1
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Charry J, Tkatchenko A. van der Waals Radii of Free and Bonded Atoms from Hydrogen (Z = 1) to Oganesson (Z = 118). J Chem Theory Comput 2024; 20:7469-7478. [PMID: 39208255 PMCID: PMC11391583 DOI: 10.1021/acs.jctc.4c00784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Reliable numerical values of van der Waals (vdW) radii are required for constructing empirical force fields, vdW-inclusive density functional, and quantum-chemical methods, as well as for implicit solvent models. However, multiple definitions exist for vdW radii, involving either equilibrium or the closest contact distances between free or bonded atoms within molecules or crystals. For the paradigmatic case of the hydrogen atom, its reported vdW radius fluctuates between 2.15 and 3.70 Bohr depending on the definition, leading to a high uncertainty in calculations and different conceptual interpretations of noncovalent interactions. In this work, we systematically review different definitions and methodologies to establish the free and bonded vdW radii for hydrogen, based on equilibrium vdW distances in noncovalently bonded molecules, enveloping electron density cutoffs, noncovalent positron bonds in hydrogen anion dimer, vacuum virtual photon cloud caused by the hydrogen atom, and atomic dipole polarizability. By doing so, we show that the vdW radius of the free hydrogen atom is 3.16 ± 0.06 Bohr. By employing the most general and elegant definition of atomic vdW radius as a function of the atomic polarizability, we tabulate consistent values of vdW radii for all atoms in the periodic table up to Z = 118.
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Affiliation(s)
- Jorge Charry
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
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2
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Červinka C. Tuning the quasi-harmonic treatment of crystalline ionic liquids within the density functional theory. J Comput Chem 2021; 43:448-456. [PMID: 34958138 DOI: 10.1002/jcc.26804] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 11/06/2022]
Abstract
Five ionic liquids are selected for benchmarking the performance of quasi-harmonic density functional theory (DFT) calculations of structural, phonon, and thermodynamic properties of their crystals. Data predicted by individual computational setups are sorted, establishing a distinct hierarchy among the first-principles approaches. PBE-D3 and B3LYP-D3 functionals are coupled with various plane wave and Gaussian-type orbital (GTO) basis sets. Propagation of the basis set superposition error and of the imperfections of both functionals into finite-temperature properties is discussed in detail. PBE-D3 together with a triple-zeta GTO basis set often yields the most accurate predictions of predicted molar volume and heat capacity with errors at 1% and 8%, respectively, representing the state-of-the-art for quasi-harmonic DFT calculations for crystalline ionic liquids. Fortuitous error cancellation between the basis-set superposition (overbinding) and PBE imperfection (overexpanding) strongly affects the overall accuracy, unlike the case of B3LYP/GTO calculations, impeding systematic convergence of the methodology towards higher accuracy.
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Affiliation(s)
- Ctirad Červinka
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Prague, Czech Republic
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3
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Gale JD, LeBlanc LM, Spackman PR, Silvestri A, Raiteri P. A Universal Force Field for Materials, Periodic GFN-FF: Implementation and Examination. J Chem Theory Comput 2021; 17:7827-7849. [PMID: 34735764 DOI: 10.1021/acs.jctc.1c00832] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In this study, the adaption of the recently published molecular GFN-FF for periodic boundary conditions (pGFN-FF) is described through the use of neighbor lists combined with appropriate charge sums to handle any dimensionality from 1D polymers to 2D surfaces and 3D solids. Numerical integration over the Brillouin zone for the calculation of π bond orders of periodic fragments is also included. Aside from adapting the GFN-FF method to handle periodicity, improvements to the method are proposed in regard to the calculation of topological charges through the inclusion of a screened Coulomb term that leads to more physical charges and avoids a number of pathological cases. Short-range damping of three-body dispersion is also included to avoid collapse of some structures. Analytic second derivatives are also formulated with respect to both Cartesian and strain variables, including prescreening of terms to accelerate the dispersion/coordination number contribution to the Hessian. The modified pGFN-FF scheme is then applied to a wide range of different materials in order to examine how well this universal model performs.
