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Lee M, Kim B, Sim M, Sogal M, Kim Y, Yu H, Burke K, Sim E. Correcting Dispersion Corrections with Density-Corrected DFT. J Chem Theory Comput 2024. [PMID: 39120872 DOI: 10.1021/acs.jctc.4c00689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Almost all empirical parametrizations of dispersion corrections in DFT use only energy errors, thereby mixing functional and density-driven errors. We introduce density and dispersion-corrected DFT (D2C-DFT), a dual-calibration approach that accounts for density delocalization errors when parametrizing dispersion interactions. We simply exclude density-sensitive reactions from the training data. We find a significant reduction in both errors and variation among several semilocal functionals and their global hybrids when tailored dispersion corrections are employed with Hartree-Fock densities.
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Affiliation(s)
- Minhyeok Lee
- Department of Chemistry, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul 03722, Korea
| | - Byeongjae Kim
- Department of Chemistry, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul 03722, Korea
| | - Mingyu Sim
- Department of Chemistry, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul 03722, Korea
| | - Mihira Sogal
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Youngsam Kim
- Department of Chemistry, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul 03722, Korea
| | - Hayoung Yu
- Department of Chemistry, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul 03722, Korea
| | - Kieron Burke
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Eunji Sim
- Department of Chemistry, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul 03722, Korea
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2
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Gray M, Herbert JM. Assessing the domain-based local pair natural orbital (DLPNO) approximation for non-covalent interactions in sizable supramolecular complexes. J Chem Phys 2024; 161:054114. [PMID: 39105555 PMCID: PMC11305816 DOI: 10.1063/5.0206533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 07/18/2024] [Indexed: 08/07/2024] Open
Abstract
The titular domain-based local pair natural orbital (DLPNO) approximation is the most widely used method for extending correlated wave function models to large molecular systems, yet its fidelity for intermolecular interaction energies in large supramolecular complexes has not been thoroughly vetted. Non-covalent interactions are sensitive to tails of the electron density and involve nonlocal dispersion that is discarded or approximated if the screening of pair natural orbitals (PNOs) is too aggressive. Meanwhile, the accuracy of the DLPNO approximation is known to deteriorate as molecular size increases. Here, we test the DLPNO approximation at the level of second-order Møller-Plesset perturbation theory (MP2) and coupled-cluster theory with singles, doubles, and perturbative triples [CCSD(T)] for a variety of large supramolecular complexes. DLPNO-MP2 interaction energies are within 3% of canonical values for small dimers with ≲10 heavy atoms, but for larger systems, the DLPNO approximation is often quite poor unless the results are extrapolated to the canonical limit where the threshold for discarding PNOs is taken to zero. Counterpoise correction proves to be essential in reducing errors with respect to canonical results. For a sequence of nanoscale graphene dimers up to (C96H24)2, extrapolated DLPNO-MP2 interaction energies agree with canonical values to within 1%, independent of system size, provided that the basis set does not contain diffuse functions; these cause the DLPNO approximation to behave erratically, such that results cannot be extrapolated in a meaningful way. DLPNO-CCSD(T) calculations are typically performed using looser PNO thresholds as compared to DLPNO-MP2, but this significantly impacts accuracy for large supramolecular complexes. Standard DLPNO-CCSD(T) settings afford errors of 2-6 kcal/mol for dimers involving coronene (C24H12) and circumcoronene (C54H18), even at the DLPNO-CCSD(T1) level.
