SMILES!

Assalamualikum everyone 😀
For this week, we would like to share about SMILES 😁
SMILES stands for "Simplified Molecular Input Line Entry System". SMILES is used to translate a chemical's three-dimensional structure into a string of symbols that is easily understood by computer software.

SMILES notation is a string of letters, numbers and other characters that specify the atoms, their connectivity, bond orders and chirality. Bare in mind that the notation has no spaces.

There are few specification rules in SMILES.

1) Atomic symbols and their SMILES notation:

Chemical names	Atomic symbols	SMILES notation
Methane	CH4	C
Water	H2O	O
Hydrogen sulfide	H2S	S
Ammonia	NH3	N
Phosphine	PH3	P
Hydrogen chloride	HCl	Cl

As for elements, they need to be shown in brackets.For example [Au] for elemental gold and [S] for elemental sulfur.

2) Bonds are represented by this symbols:

Bonds	Symbols	Examples
Single	-	No need to be written in SMILES notation
Double	=	C=O
Triple	#	C#N
Aromatics	:	No need to be written in SMILES notation

3) Branches are specified by enclosures in parentheses

   Triethylamine 

CCN(CC)CC

4) Cyclic structures are represented by breaking one single or double (aromatic) bond in each ring. 

• Ring-opening 

The steps are:

1.  Break one single bond in each ring
2.  Number in any order
3.  Same number indicates start and end of the ring
4.  The numbers entered immediately

Ring opening of cyclohexane

• Ring-closure

The steps are:

1. Atoms in aromatic ring are specified by lower case letters.
2. Number in any order.
3. An atom can be associated with two consecutive numbers.
4. Aromatic bonds may always be omitted.

We also got to learn how to draw chemical structure using ChemSketch software. you can download it here → ChemSketch

We hope all of you learn something from what we shared today. That's all for today. See you soon! 💞