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Affiliation(s)
- Julian D Gale
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University, PO Box U1987, Perth, Western Australia 6845, Australia
| | - Luc M LeBlanc
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University, PO Box U1987, Perth, Western Australia 6845, Australia
| | - Peter R Spackman
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University, PO Box U1987, Perth, Western Australia 6845, Australia
| | - Alessandro Silvestri
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University, PO Box U1987, Perth, Western Australia 6845, Australia
| | - Paolo Raiteri
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University, PO Box U1987, Perth, Western Australia 6845, Australia
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4
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Blaško M, Pašteka LF, Urban M. DFT Functionals for Modeling of Polyethylene Chains Cross-Linked by Metal Atoms. DLPNO-CCSD(T) Benchmark Calculations. J Phys Chem A 2021; 125:7382-7395. [PMID: 34428051 DOI: 10.1021/acs.jpca.1c04793] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Density functional theory (DFT) functionals for calculations of binding energies (BEs) of the polyethylene (PE) chains cross-linked by selected metal atoms (M) are benchmarked against DLPNO-CCSD(T) and DLPNO-CCSD(T1) data. PEX-M-PEX complexes as compared with plain parallel PEX···PEX chains with X = 3-9 carbon atoms are model species characterized by a cooperative effect of covalent C-M-C bonds and interchain dispersion interactions. The accuracy of DLPNO-CC methods was assessed by a comparison of BEs with the canonical CCSD(T) results for small PE3-M-PE3 complexes. Functionals for PEX···PEX and closed-shell PEX-M-PEX complexes (M = Be, Mg, Zn) were benchmarked against DLPNO-CCSD(T) BEs; open-shell complexes (M = Li, Ag, Au) were benchmarked against the DLPNO-CCSD(T1) method with iterative triples. Three dispersion corrections were combined with 25 DFT functionals for calculations of BEs with respect to PEX-M and PEX fragments employing def2-TZVPP and def2-QZVPP basis sets. Accuracy to within 5% for the closed-shell PEX-M-PEX complexes was achieved with five functionals. Less accurate are functionals for the open-shell PEX-M-PEX complexes; only two functionals deviate by less than 15% from DLPNO-CCSD(T1). Particularly problematic were PEX-Li-PEX complexes. A reasonable overall performance across all complexes in terms of the mean absolute percentage error is found for the range-separated hybrid functionals ωB97X-D3 and CAM-B3LYP/D3(BJ)-ABC.
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Affiliation(s)
- Martin Blaško
- FunGlass, A. Dubček University of Trenčín, Študentská 2, 911 50 Trenčín, Slovakia
| | - Lukáš F Pašteka
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Miroslav Urban
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
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5
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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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6
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Petersson GA, Frisch MJ, Dobek F, Zulueta B. Three-Body Dispersion Corrections to the Spherical Atom Model: The PFD-3B Density Functional. J Phys Chem A 2020; 124:10296-10311. [DOI: 10.1021/acs.jpca.0c05940] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- George A. Petersson
- Institute for Computational Molecular Science, Temple University, 1925 N. 12th Street, Philadelphia, Pennsylvania 19122, United States
| | - Michael J. Frisch
- Gaussian, Inc., 340 Quinnipiac Street Building 40, Wallingford, Connecticut 06492, United States
| | - Frank Dobek
- Hall-Atwater Laboratories of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
| | - Barbaro Zulueta
- Institute for Computational Molecular Science, Temple University, 1925 N. 12th Street, Philadelphia, Pennsylvania 19122, United States
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7
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Gonthier JF, Head-Gordon M. Assessing Electronic Structure Methods for Long-Range Three-Body Dispersion Interactions: Analysis and Calculations on Well-Separated Metal Atom Trimers. J Chem Theory Comput 2019; 15:4351-4361. [PMID: 31283231 DOI: 10.1021/acs.jctc.9b00050] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Three-body dispersion interactions are much weaker than their two-body counterpart. However, their importance grows quickly as the number of interacting monomers rises. To explore the numerical performance of correlation methods for long-range three-body dispersion, we performed calculations on eight very simple dispersion-dominated model metal trimers: Na3, Mg3, Zn3, Cd3, Hg3, Cu3, Ag3, and Au3. One encouraging aspect is that relatively small basis sets of augmented triple-ζ size appear to be adequate for three-body dispersion in the long-range. Coupled cluster calculations were performed at high levels to assess MP3, CCSD, CCSD(T), empirical density functional theory dispersion (D3), and the many-body dispersion (MBD) approach. We found that the accuracy of CCSD(T) was generally significantly lower than for two-body interactions, with errors sometimes reaching 20% in the investigated systems, while CCSD and particularly MP3 were generally more erratic. MBD is found to perform better than D3 at large distances, whereas the opposite is true at shorter distances. When computing reference numbers for three-body dispersion, care should be taken to appropriately represent the effect of the connected triple excitations, which are significant in most cases and incompletely approximated by CCSD(T).