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Affiliation(s)
- Montgomery Gray
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - John M. Herbert
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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3
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Wei Y, Debnath S, Weber JL, Mahajan A, Reichman DR, Friesner RA. Scalable Ab Initio Electronic Structure Methods with Near Chemical Accuracy for Main Group Chemistry. J Phys Chem A 2024; 128:5796-5807. [PMID: 38970826 DOI: 10.1021/acs.jpca.4c02853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2024]
Abstract
This study evaluates the precision of widely recognized quantum chemical methodologies, CCSD(T), DLPNO-CCSD(T), and localized ph-AFQMC, for determining the thermochemistry of main group elements. DLPNO-CCSD(T) and localized ph-AFQMC, which offer greater scalability compared to canonical CCSD(T), have emerged over the past decade as pivotal in producing precise benchmark chemical data. Our investigation includes closed-shell, neutral molecules, focusing on their heat of formation and atomization energy sourced from four specific small molecule data sets. First, we selected molecules from the G2 and G3 data sets, noted for their reliable experimental heat of formation data. Additionally, we incorporate molecules from the W4-11 and W4-17 sets, which provide high-level theoretical reference values for atomization energy at 0 K. Our findings reveal that both DLPNO-CCSD(T) and ph-AFQMC methods are capable of achieving a root-mean-square deviation of less than 1 kcal/mol across the combined data set, aligning with the threshold for chemical accuracy. Moreover, we make efforts to confine the maximum deviations within 2 kcal/mol, a degree of precision that significantly broadens the applicability of these methods in fields such as biology and materials science.
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Affiliation(s)
- Yujing Wei
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Sibali Debnath
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - John L Weber
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Ankit Mahajan
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - David R Reichman
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Richard A Friesner
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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4
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Menezes F, Popowicz GM. When catchers meet - a computational study on the dimerization of the Buckycatcher. Phys Chem Chem Phys 2023; 25:24031-24041. [PMID: 37646477 DOI: 10.1039/d3cp02903d] [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
We study the dimerization of the buckycatcher in gas phase and in toluene. We created an extensive library of 36 different complexes, which were characterized at semi-empirical and DFT levels. Semi-empirical geometries and dimerization energies compare well against reference data or Density Functional Theory calculations we performed. Born-Oppenheimer molecular dynamics was used to understand what happens when two molecules of the buckycatcher meet, allowing us to infer on the lack of kinetic barriers when dimers form. Thermodynamically, it is possible that room temperature solutions contain dimerized buckycatcher. Using a very simple exchange model, it is shown, however, that dimerization cannot compete thermodynamically against complexation with fullerenes, which accounts for experimental observations.
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Affiliation(s)
- Filipe Menezes
- Institute of Structural Biology, Helmholtz Munich, Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.
| | - Grzegorz Maria Popowicz
- Institute of Structural Biology, Helmholtz Munich, Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.
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5
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Carter-Fenk K, Head-Gordon M. Repartitioned Brillouin-Wigner perturbation theory with a size-consistent second-order correlation energy. J Chem Phys 2023; 158:234108. [PMID: 37338032 PMCID: PMC10284609 DOI: 10.1063/5.0150033] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023] Open
Abstract
Second-order Møller-Plesset perturbation theory (MP2) often breaks down catastrophically in small-gap systems, leaving much to be desired in its performance for myriad chemical applications such as noncovalent interactions, thermochemistry, and dative bonding in transition metal complexes. This divergence problem has reignited interest in Brillouin-Wigner perturbation theory (BWPT), which is regular at all orders but lacks size consistency and extensivity, severely limiting its application to chemistry. In this work, we propose an alternative partitioning of the Hamiltonian that leads to a regular BWPT perturbation series that, through the second order, is size-extensive, size-consistent (provided its Hartree-Fock reference is also), and orbital invariant. Our second-order size-consistent Brillouin-Wigner (BW-s2) approach can describe the exact dissociation limit of H2 in a minimal basis set, regardless of the spin polarization of the reference orbitals. More broadly, we find that BW-s2 offers improvements relative to MP2 for covalent bond breaking, noncovalent interaction energies, and metal/organic reaction energies, although rivaling coupled-cluster with single and double substitutions for thermochemical properties.
