ReviewJournal of computer-aided molecular design2023
Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory.
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.
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.
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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.
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Who cites it
5 citing papers in PubMed.
- Automating Model Building for SPM Images of Biomolecules Using MISO.Journal of chemical information and modeling · 2026Article
- Comprehensive Investigation of Polymorphic Stability and Phase Transformation Kinetics in Tegoprazan.Pharmaceutics · 2025Article
- Conformational Profile of Galactose-α-1,3-Galactose (α-Gal) and Structural Basis of Its Immunological Response.Chemistry (Weinheim an der Bergstrasse, Germany) · 2025Article
- Assessing the domain-based local pair natural orbital (DLPNO) approximation for non-covalent interactions in sizable supramolecular complexes.The Journal of chemical physics · 2024Article
- Identification of Peptidoglycan Glycosyltransferase FtsI as a Potential Drug Target againstCurrent pharmaceutical design · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
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
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