Evidence map›Paper›PMID 39087913›Full record

ArticleThe journal of physical chemistry. B2024

Benchmarking Quantum Mechanical Levels of Theory for Valence Parametrization in Force Fields.

Pavan Kumar Behara, Hyesu Jang, Joshua T Horton, Trevor Gokey, David L Dotson, Simon Boothroyd, Christopher I Bayly, Daniel J Cole, Lee-Ping Wang, David L Mobley

Abstract read
In one paragraph

Article in The journal of physical chemistry. B, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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

8 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Article
  6. Article
  7. Article
  8. Article
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

10 authors.

Pavan Kumar BeharaCenter for Neurotherapeutics, University of California, Irvine, California 92697, United States.ORCID 0000-0001-6583-2148
Hyesu JangChemistry Department, University of California at Davis, Davis, California 95616, United States.
Joshua T HortonSchool of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K.
Trevor GokeyDepartment of Chemistry, University of California, Irvine, California 92697, United States.
David L DotsonThe Open Force Field Initiative, Open Molecular Software Foundation, Davis, California 95616, United States.
Simon BoothroydBoothroyd Scientific Consulting Ltd., London WC2H 9JQ, U.K.
Christopher I BaylyOpenEye Scientific Software, Santa Fe, New Mexico 87508, United States.
Daniel J ColeSchool of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K.
Lee-Ping WangChemistry Department, University of California at Davis, Davis, California 95616, United States.ORCID 0000-0003-3072-9946
David L MobleyCenter for Neurotherapeutics, University of California, Irvine, California 92697, United States.ORCID 0000-0002-1083-5533

Funding

Open data-driven infrastructure for building biomolecular force fields for predictive biophysics and drug designR01GM132386 · NIGMS · UNIVERSITY OF COLORADO · PI SHIRTS, MICHAEL R · 2020 to 2023
$3.1M
Accelerating drug discovery via ML-guided iterative design and optimizationR35GM148236 · NIGMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI David Lowell Mobley · 2023 to 2026
$2.2M
NIGMS NIH HHS R01 GM132386NIGMS NIH HHS R35 GM148236
6 · The paper itself

Abstract

A wide range of density functional methods and basis sets are available to derive the electronic structure and properties of molecules. Quantum mechanical calculations are too computationally intensive for routine simulation of molecules in the condensed phase, prompting the development of computationally efficient force fields based on quantum mechanical data. Parametrizing general force fields, which cover a vast chemical space, necessitates the generation of sizable quantum mechanical data sets with optimized geometries and torsion scans. To achieve this efficiently, choosing a quantum mechanical method that balances computational cost and accuracy is crucial. In this study, we seek to assess the accuracy of quantum mechanical theory for specific properties such as conformer energies and torsion energetics. To comprehensively evaluate various methods, we focus on a representative set of 59 diverse small molecules, comparing approximately 25 combinations of functional and basis sets against the reference level coupled cluster calculations at the complete basis set limit.

Identifiers

PMID39087913
PMCPMC11331531

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

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.