Ab Initio Extended Hartree–Fock plus Dispersion Method Applied to Dimers with Hundreds of Atoms

Garcia, Javier; Szalewicz, Krzysztof

doi:10.1021/acs.jpca.9b11900

Cited by 12 publications

(15 citation statements)

References 71 publications

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“…Table includes comparisons of D as 20 with D as 10 on several other benchmark sets, namely, S66, S66x8, IonHB, UD-ARL, and S12L (with the dimer C7a omitted). All values presented in Table are taken from ref (see ref for computational details) and show that D as 20 gives systematically more accurate dispersion energies than D as 10 , although the improvements are generally not large. The only exception is IonHB, where MURE is 0.7% larger in the case of D as 20 , but MUE is 0.02 kcal·mol –1 smaller.…”

Section: Resultsmentioning

confidence: 99%

Extension of an Atom–Atom Dispersion Function to Halogen Bonds and Its Use for Rational Design of Drugs and Biocatalysts

et al. 2021

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A dispersion function D as in the form of a damped atom–atom asymptotic expansion fitted to ab initio dispersion energies from symmetry-adapted perturbation theory was improved and extended to systems containing heavier halogen atoms. To illustrate its performance, the revised D as function was implemented in the multipole first-order electrostatic and second-order dispersion (MED) scoring model. The extension has allowed applications to a much larger set of biocomplexes than it was possible with the original D as . A reasonable correlation between MED and experimentally determined inhibitory activities was achieved in a number of test cases, including structures featuring nonphysically shortened intermonomer distances, which constitute a particular challenge for binding strength predictions. Since the MED model is also computationally efficient, it can be used for reliable and rapid assessment of the ligand affinity or multidimensional scanning of amino acid side-chain conformations in the process of rational design of novel drugs or biocatalysts.

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Section: Resultsmentioning

confidence: 99%

Extension of an Atom–Atom Dispersion Function to Halogen Bonds and Its Use for Rational Design of Drugs and Biocatalysts

et al. 2021

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“…One may ask why pDFT+D calculations are needed to improve the rankings, while several comparisons on benchmark interaction energies, see, e.g., refs. 42 , 43 , show that SAPT(DFT) is nearly as accurate as CCSD(T) and more accurate than DFT+D methods. The main reason is that what is used in CSPs are aiFFs, and they include additional uncertainties due to fitting.…”

Section: Resultsmentioning

confidence: 99%

“…SAPT(DFT) and CCSD(T) calculations scale as and with system size, respectively, where n is the number of electrons, and for dimers with a couple dozens of atoms, SAPT(DFT) calculations are about two orders of magnitude less expensive than CCSD(T) calculations. The recently developed new SAPT(DFT) algorithms and effective computer codes 35 , 42 can be used to compute thousands of grid points for dimers with ~100-atom monomers using reasonable computer resources and being able to achieve this in a few days if a sufficient number of computer cores are available.…”

Section: Methodsmentioning

confidence: 99%

“…Thus, both the ab initio method and the fit to interaction energies computed using this method must have sufficiently small uncertainties. In calculations of dimer interaction energies, the variant of SAPT used by us (see “Methods”) is nearly as accurate 35 , 42 , 43 as the coupled cluster method with single, double, and noniterative triple excitations, CCSD(T), the “gold-standard” method of electronic structure theory, but is significantly less expensive. To prevent loss of accuracy due to fitting, the form of the fitting function has to be significantly more involved than those of empirical FFs that are typically built from Lennard-Jones plus Coulomb potentials, see “Methods”.…”

Section: Introductionmentioning

confidence: 99%

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Reliable crystal structure predictions from first principles

Nikhar

Szalewicz

2022

Nat Commun

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An inexpensive and reliable method for molecular crystal structure predictions (CSPs) has been developed. The new CSP protocol starts from a two-dimensional graph of crystal’s monomer(s) and utilizes no experimental information. Using results of quantum mechanical calculations for molecular dimers, an accurate two-body, rigid-monomer ab initio-based force field (aiFF) for the crystal is developed. Since CSPs with aiFFs are essentially as expensive as with empirical FFs, tens of thousands of plausible polymorphs generated by the crystal packing procedures can be optimized. Here we show the robustness of this protocol which found the experimental crystal within the 20 most stable predicted polymorphs for each of the 15 investigated molecules. The ranking was further refined by performing periodic density-functional theory (DFT) plus dispersion correction (pDFT+D) calculations for these 20 top-ranked polymorphs, resulting in the experimental crystal ranked as number one for all the systems studied (and the second polymorph, if known, ranked in the top few). Alternatively, the polymorphs generated can be used to improve aiFFs, which also leads to rank one predictions. The proposed CSP protocol should result in aiFFs replacing empirical FFs in CSP research.

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“…The HF-3c method uses three separate geometry-dependent formulas 38,39 to add energy corrections ("3c") for the various deficiencies of minimal basis set HF: one to account for some of the missing dispersion interactions, and two to mitigate the effects of basis set incompleteness errors. Several other techniques have been proposed in the literature [40][41][42][43][44][45][46][47][48][49][50][51][52][53][54] , reflecting the interest in developing computationally inexpensive methods for large systems.…”

Section: Introductionmentioning

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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Ab Initio Extended Hartree–Fock plus Dispersion Method Applied to Dimers with Hundreds of Atoms

Cited by 12 publications

References 71 publications

Extension of an Atom–Atom Dispersion Function to Halogen Bonds and Its Use for Rational Design of Drugs and Biocatalysts

Extension of an Atom–Atom Dispersion Function to Halogen Bonds and Its Use for Rational Design of Drugs and Biocatalysts

Reliable crystal structure predictions from first principles

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

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