1
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Urban L, Laqua H, Thompson TH, Ochsenfeld C. Efficient Exploitation of Numerical Quadrature with Distance-Dependent Integral Screening in Explicitly Correlated F12 Theory: Linear Scaling Evaluation of the Most Expensive RI-MP2-F12 Term. J Chem Theory Comput 2024; 20:3706-3718. [PMID: 38626443 PMCID: PMC11099969 DOI: 10.1021/acs.jctc.4c00193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/23/2024] [Accepted: 03/25/2024] [Indexed: 04/18/2024]
Abstract
We present a linear scaling atomic orbital based algorithm for the computation of the most expensive exchange-type RI-MP2-F12 term by employing numerical quadrature in combination with CABS-RI to avoid six-center-three-electron integrals. Furthermore, a robust distance-dependent integral screening scheme, based on integral partition bounds [Thompson, T. H.; Ochsenfeld, C. J. Chem. Phys. 2019, 150, 044101], is used to drastically reduce the number of the required three-center-one-electron integrals substantially. The accuracy of our numerical quadrature/CABS-RI approach and the corresponding integral screening is thoroughly assessed for interaction and isomerization energies across a variety of numerical integration grids. Our method outperforms the standard density fitting/CABS-RI approach with errors below 1 μEh even for small grid sizes and moderate screening thresholds. The choice of the grid size and screening threshold allows us to tailor our ansatz to a desired accuracy and computational efficiency. We showcase the approach's effectiveness for the chemically relevant system valinomycin, employing a triple-ζ F12 basis set combination (C54H90N6O18, 5757 AO basis functions, 10,266 CABS basis functions, 735,783 grid points). In this context, our ansatz achieves higher accuracy combined with a 135× speedup compared to the classical density fitting based variant, requiring notably less computation time than the corresponding RI-MP2 calculation. Additionally, we demonstrate near-linear scaling through calculations on linear alkanes. We achieved an 817-fold acceleration for C80H162 and an extrapolated 28,765-fold acceleration for C200H402, resulting in a substantially reduced computational time for the latter─from 229 days to just 11.5 min. Our ansatz may also be adapted to the remaining MP2-F12 terms, which will be the subject of future work.
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Affiliation(s)
- Lars Urban
- Chair
of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), D-81377 Munich, Germany
- Max
Planck Institute for Solid State Research, D-70569 Stuttgart, Germany
| | - Henryk Laqua
- Chair
of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), D-81377 Munich, Germany
| | - Travis H. Thompson
- Chair
of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), D-81377 Munich, Germany
| | - Christian Ochsenfeld
- Chair
of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), D-81377 Munich, Germany
- Max
Planck Institute for Solid State Research, D-70569 Stuttgart, Germany
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2
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Nakajima Y, Ohmura T, Seino J. Using atomic clustering based on structural and electronic descriptors that consider surrounding environment to evaluate local properties of DFT functionals. J Comput Chem 2024. [PMID: 38686778 DOI: 10.1002/jcc.27375] [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: 11/12/2023] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024]
Abstract
We developed a method for evaluating the accuracies of the local properties of DFT functionals in detail using a clustering method based on machine learning and structural/electronic descriptors. We generated 36 clusters consistent with human intuition using 30,436 carbon atoms from the QM9 dataset. The results were used to evaluate 13C NMR chemical shifts calculated using 84 DFT functionals. Carbon atoms were grouped based on their similar environments, reducing errors within these groups. This enables more accurate assessment of the accuracy using a specific DFT functional. Therefore, the present atomic clustering provides more detailed insight into accuracy verification.
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Affiliation(s)
- Yuya Nakajima
- Waseda Research Institute for Science and Engineering, Tokyo, Japan
| | - Takuto Ohmura
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Junji Seino
- Waseda Research Institute for Science and Engineering, Tokyo, Japan
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
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3
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Li H, Brémond E, Sancho-García JC, Pérez-Jiménez ÁJ, Scalmani G, Frisch MJ, Adamo C. Axial-equatorial equilibrium in substituted cyclohexanes: a DFT perspective on a small but complex problem. Phys Chem Chem Phys 2024; 26:8094-8105. [PMID: 38384253 DOI: 10.1039/d3cp06141h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
In Chemistry, complexity is not necessarily associated to large systems, as illustrated by the textbook example of axial-equatorial equilibrium in mono-substituted cyclohexanes. The difficulty in modelling such a simple isomerization is related to the need for reproducing the delicate balance between two forces, with opposite effects, namely the attractive London dispersion and the repulsive steric interactions. Such balance is a stimulating challenge for density-functional approximations and it is systematically explored here by considering 20 mono-substituted cyclohexanes. In comparison to highly accurate CCSD(T) reference calculations, their axial-equatorial equilibrium is studied with a large set of 48 exchange-correlation approximations, spanning from semilocal to hybrid to more recent double hybrid functionals. This dataset, called SAV20 (as Steric A-values for 20 molecules), allows to highlight the difficulties encountered by common and more original DFT approaches, including those corrected for dispersion with empirical potentials, the 6-31G*-ACP model, and our cost-effective PBE-QIDH/DH-SVPD protocol, in modeling these challenging interactions. Interestingly, the performance of the approaches considered in this contribution on the SAV20 dataset does not correlate with that obtained with other more standard datasets, such as S66, IDISP or NC15, thus indicating that SAV20 covers physicochemical features not already considered in previous noncovalent interaction benchmarks.
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Affiliation(s)
- Hanwei Li
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Health and Life Sciences, F-75005 Paris, France.
| | - Eric Brémond
- Université Paris Cité, ITODYS, CNRS, F-75006 Paris, France
| | | | | | | | | | - Carlo Adamo
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Health and Life Sciences, F-75005 Paris, France.
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4
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Li W, Wang Y, Ni Z, Li S. Cluster-in-Molecule Local Correlation Method for Dispersion Interactions in Large Systems and Periodic Systems. Acc Chem Res 2023; 56:3462-3474. [PMID: 37991873 DOI: 10.1021/acs.accounts.3c00538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
ConspectusThe noncovalent interactions, including dispersion interactions, control the structures and stabilities of complex chemical systems, including host-guest complexes and the adsorption process of molecules on the solid surfaces. The density functional theory (DFT) with empirical dispersion correction is now the working horse in many areas of applications. Post-Hartree-Fock (post-HF) methods have been well recognized to provide more accurate descriptions in a systematic way. However, traditional post-HF methods are mainly limited to small- or medium-sized systems, and their applications to periodic condensed phase systems are still very limited due to their expensive computational costs.To extend post-HF calculations to large molecules, the cluster-in-molecule (CIM) local correlation approach has been established, allowing highly accurate electron correlation calculations that are routinely available for very large systems. In the CIM approach, the electron correlation energy of a large molecule could be obtained from electron correlation calculations on a series of clusters, each of which contains a subset of occupied and virtual localized molecular orbitals. The CIM method could be massively and efficiently parallelized on general computer clusters. The CIM method has been implemented at various electron correlation levels, including second-order Mo̷ller-Plesset perturbation theory (MP2), coupled cluster singles and doubles (CCSD), CCSD with perturbative triples correction [CCSD(T)], etc. The CIM-MP2 energy gradient algorithm was developed and applied to the geometry optimizations of large systems. The CIM method has also been extended to condensed-phase systems under periodic boundary conditions (PBC-CIM). For periodic systems, the correlation energy per unit cell could be evaluated with correlation energy contributions from a series of clusters that are built with localized Wannier functions.CIM-based electron correlation calculations have been employed to investigate a number of chemical problems in which the dispersion interaction is important. CIM-based post-HF methods including CIM domain-based local pair natural orbital (DLPNO) CCSD(T) are applied to compute the relative or binding energies of biological systems or supramolecular complexes, the reaction barrier in a relatively complex chemical reaction. The CIM-MP2 method is used to obtain the optimized geometry of large systems. CIM-based post-HF calculations have also been used to compute the cohesive energies of molecular crystals and adsorption energies of molecules on the solid surfaces. The CIM and its PBC variant are expected to become a powerful theoretical tool for accurate calculations of the energies and structures for a broad range of large systems and condensed-phase systems with significant dispersion interactions.
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Affiliation(s)
- Wei Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Yuqi Wang
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Zhigang Ni
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, People's Republic of China
| | - Shuhua Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
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5
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Zhugayevych A, Sun W, van der Heide T, Lien-Medrano CR, Frauenheim T, Tretiak S. Benchmark Data Set of Crystalline Organic Semiconductors. J Chem Theory Comput 2023; 19:8481-8490. [PMID: 37969072 PMCID: PMC10688188 DOI: 10.1021/acs.jctc.3c00861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/17/2023]
Abstract
This work reports a Benchmark Data set of Crystalline Organic Semiconductors to test calculations of the structural and electronic properties of these materials in the solid state. The data set contains 67 crystals consisting of mostly rigid molecules with a single dominant conformer, covering the majority of known structural types. The experimental crystal structure is available for the entire data set, whereas zero-temperature unit cell volume can be reliably estimated for a subset of 28 crystals. Using this subset, we benchmark r2SCAN-D3 and PBE-D3 density functionals. Then, for the entire data set, we benchmark approximate density functional theory (DFT) methods, including GFN1-xTB and DFTB3(3ob-3-1), with various dispersion corrections against r2SCAN-D3. Our results show that r2SCAN-D3 geometries are accurate within a few percent, which is comparable to the statistical uncertainty of experimental data at a fixed temperature, but the unit cell volume is systematically underestimated by 2% on average. The several times faster PBE-D3 provides an unbiased estimate of the volume for all systems except for molecules with highly polar bonds, for which the volume is substantially overestimated in correlation with the underestimation of atomic charges. Considered approximate DFT methods are orders of magnitude faster and provide qualitatively correct but overcompressed crystal structures unless the dispersion corrections are fitted by unit cell volume.
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Affiliation(s)
- Andriy Zhugayevych
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Wenbo Sun
- Bremen
Center for Computational Materials Science, Am Fallturm 1, 28359 Bremen, Germany
| | - Tammo van der Heide
- Bremen
Center for Computational Materials Science, Am Fallturm 1, 28359 Bremen, Germany
| | | | - Thomas Frauenheim
- Bremen
Center for Computational Materials Science, Am Fallturm 1, 28359 Bremen, Germany
| | - Sergei Tretiak
- Los
Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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6
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Friede M, Ehlert S, Grimme S, Mewes JM. Do Optimally Tuned Range-Separated Hybrid Functionals Require a Reparametrization of the Dispersion Correction? It Depends. J Chem Theory Comput 2023; 19:8097-8107. [PMID: 37955590 DOI: 10.1021/acs.jctc.3c00717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
For ground- and excited-state studies of large molecules, it is the state of the art to combine (time-dependent) DFT with dispersion-corrected range-separated hybrid functionals (RSHs), which ensures an asymptotically correct description of exchange effects and London dispersion. Specifically for studying excited states, it is common practice to tune the range-separation parameter ω (optimal tuning), which can further improve the accuracy. However, since optimal tuning essentially changes the functional, it is unclear if and how much the parameters used for the dispersion correction depend on the chosen ω value. To answer this question, we explore this interdependency by refitting the DFT-D4 dispersion model for six established RSHs over a wide range of ω values (0.05-0.45 a0-1) using a set of noncovalently bound molecular complexes. The results reveal some surprising differences among the investigated functionals: While PBE-based RSHs and ωB97M-D4 generally exhibit a weak interdependency and robust performance over a wide range of ω values, B88-based RSHs, specifically LC-BLYP, are strongly affected. For these, even a minor reduction of ω from the default value manifests in strong systematic overbinding and poor performance in the typical range of optimally tuned ω values. Finally, we discuss strategies to mitigate these issues and reflect the results in the context of the employed D4 parameter optimization algorithm and fit set, outlining strategies for future improvements.
