Crystallography Open Database: History, Development, and Perspectives

Gražulis, S.; Merkys, Andrius; Vaitkus, Antanas; Chateigner, Daniel; Lutterotti, Luca; Moeck, Peter; Quirós, Miguel; Downs, Robert T.; Kaminsky, Werner; Bail, A. Le

doi:10.1002/9783527802265.ch1

Cited by 6 publications

(2 citation statements)

References 63 publications

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“…In this work, we outline an extensive effort to analyze the conformers and torsional angle preferences of more than 3 million organic small molecules, using exhaustive sampling using the GFN2-xTB method across both the experimental Crystallographic Open Database (COD) and multiple sets of small molecules, including PubChemQC . We compare the potential bias between the crystallographic and gas-phase geometries and individual torsion patterns, including analysis with ωB97X-D3 with the def2-SVP basis set. , …”

Section: Introductionmentioning

confidence: 99%

Systematic Comparison of Experimental Crystallographic Geometries and Gas-Phase Computed Conformers for Torsion Preferences

Folmsbee,

Koes,

Hutchison

2023

J. Chem. Inf. Model.

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We performed exhaustive torsion sampling on more than 3 million compounds using the GFN2-xTB method and performed a comparison of experimental crystallographic and gas-phase conformers. Many conformer sampling methods derive torsional angle distributions from experimental crystallographic data, limiting the torsion preferences to molecules that must be stable, synthetically accessible, and able to be crystallized. In this work, we evaluate the differences in torsional preferences of experimental crystallographic geometries and gas-phase computed conformers from a broad selection of compounds to determine whether torsional angle distributions obtained from semiempirical methods are suitable priors for conformer sampling. We find that differences in torsion preferences can be mostly attributed to a lack of available experimental crystallographic data with small deviations derived from gas-phase geometry differences. GFN2 demonstrates the ability to provide accurate and reliable torsional preferences that can provide a basis for new methods free from the limitations of experimental data collection. We provide Gaussian-based fits and sampling distributions suitable for torsion sampling and propose an alternative to the widely used “experimental torsion and knowledge distance geometry” (ETKDG) method using quantum torsion-derived distance geometry (QTDG) methods.

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Section: Introductionmentioning

confidence: 99%

Systematic Comparison of Experimental Crystallographic Geometries and Gas-Phase Computed Conformers for Torsion Preferences

Folmsbee,

Koes,

Hutchison

2023

J. Chem. Inf. Model.

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show abstract

“…In this work, we outline an extensive effort to analyze the conformers and torsional angle preferences of more than 3 million organic small molecules, using exhaustive sampling using the GFN2-xTB method across both the experimental Crystallographic Open Database 33 (COD) and multiple sets of small molecules, including PubChemQC. 30 We compare the potential bias between the crystallographic and gas-phase geometries and individual torsion patterns, including analysis with ωB97X-D3 34 with the def2-SVP basis set.…”

Section: Introductionmentioning

confidence: 99%

Systematic Comparison of Experimental Crystallographic Geometries and Gas-Phase Computed Conformers for Torsion Preferences

Folmsbee,

Koes,

Hutchison

2023

Preprint

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We have performed exhaustive torsion sampling on more than 3 million compounds using the GFN2 method and performed a comparison of experimental crystallographic and gas-phase conformers. Many conformer sampling methods derive torsional angle distributions from experimental crystallographic data, limiting the torsion preferences to molecules that must be stable, synthetically accessible, and able to be crystallized. In this work, we evaluate the differences in torsional preferences of experimental crystallographic geometries and gas-phase computed conformers from a broad selection of compounds to determine whether torsional angle distributions obtained from semi-empirical methods are suitable for conformer sampling. We find that differences in torsion preferences can be mostly attributed to a lack of available experimental crystallographic data, with some deviations derived from gas-phase geometry differences. GFN2 demonstrates the ability to provide accurate and reliable torsional preferences that can provide a basis for new methods free from limitations of experimental data collection. We provide Gaussian-based fits and sampling distributions suitable for torsion sampling, and propose an alternative to ETKDG using quantum-torsion derived distance geometry methods (QTDG).

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Study of neodymium addition on the magnetic and structural properties of strontium hexaferrite synthesized by the Pechini method

Ramírez-Ayala

Guerrero

Herrera‐González

et al. 2023

Journal of Magnetism and Magnetic Materials

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Crystallography Open Database: History, Development, and Perspectives

Cited by 6 publications

References 63 publications

Systematic Comparison of Experimental Crystallographic Geometries and Gas-Phase Computed Conformers for Torsion Preferences

Systematic Comparison of Experimental Crystallographic Geometries and Gas-Phase Computed Conformers for Torsion Preferences

Systematic Comparison of Experimental Crystallographic Geometries and Gas-Phase Computed Conformers for Torsion Preferences

Study of neodymium addition on the magnetic and structural properties of strontium hexaferrite synthesized by the Pechini method

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