Evidence map›Paper›PMID 38319296›Full record

ArticleJournal of chemical information and modeling2024

From Organic Fragments to Photoswitchable Catalysts: The OFF-ON Structural Repository for Transferable Kernel-Based Potentials.

Frédéric Célerse, Matthew D Wodrich, Sergi Vela, Simone Gallarati, Raimon Fabregat, Veronika Juraskova, Clémence Corminboeuf

Abstract read
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Article in Journal of chemical information and modeling, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0cells of the map it votes in
0citing papers in PubMed
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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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

7 authors.

Frédéric CélerseLaboratory for Computational Molecular Design (LCMD), Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland.ORCID 0000-0001-8584-6547
Matthew D WodrichLaboratory for Computational Molecular Design (LCMD), Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland.ORCID 0000-0002-6006-671X
Sergi VelaLaboratory for Computational Molecular Design (LCMD), Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland.ORCID 0000-0002-3431-2470
Simone GallaratiLaboratory for Computational Molecular Design (LCMD), Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland.
Raimon FabregatLaboratory for Computational Molecular Design (LCMD), Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland.
Veronika JuraskovaLaboratory for Computational Molecular Design (LCMD), Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland.
Clémence CorminboeufLaboratory for Computational Molecular Design (LCMD), Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland.ORCID 0000-0001-7993-2879

Funding

European Research Council
6 · The paper itself

Abstract

Structurally and conformationally diverse databases are needed to train accurate neural networks or kernel-based potentials capable of exploring the complex free energy landscape of flexible functional organic molecules. Curating such databases for species beyond "simple" drug-like compounds or molecules composed of well-defined building blocks (e.g., peptides) is challenging as it requires thorough chemical space mapping and evaluation of both chemical and conformational diversities. Here, we introduce the OFF-ON (organic fragments from organocatalysts that are non-modular) database, a repository of 7869 equilibrium and 67,457 nonequilibrium geometries of organic compounds and dimers aimed at describing conformationally flexible functional organic molecules, with an emphasis on photoswitchable organocatalysts. The relevance of this database is then demonstrated by training a local kernel regression model on a low-cost semiempirical baseline and comparing it with a PBE0-D3 reference for several known catalysts, notably the free energy surfaces of exemplary photoswitchable organocatalysts. Our results demonstrate that the OFF-ON data set offers reliable predictions for simulating the conformational behavior of virtually any (photoswitchable) organocatalyst or organic compound composed of H, C, N, O, F, and S atoms, thereby opening a computationally feasible route to explore complex free energy surfaces in order to rationalize and predict catalytic behavior.

Indexed as

Neural Networks, ComputerPeptidesDatabases, FactualEntropyOrganic ChemicalsOrganic ChemicalsPeptides

Identifiers

PMID38319296
PMCPMC10900300

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Registered trials

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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.