Evidence map›Paper›PMID 37597063›Full record

ReviewJournal of computer-aided molecular design2023

Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory.

Ioannis Stylianakis, Nikolaos Zervos, Jenn-Huei Lii, Dimitrios A Pantazis, Antonios Kolocouris

Erratum issuedAbstract readReview
In one paragraph

Review in Journal of computer-aided molecular design, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

  1. Automating Model Building for SPM Images of Biomolecules Using MISO.Journal of chemical information and modeling · 2026
    Article
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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

5 authors.

Ioannis StylianakisDepartment of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece.
Nikolaos ZervosDepartment of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece.
Jenn-Huei LiiDepartment of Chemistry, National Changhua University of Education, Changhua City, Taiwan.
Dimitrios A PantazisMax-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany.ORCID http://orcid.org/0000-0002-2146-9065
Antonios KolocourisDepartment of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece. ankol@pharm.uoa.gr.ORCID http://orcid.org/0000-0001-6110-1903

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

We selected 145 reference organic molecules that include model fragments used in computer-aided drug design. We calculated 158 conformational energies and barriers using force fields, with wide applicability in commercial and free softwares and extensive application on the calculation of conformational energies of organic molecules, e.g. the UFF and DREIDING force fields, the Allinger's force fields MM3-96, MM3-00, MM4-8, the MM2-91 clones MMX and MM+, the MMFF94 force field, MM4, ab initio Hartree-Fock (HF) theory with different basis sets, the standard density functional theory B3LYP, the second-order post-HF MP2 theory and the Domain-based Local Pair Natural Orbital Coupled Cluster DLPNO-CCSD(T) theory, with the latter used for accurate reference values. The data set of the organic molecules includes hydrocarbons, haloalkanes, conjugated compounds, and oxygen-, nitrogen-, phosphorus- and sulphur-containing compounds. We reviewed in detail the conformational aspects of these model organic molecules providing the current understanding of the steric and electronic factors that determine the stability of low energy conformers and the literature including previous experimental observations and calculated findings. While progress on the computer hardware allows the calculations of thousands of conformations for later use in drug design projects, this study is an update from previous classical studies that used, as reference values, experimental ones using a variety of methods and different environments. The lowest mean error against the DLPNO-CCSD(T) reference was calculated for MP2 (0.35 kcal mol

Indexed as

SoftwareMolecular ConformationPhysical PhenomenaThermodynamicsB3LYPConformational energiesDLPNO-CCSD(T)Force fieldsOrganic molecules

Identifiers

PMID37597063
PMCPMC10618395

What OpenQuestion holds

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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.