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Affiliation(s)
- Kevin Carter-Fenk
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
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6
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Grygier P, Pustelny K, Nowak J, Golik P, Popowicz GM, Plettenburg O, Dubin G, Menezes F, Czarna A. Silmitasertib (CX-4945), a Clinically Used CK2-Kinase Inhibitor with Additional Effects on GSK3β and DYRK1A Kinases: A Structural Perspective. J Med Chem 2023; 66:4009-4024. [PMID: 36883902 PMCID: PMC10041529 DOI: 10.1021/acs.jmedchem.2c01887] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
A clinical casein kinase 2 inhibitor, CX-4945 (silmitasertib), shows significant affinity toward the DYRK1A and GSK3β kinases, involved in down syndrome phenotypes, Alzheimer's disease, circadian clock regulation, and diabetes. This off-target activity offers an opportunity for studying the effect of the DYRK1A/GSK3β kinase system in disease biology and possible line extension. Motivated by the dual inhibition of these kinases, we solved and analyzed the crystal structures of DYRK1A and GSK3β with CX-4945. We built a quantum-chemistry-based model to rationalize the compound affinity for CK2α, DYRK1A, and GSK3β kinases. Our calculations identified a key element for CK2α's subnanomolar affinity to CX-4945. The methodology is expandable to other kinase selectivity modeling. We show that the inhibitor limits DYRK1A- and GSK3β-mediated cyclin D1 phosphorylation and reduces kinase-mediated NFAT signaling in the cell. Given the CX-4945's clinical and pharmacological profile, this inhibitory activity makes it an interesting candidate with potential for application in additional disease areas.
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Affiliation(s)
- Przemyslaw Grygier
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland
| | - Katarzyna Pustelny
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland
| | - Jakub Nowak
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland
| | | | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum Muenchen, Ingolstaedter Landstrasse 1, Neuherberg 85764, Germany
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstrasse 4, Garching 85747, Germany
| | - Oliver Plettenburg
- Institute of Medicinal Chemistry, Helmholtz Munich, Ingolstaedter Landstrasse 1, Neuherberg 85764, Germany
- Institute of Organic Chemistry, Centre of Biomolecular Drug Research (BMWZ) and Laboratory of Nano and Quantum Engineering (LNQE), Leibniz University Hannover, Schneiderberg 1b, Hannover 30167, Germany
- German Center for Diabetes Research (DZD), Ingolstaedter Landstrasse 1, Neuherberg 85764, Germany
- Institute of Lung Health (ILH), Aulweg 130, Giessen 35392, Germany
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland
| | - Filipe Menezes
- Institute of Structural Biology, Helmholtz Zentrum Muenchen, Ingolstaedter Landstrasse 1, Neuherberg 85764, Germany
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstrasse 4, Garching 85747, Germany
| | - Anna Czarna
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland
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Menezes F, Popowicz GM. A Buckycatcher in Solution-A Computational Perspective. Molecules 2023; 28:molecules28062841. [PMID: 36985812 PMCID: PMC10056437 DOI: 10.3390/molecules28062841] [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: 02/24/2023] [Revised: 03/17/2023] [Accepted: 03/19/2023] [Indexed: 03/30/2023] Open
Abstract
In this work, we study the buckycatcher (C60H28) in solution using quantum chemical models. We investigate the conformational equilibria in several media and the effects that molecules of solvent might have in interconversion barriers between the different conformers. These are studied in a hypothetical gas phase, in the dielectric of a solvent, as well as with hybrid solvation. In the latter case, due to a disruption of π-stacking interactions, the transition states are destabilized. We also evaluate the complexation of the buckycatcher with solvent-like molecules. In most cases studied, there should be no adducts formed because the enthalpy driving force cannot overcome entropic penalties.
