IUPAC name functionalities in MarvinSketch

Importing a IUPAC name (Name to Structure)

You can easily import a molecule by importing the name directly into MarvinSketch.

1. A simple method is to select the name in the text of any page and drag&drop or copy&paste it to MarvinSketch.
2. Select the Enter IUPAC name from the Edit menu, and paste the name into the text field.
3. Open a text file (.name) containing IUPAC names (one per row). MarvinView will open all structures, MarvinSketch will ask you to select one structure (by its index number).
   

Notes:

• Some names contain non-ASCII characters or formatting. These are imported into Marvin names by reformulating the name. Two examples of this feature:

  	ring-numbering (superscripts)	non-standard valence (Greek letter)
  Structure
  Standard name	pentacyclo[6.4.0.02,7.03,6.09,12]dodecane	1λ14-thiopyran-1-carboxylic acid
  Marvin name	pentacyclo[6.4.0.0^{2,7}.0^{3,6}.0^{9,12}]dodecane	1$1^{4}-thiopyran-1-carboxylic acid
  Changed	superscript to ^{ }	λ to $1

  
  
• Name import is only available for a single molecule with the free MarvinSketch desktop application. For batch opening in MarvinView (from a text file) you will need the IUPAC Name Plugin licence.

Dynamic IUPAC name changes while drawing a structure (structure to name)

If IUPAC name is inserted to the canvas (Insert -> IUPAC name) you will see the name changing whenever you alter a molecule. See this animation.

The snapshot below shows a molecule taken from the IUPAC specification, with its name computed by Marvin.

Note that batch name generation is only available with the IUPAC Name Plugin licence.

Features

• Chains, Monocycles
• Retained/traditional names for ring systems with and without heteroatoms
• Spiro ring systems
• All cases of von Bayer nomenclature for bridged ring systems
• Fused ring systems (linear fused ring systems are named using the fused nomenclature, others using von Bayer nomenclature)
• Ethers
• Common characteristic groups
• Ionic compounds
• Compounds with one radical
• Unlimited number of atoms and rings
• All atom types
• Substitutive nomenclature
• Stereochemistry

Current limitations

• Molecules containing multiple radicals (e.g. ethane-1,2-diyl) are not supported yet.
• Stereo descriptors (r) and (s) are not supported (as in the whole of marvin).
• Amino-acids and peptides are supported only when the amino-acids are represented as groups.
• Isotopes are not supported
• Some aspects of nomenclature are only partially implemented, in particular complex cases of fused systems and multiplicative nomenclature. In those cases, a less straightforward but chemically correct name will be generated.