Two Dimentional Molecular Representation

Two Dimensional Molecular Representation

Molecular search in RMG

Smiles: simplified molecular-input line-entry system

A line notation for describing the structure of chemical species using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules.

All we need to do is write the backbone, hydrogens are auto-completed.

Syntax Examples:

• Describing a free radical:
Use []. In the rectangular parenthesis, next to the main element, specify how many other elements and what elements are connected.

For example, writing [CH2]CC gives:



• Branching:
Use (). In the parenthesis, next to the main element, specify how many other elements and what elements are connected.

For example, writing CC(C)CC gives:



• Rings:
Write a number next to each element that are connected to one another.

For example, writing C1CCCCC1C gives:



• Formal Charge:
Use []. In the rectangular parenthesis, next to the main element, write the appropriate charge [+] or [-] and specify how many other elements and what elements are connected.

For example, writing [N+][O-] gives:



• Double Bond:
Use =. For example, writing C=C gives:



• Triple Bond:
Use #. For example, writing N#N gives:

For further Examples and applications of further molecule descriptions like: Aromaticity etc .

Adjacency List:

Letter explanations:

u- unpaired electrons

p- lone pairs

c- formal charge