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Affiliation(s)
- Jérôme F Gonthier
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry , University of California , Berkeley , California 94720 , United States.,Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
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8
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Carter-Fenk K, Lao KU, Liu KY, Herbert JM. Accurate and Efficient ab Initio Calculations for Supramolecular Complexes: Symmetry-Adapted Perturbation Theory with Many-Body Dispersion. J Phys Chem Lett 2019; 10:2706-2714. [PMID: 31063380 DOI: 10.1021/acs.jpclett.9b01156] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Symmetry-adapted perturbation theory (SAPT) provides a chemically meaningful energy decomposition scheme for nonbonded interactions that is useful for interpretive purposes. Although formally a dimer theory, we have previously introduced an "extended" version (XSAPT) that incorporates many-body polarization via self-consistent charge embedding. Here, we extend the XSAPT methodology to include nonadditive dispersion, using a modified form of the many-body dispersion (MBD) method of Tkatchenko and co-workers. Dispersion interactions beyond the pairwise atom-atom approximation improve total interaction energies even in small systems, and for large π-stacked complexes these corrections can amount to several kilocalories per mole. The XSAPT+MBD method introduced here achieves errors of ≲1 kcal/mol (as compared to high-level ab initio benchmarks) for the L7 data set of large dispersion-bound complexes and ≲4 kcal/mol (as compared to experiment) for the S30L data set of host-guest complexes. This is superior to the best contemporary density functional methods for noncovalent interactions, at comparable or lower cost. XSAPT+MBD represents a promising method for application to supramolecular assemblies, including protein-ligand binding.
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Affiliation(s)
- Kevin Carter-Fenk
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Ka Un Lao
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Kuan-Yu Liu
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
| | - John M Herbert
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
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9
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Lao KU, Herbert JM. A Simple Correction for Nonadditive Dispersion within Extended Symmetry-Adapted Perturbation Theory (XSAPT). J Chem Theory Comput 2018; 14:5128-5142. [DOI: 10.1021/acs.jctc.8b00527] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ka Un Lao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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10
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Lao KU, Herbert JM. Atomic Orbital Implementation of Extended Symmetry-Adapted Perturbation Theory (XSAPT) and Benchmark Calculations for Large Supramolecular Complexes. J Chem Theory Comput 2018; 14:2955-2978. [DOI: 10.1021/acs.jctc.8b00058] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ka Un Lao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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11
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Blaško M, Mach P, Antušek A, Urban M. DFT Modeling of Cross-Linked Polyethylene: Role of Gold Atoms and Dispersion Interactions. J Phys Chem A 2018; 122:1496-1503. [DOI: 10.1021/acs.jpca.7b12232] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martin Blaško
- Department
of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynská Dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Pavel Mach
- Department
of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics
and Informatics, Comenius University, Mlynská Dolina, 84248 Bratislava, Slovakia
| | - Andrej Antušek
- Advanced
Technologies Research Institute, Faculty of Materials Science and
Technology in Trnava, Slovak University of Technology in Bratislava, Bottova 25, 917 24 Trnava, Slovakia
| | - Miroslav Urban
- Department
of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynská Dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia
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