SMILES Notation Guide

1. Atoms:

• Organic subset (B, C, N, O, P, S, F, Cl, Br, I) are represented by their element symbols.
• Brackets are used for atoms outside the organic subset or when showing charge/hydrogen count, e.g., [Na], [S+], [H].

2. Bonds:

• Single bonds are not shown or represented by '-'.
• Double bonds are '=', triple bonds are '#', and aromatic bonds are ':'.

3. Branches:

• Enclosed in parentheses.
• Example: Ethanol (C-C-O) is CC(O).

4. Rings:

• Atoms in a ring are connected by a number following the atoms in the ring.
• Example: Benzene (C6H6) is C1=CC=CC=C1.

5. Charges:

• Represented by + or - after the element. Multiple charges are shown by repeating the sign, e.g., [N+], [O-], [Fe+++].

6. Stereochemistry:

• '@' for anticlockwise and '@@' for clockwise chirality.
• Example: L-alanine is NC@@HC(=O)O.

7. Isotopes:

• Shown by a number prefix. Example: Deuterium-labeled methane is [2H]C.

For more details, refer to the official SMILES specification.