Evidence map›Paper›PMID 36792512›Full record

ArticleThe Journal of chemical physics2023

Reparameterization of the chemical-potential equalization model with DFTB3: A practical balance between accuracy and transferability.

Van-Quan Vuong, Qiang Cui

Abstract read
In one paragraph

Article in The Journal of chemical physics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

2 authors.

Van-Quan VuongDepartment of Chemistry, Boston University, Boston, Massachusetts 02215, USA.ORCID 0000-0001-8580-8532
Qiang CuiDepartment of Chemistry, Boston University, Boston, Massachusetts 02215, USA.ORCID 0000-0001-6214-5211

Funding

Computational Analysis of Enzyme Catalysis and RegulationR35GM141930 · NIGMS · BOSTON UNIVERSITY (CHARLES RIVER CAMPUS) · PI Qiang Cui · 2021 to 2026
$2.7M
NIGMS NIH HHS R35 GM141930
6 · The paper itself

Abstract

To improve the performance of the third-order density-functional tight-binding method (DFTB3) for non-covalent interactions involving organic and biological molecules, a chemical-potential equalization (CPE) approach was introduced [J. Phys. Chem. A, 116, 9131 (2012)] and parameterized for the H, C, N, O, and S chemical elements [J. Chem. Phys., 143, 084123 (2015)]. Based largely on equilibrium structures, the parameterized DFTB3/CPE models were shown to exhibit improvements in molecular polarizabilities and intermolecular interactions. With more extensive analyses, however, we observe here that the available DFTB3/CPE models have two critical limitations: (1) they lead to sharply varying potential energy surfaces, thus causing numerical instability in molecular dynamics (MD) simulations, and (2) they lead to spurious interactions at short distances for some dimer complexes. These shortcomings are attributed to the employed screening functions and the overfitting of CPE parameters. In this work, we introduce a new strategy to simplify the parameterization procedure and significantly reduce free parameters down to four global (i.e., independent of element type) ones. With this strategy, two new models, DFTB3/CPE(r) and DFTB3/CPE(r

Identifiers

PMID36792512
PMCPMC9928490

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.