Chemical space as a unifying theme for chemistry

Journal of Cheminformatics, Journal Year: 2025, Volume and Issue: 17(1)

Published: Jan. 16, 2025

Chemistry has diversified from a basic understanding of the elements to studying millions highly diverse molecules and materials, which together are conceptualized as chemical space. A map this space where distances represent similarities between compounds can mutual relationships different subfields chemistry help discipline be viewed understood globally.

Language: Английский

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Clc-db: an open-source online database of chiral ligands and catalysts

Journal of Cheminformatics, Journal Year: 2025, Volume and Issue: 17(1)

Published: April 3, 2025

Language: Английский

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molli: A General-Purpose Python Toolkit for Combinatorial Small Molecule Library Generation, Manipulation, and Feature Extraction.

Published: Aug. 12, 2024

The construction, management and analysis of large in silico molecular libraries is critical many areas modern chemistry. Herein, we introduce the MOLecular LIibrary toolkit, “molli”, which a Python 3 cheminformatics module that provides streamlined interface for manipulating libraries. Three-dimensional, combinatorial molecule can be expanded directly from two-dimensional chemical structure fragments stored CDXML files with high stereochemical fidelity. Geometry optimization, property calculation, conformer generation are executed by interfacing widely used computational chemistry programs such as OpenBabel, RDKit, ORCA, NWChem, xTB/CREST. Conformer-dependent grid-based feature calculators provide numerical representation, to robust three-dimensional visualization tools comprehensive images enhance human understanding thousands members. package includes command-line addition classes streamline frequently workflows. Parallel performance benchmarked on various hardware platforms, common workflows demonstrated different tasks ranging optimized descriptor calculation catalyst an NMR shift prediction workflow files.

Language: Английский

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Synthesis of Some New Chiral Triazole-oxazoline Derivatives

Current Organic Synthesis, Journal Year: 2024, Volume and Issue: 22(1), P. 136 - 142

Published: July 12, 2024

: Some new (S)-2-[1-aryl-5-methyl-1H-1,2,3-triazol-4-yl]-4-benzyl-4,5-dihydro-ox-azoline were synthesized by the reaction of (S)-N-(1-hydroxy-3-phenylpropan-2-yl)-1-aryl-5-methyl-1H-1,2,3-triazole-4-carboxamides which prepared from aromatic amine as start-ing materials, with p-toluenesulfonyl chloride, triethylamine and DMAP. The structures characterized 1H NMR, 13C MS IR. chiral triazole-oxazoline was used a ligand in Diels-Alder asymmetric catalytic between 3-allyl-1,3-ox-azolidin-2-ketone 2-methyl-1,3-butadiene, using PdCl2 catalyst. (S)-3-(4-methylcyclo-hexe-3-ene-1-formyl)-1,3-oxazolidin-2-one obtained. Background: ligands are rarely reported. Objective: aim study to synthsize some (S)-4-benzyl-2-(1-aryl-5-methyl-1H-1,2,3-triazole-4-yl)-4,5-dihydrooxazoline (5a-g). Methods: one-pot methods oriented synthesis adopted. This provides sim-ple effective method for derivatives. Results: (5a-g) cyclization 3-allyl-1,3-oxazolidin-2-ketone 2-methyl-1,3-butadiene catalyzed (S)-4-triazole-oxazoline ligands. Conclusion: (S)-4-benzyl-2-(1-aryl-5-methyl-1H-1,2,3-triazole-4-yl)-4,5-dihydro-oxazoline corresponding N-[(S)-1-hydroxy-3-phenylpropan-2-yl]-1-aryl-5-methyl-1H-1,2,3-triazole-4-formamide, through method. After preliminary evaluation, triazoline-oxazoline ligands, 1,2,3-triazole rings, like pyridine-type materials saved replace one oxazoline ring di-oxazoline reactions.

Language: Английский

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molli: A General Purpose Python Toolkit for Combinatorial Small Molecule Library Generation, Manipulation, and Feature Extraction

Journal of Chemical Information and Modeling, Journal Year: 2024, Volume and Issue: 64(21), P. 8083 - 8090

Published: Oct. 23, 2024

The construction, management, and analysis of large in silico molecular libraries is critical many areas modern chemistry. Herein, we introduce the MOLecular LIibrary toolkit, "molli", which a Python 3 cheminformatics module that provides streamlined interface for manipulating libraries. Three-dimensional, combinatorial molecule can be expanded directly from two-dimensional chemical structure fragments stored CDXML files with high stereochemical fidelity. Geometry optimization, property calculation, conformer generation are executed by interfacing widely used computational chemistry programs such as OpenBabel, RDKit, ORCA, NWChem, xTB/CREST. Conformer-dependent grid-based feature calculators provide numerical representation to robust three-dimensional visualization tools comprehensive images enhance human understanding thousands members. package includes command-line addition classes streamline frequently workflows. Parallel performance benchmarked on various hardware platforms, common workflows demonstrated different tasks ranging optimized descriptor calculation catalyst an NMR shift prediction workflow files.

Language: Английский

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