G.P.O. Box U1987, Perth 6845, Western Australia, Australia
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Xu S, Wang QD, Sun MM, Yin G, Liang J. Benchmark calculations for bond dissociation energies and enthalpy of formation of chlorinated and brominated polycyclic aromatic hydrocarbons. RSC Adv 2021; 11:29690-29701. [PMID: 35479574 PMCID: PMC9040899 DOI: 10.1039/d1ra05391d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 08/31/2021] [Indexed: 01/22/2023] Open
Abstract
Thermodynamic properties, i.e., bond dissociation energies and enthalpy of formation, of chlorinated and brominated polycyclic aromatic hydrocarbons play a fundamental role in understanding their formation mechanisms and reactivity. Computational electronic structure calculations routinely used to predict thermodynamic properties of various species are limited for these compounds due to large computational cost to obtain accurate results by employing high-level wave function theory methods. In this work, a number of composite model chemistry methods (CBS-QB3, G3MP2, G3, and G4) are used to compute bond dissociation energies and enthalpies of formation of small to medium-size chlorinated and brominated polycyclic aromatic hydrocarbon compounds. The enthalpy of formation is derived via the atomization method and compared against the recommended values. Statistical analysis indicates that G4 is the best method. For comparison, three commonly used density functional theory (DFT) methods (M06-2X, ωB97X-D and B2PLYP-D3) with various basis sets including 6-311++G(d, p), cc-pVTZ, and cc-pVQZ in the prediction of bond dissociation energies and enthalpies of formation have been tested using the optimized geometries at the same M06-2X/6-311++G(d, p) level of theory. It is found that ωB97X-D/6-311++G(d, p) shows the best performance in computing the bond dissociation energies, while ωB97X-D/cc-pVTZ exhibits the best prediction in enthalpy of formation of the studied reaction systems. The structural effect on the bond dissociation energies and enthalpy of formation of chlorinated and brominated polycyclic aromatic hydrocarbons are then systematically analyzed. Based on comparisons of the various methods, reliable DFT methods are recommended for future theoretical studies on large chlorinated and brominated polycyclic aromatic hydrocarbons considering both accuracy and computational cost. This work, to the authors' knowledge, is the first to systematically benchmark theoretical methods for the accurate prediction of thermodynamic properties for chlorinated and brominated polycyclic aromatic hydrocarbons. Benchmark calculations using state-of-the-art DFT functionals and composite methods for bond dissociation energy and enthalpy of formation of halogenated polycyclic aromatic hydrocarbons are performed.![]()
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Affiliation(s)
- Shenying Xu
- Faculty of Materials and Chemical Engineering, Yibin University Yibin Sichuan 644000 People's Republic of China
| | - Quan-De Wang
- Faculty of Materials and Chemical Engineering, Yibin University Yibin Sichuan 644000 People's Republic of China .,Low Carbon Energy Institute and School of Chemical Engineering, China University of Mining and Technology Xuzhou 221008 People's Republic of China
| | - Mao-Mao Sun
- Low Carbon Energy Institute and School of Chemical Engineering, China University of Mining and Technology Xuzhou 221008 People's Republic of China
| | - Guoliang Yin
- Faculty of Materials and Chemical Engineering, Yibin University Yibin Sichuan 644000 People's Republic of China
| | - Jinhu Liang
- Faculty of Materials and Chemical Engineering, Yibin University Yibin Sichuan 644000 People's Republic of China .,School of Environment and Safety Engineering, North University of China Taiyuan 030051 People's Republic of China
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Abstract
We calculate complete basis set (CBS) limit-extrapolated ionization potentials (IPs) and electron affinities (EA) with Slater-type basis sets for the molecules in the GW100 database. To this end, we present two new Slater-type orbital (STO) basis sets of triple-(TZ) and quadruple-ζ (QZ) quality, whose polarization is adequate for correlated-electron methods and which contain extra diffuse functions to be able to correctly calculate EAs of molecules with a positive lowest unoccupied molecular orbital (LUMO). We demonstrate that going from TZ to QZ quality consistently reduces the basis set error of our computed IPs and EAs, and we conclude that a good estimate of these quantities at the CBS limit can be obtained by extrapolation. With mean absolute deviations (MAD) from 70 to 85 meV, our CBS limit-extrapolated IP are in good agreement with results from FHI-AIMS, TURBOMOLE, VASP, and WEST, while they differ by more than 130 meV on average from nanoGW. With a MAD of 160 meV, our EA are also in good agreement with the WEST code. Especially for systems with positive LUMOs, the agreement is excellent. With respect to other codes, the STO-type basis sets generally underestimate EAs of small molecules with strongly bound LUMOs. With 62 meV for IPs and 93 meV for EAs, we find much better agreement with CBS limit-extrapolated results from FHI-AIMS for a set of 250 medium to large organic molecules.
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Affiliation(s)
- Arno Förster
- Theoretical Chemistry, Vrije
Universiteit, De Boelelaan
1083, NL-1081 HV Amsterdam, The Netherlands
| | - Lucas Visscher
- Theoretical Chemistry, Vrije
Universiteit, De Boelelaan
1083, NL-1081 HV Amsterdam, The Netherlands
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Cao X, Tian P. "Dividing and Conquering" and "Caching" in Molecular Modeling. Int J Mol Sci 2021; 22:5053. [PMID: 34068835 PMCID: PMC8126232 DOI: 10.3390/ijms22095053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 11/17/2022] Open
Abstract
Molecular modeling is widely utilized in subjects including but not limited to physics, chemistry, biology, materials science and engineering. Impressive progress has been made in development of theories, algorithms and software packages. To divide and conquer, and to cache intermediate results have been long standing principles in development of algorithms. Not surprisingly, most important methodological advancements in more than half century of molecular modeling are various implementations of these two fundamental principles. In the mainstream classical computational molecular science, tremendous efforts have been invested on two lines of algorithm development. The first is coarse graining, which is to represent multiple basic particles in higher resolution modeling as a single larger and softer particle in lower resolution counterpart, with resulting force fields of partial transferability at the expense of some information loss. The second is enhanced sampling, which realizes "dividing and conquering" and/or "caching" in configurational space with focus either on reaction coordinates and collective variables as in metadynamics and related algorithms, or on the transition matrix and state discretization as in Markov state models. For this line of algorithms, spatial resolution is maintained but results are not transferable. Deep learning has been utilized to realize more efficient and accurate ways of "dividing and conquering" and "caching" along these two lines of algorithmic research. We proposed and demonstrated the local free energy landscape approach, a new framework for classical computational molecular science. This framework is based on a third class of algorithm that facilitates molecular modeling through partially transferable in resolution "caching" of distributions for local clusters of molecular degrees of freedom. Differences, connections and potential interactions among these three algorithmic directions are discussed, with the hope to stimulate development of more elegant, efficient and reliable formulations and algorithms for "dividing and conquering" and "caching" in complex molecular systems.
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Affiliation(s)
- Xiaoyong Cao
- School of Life Sciences, Jilin University, Changchun 130012, China;
| | - Pu Tian
- School of Life Sciences, Jilin University, Changchun 130012, China;
- School of Artificial Intelligence, Jilin University, Changchun 130012, China
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