SMILE  ?

      this one?   

Link : Smile Image

        

= NOPE

what is it???

        Before this I only know what is molecular structure of chemistry which usually seen at the cover of chemistry’s books or examination sheet of paper, however, I don’t even know how to draw it. Do you know what, I think that is a simply way which draw it directly by hand with pen or pencil, oppss.... but how to make it using computer? And what is the system used to make the molecular structure? Luckily, I learn it in computer in science (KOS 1110) subject.....
Huhuhuhu, now I know the secret on how to make it using computer, by using ACD/ChemSketch Software and Simplified Molecular Input Line Entry System (SMILE), which is easier.

         First thing to do, you must have the ACD/ChemSkecth(Freeware) which you may download it at the internet. 

 The ACD/ChemSketch (Freeware) Software

Second thing to do, you also need the ACD/ChemSketch’s Tutorial (version 8.0 for Microsoft window) so that you will be able to draw the chemical structure and the graphical image professionally.

The ACD/ChemSketch Manual  pdf

The Structure Mode Screen

      SMILE  is stand for Simplified Molecular Input Line Entry System, a simple yet comprehensive chemical language in which molecules and reactions can be specified using ASCII characters representing atom and bond symbols which is widely used and it is computationally efficient. SMILE strings can be imported by most molecule editors for conversion back into two-dimensional drawing or three-dimensional models of the molecules.

     SMILES contains the same information as is found in an extended connection table but with several advantages.SMILES supports all elements in the periodic table. An atom is represented using its respective atomic symbol. Upper case letters refer to non-aromatic atom; lower case letters refer to aromatic atoms. If the atomic has more than one letter th second letter must be lower case.Besides, SMILES  used the hydrogen-suppressed molecular graphs (HSMG).

     On the other hand, in terms of a graph-based computational procedure, SMILES is a string obtained by printing the symbol nodes encountered in a depth-first tree traversal of a chemical graph. The chemical graph is first trimmed to remove hydrogen atoms and cycles are broken to turn it into a spanning tree, where, cycles have been broken, numeric suffix labels are included to indicate the connected nodes. Parentheses are used to indicate point of branching on the tree.


SMILES are divided into 2 term that are Conical SMILES term and Isomeric SMILES term. The differences between both of this may be seen as follow:

Canonical SMILES	Isomeric SMILES
Rules for ensuring that each distinct chemical molecule has a single unique SMILES representation	Extensions to support the specification of isotopes, chirality and configuration about double bond
Application : Indexing Ensuring uniqueness of molecules in a database	Application : Allow rigorous partial specification of chirality

Bond are denoted as shown:

   

-	Single Bond
=	Double Bond
#	Triple Bond
*	Aromatic Bond
.	Disconnected Structure

link : www.indiana.edu/~cheminfo/gw/SMILESNEW1.ppt

Smile branches

·         Represented by enclosure in parentheses

• Can be nested or stacked
• Examples:

      Fluoroform

      C(F)(F)F or FC(F)F

      Branches may be stacked.  

Smiles Atoms

•          Use normal chemical symbols

•          Add punctuation symbols if necessary

•          No super- or subscripts

Smile bonds

•         Single bonds are denoted by a dash, `-'. Single bond symbols and aromatic bond symbols (`:') may be omitted : Ethanol (C-C-O)

      

•      Double bonds are denoted by an equals sign `=' : Carbon Dioxide (O=C=O)

•        Triple bonds are denoted by a pound sign `#' : Hydrogen Cyanide (C#N)

Smiles Symbols

•          String of alphanumeric characters and certain punctuation symbols

•          Terminates at the first space encountered when read left to right

•          The ORGANIC SUBSET:

                                              B, C, N, O, P, S, F, Cl, Br, I

Other Smiles Atoms

•          Aliphatic or nonaromatic carbon:  C

                     1.     Cyclohexane: C1CCCCC1

  •          Atom in aromatic ring: lowercase letter

                   

                    2.      Benzene : c1ccccc1

                                                       

  Smiles Charge

•          Specify attached hydrogens and charges in square brackets

•          Number of attached hydrogens is the symbol H followed by optional digit

•          Example

1.          Proton [H+]
2. 
   

           2.    Ammonium Ion [NH4+]

  

     Cyclic Structures

•          Numbers indicate start and stop of ring

•          Same number indicates start and end of the ring, entered immediately following the start/end atoms

•          Only numbers 1 – 9 are used

•          A number should appear only twice

•          Atom can be associated w. 2 consecutive numbers, e.g.,  Napthalene : c12ccccc1cccc2

     Further Restriction

•         A branch cannot begin a SMILES notation

•         A branch cannot immediately follow a double- or triple-bond symbol

•         Example: C=(CC)C is invalid, but

•         C(=CC)C or C(CC)=C are valid SMILES

    Smiles Fragment

1.     Nitro > N(=O)(=O)
2.     Nitrate > ON(=O)(=O)
3.     cyanide > C#N
4.     Azide > N=N#N
5. 
   

    Isomeric and Chiral Smiles

•          Isomeric configuration indicated by forward and backward slashes: /  \

•          Examples:

–        trans-difluoroethene:  F/C=C/F

•          The F's are on "opposite sides" of the double bond

                    –        cis-difluoroethene: cis-difluoroethene

                                    .   The F's are on the "same side" of the double bond

               •      Chirality indicated by the “@” symbol

               •       Example : L-alanine >  N[C@@H](C)C(=O)O

 

   An application for SMILE

• 
  
•      JMDraw/SMILESViewer (Christoph Steinbeck)
•          JME Molecular Editor (Peter Ertl)
•          STN Express (SMILES as output)
•         Tripos (dbtranslate: SMILES to MOL)
•       Marvin (Ferenc Csizmadia)
•        http://chemaxon.com/marvin/
•       CACTVS http://www2.ccc.uni-erlangen.de/cactvs/
•      SMILESCAS Database
•      http://www.syrres.com/esc/smilecas.htm
•     Over 103,000 SMILES notations
•       Input CAS Registry Number
•       Leads to SMILES and thence to a structure search

        

       Here are some exercises that we did :)