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Affiliation(s)
- Marvin Friede
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Sebastian Ehlert
- AI4Science, Microsoft Research, Evert van de Beekstraat 354, 1118 CZ Schiphol, The Netherlands
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Jan-Michael Mewes
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
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7
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Lemke Y, Ochsenfeld C. Highly accurate σ- and τ-functionals for beyond-RPA methods with approximate exchange kernels. J Chem Phys 2023; 159:194104. [PMID: 37966000 DOI: 10.1063/5.0173042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 10/12/2023] [Indexed: 11/16/2023] Open
Abstract
σ-Functionals are promising new developments for the Kohn-Sham correlation energy based upon the direct Random Phase Approximation (dRPA) within the adiabatic connection formalism, providing impressive improvements over dRPA for a broad range of benchmarks. However, σ-functionals exhibit a high amount of self-interaction inherited from the approximations made within dRPA. Inclusion of an exchange kernel in deriving the coupling-strength-dependent density-density response function leads to so-called τ-functionals, which - apart from a fourth-order Taylor series expansion - have only been realized in an approximate fashion so far to the best of our knowledge, most notably in the form of scaled σ-functionals. In this work, we derive, optimize, and benchmark three types of σ- and τ-functionals including approximate exchange effects in the form of an antisymmetrized Hartree kernel. These functionals, based on a second-order screened exchange type contribution in the adiabatic connection formalism, the electron-hole time-dependent Hartree-Fock kernel (eh-TDHF) otherwise known as RPA with exchange (RPAx), and an approximation thereof known as approximate exchange kernel (AXK), are optimized on the ASCDB database using two new parametrizations named A1 and A2. In addition, we report a first full evaluation of σ- and τ-functionals on the GMTKN55 database, revealing our exchange-including functionals to considerably outperform existing σ-functionals while being highly competitive with some of the best double-hybrid functionals of the original GMTKN55 publication. In particular, the σ-functionals based on AXK and τ-functionals based on RPAx with PBE0 reference stand out as highly accurate approaches for a wide variety of chemically relevant problems.
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Affiliation(s)
- Yannick Lemke
- Chair of Theoretical Chemistry, Department of Chemistry, Ludwig-Maximilians-Universität München (LMU), Butenandtstr. 5-13, D-81377 Munich, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, Ludwig-Maximilians-Universität München (LMU), Butenandtstr. 5-13, D-81377 Munich, Germany
- Max-Planck-Institute for Solid State Research, Heisenbergstr. 1, D-70569 Stuttgart, Germany
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8
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Thürlemann M, Riniker S. Hybrid classical/machine-learning force fields for the accurate description of molecular condensed-phase systems. Chem Sci 2023; 14:12661-12675. [PMID: 38020395 PMCID: PMC10646964 DOI: 10.1039/d3sc04317g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Electronic structure methods offer in principle accurate predictions of molecular properties, however, their applicability is limited by computational costs. Empirical methods are cheaper, but come with inherent approximations and are dependent on the quality and quantity of training data. The rise of machine learning (ML) force fields (FFs) exacerbates limitations related to training data even further, especially for condensed-phase systems for which the generation of large and high-quality training datasets is difficult. Here, we propose a hybrid ML/classical FF model that is parametrized exclusively on high-quality ab initio data of dimers and monomers in vacuum but is transferable to condensed-phase systems. The proposed hybrid model combines our previous ML-parametrized classical model with ML corrections for situations where classical approximations break down, thus combining the robustness and efficiency of classical FFs with the flexibility of ML. Extensive validation on benchmarking datasets and experimental condensed-phase data, including organic liquids and small-molecule crystal structures, showcases how the proposed approach may promote FF development and unlock the full potential of classical FFs.
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Affiliation(s)
- Moritz Thürlemann
- Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir-Prelog-Weg 2 Zürich 8093 Switzerland
| | - Sereina Riniker
- Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir-Prelog-Weg 2 Zürich 8093 Switzerland
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9
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Neugebauer H, Pinski P, Grimme S, Neese F, Bursch M. Assessment of DLPNO-MP2 Approximations in Double-Hybrid DFT. J Chem Theory Comput 2023; 19:7695-7703. [PMID: 37862406 PMCID: PMC10653103 DOI: 10.1021/acs.jctc.3c00896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Indexed: 10/22/2023]
Abstract
The unfavorable scaling (N5) of the conventional second-order Møller-Plesset theory (MP2) typically prevents the application of double-hybrid (DH) density functionals to large systems with more than 100 atoms. A prominent approach to reduce the computational demand of electron correlation methods is the domain-based local pair natural orbital (DLPNO) approximation that is successfully used in the framework of DLPNO-CCSD(T). Its extension to MP2 [Pinski P.; Riplinger, C.; Valeev, E. F.; Neese, F. J. Chem. Phys. 2015, 143, 034108.] paved the way for DLPNO-based DH (DLPNO-DH) methods. In this work, we assess the accuracy of the DLPNO-DH approximation compared to conventional DHs on a large number of 7925 data points for thermochemistry and 239 data points for structural features, including main-group and transition-metal systems. It is shown that DLPNO-DH-DFT can be applied successfully to perform energy calculations and geometry optimizations for large molecules at a drastically reduced computational cost. Furthermore, PNO space extrapolation is shown to be applicable, similar to its DLPNO-CCSD(T) counterpart, to reduce the remaining error.
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Affiliation(s)
- Hagen Neugebauer
- Mulliken
Center for Theoretical Chemistry, Clausius Institute for Physical
and Theoretical Chemistry, University of
Bonn, Beringstraße 4, D-53115 Bonn, Germany
| | - Peter Pinski
- HQS
Quantum Simulations GmbH, Rintheimer Straße 23, D-76131 Karlsruhe, Germany
| | - Stefan Grimme
- Mulliken
Center for Theoretical Chemistry, Clausius Institute for Physical
and Theoretical Chemistry, University of
Bonn, Beringstraße 4, D-53115 Bonn, Germany
| | - Frank Neese
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Markus Bursch
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
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10
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Carter-Fenk K, Shee J, Head-Gordon M. Optimizing the regularization in size-consistent second-order Brillouin-Wigner perturbation theory. J Chem Phys 2023; 159:171104. [PMID: 37933781 PMCID: PMC10752296 DOI: 10.1063/5.0174923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/09/2023] [Indexed: 11/08/2023] Open
Abstract
Despite its simplicity and relatively low computational cost, second-order Møller-Plesset perturbation theory (MP2) is well-known to overbind noncovalent interactions between polarizable monomers and some organometallic bonds. In such situations, the pairwise-additive correlation energy expression in MP2 is inadequate. Although energy-gap dependent amplitude regularization can substantially improve the accuracy of conventional MP2 in these regimes, the same regularization parameter worsens the accuracy for small molecule thermochemistry and density-dependent properties. Recently, we proposed a repartitioning of Brillouin-Wigner perturbation theory that is size-consistent to second order (BW-s2), and a free parameter (α) was set to recover the exact dissociation limit of H2 in a minimal basis set. Alternatively α can be viewed as a regularization parameter, where each value of α represents a valid variant of BW-s2, which we denote as BW-s2(α). In this work, we semi-empirically optimize α for noncovalent interactions, thermochemistry, alkane conformational energies, electronic response properties, and transition metal datasets, leading to improvements in accuracy relative to the ab initio parameterization of BW-s2 and MP2. We demonstrate that the optimal α parameter (α = 4) is more transferable across chemical problems than energy-gap-dependent regularization parameters. This is attributable to the fact that the BW-s2(α) regularization strength depends on all of the information encoded in the t amplitudes rather than just orbital energy differences. While the computational scaling of BW-s2(α) is iterative O(N5), this effective and transferable approach to amplitude regularization is a promising route to incorporate higher-order correlation effects at second-order cost.
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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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11
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Graf D, Thom AJW. Corrected density functional theory and the random phase approximation: Improved accuracy at little extra cost. J Chem Phys 2023; 159:174106. [PMID: 37921249 DOI: 10.1063/5.0168569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023] Open
Abstract
We recently introduced an efficient methodology to perform density-corrected Hartree-Fock density functional theory [DC(HF)-DFT] calculations and an extension to it we called "corrected" HF DFT [C(HF)-DFT] [Graf and Thom, J. Chem. Theory Comput. 19 5427-5438 (2023)]. In this work, we take a further step and combine C(HF)-DFT, augmented with a straightforward orbital energy correction, with the random phase approximation (RPA). We refer to the resulting methodology as corrected HF RPA [C(HF)-RPA]. We evaluate the proposed methodology across various RPA methods: direct RPA (dRPA), RPA with an approximate exchange kernel, and RPA with second-order screened exchange. C(HF)-dRPA demonstrates very promising performance; for RPA with exchange methods, on the other hand, we often find over-corrections.
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Affiliation(s)
- Daniel Graf
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, England
| | - Alex J W Thom
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, England
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12
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Hermann J, Stöhr M, Góger S, Chaudhuri S, Aradi B, Maurer RJ, Tkatchenko A. libMBD: A general-purpose package for scalable quantum many-body dispersion calculations. J Chem Phys 2023; 159:174802. [PMID: 37933783 DOI: 10.1063/5.0170972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 10/17/2023] [Indexed: 11/08/2023] Open
Abstract
Many-body dispersion (MBD) is a powerful framework to treat van der Waals (vdW) dispersion interactions in density-functional theory and related atomistic modeling methods. Several independent implementations of MBD with varying degree of functionality exist across a number of electronic structure codes, which both limits the current users of those codes and complicates dissemination of new variants of MBD. Here, we develop and document libMBD, a library implementation of MBD that is functionally complete, efficient, easy to integrate with any electronic structure code, and already integrated in FHI-aims, DFTB+, VASP, Q-Chem, CASTEP, and Quantum ESPRESSO. libMBD is written in modern Fortran with bindings to C and Python, uses MPI/ScaLAPACK for parallelization, and implements MBD for both finite and periodic systems, with analytical gradients with respect to all input parameters. The computational cost has asymptotic cubic scaling with system size, and evaluation of gradients only changes the prefactor of the scaling law, with libMBD exhibiting strong scaling up to 256 processor cores. Other MBD properties beyond energy and gradients can be calculated with libMBD, such as the charge-density polarization, first-order Coulomb correction, the dielectric function, or the order-by-order expansion of the energy in the dipole interaction. Calculations on supramolecular complexes with MBD-corrected electronic structure methods and a meta-review of previous applications of MBD demonstrate the broad applicability of the libMBD package to treat vdW interactions.
