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Thursday, March 12, 2015

[ SMILES NOTATION ]


Simplified Molecular-Input Line-Entry System 

It is a specification in form of a line notation for describing the structure of chemical species using short ASCII strings  that can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules.

In July 2006, the IUPAC introduced the InChI as a standard for formula representation. SMILES is generally considered to have the advantage of being slightly more human-readable than InChI. It also has a wide base of software support with extensive theoretical backing.



The term SMILES refers to a line notation for encoding molecular structures and specific instances should strictly be called SMILES strings. However, the term SMILES is also commonly used to refer to both a single SMILES string and a number of SMILES strings which are the exact meaning is usually apparent from the context.


FOR EXAMPLE…

CATEGORY
DESCRIPTION
ATOMS 
  •           Atoms are represented by the standard abbreviation of the chemical elements, in square brackets, such as [Au] for gold.


  •           An atom holding one or more electrical charges is enclosed in brackets. For hydrogen, followed by the symbol H if it is bonded to one or more atoms, followed by the number of hydrogen atoms as


  •           Then, followed  by the sign '+' for a positive charge or by '-' for a negative charge in the same brackets.



BONDS
  •           Bonds between aliphatic atoms are assumed to be single


  •           Double, triple, and quadruple bonds are represented by the symbols '=', '#', and '$' respectively as illustrated by the SMILES :


  •      O=C=O (carbon dioxide),
  •      C#N (hydrogen cyanide)
  •      [Ga-]$[As+] (gallium arsenide).



  •           Ring closure labels are used to indicate connectivity between non-adjacent atoms in the SMILES string, 


STEREOCHEMISTRY
  •           Configuration around double bonds is specified using the characters "/" and "\"


  •           For example, F/C=C/F (see depiction) is one representation of trans-difluoroethene, in which the fluorine atoms are on opposite sides of the double bond, 




NOT  JUST A SIMPLE SMILE RITE...CHILL!!

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