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June, 2007

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IUPAC Naming. Daniel Bonniot. June, 2007. IUPAC Naming. Available in Marvin since 4.1.7 (April 2007) Present several ways to use it Evaluation Work in progress. Different Nomenclatures. Traditional name: isobutane IUPAC name: 2-methylpropane. Different Nomenclatures.

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June, 2007

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  1. IUPAC Naming Daniel Bonniot June, 2007

  2. IUPAC Naming • Available in Marvin since 4.1.7 (April 2007) • Present several ways to use it • Evaluation • Work in progress

  3. Different Nomenclatures • Traditional name: isobutane • IUPAC name: 2-methylpropane

  4. Different Nomenclatures • Traditional name: isobutane • IUPAC name: 2-methylpropane • IUPAC name: ethyl methyl ketone • Preferred IUPAC name: but-2-one

  5. Our nomenclature options • Currently two options: • Preferred (default) • Traditional • Open to custom needs

  6. Plugin (MView, MSketch)‏ • Demo

  7. Real time label (MSketch 4.2)‏ • Updated automatically • Automatic or manual placement • Demo

  8. Batch naming • Using MarvinView: File/Save as: IUPAC Name • On the command line: molconvert name inputs.mol -o names.txt • Adding names as an additional field to a SDfile cxcalc -S name input.sdf -o named.sdf • Batch naming requires a license key

  9. Instant JChem 2 • Requires updated IJC 2 • Demo

  10. Independent Evaluation • 193 molecules chosen by a chemist • Names produced for all, no failures • 187 correct names • 5 with missing stereo information (3 fixed since, remaining need r/s stereo) • 1 wrong name, fixed • ACD/Labs: 2 failures & 1+ wrong • ChemOffice: 10 failures

  11. Evaluation (automated)‏ • Pubchem: 23,000 molecules, average 30 atoms per molecule • Speed: 90 names/second • Names generated: 99.8% • Using name to structure, virtually no “wrong” name

  12. Work in progress • More extensive support for traditional nomenclature • Specific naming, depending on requests (sugars, natural products, ...) • Name import (name to structure)

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