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Affiliation(s)
- Jan Hermann
- Department of Mathematics and Computer Science, FU Berlin, 14195 Berlin, Germany
| | - Martin Stöhr
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Szabolcs Góger
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Shayantan Chaudhuri
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Bálint Aradi
- Bremen Center for Computational Materials Science, University of Bremen, 28359 Bremen, Germany
| | - Reinhard J Maurer
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
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13
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Franzke Y, Holzer C, Andersen JH, Begušić T, Bruder F, Coriani S, Della Sala F, Fabiano E, Fedotov DA, Fürst S, Gillhuber S, Grotjahn R, Kaupp M, Kehry M, Krstić M, Mack F, Majumdar S, Nguyen BD, Parker SM, Pauly F, Pausch A, Perlt E, Phun GS, Rajabi A, Rappoport D, Samal B, Schrader T, Sharma M, Tapavicza E, Treß RS, Voora V, Wodyński A, Yu JM, Zerulla B, Furche F, Hättig C, Sierka M, Tew DP, Weigend F. TURBOMOLE: Today and Tomorrow. J Chem Theory Comput 2023; 19:6859-6890. [PMID: 37382508 PMCID: PMC10601488 DOI: 10.1021/acs.jctc.3c00347] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Indexed: 06/30/2023]
Abstract
TURBOMOLE is a highly optimized software suite for large-scale quantum-chemical and materials science simulations of molecules, clusters, extended systems, and periodic solids. TURBOMOLE uses Gaussian basis sets and has been designed with robust and fast quantum-chemical applications in mind, ranging from homogeneous and heterogeneous catalysis to inorganic and organic chemistry and various types of spectroscopy, light-matter interactions, and biochemistry. This Perspective briefly surveys TURBOMOLE's functionality and highlights recent developments that have taken place between 2020 and 2023, comprising new electronic structure methods for molecules and solids, previously unavailable molecular properties, embedding, and molecular dynamics approaches. Select features under development are reviewed to illustrate the continuous growth of the program suite, including nuclear electronic orbital methods, Hartree-Fock-based adiabatic connection models, simplified time-dependent density functional theory, relativistic effects and magnetic properties, and multiscale modeling of optical properties.
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Affiliation(s)
- Yannick
J. Franzke
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Christof Holzer
- Institute
of Theoretical Solid State Physics, Karlsruhe
Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - Josefine H. Andersen
- DTU
Chemistry, Department of Chemistry, Technical
University of Denmark, Kemitorvet Building 207, DK-2800 Kongens Lyngby, Denmark
| | - Tomislav Begušić
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Florian Bruder
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Sonia Coriani
- DTU
Chemistry, Department of Chemistry, Technical
University of Denmark, Kemitorvet Building 207, DK-2800 Kongens Lyngby, Denmark
| | - Fabio Della Sala
- Institute
for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, 73100 Lecce, Italy
- Center for
Biomolecular Nanotechnologies @UNILE, Istituto
Italiano di Tecnologia, Via Barsanti, 73010 Arnesano, Italy
| | - Eduardo Fabiano
- Institute
for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, 73100 Lecce, Italy
- Center for
Biomolecular Nanotechnologies @UNILE, Istituto
Italiano di Tecnologia, Via Barsanti, 73010 Arnesano, Italy
| | - Daniil A. Fedotov
- DTU
Chemistry, Department of Chemistry, Technical
University of Denmark, Kemitorvet Building 207, DK-2800 Kongens Lyngby, Denmark
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Susanne Fürst
- Institut
für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7, Technische Universität Berlin, Straße des 17 Juni 135, 10623, Berlin, Germany
| | - Sebastian Gillhuber
- Institute
of Inorganic Chemistry, Karlsruhe Institute
of Technology (KIT), Engesserstr. 15, 76131 Karlsruhe, Germany
| | - Robin Grotjahn
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Martin Kaupp
- Institut
für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7, Technische Universität Berlin, Straße des 17 Juni 135, 10623, Berlin, Germany
| | - Max Kehry
- Institute
of Physical Chemistry, Karlsruhe Institute
of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Marjan Krstić
- Institute
of Theoretical Solid State Physics, Karlsruhe
Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - Fabian Mack
- Institute
of Physical Chemistry, Karlsruhe Institute
of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Sourav Majumdar
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Brian D. Nguyen
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Shane M. Parker
- Department
of Chemistry, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio 44106 United States
| | - Fabian Pauly
- Institute
of Physics, University of Augsburg, Universitätsstr. 1, 86159 Augsburg, Germany
| | - Ansgar Pausch
- Institute
of Physical Chemistry, Karlsruhe Institute
of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Eva Perlt
- Otto-Schott-Institut
für Materialforschung, Friedrich-Schiller-Universität
Jena, Löbdergraben
32, 07743 Jena, Germany
| | - Gabriel S. Phun
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Ahmadreza Rajabi
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Dmitrij Rappoport
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Bibek Samal
- Department
of Chemical Sciences, Tata Institute of
Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Tim Schrader
- Otto-Schott-Institut
für Materialforschung, Friedrich-Schiller-Universität
Jena, Löbdergraben
32, 07743 Jena, Germany
| | - Manas Sharma
- Otto-Schott-Institut
für Materialforschung, Friedrich-Schiller-Universität
Jena, Löbdergraben
32, 07743 Jena, Germany
| | - Enrico Tapavicza
- Department
of Chemistry and Biochemistry, California
State University, Long Beach, 1250 Bellflower Boulevard, Long
Beach, California 90840-9507, United States
| | - Robert S. Treß
- Lehrstuhl
für Theoretische Chemie, Ruhr-Universität
Bochum, 44801 Bochum, Germany
| | - Vamsee Voora
- Department
of Chemical Sciences, Tata Institute of
Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Artur Wodyński
- Institut
für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7, Technische Universität Berlin, Straße des 17 Juni 135, 10623, Berlin, Germany
| | - Jason M. Yu
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Benedikt Zerulla
- Institute
of Nanotechnology, Karlsruhe Institute of
Technology (KIT), Hermann-von-Helmholtz-Platz
1, 76344 Eggenstein-Leopoldshafen Germany
| | - Filipp Furche
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Christof Hättig
- Lehrstuhl
für Theoretische Chemie, Ruhr-Universität
Bochum, 44801 Bochum, Germany
| | - Marek Sierka
- Otto-Schott-Institut
für Materialforschung, Friedrich-Schiller-Universität
Jena, Löbdergraben
32, 07743 Jena, Germany
| | - David P. Tew
- Physical
and Theoretical Chemistry Laboratory, University
of Oxford, South Parks
Road, Oxford OX1 3QZ, United Kingdom
| | - Florian Weigend
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
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14
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Daas KJ, Kooi DP, Peters NC, Fabiano E, Della Sala F, Gori-Giorgi P, Vuckovic S. Regularized and Opposite Spin-Scaled Functionals from Møller-Plesset Adiabatic Connection─Higher Accuracy at Lower Cost. J Phys Chem Lett 2023; 14:8448-8459. [PMID: 37721318 DOI: 10.1021/acs.jpclett.3c01832] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Noncovalent interactions (NCIs) play a crucial role in biology, chemistry, material science, and everything in between. To improve pure quantum-chemical simulations of NCIs, we propose a methodology for constructing approximate correlation energies by combining an interpolation along the Møller-Plesset adiabatic connection (MP AC) with a regularization and spin-scaling strategy applied to MP2 correlation energies. This combination yields cosκos-SPL2, which exhibits superior accuracy for NCIs compared to any of the individual strategies. With the N4 formal scaling, cosκos-SPL2 is competitive or often outperforms more expensive dispersion-corrected double hybrids for NCIs. The accuracy of cosκos-SPL2 particularly shines for anionic halogen bonded complexes, where it surpasses standard dispersion-corrected DFT by a factor of 3 to 5.
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Affiliation(s)
- Kimberly J Daas
- Department of Chemistry & Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
| | - Derk P Kooi
- Department of Chemistry & Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
- Microsoft Research AI4Science, Evert van de Beekstraat 354, 1118CZ Schiphol, The Netherlands
| | - Nina C Peters
- Department of Chemistry & Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
| | - Eduardo Fabiano
- Institute for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, 73100 Lecce, Italy
- Center for Biomolecular Nanotechnologies, Istituto Italiano di Tecnologia, 73010 Arnesano, Italy
| | - Fabio Della Sala
- Institute for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, 73100 Lecce, Italy
- Center for Biomolecular Nanotechnologies, Istituto Italiano di Tecnologia, 73010 Arnesano, Italy
| | - Paola Gori-Giorgi
- Department of Chemistry & Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
- Microsoft Research AI4Science, Evert van de Beekstraat 354, 1118CZ Schiphol, The Netherlands
| | - Stefan Vuckovic
- Department of Chemistry, Faculty of Science and Medicine, Université de Fribourg/Universität Freiburg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
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15
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Czernek J, Brus J. On the Intermolecular Interactions in Thiophene-Cored Single-Stacking Junctions. Int J Mol Sci 2023; 24:13349. [PMID: 37686156 PMCID: PMC10487960 DOI: 10.3390/ijms241713349] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
There have been attempts, both experimental and based on density-functional theory (DFT) modeling, at understanding the factors that govern the electronic conductance behavior of single-stacking junctions formed by pi-conjugated materials in nanogaps. Here, a reliable description of relevant stacked configurations of some thiophene-cored systems is provided by means of high-level quantum chemical approaches. The minimal structures of these configurations, which are found using the dispersion-corrected DFT approach, are employed in calculations that apply the coupled cluster method with singles, doubles and perturbative triples [CCSD(T)] and extrapolations to the complete basis set (CBS) limit in order to reliably quantify the strength of intermolecular binding, while their physical origin is investigated using the DFT-based symmetry-adapted perturbation theory (SAPT) of intermolecular interactions. In particular, for symmetrized S-Tn dimers (where "S" and "T" denote a thiomethyl-containing anchor group and a thiophene segment comprising "n" units, respectively), the CCSD(T)/CBS interaction energies are found to increase linearly with n ≤ 6, and significant conformational differences between the flanking 2-thiophene group in S-T1 and S-T2 are described by the CCSD(T)/CBS and SAPT/CBS computations. These results are put into the context of previous work on charge transport properties of S-Tn and other types of supramolecular junctions.
