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stereonotations [2012/10/13 16:59]
sanmark
stereonotations [2012/10/15 14:27] (current)
sanmark
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 Stereo configurations of molecules in the mcule database are standardized and displayed at mcule.com accordingly. Here we give a description of our drawing standards, which are necessary to interpret stereo configurations in the mcule database correctly. Stereo configurations of molecules in the mcule database are standardized and displayed at mcule.com accordingly. Here we give a description of our drawing standards, which are necessary to interpret stereo configurations in the mcule database correctly.
  
-The mcule database currently supports the representation of the two most common forms of stereoisomerism: optical isomerism and cis-trans isomerism. Configuration of optical isomers is usually specified and displayed using special bond types at the tetrahedral centers, whereas cis-trans configurations are primarily represented by 2D geometry.+The mcule database currently supports the representation of the two most common forms of stereoisomerism: [[http://en.wikipedia.org/wiki/Optical_isomers|optical isomerism]] and [[http://en.wikipedia.org/wiki/Cis-trans_isomerism|cis-trans isomerism]]. Configuration of optical isomers is usually specified and displayed using special bond types at the tetrahedral centers, whereas cis-trans configurations are primarily represented by 2D geometry.
  
 ===Cis-trans configuration=== ===Cis-trans configuration===
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 The mcule registration system supports the distinction between unknown and unspecified/undefined cis-trans configurations. Unknown cis-trans configuration represents a structure having either E or Z configuration but definitely one of them. In unspecified/undefined cases the structure can also represent the mixture of the cis and trans isomers. The mcule registration system supports the distinction between unknown and unspecified/undefined cis-trans configurations. Unknown cis-trans configuration represents a structure having either E or Z configuration but definitely one of them. In unspecified/undefined cases the structure can also represent the mixture of the cis and trans isomers.
  
-Although the mcule registration system can distinguish between unknown and unspecified/undefined cases, the currently implemented molecule editor and visualization tools (ChemWriter and ChemVector) don’t provide different bond types for these two configuration types. Unknown and unspecified/undefined cis-trans configurations are therefore both displayed by crossed double bond. If unspecified double bonds are present, we indicate them in the comment field of the compound index pages.+Although the mcule registration system can distinguish between unknown and unspecified/undefined cases, the currently implemented molecule editor and visualization tools (ChemWriter and ChemVector) don’t provide different bond types for these two configuration types. Unknown and unspecified/undefined cis-trans configurations are therefore both displayed by crossed double bond.
  
 ===Tetrahedral configuration=== ===Tetrahedral configuration===
stereonotations.1350140360.txt.gz · Last modified: 2012/10/13 16:59 by sanmark