organic-chemistry - SKILL.md Agent Skill

name: organic-chemistry description: Chemistry of carbon compounds license: MIT compatibility: opencode metadata: audience: organic chemists, researchers, students category: chemistry

What I do

Study carbon-based compounds and reactions
Analyze organic reaction mechanisms
Design synthetic routes
Characterize organic molecules
Investigate stereochemistry
Develop new synthetic methods

When to use me

When studying organic reactions
When designing syntheses
When analyzing mechanisms
When working with functional groups
When determining stereochemistry
When characterizing organic compounds

Key Concepts

Functional Groups

Class	Structure	Example
Alkane	C-H, C-C	CH₄
Alkene	C=C	C₂H₄
Alkyne	C≡C	C₂H₂
Alcohol	-OH	C₂H₅OH
Ether	R-O-R'	diethyl ether
Aldehyde	-CHO	CH₃CHO
Ketone	R-CO-R'	acetone
Carboxylic acid	-COOH	acetic acid
Amine	-NH₂	ethylamine

Reaction Mechanisms

# Example: SN1 vs SN2 reaction analysis
def reaction_type(substrate, nucleophile, solvent):
    """
    Determine likely mechanism.
    """
    # SN2: Primary alkyl halide, strong nucleophile, polar aprotic
    if substrate in ['methyl', 'primary'] and nucleophile == 'strong':
        return 'SN2'
    
    # SN1: Tertiary alkyl halide, weak nucleophile, polar protic
    elif substrate == 'tertiary' and nucleophile == 'weak':
        return 'SN1'
    
    # E2: Strong base, anti-periplanar H
    elif nucleophile == 'strong_base':
        return 'E2'
    
    return 'mixture'

Stereochemistry

Chiral centers
Enantiomers vs diastereomers
R/S configuration
E/Z isomerism (alkenes)
Meso compounds
Optical activity

Synthesis Strategies

Retrosynthetic analysis
Functional group transformations
Protecting groups
Carbon-carbon bond formation
Oxidation/reduction
Stereocontrol