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Affiliation(s)
- Jiří Czernek
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovsky Square 2, 16200 Prague, Czech Republic;
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16
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Villot C, Huang T, Lao KU. Accurate prediction of global-density-dependent range-separation parameters based on machine learning. J Chem Phys 2023; 159:044103. [PMID: 37486048 DOI: 10.1063/5.0157340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023] Open
Abstract
In this work, we develop an accurate and efficient XGBoost machine learning model for predicting the global-density-dependent range-separation parameter, ωGDD, for long-range corrected functional (LRC)-ωPBE. This ωGDDML model has been built using a wide range of systems (11 466 complexes, ten different elements, and up to 139 heavy atoms) with fingerprints for the local atomic environment and histograms of distances for the long-range atomic correlation for mapping the quantum mechanical range-separation values. The promising performance on the testing set with 7046 complexes shows a mean absolute error of 0.001 117 a0-1 and only five systems (0.07%) with an absolute error larger than 0.01 a0-1, which indicates the good transferability of our ωGDDML model. In addition, the only required input to obtain ωGDDML is the Cartesian coordinates without electronic structure calculations, thereby enabling rapid predictions. LRC-ωPBE(ωGDDML) is used to predict polarizabilities for a series of oligomers, where polarizabilities are sensitive to the asymptotic density decay and are crucial in a variety of applications, including the calculations of dispersion corrections and refractive index, and surpasses the performance of all other popular density functionals except for the non-tuned LRC-ωPBE. Finally, LRC-ωPBE (ωGDDML) combined with (extended) symmetry-adapted perturbation theory is used in calculating noncovalent interactions to further show that the traditional ab initio system-specific tuning procedure can be bypassed. The present study not only provides an accurate and efficient way to determine the range-separation parameter for LRC-ωPBE but also shows the synergistic benefits of fusing the power of physically inspired density functional LRC-ωPBE and the data-driven ωGDDML model.
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Affiliation(s)
- Corentin Villot
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, USA
| | - Tong Huang
- 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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17
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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: 3] [Impact Index Per Article: 3.0] [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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18
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Spadetto E, Philipsen PHT, Förster A, Visscher L. Toward Pair Atomic Density Fitting for Correlation Energies with Benchmark Accuracy. J Chem Theory Comput 2023; 19:1499-1516. [PMID: 36787494 PMCID: PMC10018742 DOI: 10.1021/acs.jctc.2c01201] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Pair atomic density fitting (PADF) has been identified as a promising strategy to reduce the scaling with system size of quantum chemical methods for the calculation of the correlation energy like the direct random-phase approximation (RPA) or second-order Møller-Plesset perturbation theory (MP2). PADF can however introduce large errors in correlation energies as the two-electron interaction energy is not guaranteed to be bounded from below. This issue can be partially alleviated by using very large fit sets, but this comes at the price of reduced efficiency and having to deal with near-linear dependencies in the fit set. One posibility is to use global density fitting (DF), but in this work, we introduce an alternative methodology to overcome this problem that preserves the intrinsically favorable scaling of PADF. We first regularize the Fock matrix by projecting out parts of the basis set which gives rise to orbital products that are hard to describe by PADF. After having thus obtained a reliable self-consistent field solution, we then also apply this projector to the orbital coefficient matrix to improve the precision of PADF-MP2 and PADF-RPA. We systematically assess the accuracy of this new approach in a numerical atomic orbital framework using Slater type orbitals (STO) and correlation consistent Gaussian type basis sets up to quintuple-ζ quality for systems with more than 200 atoms. For the small and medium systems in the S66 database we show the maximum deviation of PADF-MP2 and PADF-RPA relative correlation energies to DF-MP2 and DF-RPA reference results to be 0.07 and 0.14 kcal/mol, respectively. When the new projector method is used, the errors only slightly increase for large molecules and also when moderately sized fit sets are used the resulting errors are well under control. Finally, we demonstrate the computational efficiency of our algorithm by calculating the interaction energies of large, non-covalently bound complexes with more than 1000 atoms and 20000 atomic orbitals at the RPA@PBE/CC-pVTZ level of theory.
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Affiliation(s)
- Edoardo Spadetto
- Software for Chemistry and Materials NV, NL-1081HV Amsterdam, The Netherlands
| | | | - Arno Förster
- Software for Chemistry and Materials NV, NL-1081HV Amsterdam, The Netherlands.,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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19
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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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20
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Phosphatidylcholine in the tear film of the eye: enhanced topical delivery of fluorometholone to the eye. INORG CHEM COMMUN 2023. [DOI: 10.1016/j.inoche.2023.110506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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21
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Kříž K, Schmidt L, Andersson AT, Walz MM, van der Spoel D. An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation. J Chem Inf Model 2023; 63:412-431. [PMID: 36630710 PMCID: PMC9875315 DOI: 10.1021/acs.jcim.2c01127] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Indexed: 01/12/2023]
Abstract
Force fields (FFs) for molecular simulation have been under development for more than half a century. As with any predictive model, rigorous testing and comparisons of models critically depends on the availability of standardized data sets and benchmarks. While such benchmarks are rather common in the fields of quantum chemistry, this is not the case for empirical FFs. That is, few benchmarks are reused to evaluate FFs, and development teams rather use their own training and test sets. Here we present an overview of currently available tests and benchmarks for computational chemistry, focusing on organic compounds, including halogens and common ions, as FFs for these are the most common ones. We argue that many of the benchmark data sets from quantum chemistry can in fact be reused for evaluating FFs, but new gas phase data is still needed for compounds containing phosphorus and sulfur in different valence states. In addition, more nonequilibrium interaction energies and forces, as well as molecular properties such as electrostatic potentials around compounds, would be beneficial. For the condensed phases there is a large body of experimental data available, and tools to utilize these data in an automated fashion are under development. If FF developers, as well as researchers in artificial intelligence, would adopt a number of these data sets, it would become easier to compare the relative strengths and weaknesses of different models and to, eventually, restore the balance in the force.
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Affiliation(s)
- Kristian Kříž
- Department
of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124Uppsala, Sweden
| | - Lisa Schmidt
- Faculty
of Biosciences, University of Heidelberg, Heidelberg69117, Germany
| | - Alfred T. Andersson
- Department
of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124Uppsala, Sweden
| | - Marie-Madeleine Walz
- Department
of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124Uppsala, Sweden
| | - David van der Spoel
- Department
of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124Uppsala, Sweden
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22
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George G, Stasyuk OA, Voityuk AA, Stasyuk AJ, Solà M. Aromaticity controls the excited-state properties of host-guest complexes of nanohoops. NANOSCALE 2023; 15:1221-1229. [PMID: 36537223 DOI: 10.1039/d2nr04037a] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
π-Conjugated organic molecules have exciting applications as materials for batteries, solar cells, light-emitting diodes, etc. Among these systems, antiaromatic compounds are of particular interest because of their smaller HOMO-LUMO energy gap compared to aromatic compounds. A small HOMO-LUMO gap is expected to facilitate charge transfer in the systems. Here we report the ground and excited-state properties of two model nanohoops that are nitrogen-doped analogs of recently synthesized [4]cyclodibenzopentalenes - tetramers of benzene-fused aromatic 1,4-dihydropyrrolo[3,2-b]pyrrole ([4]DHPP) and antiaromatic pyrrolo[3,2-b]pyrrole ([4]PP). Their complexes with C60 fullerene show different behavior upon photoexcitation, depending on the degree of aromaticity. [4]DHPP acts as an electron donor, whereas [4]PP is a stronger electron acceptor than C60. The ultrafast charge separation combined with the slow charge recombination that we found for [4]PP⊃C60 indicates a long lifetime of the charge transfer state.
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Affiliation(s)
- G George
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, C/ Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain.
| | - O A Stasyuk
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, C/ Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain.
| | - A A Voityuk
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, C/ Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain.
| | - A J Stasyuk
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, C/ Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain.
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - M Solà
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, C/ Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain.
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23
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Thürlemann M, Böselt L, Riniker S. Regularized by Physics: Graph Neural Network Parametrized Potentials for the Description of Intermolecular Interactions. J Chem Theory Comput 2023; 19:562-579. [PMID: 36633918 PMCID: PMC9878731 DOI: 10.1021/acs.jctc.2c00661] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Indexed: 01/13/2023]
Abstract
Simulations of molecular systems using electronic structure methods are still not feasible for many systems of biological importance. As a result, empirical methods such as force fields (FF) have become an established tool for the simulation of large and complex molecular systems. The parametrization of FF is, however, time-consuming and has traditionally been based on experimental data. Recent years have therefore seen increasing efforts to automatize FF parametrization or to replace FF with machine-learning (ML) based potentials. Here, we propose an alternative strategy to parametrize FF, which makes use of ML and gradient-descent based optimization while retaining a functional form founded in physics. Using a predefined functional form is shown to enable interpretability, robustness, and efficient simulations of large systems over long time scales. To demonstrate the strength of the proposed method, a fixed-charge and a polarizable model are trained on ab initio potential-energy surfaces. Given only information about the constituting elements, the molecular topology, and reference potential energies, the models successfully learn to assign atom types and corresponding FF parameters from scratch. The resulting models and parameters are validated on a wide range of experimentally and computationally derived properties of systems including dimers, pure liquids, and molecular crystals.
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Affiliation(s)
- Moritz Thürlemann
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Lennard Böselt
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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24
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Müller M, Hansen A, Grimme S. ωB97X-3c: A composite range-separated hybrid DFT method with a molecule-optimized polarized valence double-ζ basis set. J Chem Phys 2023; 158:014103. [PMID: 36610980 DOI: 10.1063/5.0133026] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A new composite density functional theory (DFT) method is presented. It is based on ωB97X-V as one of the best-performing density functionals for the GMTKN55 thermochemistry database and completes the family of "3c" methods toward range-separated hybrid DFT. This method is consistently available for all elements up to Rn (Z = 1-86). Its further key ingredients are a polarized valence double-ζ (vDZP) Gaussian basis set, which was fully optimized in molecular DFT calculations, in combination with large-core effective core potentials and a specially adapted D4 dispersion correction. Unlike most existing double-ζ atomic orbital sets, vDZP shows only small basis set superposition errors (BSSEs) and can compete with standard sets of triple-ζ quality. Small residual BSSE effects are efficiently absorbed by the D4 damping scheme, which overall eliminates the need for an explicit treatment or empirical corrections for BSSE. Thorough tests on a variety of thermochemistry benchmark sets show that the new composite method, dubbed ωB97X-3c, is on par with or even outperforms standard hybrid DFT methods in a quadruple-zeta basis set at a small fraction of the computational cost. Particular strengths of this method are the description of non-covalent interactions and barrier heights, for which it is among the best-performing density functionals overall.