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Affiliation(s)
- Filipe Menezes
- Institute of Structural Biology, Helmholtz Zentrum Muenchen, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum Muenchen, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
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8
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Li W, Wang D, Lao KU, Wang X. Inclusion Complexation of S-Nitrosoglutathione for Sustained Nitric Oxide Release from Catheter Surfaces: A Strategy to Prevent and Treat Device-Associated Infections. ACS Biomater Sci Eng 2023; 9:1694-1705. [PMID: 36542753 DOI: 10.1021/acsbiomaterials.2c01284] [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: 12/24/2022]
Abstract
S-Nitrosoglutathione (GSNO) is a nontoxic nitric oxide (NO)-donating compound that occurs naturally in the human body. The use of GSNO to deliver exogenous NO for therapeutic and protective applications is limited by the high lability of dissolved GSNO in aqueous formulations. In this paper, we report a host-guest chemistry-based strategy to modulate the GSNO reactivity and NO release kinetics for the design of anti-infective catheters and hydrogels. Cyclodextrins (CDs) are host molecules that are typically used to encapsulate hydrophobic guest molecules into their hydrophobic cavities. However, we found that CDs form inclusion complexes with GSNO, an extremely hydrophilic molecule with a solubility of over 1 M at physiological pH. More interestingly, the host-guest complexation reduces the decomposition reactivity of GSNO in the order of αCD > γCD > hydroxypropyl βCD. The lifetime of 0.1 M GSNO is increased to up to 15 days in the presence of CDs at 37 °C, which is more than twice the lifetime of free GSNO. Quantum chemistry calculations indicate that GSNO in αCD undergoes a conformational change that significantly reduces the S-NO bond distance and increases its stability. The calculated S-NO bond dissociation enthalpies of free and complexed GSNO well agree with the experimentally observed GSNO decomposition kinetics. The NO release from GSNO-CD solutions, compared to GSNO solutions, has suppressed initial bursts and extended durations, enhancing the safety and efficacy of NO-based therapies and device protections. In an example application as an anti-infective lock solution for intravascular catheters, the GSNO-αCD solution exhibits potent antibacterial activities for both planktonic and biofilm bacteria, both intraluminal and extraluminal environments, both prevention and treatment of infections, and against multiple bacterial strains, including a multidrug-resistant strain. In addition to solutions, the inclusion complexation also enables the preparation of GSNO hydrogels with enhanced stability and improved antibacterial efficacy. Since methods to suppress and control the GSNO decomposition rate are rare, this supramolecular strategy provides new opportunities for the formulation and application of this natural NO donor.
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Affiliation(s)
- Wuwei Li
- Department of Chemistry, Virginia Commonwealth University, 1001 W. Main Street, Richmond, Virginia 23284, United States
| | - Danyang Wang
- Department of Chemistry, Virginia Commonwealth University, 1001 W. Main Street, Richmond, Virginia 23284, United States
| | - Ka Un Lao
- Department of Chemistry, Virginia Commonwealth University, 1001 W. Main Street, Richmond, Virginia 23284, United States
| | - Xuewei Wang
- Department of Chemistry, Virginia Commonwealth University, 1001 W. Main Street, Richmond, Virginia 23284, United States
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9
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Villot C, Lao KU. Electronic structure theory on modeling short-range noncovalent interactions between amino acids. J Chem Phys 2023; 158:094301. [PMID: 36889981 DOI: 10.1063/5.0138032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
While short-range noncovalent interactions (NCIs) are proving to be of importance in many chemical and biological systems, these atypical bindings happen within the so-called van der Waals envelope and pose an enormous challenge for current computational methods. We introduce SNCIAA, a database of 723 benchmark interaction energies of short-range noncovalent interactions between neutral/charged amino acids originated from protein x-ray crystal structures at the "gold standard" coupled-cluster with singles, doubles, and perturbative triples/complete basis set [CCSD(T)/CBS] level of theory with a mean absolute binding uncertainty less than 0.1 kcal/mol. Subsequently, a systematic assessment of commonly used computational methods, such as the second-order Møller-Plesset theory (MP2), density functional theory (DFT), symmetry-adapted perturbation theory (SAPT), composite electronic-structure methods, semiempirical approaches, and the physical-based potentials with machine learning (IPML) on SNCIAA is carried out. It is shown that the inclusion of dispersion corrections is essential even though these dimers are dominated by electrostatics, such as hydrogen bondings and salt bridges. Overall, MP2, ωB97M-V, and B3LYP+D4 turned out to be the most reliable methods for the description of short-range NCIs even in strongly attractive/repulsive complexes. SAPT is also recommended in describing short-range NCIs only if the δMP2 correction has been included. The good performance of IPML for dimers at close-equilibrium and long-range conditions is not transferable to the short-range. We expect that SNCIAA will assist the development/improvement/validation of computational methods, such as DFT, force-fields, and ML models, in describing NCIs across entire potential energy surfaces (short-, intermediate-, and long-range NCIs) on the same footing.
