Benchmarking London dispersion corrected density functional theory for noncovalent ion-pi interactions

Spicher, Sebastian; Caldeweyher, Eike; Hansen, Andreas

doi:10.26434/chemrxiv.13497135.v2

Cited by 2 publications

(3 citation statements)

References 113 publications

(154 reference statements)

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“…5% for the LNCI16 set, which further confirms its generally good performance for non-covalently bound systems. 85 99 In terms of accuracy, PBEh-3c performs second best among all the tested methods, and more importantly, it converges for all systems of the LNCI16 set. For the subset where the (meta-)GGA DFAs also converged, PBEh-3c achieved a relMAD of 8.9%.…”

Section: Resultsmentioning

confidence: 95%

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Efficient Computation of the Interaction Energies of Very Large Non-covalently Bound Complexes

Gorges¹,

Bädorf²,

Hansen³

et al. 2022

Synlett

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We 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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Section: Resultsmentioning

confidence: 95%

“… a MAD values for ωB97X-3c, ωB97X-D4/QZ (with revised D4 parametrization 41 ), and the popular B3LYP-D4/QZ method for NCI benchmark sets S30L, 19 IONPI19, 99 L7, 18 100 S66, 101 R160x6, 102 and HB300SPX. 103 ωB97X-3c and ωB97X-D4 values are taken from Ref.…”

Section: Generation Of Reference Valuesmentioning

confidence: 99%

Efficient Computation of the Interaction Energies of Very Large Non-covalently Bound Complexes

Gorges¹,

Bädorf²,

Hansen³

et al. 2022

Synlett

Self Cite

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“…62 This method was used for its high accuracy proven in benchmark studies 63−65 and also since dispersion-corrected double-hybrid DFT methods are recommended for the description of noncovalent anion•••π interactions. 66 The DFT quadrature grid GRID5 was used. The RI approximation for Coulomb integrals (RI-J) and COSX (chain-of-spheres exchange) approximation for exchange integrals with the accurate GRIDX6 grid were employed with the automatic construction of the auxiliary basis set (AutoAux keyword).…”

Section: Potential Energymentioning

confidence: 99%

Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions

Mráziková

Kruse

Mlýnský

et al. 2022

J. Chem. Inf. Model.

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Phosphate•••π, also called anion•••π, contacts occur between nucleobases and anionic phosphate oxygens (OP2) in r(GNRA) and r(UNNN) U-turn motifs (N = A,G,C,U; R = A,G). These contacts were investigated using state-of-the-art quantum-chemical methods (QM) to characterize their physicochemical properties and to serve as a reference to evaluate AMBER force field (AFF) performance. We found that phosphate•••π interaction energies calculated with the AFF for dimethyl phosphate•••nucleobase model systems are less stabilizing in comparison with double-hybrid DFT and that minimum contact distances are larger for all nucleobases. These distance stretches are also observed in large-scale AFF vs QM/MM computations and classical molecular dynamics (MD) simulations on several r(gcGNRAgc) tetraloop hairpins when compared to experimental data extracted from X-ray/cryo-EM structures (res. ≤ 2.5 Å) using the WebFR3D bioinformatic tool. MD simulations further revealed shifted OP2/nucleobase positions. We propose that discrepancies between the QM and AFF result from a combination of missing polarization in the AFF combined with too large AFF Lennard-Jones (LJ) radii of nucleobase carbon atoms in addition to an exaggerated short-range repulsion of the r −12 LJ repulsive term. We compared these results with earlier data gathered on lone pair•••π contacts in CpG Z-steps occurring in r(UNCG) tetraloops. In both instances, charge transfer calculations do not support any significant n → π* donation effects. We also investigated thiophosphate•••π contacts that showed reduced stabilizing interaction energies when compared to phosphate•••π contacts. Thus, we challenge suggestions that the experimentally observed enhanced thermodynamic stability of phosphorothioated r(GNRA) tetraloops can be explained by larger London dispersion.

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Benchmarking London dispersion corrected density functional theory for noncovalent ion-pi interactions

Cited by 2 publications

References 113 publications

Efficient Computation of the Interaction Energies of Very Large Non-covalently Bound Complexes

Efficient Computation of the Interaction Energies of Very Large Non-covalently Bound Complexes

Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions

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