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Affiliation(s)
- Marcel Müller
- Mulliken Center for Theoretical Chemistry, Clausius-Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Clausius-Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Clausius-Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
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25
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Santra G, Martin JM. Performance of Localized-Orbital Coupled-Cluster Approaches for the Conformational Energies of Longer n-Alkane Chains. J Phys Chem A 2022; 126:9375-9391. [PMID: 36508714 PMCID: PMC9791657 DOI: 10.1021/acs.jpca.2c06407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We report an update and enhancement of the ACONFL (conformer energies of large alkanes [J. Phys. Chem. A2022,126, 3521-3535]) dataset. For the ACONF12 (n-dodecane) subset, we report basis set limit canonical coupled-cluster with singles, doubles, and perturbative triples [i.e., CCSD(T)] reference data obtained from the MP2-F12/cc-pV{T,Q}Z-F12 extrapolation, [CCSD(F12*)-MP2-F12]/aug-cc-pVTZ-F12, and a (T) correction from conventional CCSD(T)/aug-cc-pV{D,T}Z calculations. Then, we explored the performance of a variety of single and composite localized-orbital CCSD(T) approximations, ultimately finding an affordable localized natural orbital CCSD(T) [LNO-CCSD(T)]-based post-MP2 correction that agrees to 0.006 kcal/mol mean absolute deviation with the revised canonical reference data. In tandem with canonical MP2-F12 complete basis set extrapolation, this was then used to re-evaluate the ACONF16 and ACONF20 subsets for n-hexadecane and n-icosane, respectively. Combining those with the revised canonical reference data for the dodecane conformers (i.e., ACONF12 subset), a revised ACONFL set was obtained. It was then used to assess the performance of different localized-orbital coupled-cluster approaches, such as pair natural orbital localized CCSD(T) [PNO-LCCSD(T)] as implemented in MOLPRO, DLPNO-CCSD(T0) and DLPNO-CCSD(T1) as implemented in ORCA, and LNO-CCSD(T) as implemented in MRCC, at their respective "Normal", "Tight", "vTight", and "vvTight" accuracy settings. For a given accuracy threshold and basis set, DLPNO-CCSD(T1) and DLPNO-CCSD(T0) perform comparably. With "VeryTightPNO" cutoffs, explicitly correlated DLPNO-CCSD(T1)-F12/VDZ-F12 is the best pick among all the DLPNO-based methods tested. To isolate basis set incompleteness from localized-orbital-related truncation errors (domain, LNOs), we have also compared the localized coupled-cluster approaches with canonical DF-CCSD(T)/aug-cc-pVTZ for the ACONF12 set. We found that gradually tightening the cutoffs improves the performance of LNO-CCSD(T), and using a composite scheme such as vTight + 0.50[vTight - Tight] improves things further. For DLPNO-CCSD(T1), "TightPNO" and "VeryTightPNO" offer a statistically similar accuracy, which gets slightly better when TCutPNO is extrapolated to the complete PNO space limit. Similar to Brauer et al.'s [Phys. Chem. Chem. Phys.2016,18 (31), 20905-20925] previous report for the S66x8 noncovalent interactions, the dispersion-corrected direct random phase approximation (dRPA)-based double hybrids perform remarkably well for the ACONFL set. While the revised reference data do not affect any conclusions on the less accurate methods, they may upend orderings for more accurate methods with error statistics on the same order as the difference between reference datasets.
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26
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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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27
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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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28
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Liang J, Zhang D, Cao Y, Xue K, Xia Y, Qi Z. Insight into pyrolysis mechanism of 1,2-propylene glycol: Based on density functional theory and wavefunction analysis. J Mol Graph Model 2022; 116:108277. [PMID: 35930820 DOI: 10.1016/j.jmgm.2022.108277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/19/2022] [Accepted: 07/14/2022] [Indexed: 12/15/2022]
Abstract
The multiple thermal decomposition mechanisms of 1,2-propylene glycol are studied through theoretical calculation and experiment, including carbon chain break, dehydrogenation and dehydration mechanism. The wavefunction is employed to analyze the decomposition process from a micro perspective. DLPNO-CCSD(T)/CBS method is engaged in establishing potential energy surface. The results reveal that the dehydration and carbon chain break mechanism are the primary pyrolysis paths, and the former is the dominant pyrolysis mechanism at low temperature, while the latter is applicable at the high temperature. The pyrolysis products are mainly acetaldehyde, propanal and acetone, which is consistent with experimental results. Besides, the comparison results of 1,2-propylene glycol and glycerol pyrolysis products indicate that the increment of hydroxyls are conducive to the generation of carbonyl compounds during the polyol thermal decomposition. This work is aimed to comprehensively investigate the pyrolysis mechanism of 1,2-propylene glycol and provide the valuable thermodynamics and kinetic data for developing efficient polyol pyrolysis technology. Furthermore, it provides a reference for choosing low-toxic tobacco humectant.
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Affiliation(s)
- Jiankang Liang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, Jiangsu, 211189, PR China
| | - Dongdong Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, Jiangsu, 211189, PR China
| | - Yi Cao
- China Tobacco Jiangsu Industrial Co., Ltd., Nanjing, Jiangsu, 210019, PR China
| | - Ke Xue
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, Jiangsu, 211189, PR China
| | - Yong Xia
- School of Packaging and Materials Engineering, Hunan University of Technology, Zhuzhou, Hunan, 412007, PR China
| | - Zhengjian Qi
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, Jiangsu, 211189, PR China.
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29
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Adekoya O, Adekoya GJ, Sadiku RE, Hamam Y, Ray SS. Density Functional Theory Interaction Study of a Polyethylene Glycol-Based Nanocomposite with Cephalexin Drug for the Elimination of Wound Infection. ACS OMEGA 2022; 7:33808-33820. [PMID: 36188269 PMCID: PMC9520710 DOI: 10.1021/acsomega.2c02347] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/26/2022] [Indexed: 05/13/2023]
Abstract
In this paper, density functional theory (DFT) simulations are used to evaluate the possible use of a graphene oxide-based poly(ethylene glycol) (GO/PEG) nanocomposite as a drug delivery substrate for cephalexin (CEX), an antibiotic drug employed to treat wound infection. First, the stable configuration of the PEGylated system was generated with a binding energy of -25.67 kcal/mol at 1.62 Å through Monte Carlo simulation and DFT calculation for a favorable adsorption site. The most stable configuration shows that PEG interacts with GO through hydrogen bonding of the oxygen atom on the hydroxyl group of PEG with the hydrogen atom of the carboxylic group on GO. Similarly, for the interaction of the CEX drug with the GO/PEG nanocomposite excipient system, the adsorption energies are computed after determining the optimal and thermodynamically favorable configuration. The nitrogen atom from the amine group of the drug binds with a hydrogen atom from the carboxylic group of the GO/PEG nanocomposite at 1.75 Å, with an adsorption energy of -36.17 kcal/mol, in the most stable drug-excipient system. Drug release for tissue regeneration at the predicted target cell is more rapid in moist conditions than in the gas phase. The solubility of the suggested drug in the aqueous media around the open wound is shown by the magnitude of the predicted solvation energy. The findings from this study theoretically validate the potential use of a GO/PEG nanocomposite for wound treatment application as a drug carrier for sustained release of the CEX drug.
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Affiliation(s)
- Oluwasegun
Chijioke Adekoya
- Institute
of Nanoengineering Research (INER), Department of Chemical, Metallurgical
and Materials Engineering, Faculty of Engineering and the Built Environment, Tshwane University of Technology, Pretoria 0001, South Africa
| | - Gbolahan Joseph Adekoya
- Institute
of Nanoengineering Research (INER), Department of Chemical, Metallurgical
and Materials Engineering, Faculty of Engineering and the Built Environment, Tshwane University of Technology, Pretoria 0001, South Africa
- Centre
for Nanostructures and Advanced Materials, DSI-CSIR Nanotechnology Innovation Centre, Council for Scientific
and Industrial Research, Pretoria 0001, South Africa
| | - Rotimi Emmanuel Sadiku
- Institute
of Nanoengineering Research (INER), Department of Chemical, Metallurgical
and Materials Engineering, Faculty of Engineering and the Built Environment, Tshwane University of Technology, Pretoria 0001, South Africa
| | - Yskandar Hamam
- Department
of Electrical Engineering, Faculty of Engineering and the Built Environment, Tshwane University of Technology, Pretoria 001, South Africa
- École
Supérieure d’Ingénieurs en Électrotechnique
et Électronique, Cité Descartes, 2 Boulevard Blaise Pascal, Noisy-le-Grand, Paris 93160, France
| | - Suprakas Sinha Ray
- Centre
for Nanostructures and Advanced Materials, DSI-CSIR Nanotechnology Innovation Centre, Council for Scientific
and Industrial Research, Pretoria 0001, South Africa
- Department
of Chemical Sciences, University of Johannesburg, Doornforntein, Johannesburg 2028, South
Africa
- , ,
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30
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Förster A. Assessment of the Second-Order Statically Screened Exchange Correction to the Random Phase Approximation for Correlation Energies. J Chem Theory Comput 2022; 18:5948-5965. [PMID: 36150190 PMCID: PMC9558381 DOI: 10.1021/acs.jctc.2c00366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
With increasing interelectronic distance, the screening
of the
electron–electron interaction by the presence of other electrons
becomes the dominant source of electron correlation. This effect is
described by the random phase approximation (RPA) which is therefore
a promising method for the calculation of weak interactions. The success
of the RPA relies on the cancellation of errors, which can be traced
back to the violation of the crossing symmetry of the 4-point vertex,
leading to strongly overestimated total correlation energies. By the
addition of second-order screened exchange (SOSEX) to the correlation
energy, this issue is substantially reduced. In the adiabatic connection
(AC) SOSEX formalism, one of the two electron–electron interaction
lines in the second-order exchange term is dynamically screened (SOSEX(W, vc)). A
related SOSEX expression in which both electron–electron interaction
lines are statically screened (SOSEX(W(0), W(0))) is obtained from the G3W2 contribution to the electronic self-energy. In contrast to SOSEX(W, vc), the
evaluation of this correlation energy expression does not require
an expensive numerical frequency integration and is therefore advantageous
from a computational perspective. We compare the accuracy of the statically
screened variant to RPA and RPA+SOSEX(W, vc) for a wide range of chemical
reactions. While both methods fail for barrier heights, SOSEX(W(0), W(0)) agrees very well with SOSEX(W, vc) for
charged excitations and noncovalent interactions where they lead to
major improvements over RPA.
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Affiliation(s)
- Arno Förster
- Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, NL-1081 HV, Amsterdam, The Netherlands
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31
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Sacchetta F, Graf D, Laqua H, Ambroise MA, Kussmann J, Dreuw A, Ochsenfeld C. An effective sub-quadratic scaling atomic-orbital reformulation of the scaled opposite-spin RI-CC2 ground-state model using Cholesky-decomposed densities and an attenuated Coulomb metric. J Chem Phys 2022; 157:104104. [DOI: 10.1063/5.0098719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An atomic-orbital reformulation of the Laplace-transformed scaled opposite-spin (SOS) coupled cluster singles and doubles (CC2) model within the resolution of the identity (RI) approximation (SOS-RI-CC2) is presented that extends its applicability to molecules with several hundreds of atoms and triple-zeta basis sets. We exploit sparse linear algebra and an attenuated Coulomb metric to decrease the disk space demands and the computational efforts. In this way, an effective sub-quadratic computational scaling is achieved with our ω-SOS-CDD-RI-CC2 model. Moreover, Cholesky decomposition of the ground-state one-electron density matrix reduces the prefactor, allowing for an early crossover with the molecular orbital formulation. The accuracy and performance of the presented method are investigated for various molecular systems.
