Atoms with Charges and Stereochemistry in SMILES Notation 🧪

Introduction ℹ️

SMILES notation provides powerful features to represent charged atoms and stereochemical configurations, essential elements in organic and inorganic chemistry.

Representing Charges ⚡

Positive Charges (+)

• Single positive charge: [X+]
• Multiple positive charges: [X+2], [X+3]

Examples:

• Ammonium Ion (NH4+): [NH4+] 🔵
• Calcium Ion (Ca2+): [Ca+2] 🟡
• Aluminum Ion (Al3+): [Al+3] 🟣

Negative Charges (-)

• Single negative charge: [X-]
• Multiple negative charges: [X-2], [X-3]

Examples:

• Chloride Ion (Cl-): [Cl-] 🟢
• Sulfate Ion (SO4 2-): [O-]S([O-])(=O)=O 🟡

Stereochemistry Configuration 🔄

Tetrahedral Centers (@)

• @ indicates counterclockwise arrangement
• @@ indicates clockwise arrangement

Key Examples:

1. L-Alanine: N[C@H](C)C(=O)O 🟨
2. D-Alanine: N[C@@H](C)C(=O)O 🟧

Important Molecules with Stereochemistry

1. Lactic Acid 🥛

   • (S)-Lactic acid: C[C@H](O)C(=O)O
   • (R)-Lactic acid: C[C@@H](O)C(=O)O

2. Amino Acids 🧬

   • L-Serine: N[C@H](CO)C(=O)O
   • D-Serine: N[C@@H](CO)C(=O)O

Tips for Working with Charges and Stereochemistry 💡

1. Always use square brackets [] for charged atoms
2. Double-check stereochemical notations
3. Remember that @ and @@ are relative to the written order of atoms

Common Applications 🔬

• Drug development
• Protein structure analysis
• Chemical database searching
• Molecular modeling

Related Topics 📚

• Chirality in organic chemistry
• Ion formation
• Stereoisomerism
• Chemical equilibrium

Keywords: SMILES notation, molecular charges, stereochemistry, chiral centers, chemical representation, molecular structure, chemical informatics