June, 2007

Daniel Bonniot

IUPAC Naming

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

• Traditional name: isobutane• IUPAC name: 2-methylpropane

• IUPAC name: ethyl methyl ketone• Preferred IUPAC name: but-2-one

Our nomenclature options

• Currently two options:– Preferred (default)– Traditional

• Open to custom needs

Plugin (MView, MSketch)

• Demo

Real time label (MSketch 4.2)

• Updated automatically• Automatic or manual placement• Demo

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 SDfilecxcalc -S name input.sdf -o named.sdf

• Batch naming requires a license key

Instant JChem 2

• Requires updated IJC 2• Demo

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

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

Work in progress

• More extensive support for traditional nomenclature

• Specific naming, depending on requests (sugars, natural products, ...)

• Name import (name to structure)