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Affiliation(s)
- F. Sacchetta
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Munich, Germany
| | - D. Graf
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Munich, Germany
| | - H. Laqua
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Munich, Germany
| | - M. A. Ambroise
- Chair of Theoretical and Computational Chemistry, Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany
| | - J. Kussmann
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Munich, Germany
| | - A. Dreuw
- Chair of Theoretical and Computational Chemistry, Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany
| | - C. Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Munich, Germany
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32
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Nagy PR, Gyevi-Nagy L, Lőrincz BD, Kállay M. Pursuing the basis set limit of CCSD(T) non-covalent interaction energies for medium-sized complexes: case study on the S66 compilation. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2109526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Péter R. Nagy
- Faculty of Chemical Technology and Biotechnology, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, Budapest, Hungary
- ELKH-BME Quantum Chemistry Research Group, Budapest, Hungary
| | - László Gyevi-Nagy
- Faculty of Chemical Technology and Biotechnology, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, Budapest, Hungary
- ELKH-BME Quantum Chemistry Research Group, Budapest, Hungary
| | - Balázs D. Lőrincz
- Faculty of Chemical Technology and Biotechnology, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, Budapest, Hungary
- ELKH-BME Quantum Chemistry Research Group, Budapest, Hungary
| | - Mihály Kállay
- Faculty of Chemical Technology and Biotechnology, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, Budapest, Hungary
- ELKH-BME Quantum Chemistry Research Group, Budapest, Hungary
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Behnle S, Richter R, Völkl L, Idzko P, Förstner A, Bozkaya U, Fink RF. Accurate Property Prediction by Second Order Perturbation Theory: The REMP and OO-REMP Hybrids. J Chem Phys 2022; 157:104111. [DOI: 10.1063/5.0105628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The prediction of molecular properties such as equilibrium structures or vibrationalwavenumbers is a routine task in computational chemistry. If very high accuracy is required, however, the use of computationally demanding ab initio wavefunction methods is mandatory. We present property calculations utilizing the REMP and OO-REMP hybrid perturbation theories showing that with the latter approach, very accurate results are obtained at second order in perturbation theory. Specifically, equilibrium structures and harmonic vibrational wavenumbers as well as dipole moments of closed and open shell molecules were calculated and compared to the best available experimental results or very accurate calculations.OO-REMP is capable of predicting bond lengths of small closed and open shell molecules with an accuracy of 0.2 pm and 0.5 pm, respectively, often within the range of experimental uncertainty. Equilibrium harmonic vibrational wavenumbers are predicted with an accuracy better than 20 cm−1 . Dipole moments of small closed and open shell molecules are reproduced with a relative error of less than 3 %. Across all investigated properties it turns out that a 20 %:80 % MP:RE mixing ratio consistently provides the best results. This is in line with our previous findings featuring closed and open shell reaction energies.
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Affiliation(s)
- Stefan Behnle
- Fachbereich II Chemie, Eberhard Karls Universität Tübingen Fachbereich II Chemie, Germany
| | - Robert Richter
- Eberhard Karls Universitat Tubingen Fachbereich II Chemie, Germany
| | - Luca Völkl
- Eberhard Karls Universitat Tubingen Fachbereich II Chemie, Germany
| | - Paul Idzko
- Eberhard Karls Universitat Tubingen Fachbereich II Chemie, Germany
| | - André Förstner
- Eberhard Karls Universitat Tubingen Fachbereich II Chemie, Germany
| | - Uğur Bozkaya
- Department of Chemistry, Hacettepe University, Turkey
| | - Reinhold F Fink
- Institute of Physical and Theoretical Chemistry, Eberhard Karls Universität Tübingen Fachbereich II Chemie, Germany
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34
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Peluso P, Chankvetadze B. Recognition in the Domain of Molecular Chirality: From Noncovalent Interactions to Separation of Enantiomers. Chem Rev 2022; 122:13235-13400. [PMID: 35917234 DOI: 10.1021/acs.chemrev.1c00846] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
It is not a coincidence that both chirality and noncovalent interactions are ubiquitous in nature and synthetic molecular systems. Noncovalent interactivity between chiral molecules underlies enantioselective recognition as a fundamental phenomenon regulating life and human activities. Thus, noncovalent interactions represent the narrative thread of a fascinating story which goes across several disciplines of medical, chemical, physical, biological, and other natural sciences. This review has been conceived with the awareness that a modern attitude toward molecular chirality and its consequences needs to be founded on multidisciplinary approaches to disclose the molecular basis of essential enantioselective phenomena in the domain of chemical, physical, and life sciences. With the primary aim of discussing this topic in an integrated way, a comprehensive pool of rational and systematic multidisciplinary information is provided, which concerns the fundamentals of chirality, a description of noncovalent interactions, and their implications in enantioselective processes occurring in different contexts. A specific focus is devoted to enantioselection in chromatography and electromigration techniques because of their unique feature as "multistep" processes. A second motivation for writing this review is to make a clear statement about the state of the art, the tools we have at our disposal, and what is still missing to fully understand the mechanisms underlying enantioselective recognition.
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Affiliation(s)
- Paola Peluso
- Istituto di Chimica Biomolecolare ICB, CNR, Sede secondaria di Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, I-07100 Sassari, Italy
| | - Bezhan Chankvetadze
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Chavchavadze Avenue 3, 0179 Tbilisi, Georgia
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35
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Villot C, Ballesteros F, Wang D, Lao KU. Coupled Cluster Benchmarking of Large Noncovalent Complexes in L7 and S12L as Well as the C 60 Dimer, DNA-Ellipticine, and HIV-Indinavir. J Phys Chem A 2022; 126:4326-4341. [PMID: 35766331 DOI: 10.1021/acs.jpca.2c01421] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this work, we report the benchmark binding energies of the seven complexes within the L7 data set, six host-guest complexes from the S12L data set, a C60 dimer, the DNA-ellipticine intercalation complex, and the largest system of the study, the HIV-indinavir system, which contained 343 atoms or 139 heavy atoms. The high-quality values reported were obtained via a focal point method that relies on the canonical form of second-order Møller-Plesset theory and the domain-based local pair natural orbital scheme for the coupled cluster with single double and perturbative triple excitations [DLPNO-CCSD(T)] extrapolated to the complete basis set (CBS) limit. The results in this work not only corroborate but also improve upon some previous benchmark values for large noncovalent complexes albeit at a relatively steep cost. Although local CCSD(T) and the largely successful fixed-node diffusion Monte Carlo (FN-DMC) have been shown to generally agree for small- to medium-size systems, a discrepancy in their reported binding energy values arises for large complexes, where the magnitude of the disagreement is a definite cause for concern. For example, the largest deviation in the L7 data set was 2.8 kcal/mol (∼10%) on the low end in C3GC. Such a deviation only grows worse in the S12L set, which showed a difference of up to 10.4 kcal/mol (∼25%) by a conservative estimation in buckycatcher-C60. The DNA-ellipticine complex also generated a disagreement of 4.4 kcal/mol (∼10%) between both state-of-the-art methods. The disagreement between local CCSD(T) and FN-DMC in large noncovalent complexes shows that it is urgently needed to have the canonical CCSD(T), the Monte Carlo CCSD(T), or the full configuration interaction quantum Monte Carlo approaches available to large systems on the hundred-atom scale to solve this dilemma. In addition, the performances of cheaper popular computational methods were assessed for the studied complexes with respect to DLPNO-CCSD(T)/CBS. r2SCAN-3c, B97M-V, and PBE0+D4 work well in large noncovalent complexes in this work, and GFN2-xTB performs well in π-π stacking complexes. B97M-V is the most reliable computationally efficient approach to predicting noncovalent interactions for large complexes, being the only one to have binding errors within the so-called 1 kcal/mol "chemical accuracy". The benchmark interaction energies of these host-guest complexes, molecular materials, and biological systems with electronic and medicinal implications provide crucial reference data for the improvement of current and future lower-cost methods.
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Affiliation(s)
- Corentin Villot
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284 United States
| | - Francisco Ballesteros
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284 United States
| | - Danyang Wang
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284 United States
| | - Ka Un Lao
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284 United States
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36
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Urban L, Laqua H, Ochsenfeld C. Highly Efficient and Accurate Computation of Multiple Orbital Spaces Spanning Fock Matrix Elements on Central and Graphics Processing Units for Application in F12 Theory. J Chem Theory Comput 2022; 18:4218-4228. [PMID: 35674337 DOI: 10.1021/acs.jctc.2c00215] [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
We employ our recently published highly efficient seminumerical exchange (sn-LinK) [Laqua, H.; Thompson, T. H.; Kussmann, J.; Ochsenfeld, C. J. Chem. Theory Comput. 2020, 16, 1456-1468] and integral-direct resolution of the identity Coulomb (RI-J) [Kussmann, J.; Laqua, H.; Ochsenfeld, C. J. Chem. Theory Comput. 2021, 17, 1512-1521] methods to significantly accelerate the computation of the demanding multiple orbital spaces spanning Fock matrix elements present in R12/F12 theory on central and graphics processing units. The errors introduced by RI-J and sn-LinK into the RI-MP2-F12 energy are thoroughly assessed for a variety of basis sets and integration grids. We find that these numerical errors are always below "chemical accuracy" (∼1 mH) even for the coarsest settings and can easily be reduced below 1 μH by employing only moderately large integration grids and RI-J basis sets. Since the number of basis functions of the multiple orbital spaces is notably larger compared with conventional Hartree-Fock theory, the efficiency gains from the superior basis scaling of RI-J and sn-LinK (O(Nbas2) instead of O(Nbas4) for both) are even more significant, with maximum speedup factors of 37 000 for RI-J and 4500 for sn-LinK. In total, the multiple orbital spaces spanning Fock matrix evaluation of the largest tested structure using a triple-ζ F12 basis set (5058 AO basis functions, 9267 CABS basis functions) is accelerated over 1575× using CPUs and over 4155× employing GPUs.
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Affiliation(s)
- Lars Urban
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), D-81377 Munich, Germany.,Max Planck Institute for Solid State Research, D-70569 Stuttgart, Germany
| | - Henryk Laqua
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), D-81377 Munich, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), D-81377 Munich, Germany.,Max Planck Institute for Solid State Research, D-70569 Stuttgart, Germany
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37
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Luňák S, Weiter M, Vala M. Complete Set of Diketopyrrolopyrrole Centrosymmetrical Cofacial Stacked Pairs. Chemphyschem 2022; 23:e202200252. [PMID: 35770507 DOI: 10.1002/cphc.202200252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/29/2022] [Indexed: 11/12/2022]
Abstract
Stacked centrosymmetrical dimers and simultaneously H-bonded and stacked hexamers of thiophene-substituted diketopyrrolopyrrole (ThDPP) were studied using DFT as models for crystals with slipped-stacked molecules in 1D columns. Eight stacked dimer arrangements were found, six of which are driven by the minimisation of electron repulsion and realised by placing the partially negatively charged atoms of the diketopyrrolopyrrole rings below the centre of an adjancent thiophene ring. Four of these stacks are related to N,N'-diacylated derivative. An analogous set of eight stacks was discovered computationally for phenyl-substituted DPP (PhDPP), four of which are known among H-bonded DPP pigments, and one more among N,N'-dialkylated PhDPP derivatives. The results shed more light on the mechanisms that drive the formation of stacks between nonaromatic (DPP) and aromatic (Th, Ph) rings. The excitation energies of the lowest four singlet states computed by TD DFT enabled excitonic coupling and energy separation between Frenkel-resonsnce-type and charge-transfer states to be established, depending on the equilibrium stack geometry.
