Interplay between test sets and statistical procedures in ranking DFT methods: The case of electron density studies

Marjewski, Alexander A.; Medvedev, Michael G.; Gerasimov, Igor S.; Panova, Maria V.; Perdew, John P.; Дмитриенко, Артем О.

doi:10.1016/j.mencom.2018.05.001

Cited by 37 publications

(23 citation statements)

References 49 publications

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“…Indeed as shown in the paper by Medvedev et al [2], the common strategy of DFT functional development tailoring molecular energetics and geometry might result in DFT functionals poorly describing electron density. While energy-based evaluation of DFT functionals' performance readily delivers natural metrics, electron density-based evaluation metrics are more ambiguous; see for discussion Marjewski et al [3] and the references therein. Though electron density also delivers some natural and experimentally observable metrics such as (deviation in calculated) dipole moment (and higher moments) as used by Hait and Head-Gordon [4].…”

Section: Introductionmentioning

confidence: 99%

Performance of the DLPNO-CCSD and recent DFT methods in the calculation of isotropic and dipolar contributions to 14N hyperfine coupling constants of nitroxide radicals

Gromov

2021

J Mol Model

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B3LYP, ωB97x, B2PLYP, and the B3LYP/N07D and PBE/N07D schemes in the calculation of the 14 N anisotropic hyper ne coupling (HFC) constants of a set of 23 nitroxide radicals is evaluated. The results are compared with those obtained with the DLPNO-CCSD method and experimental HFC values. Harmonic contribution to the 14 N HFC vibrational correction was calculated at the revPBE0/def2-TZVPP level and included in the evaluation. With the vibrational correction, the DLPNO-CCSD method yielded HFC values in good agreement with the experiment (MAD = 0.3 G for the dipole-dipole contribution and MAD = 0.8 G for the contact coupling contribution). The best DFT results are obtained using the M06 functional with mean absolute deviation (MAD) = 0.2 G for the dipole-dipole contribution and MAD = 0.7 G for the contact coupling contribution. In general, vibrational correction signi cantly improved most DFT functionals' performance but did not change its overall ranking.

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Section: Introductionmentioning

confidence: 99%

Performance of the DLPNO-CCSD and recent DFT methods in the calculation of isotropic and dipolar contributions to 14N hyperfine coupling constants of nitroxide radicals

Gromov

2021

J Mol Model

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“…[22] The PBE0 functional is known to provide accurate results for organic reactions and has been shown to be well grounded in theory. [23][24][25] Transition states searches for the hydride shift transition states were performed starting from pre-optimized [26] structures where both C…H distances with the transferring hydride were constrained at ~1.4 Å. Oxygen compound O-2 a was excluded from calculation due to the absence of the experimental data about hydride shift rate.…”

Section: Resultsmentioning

confidence: 99%

BF₃ Mediated [1,5]‐Hydride Shift Triggered Cyclization: Thioethers Join the Game

Zaitseva¹,

Smirnov

Timashev

et al. 2022

Eur J Org Chem

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2-(2-(Benzylthio)benzylidene)malonates can undergo the 1,5hydride shift triggered cyclization resulting in thiachromanes in 45-84 % yield. Boron trifluoride as a reaction promotor is the key to success. DFT calculations revealed that the reaction proceeds via a chelate BF2 complex, which was confirmed by NMR-analysis. Experimental and theoretical comparison of nitro-gen, sulfur and carbon analogues revealed that sulfur derivatives have the highest activation barrier for the hydride transfer due to the unfavorable transition state geometry, which explains the lack of previous reports on 1,5-hydride shifts in (alkylthio)styrenes.

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“…DFT calculations were performed at PBE0-D3 theory level [ 64 , 65 ] in def2-TZVP basis set [ 66 ] with water solvation effects included, using the solvation model based on density (SMD) [ 67 ] and standard convergence criteria of 1.5 × 10 −5 Harthree/Bohr in Gaussian09 D.01 [ 68 ] software. PBE0 functional is known to provide accurate results in carbohydrate modeling [ 9 , 69 ] and was recently shown to be well-grounded in theory [ 70 , 71 ]. After optimization convergence, harmonic frequencies were computed at the same level of theory to ensure that located structures correspond to the expected types of stationary points (minima) and were subsequently utilized to compute quasi-harmonic [ 72 , 73 ] free energies, using GoodVibes program [ 74 ].…”

Section: Methodsmentioning

confidence: 99%

Comparison of Methods for Bulk Automated Simulation of Glycosidic Bond Conformations

Stroylov

Panova

Toukach

2020

IJMS

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Six empirical force fields were tested for applicability to calculations for automated carbohydrate database filling. They were probed on eleven disaccharide molecules containing representative structural features from widespread classes of carbohydrates. The accuracy of each method was queried by predictions of nuclear Overhauser effects (NOEs) from conformational ensembles obtained from 50 to 100 ns molecular dynamics (MD) trajectories and their comparison to the published experimental data. Using various ranking schemes, it was concluded that explicit solvent MM3 MD yielded non-inferior NOE accuracy with newer GLYCAM-06, and ultimately PBE0-D3/def2-TZVP (Triple-Zeta Valence Polarized) Density Functional Theory (DFT) simulations. For seven of eleven molecules, at least one empirical force field with explicit solvent outperformed DFT in NOE prediction. The aggregate of characteristics (accuracy, speed, and compatibility) made MM3 dynamics with explicit solvent at 300 K the most favorable method for bulk generation of disaccharide conformation maps for massive database filling.

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Interplay between test sets and statistical procedures in ranking DFT methods: The case of electron density studies

Cited by 37 publications

References 49 publications

Performance of the DLPNO-CCSD and recent DFT methods in the calculation of isotropic and dipolar contributions to 14N hyperfine coupling constants of nitroxide radicals

Performance of the DLPNO-CCSD and recent DFT methods in the calculation of isotropic and dipolar contributions to 14N hyperfine coupling constants of nitroxide radicals

BF₃ Mediated [1,5]‐Hydride Shift Triggered Cyclization: Thioethers Join the Game

Comparison of Methods for Bulk Automated Simulation of Glycosidic Bond Conformations

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Interplay between test sets and statistical procedures in ranking DFT methods: The case of electron density studies

Cited by 37 publications

References 49 publications

Performance of the DLPNO-CCSD and recent DFT methods in the calculation of isotropic and dipolar contributions to 14N hyperfine coupling constants of nitroxide radicals

Performance of the DLPNO-CCSD and recent DFT methods in the calculation of isotropic and dipolar contributions to 14N hyperfine coupling constants of nitroxide radicals

BF3 Mediated [1,5]‐Hydride Shift Triggered Cyclization: Thioethers Join the Game

Comparison of Methods for Bulk Automated Simulation of Glycosidic Bond Conformations

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Product

Resources

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BF₃ Mediated [1,5]‐Hydride Shift Triggered Cyclization: Thioethers Join the Game