Importance of model size in quantum mechanical studies of DNA intercalation

Harding, Drew P.; Kingsley, Laura J.; Spraggon, Glen; Wheeler, Steven E.

doi:10.1002/jcc.26164

Cited by 6 publications

(25 citation statements)

References 70 publications

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“…Turning to a comparison with results for the minimal-basis method HF-3c [128], we see that the MAD value for HF-3c, at 2.00 kcal mol −1 , is more than double that for CX. In other words, CX competes well with the best hybrid results of reference [128], and offers a path to acceleration that gives improved predictability compared to the HF-3c minimal-basis-set approach.…”

Section: Systemmentioning

confidence: 97%

“…The comparison is made against the CCSD(T)-extrapolated results from reference [128], and with their B3LYP-D3, and HF-3c results. The three intercalants have PDB codes 1K9G, 1DL8 and 1Z3F and are here (and in reference [128]) denoted '1', '2', and '3' (see top and middle panels of figure 6). The latter molecule includes a nitrogen atom that can be protonated and this is also included in the set of calculations, the protonated molecule is denoted '3 + '.…”

Section: Dna-intercalation Energiesmentioning

confidence: 99%

“…The intercalant in the (top panel) (1Z3F, henceforth denoted '3') is also studied in a modified form '3 + ' where a proton is added at the nitrogen identified by a red circle. The alternative intercalants shown in the (middle left and right panels), 1DL8 and 1K9G, are denoted '2' and '1' respectively[128]. Finally, the PVDF forms (bottom row) are studied in crystals forms, see figure8below, and table 7.…”

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confidence: 99%

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Hard and soft materials: putting consistent van der Waals density functionals to work

et al. 2022

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We present the idea and illustrate potential benefits of having a tool chain of closely related regular, unscreened and screened hybrid exchange-correlation (XC) functionals, all within the consistent formulation of the van der Waals density functional (vdW-DF) method [JPCM 32, 393001 (2020)]. Use of this chain of nonempirical XC functionals allows us to map when the inclusion of truly nonlocal exchange and of truly nonlocal correlation is important. Here we begin the mapping by addressing hard and soft material challenges: magnetic elements, perovskites, and biomolecular problems. We also predict the structure and polarization for a ferroelectric polymer. To facilitate this work and future broader explorations, we present a stress formulation for spin vdW-DF and illustrate the use of a simple stability-modeling scheme. The modeling supplements DFT (with a specific XC functional) by asserting whether the finding of a soft mode (an imaginary-frequency vibrational mode, ubiquitous in perovskites and soft matter) implies an actual DFT-based prediction of a low-temperature transformation.

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Section: Systemmentioning

confidence: 97%

Section: Dna-intercalation Energiesmentioning

confidence: 99%

mentioning

confidence: 99%

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Hard and soft materials: putting consistent van der Waals density functionals to work

et al. 2022

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“…The Biomolecule-Biomolecule subset contains model systems representative of nucleotide-nucleotide interactions as well as protein fragments interacting with carbohydrates, nucleotides, drugs, water, and with other proteins. Such interactions are relevant in applications like protein folding 241,242 , protein structure refinement 243,244 , protein-ligand binding [245][246][247] , intercalation 248 , nucleobase stacking 249 , and protein hydration 250 , to name a few. Uncorrected minimal or double-ζ basis set HF-D3 in general overestimate the interaction energies in this subset, and application of the ACPs reduces this overestimation and decreases the error spread and SDs.…”

Section: (I) Non-covalent Interaction Energiesmentioning

confidence: 99%

Fast and accurate quantum mechanical modeling of large molecular systems using small basis set Hartree–Fock methods corrected with atom-centered potentials

Prasad

Otero-de-la-Roza

DiLabio

2022

Preprint

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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 bio-organic 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 (73832 data points) of non-covalent properties (interaction and conformational energies) and validated additionally on a set of 32048 data points. All reference data is 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 non-covalent 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 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 non-covalent 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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“…The study of DNA fragments and of their assembly from building blocks is a rich research field. It is a goal of the overall vdW-DF method and long-term research program to realize accurate computationally effective studies of structure, of defects and intercalation [136], of fluorescence-marker base substitutions [137,138], as well as of molecular dynamics to determine the entropic effects [139]. All of these problems are interesting for biochemistry in their own right.…”

Section: Biochemistry Testing and Organic Ferroelectricsmentioning

confidence: 99%

Hard and soft materials: Putting consistent van der Waals density functionals to work

Frostenson¹,

Granhed²,

Shukla³

et al. 2021

Preprint

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We present the idea and illustrate potential benefits of having a tool chain of closely related regular, unscreened and screened hybrid exchange-correlation (XC) functionals, all within the consistent formulation of the van der Waals density functional (vdW-DF) method [JPCM 32, 393001 (2020)]. Use of this chain of nonempirical XC functionals allows us to map when the inclusion of truly nonlocal exchange and of truly nonlocal correlation is important. Here we begin the mapping by addressing hard and soft material challenges: magnetic elements, perovskites, and biomolecular problems. We also predict the structure and polarization for a ferroelectric polymer. To facilitate this work and future broader explorations, we furthermore present a stress formulation for spin vdW-DF and illustrate use of a simple stability-modeling scheme to assert when the prediction of a soft mode (an imaginary-frequency vibrational mode, ubiquitous in perovskites and soft matter) implies a prediction of an actual low-temperature transformation.

show abstract

Importance of model size in quantum mechanical studies of DNA intercalation

Cited by 6 publications

References 70 publications

Hard and soft materials: putting consistent van der Waals density functionals to work

Hard and soft materials: putting consistent van der Waals density functionals to work

Fast and accurate quantum mechanical modeling of large molecular systems using small basis set Hartree–Fock methods corrected with atom-centered potentials

Hard and soft materials: Putting consistent van der Waals density functionals to work

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