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Affiliation(s)
- Stanislav Luňák
- Brno University of Technology: Vysoke uceni technicke v Brne, Faculty of Chemistry, Purkyňova 464/118, 61200, Brno, CZECH REPUBLIC
| | - Martin Weiter
- Brno University of Technology: Vysoke uceni technicke v Brne, Faculty of Chemistry, Purkyňova 464/118, 61200, Brno, CZECH REPUBLIC
| | - Martin Vala
- Brno University of Technology: Vysoke uceni technicke v Brne, Faculty of Chemistry, Purkyňova 464/118, 61200, Brno, CZECH REPUBLIC
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38
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Gasevic T, Stückrath JB, Grimme S, Bursch M. Optimization of the r 2SCAN-3c Composite Electronic-Structure Method for Use with Slater-Type Orbital Basis Sets. J Phys Chem A 2022; 126:3826-3838. [PMID: 35654439 PMCID: PMC9255700 DOI: 10.1021/acs.jpca.2c02951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The "Swiss army knife" composite density functional electronic-structure method r2SCAN-3c (J. Chem. Phys. 2021, 154, 064103) is extended and optimized for the use with Slater-type orbital basis sets. The meta generalized-gradient approximation (meta-GGA) functional r2SCAN by Furness et al. is combined with a tailor-made polarized triple-ζ Slater-type atomic orbital (STO) basis set (mTZ2P), the semiclassical London dispersion correction (D4), and a geometrical counterpoise (gCP) correction. Relativistic effects are treated explicitly with the scalar-relativistic zeroth-order regular approximation (SR-ZORA). The performance of the new implementation is assessed on eight geometry and 74 energy benchmark sets, including the extensive GMTKN55 database as well as recent sets such as ROST61 and IONPI19. In geometry optimizations, the STO-based r2SCAN-3c is either on par with or more accurate than the hybrid density functional approximation M06-2X-D3(0)/TZP. In energy calculations, the overall accuracy is similar to the original implementation of r2SCAN-3c with Gaussian-type atomic orbitals (GTO), but basic properties, intermolecular noncovalent interactions, and barrier heights are better described with the STO approach, resulting in a lower weighted mean absolute deviation (WTMAD-2(STO) = 7.15 vs 7.50 kcal mol-1 with the original method) for the GMTKN55 database. The STO-optimized r2SCAN-3c outperforms many conventional hybrid/QZ approaches in most common applications at a fraction of their cost. The reliable, robust, and accurate r2SCAN-3c implementation with STOs is a promising alternative to the original implementation with GTOs and can be generally used for a broad field of quantum chemical problems.
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Affiliation(s)
- Thomas Gasevic
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
| | - Julius B Stückrath
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
| | - Markus Bursch
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
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39
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Huang HH, Wang YS, Chao SD. A Minimum Quantum Chemistry CCSD(T)/CBS Data Set of Dimeric Interaction Energies for Small Organic Functional Groups: Heterodimers. ACS OMEGA 2022; 7:20059-20080. [PMID: 35722020 PMCID: PMC9201891 DOI: 10.1021/acsomega.2c01888] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
We extend our previous quantum chemistry calculations of interaction energies for 31 homodimers of small organic functional groups (the SOFG-31 data set) by including 239 heterodimers with monomers selected within the SOFG-31 data set, thus resulting in the SOFG-31+239 data set. The minimum-level theoretical scheme contains (1) the basis set superposition error corrected supermolecule (BSSE-SM) approach for intermolecular interactions; (2) the second-order Møller-Plesset perturbation theory (MP2) with the Dunning's aug-cc-pVXZ (X = D, T, Q) basis sets for the geometry optimization and correlation energy calculations; and (3) the single-point energy calculations with the coupled cluster with single, double, and perturbative triple excitations method at the complete basis set limit [CCSD(T)/CBS] using the well-tested extrapolation methods for the MP2 energy calibrations. In addition, we have performed a parallel series of energy decomposition calculations based on the symmetry adapted perturbation theory (SAPT) in order to gain chemical insights. That the above procedure cannot be further reduced has been proven to be very crucial for constructing reliable data sets of interaction energies. The calculated CCSD(T)/CBS interaction energy data can serve as a benchmark for testing or training less accurate but more efficient calculation methods, such as the electronic density functional theory. As an application, we employ a segmental SAPT model previously developed for the SOFG-31 data set to predict binding energies of large heterodimer complexes. These model energy "quanta" can be used in coarse-grained molecular dynamics simulations by avoiding large-scale calculations.
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Affiliation(s)
- Hsing-Hsiang Huang
- Institute
of Applied Mechanics, National Taiwan University, Taipei 10617, Taiwan R.O.C.
| | - Yi-Siang Wang
- School
of Chemistry & Biochemistry, Georgia
Institute of Technology, Atlanta, Georgia 30332, United States
| | - Sheng D. Chao
- Institute
of Applied Mechanics, National Taiwan University, Taipei 10617, Taiwan R.O.C.
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40
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Lemke Y, Kussmann J, Ochsenfeld C. Efficient Integral-Direct Methods for Self-Consistent Reduced Density Matrix Functional Theory Calculations on Central and Graphics Processing Units. J Chem Theory Comput 2022; 18:4229-4244. [DOI: 10.1021/acs.jctc.2c00231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Y. Lemke
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 5−13, D-81377 Munich, Germany
| | - J. Kussmann
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 5−13, D-81377 Munich, Germany
| | - C. Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 5−13, D-81377 Munich, Germany
- Max Planck Institute for Solid State Research, Heisenbergstr. 1, D-70569 Stuttgart, Germany
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41
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Kern M, Škulj S, Rožman M. Adsorption of a wide variety of antibiotics on graphene-based nanomaterials: A modelling study. CHEMOSPHERE 2022; 296:134010. [PMID: 35181425 DOI: 10.1016/j.chemosphere.2022.134010] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/04/2022] [Accepted: 02/13/2022] [Indexed: 06/14/2023]
Abstract
The knowledge on the sorption behaviour of antibiotics on nanomaterials is limited, especially regarding the reaction mechanism on the surface of carbon nanomaterials, which may determine both the adsorptive capacity and regeneration efficiency of graphene adsorbers. In this work, we used molecular modelling to generate the most comprehensive (to date) adsorption dataset for pristine and functionalised graphene interacting with 8 β-lactams, 3 macrolide, 12 quinolone, 4 tetracycline, 15 sulphonamide, trimethoprim, 2 lincosamide, 2 phenicole and 4 nitroimidazole antibiotics, and their transformation products in water and n-octanol. Results show that various non-covalent interactions that operate simultaneously, including van der Waals dispersion forces, π-interactions, hydrophobic interaction and hydrogen bonding, facilitate adsorption. The molecular properties of antibiotics and graphene/graphene oxide, as well as the composition of the background solution regulate the magnitude of these interactions. Our findings demonstrate that the most efficient method for the removal of antibiotics from aquatic environments is the use of graphene at environmental pH. The subsequent regeneration of the sorbent is best achieved through washing with slightly basic (pH 8-10) non-polar solvents. The obtained theoretical insights expand and complement experimental observations and provide important information that can contribute to further exploration into the adsorbent properties of graphene-based materials, and towards the development of predictive adsorption models.
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Affiliation(s)
- Matej Kern
- Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia.
| | - Sanja Škulj
- Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia.
| | - Marko Rožman
- Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia.
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42
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Bertolini S, Jacob T. Elucidating active sites and decomposition mechanisms for oxythiomolybdate clusters (Mo
2
O
2
S
x
, x = 6;8) as catalyzers for hydrogen evolution reactions. ELECTROCHEMICAL SCIENCE ADVANCES 2022. [DOI: 10.1002/elsa.202100088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Samuel Bertolini
- Institute of Electrochemistry Faculty of Natural Sciences Ulm University Albert‐Einstein‐Allee 47 Ulm Germany
| | - Timo Jacob
- Institute of Electrochemistry Faculty of Natural Sciences Ulm University Albert‐Einstein‐Allee 47 Ulm Germany
- Helmholtz‐Institute Ulm (HIU), Electrochemical Energy Storage Ulm Germany
- Karlsruhe Institute of Technology (KIT) Karlsruhe Germany
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43
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Brémond E, Li H, Sancho-García JC, Adamo C. Double Hybrids and Noncovalent Interactions: How Far Can We Go? J Phys Chem A 2022; 126:2590-2599. [PMID: 35438491 DOI: 10.1021/acs.jpca.2c01193] [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
The accurate evaluation of weak noncovalent interactions in large, that is those containing up to thousand atoms, molecular systems represents a difficult challenge for any quantum chemical method. Indeed, some approximations are often introduced to render affordable these calculations. Here, we consider the PBE-QIDH/DH-SVPD protocol, combining a nonempirical double hybrid functional (PBE-QIDH) with a small basis set (DH-SVPD) tailored for noncovalent interactions with a double aim: (i) explore the robustness and accuracy of this protocol with respect to other Density Functional Approximations; (ii) illustrate how its performances are affected by the computational parameters underlying the calculation of the exact exchange and the Coulomb contribution, as well as the perturbative term. To this end, we consider three data sets, namely S66, L7, and CiM13, incorporating molecules of increasing size. On the bright side, our results suggest that the PBE-QIDH/DH-SVPD protocol is particularly accurate for large systems such as those contained in the CiM13 set (up to more than 1000 atoms and 14 000 basis functions), for which the DLPNO approximation leads to a significant speed-up for the evaluation of the perturbative correlation term. However, our analysis also points out the limit of this statistical exercise, when the quality of the reference data cannot be easily assessed, due to the size of the molecular complexes involved, and when the number of molecules is limited.
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Affiliation(s)
- Eric Brémond
- Université de Paris, ITODYS, CNRS, F-75006 Paris, France
| | - Hanwei Li
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Health and Life Sciences, F-75005 Paris, France
| | | | - Carlo Adamo
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Health and Life Sciences, F-75005 Paris, France.,Institut Universitaire de France, 103 Boulevard Saint Michel, F-75005 Paris, France
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44
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Chan B, Dawson W, Nakajima T. Searching for a Reliable Density Functional for Molecule-Environment Interactions, Found B97M-V/def2-mTZVP. J Phys Chem A 2022; 126:2397-2406. [PMID: 35390254 DOI: 10.1021/acs.jpca.2c02032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the present study, we have examined density functional theory methods for the calculation of the interaction energy between a small molecule and its environment. For simple systems such as a neutral solute in a neutral solvent, good accuracy can be attained using low-cost "3c" methods, in particular r2SCAN-3c. When part(s) of the system is charged, the accurate computation of the interactions is more challenging. In these cases, we find the B97M-V/def2-mTZVP method to agree well with reference values; it also shows good accuracy for the more straightforward neutral systems. Thus, B97M-V/def2-mTZVP provides a means for accurate and low-cost computation of interaction energies, notably the binding between a substrate or a drug molecule and an enzyme, which may facilitate rational drug design.