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Affiliation(s)
- Corentin Villot
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, USA
| | - Ka Un Lao
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, USA
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10
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A Cost Effective Scheme for the Highly Accurate Description of Intermolecular Binding in Large Complexes. Int J Mol Sci 2022; 23:ijms232415773. [PMID: 36555413 PMCID: PMC9780852 DOI: 10.3390/ijms232415773] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/23/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022] Open
Abstract
There has been a growing interest in quantitative predictions of the intermolecular binding energy of large complexes. One of the most important quantum chemical techniques capable of such predictions is the domain-based local pair natural orbital (DLPNO) scheme for the coupled cluster theory with singles, doubles, and iterative triples [CCSD(T)], whose results are extrapolated to the complete basis set (CBS) limit. Here, the DLPNO-based focal-point method is devised with the aim of obtaining CBS-extrapolated values that are very close to their canonical CCSD(T)/CBS counterparts, and thus may serve for routinely checking a performance of less expensive computational methods, for example, those based on the density-functional theory (DFT). The efficacy of this method is demonstrated for several sets of noncovalent complexes with varying amounts of the electrostatics, induction, and dispersion contributions to binding (as revealed by accurate DFT-based symmetry-adapted perturbation theory (SAPT) calculations). It is shown that when applied to dimeric models of poly(3-hydroxybutyrate) chains in its two polymorphic forms, the DLPNO-CCSD(T) and DFT-SAPT computational schemes agree to within about 2 kJ/mol of an absolute value of the interaction energy. These computational schemes thus should be useful for a reliable description of factors leading to the enthalpic stabilization of extended systems.
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11
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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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12
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Gray M, Bowling PE, Herbert JM. Systematic Evaluation of Counterpoise Correction in Density Functional Theory. J Chem Theory Comput 2022; 18:6742-6756. [PMID: 36251499 DOI: 10.1021/acs.jctc.2c00883] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A widespread belief persists that the Boys-Bernardi function counterpoise (CP) procedure "overcorrects" supramolecular interaction energies for the effects of basis-set superposition error. To the extent that this is true for correlated wave function methods, it is usually an artifact of low-quality basis sets. The question has not been considered systematically in the context of density functional theory, however, where basis-set convergence is generally less problematic. We present a systematic assessment of the CP procedure for a representative set of functionals and basis sets, considering both benchmark data sets of small dimers and larger supramolecular complexes. The latter include layered composite polymers with ∼150 atoms and ligand-protein models with ∼300 atoms. Provided that CP correction is used, we find that intermolecular interaction energies of nearly complete-basis quality can be obtained using only double-ζ basis sets. This is less expensive as compared to triple-ζ basis sets without CP correction. CP-corrected interaction energies are less sensitive to the presence of diffuse basis functions as compared to uncorrected energies, which is important because diffuse functions are expensive and often numerically problematic for large systems. Our results upend the conventional wisdom that CP "overcorrects" for basis-set incompleteness. In small basis sets, CP correction is mandatory in order to demonstrate that the results do not rest on error cancellation.
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Affiliation(s)
- Montgomery Gray
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio43210, United States
| | - Paige E Bowling
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio43210, United States.,Biophysics Graduate Program, The Ohio State University, Columbus, Ohio43210, United States
| | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio43210, United States.,Biophysics Graduate Program, The Ohio State University, Columbus, Ohio43210, United States
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13
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Gorges J, Grimme S, Hansen A. Reliable prediction of association (free) energies of supramolecular complexes with heavy main group elements – the HS13L benchmark set. Phys Chem Chem Phys 2022; 24:28831-28843. [DOI: 10.1039/d2cp04049b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We introduce a set of 13 supramolecular complexes featuring diverse non-covalent interactions with heavy main group elements (Zn, As, Se, Te, Br, I), high charges (−2 up to +4), and large systems with up to 266 atoms (HS13L).
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Affiliation(s)
- Johannes Gorges
- Mulliken Center for Theoretical Chemistry, Clausius-Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Clausius-Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Clausius-Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
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