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Affiliation(s)
- Bun Chan
- Graduate School of Engineering, Nagasaki University, Bunkyo 1-14, Nagasaki 852-8521, Japan
| | - William Dawson
- RIKEN Center for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe 650-0047, Japan
| | - Takahito Nakajima
- RIKEN Center for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe 650-0047, Japan
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45
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Altun A, Neese F, Bistoni G. Open-Shell Variant of the London Dispersion-Corrected Hartree-Fock Method (HFLD) for the Quantification and Analysis of Noncovalent Interaction Energies. J Chem Theory Comput 2022; 18:2292-2307. [PMID: 35167304 PMCID: PMC9009084 DOI: 10.1021/acs.jctc.1c01295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The London dispersion
(LD)-corrected Hartree–Fock (HF) method
(HFLD) is an ab initio approach for the quantification
and analysis of noncovalent interactions (NCIs) in large systems that
is based on the domain-based local pair natural orbital coupled-cluster
(DLPNO-CC) theory. In the original HFLD paper, we discussed the implementation,
accuracy, and efficiency of its closed-shell variant. Herein, an extension
of this method to open-shell molecular systems is presented. Its accuracy
is tested on challenging benchmark sets for NCIs, using CCSD(T) energies
at the estimated complete basis set limit as reference. The HFLD scheme
was found to be as accurate as the best-performing dispersion-corrected
exchange-correlation functionals, while being nonempirical and equally
efficient. In addition, it can be combined with the well-established
local energy decomposition (LED) for the analysis of NCIs, thus yielding
additional physical insights.
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Affiliation(s)
- Ahmet Altun
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Giovanni Bistoni
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany.,Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
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46
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Prasad VK, Otero-de-la-Roza A, DiLabio GA. Small-Basis Set Density-Functional Theory Methods Corrected with Atom-Centered Potentials. J Chem Theory Comput 2022; 18:2913-2930. [PMID: 35412817 DOI: 10.1021/acs.jctc.2c00036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Density functional theory (DFT) is currently the most popular method for modeling noncovalent interactions and thermochemistry. The accurate calculation of noncovalent interaction energies, reaction energies, and barrier heights requires choosing an appropriate functional and, typically, a relatively large basis set. Deficiencies of the density-functional approximation and the use of a limited basis set are the leading sources of error in the calculation of noncovalent and thermochemical properties in molecular systems. In this article, we present three new DFT methods based on the BLYP, M06-2X, and CAM-B3LYP functionals in combination with the 6-31G* basis set and corrected with atom-centered potentials (ACPs). ACPs are one-electron potentials that have the same form as effective-core potentials, except they do not replace any electrons. The ACPs developed in this work are used to generate energy corrections to the underlying DFT/basis-set method such that the errors in predicted chemical properties are minimized while maintaining the low computational cost of the parent methods. ACPs were developed for the elements H, B, C, N, O, F, Si, P, S, and Cl. The ACP parameters were determined using an extensive training set of 118655 data points, mostly of complete basis set coupled-cluster level quality. The target molecular properties for the ACP-corrected methods include noncovalent interaction energies, molecular conformational energies, reaction energies, barrier heights, and bond separation energies. The ACPs were tested first on the training set and then on a validation set of 42567 additional data points. We show that the ACP-corrected methods can predict the target molecular properties with accuracy close to complete basis set wavefunction theory methods, but at a computational cost of double-ζ DFT methods. This makes the new BLYP/6-31G*-ACP, M06-2X/6-31G*-ACP, and CAM-B3LYP/6-31G*-ACP methods uniquely suited to the calculation of noncovalent, thermochemical, and kinetic properties in large molecular systems.
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Affiliation(s)
- Viki Kumar Prasad
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia V1V 1V7, Canada
| | - Alberto Otero-de-la-Roza
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, MALTA Consolider Team, Oviedo E-33006, Spain
| | - Gino A DiLabio
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia V1V 1V7, Canada
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47
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Behnle S, Fink RF. UREMP, RO-REMP, and OO-REMP: Hybrid perturbation theories for open-shell electronic structure calculations. J Chem Phys 2022; 156:124103. [DOI: 10.1063/5.0081285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An accurate description of the electron correlation energy in closed- and open-shell molecules is shown to be obtained by a second-order perturbation theory (PT) termed REMP. REMP is a hybrid of the Retaining the Excitation degree (RE) and the Møller–Plesset (MP) PTs. It performs particularly encouragingly in an orbital-optimized variant (OO-REMP) where the reference wavefunction is given by an unrestricted Slater determinant whose spin orbitals are varied such that the total energy becomes a minimum. While the approach generally behaves less satisfactorily with unrestricted Hartree–Fock references, reasonable performance is observed for restricted Hartree–Fock and restricted open-shell Hartree–Fock references. Inclusion of single excitations to OO-REMP is investigated and found—as in similar investigations—to be dissatisfying as it deteriorates performance. For the non-multireference subset of the accurate W4-11 benchmark set of Karton et al. [Chem. Phys. Lett. 510, 165–178 (2011)], OO-REMP predicts most atomization and reaction energies with chemical accuracy (1 kcal mol−1) if complete-basis-set extrapolation with augmented and core-polarized basis sets is used. For the W4-11 related test-sets, the error estimates obtained with the OO-REMP method approach those of coupled-cluster with singles, doubles and perturbative triples [CCSD(T)] within 20%–35%. The best performance of OO-REMP is found for a mixing ratio of 20%:80% MP:RE, which is essentially independent of whether radical stabilization energies, barrier heights, or reaction energies are investigated. Orbital optimization is shown to improve the REMP approach for both closed and open shell cases and outperforms coupled-cluster theory with singles and doubles (CCSD), spin-component scaled Møller-Plesset theory at second order (SCS-MP2), and density functionals, including double hybrids in all the cases considered.
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Affiliation(s)
- Stefan Behnle
- Institute for Physical and Theoretical Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | - Reinhold F. Fink
- Institute for Physical and Theoretical Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
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48
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Prasad VK, Otero-de-la-Roza A, DiLabio GA. Fast and Accurate Quantum Mechanical Modeling of Large Molecular Systems Using Small Basis Set Hartree-Fock Methods Corrected with Atom-Centered Potentials. J Chem Theory Comput 2022; 18:2208-2232. [PMID: 35313106 DOI: 10.1021/acs.jctc.1c01128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
There has been significant interest in developing fast and accurate quantum mechanical methods for modeling large molecular systems. In this work, by utilizing a machine learning regression technique, we have developed new low-cost quantum mechanical approaches to model large molecular systems. The developed approaches rely on using one-electron Gaussian-type functions called atom-centered potentials (ACPs) to correct for the basis set incompleteness and the lack of correlation effects in the underlying minimal or small basis set Hartree-Fock (HF) methods. In particular, ACPs are proposed for ten elements common in organic and bioorganic chemistry (H, B, C, N, O, F, Si, P, S, and Cl) and four different base methods: two minimal basis sets (MINIs and MINIX) plus a double-ζ basis set (6-31G*) in combination with dispersion-corrected HF (HF-D3/MINIs, HF-D3/MINIX, HF-D3/6-31G*) and the HF-3c method. The new ACPs are trained on a very large set (73 832 data points) of noncovalent properties (interaction and conformational energies) and validated additionally on a set of 32 048 data points. All reference data are of complete basis set coupled-cluster quality, mostly CCSD(T)/CBS. The proposed ACP-corrected methods are shown to give errors in the tenths of a kcal/mol range for noncovalent interaction energies and up to 2 kcal/mol for molecular conformational energies. More importantly, the average errors are similar in the training and validation sets, confirming the robustness and applicability of these methods outside the boundaries of the training set. In addition, the performance of the new ACP-corrected methods is similar to complete basis set density functional theory (DFT) but at a cost that is orders of magnitude lower, and the proposed ACPs can be used in any computational chemistry program that supports effective-core potentials without modification. It is also shown that ACPs improve the description of covalent and noncovalent bond geometries of the underlying methods and that the improvement brought about by the application of the ACPs is directly related to the number of atoms to which they are applied, allowing the treatment of systems containing some atoms for which ACPs are not available. Overall, the ACP-corrected methods proposed in this work constitute an alternative accurate, economical, and reliable quantum mechanical approach to describe the geometries, interaction energies, and conformational energies of systems with hundreds to thousands of atoms.
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Affiliation(s)
- Viki Kumar Prasad
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia, Canada V1V 1V7
| | - Alberto Otero-de-la-Roza
- MALTA Consolider Team, Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, E-33006 Oviedo, Spain
| | - Gino A DiLabio
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia, Canada V1V 1V7
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Gray M, Herbert JM. Comprehensive Basis-Set Testing of Extended Symmetry-Adapted Perturbation Theory and Assessment of Mixed-Basis Combinations to Reduce Cost. J Chem Theory Comput 2022; 18:2308-2330. [PMID: 35289608 DOI: 10.1021/acs.jctc.1c01302] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Hybrid or "extended" symmetry-adapted perturbation theory (XSAPT) replaces traditional SAPT's treatment of dispersion with better performing alternatives while at the same time extending two-body (dimer) SAPT to a many-body treatment of polarization using a self-consistent charge embedding procedure. The present work presents a systematic study of how XSAPT interaction energies and energy components converge with respect to the choice of Gaussian basis set. Errors can be reduced in a systematic way using correlation-consistent basis sets, with aug-cc-pVTZ results converged within <0.1 kcal/mol. Similar (if slightly less systematic) behavior is obtained using Karlsruhe basis sets at much lower cost, and we introduce new versions with limited augmentation that are even more efficient. Pople-style basis sets, which are more efficient still, often afford good results if a large number of polarization functions are included. The dispersion models used in XSAPT afford much faster basis-set convergence as compared to the perturbative description of dispersion in conventional SAPT, meaning that "compromise" basis sets (such as jun-cc-pVDZ) are no longer required and benchmark-quality results can be obtained using triple-ζ basis sets. The use of diffuse functions proves to be essential, especially for the description of hydrogen bonds. The "δ(Hartree-Fock)" correction for high-order induction can be performed in double-ζ basis sets without significant loss of accuracy, leading to a mixed-basis approach that offers 4× speedup over the existing (cubic scaling) XSAPT approach.
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Affiliation(s)
- Montgomery Gray
- 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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Kutskaya AM, Serkov SA, Voronin VV, Ledovskaya MS, Polynski MV. Negligible Substituent Effect as Key to Synthetic Versatility: a Computational‐Experimental Study of Vinyl Ethers Addition to Nitrile Oxides. ChemistrySelect 2022. [DOI: 10.1002/slct.202200174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Anastasia M. Kutskaya
- Institute of Chemistry Saint Petersburg State University Universitetsky Prospect 26 Saint Petersburg 198504 Russia
| | - Semyon A. Serkov
- Institute of Chemistry Saint Petersburg State University Universitetsky Prospect 26 Saint Petersburg 198504 Russia
| | - Vladimir V. Voronin
- Institute of Chemistry Saint Petersburg State University Universitetsky Prospect 26 Saint Petersburg 198504 Russia
| | - Maria S. Ledovskaya
- Institute of Chemistry Saint Petersburg State University Universitetsky Prospect 26 Saint Petersburg 198504 Russia
| | - Mikhail V. Polynski
- Institute of Chemistry Saint Petersburg State University Universitetsky Prospect 26 Saint Petersburg 198504 Russia
- Zelinsky Institute of Organic Chemistry Russian Academy of Sciences Leninsky Prospect 47 Moscow 119991 Russia
- MSU Faculty of Chemistry Leninskiye Gory 1–3 Moscow 119991 Russia
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