# Organic

> Functional Groups & Reactivity

- Skill: `neuralblitz/organic` (Agent Skill)
- Install (CLI): `npx skillmds@latest add neuralblitz/organic`
- Raw SKILL.md: https://api.skillmd.com/api/skills/neuralblitz/organic/raw
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- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: NeuralBlitz (https://skillmd.com/u/neuralblitz)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/neuralblitz/organic

---


## Functional Groups & Reactivity

### Priority in Nomenclature (Highest to Lowest)

| priority | Functional Group | Suffix | Example |
|----------|------------------|--------|---------|
| 1 | Carboxylic acid | -oic acid | Acetic acid |
| 2 | Ester | -oate | Ethyl acetate |
| 3 | Amide | -amide | Acetamide |
| 4 | Nitrile | -nitrile | Acetonitrile |
| 5 | Aldehyde | -al | Acetaldehyde |
| 6 | Ketone | -one | Acetone |
| 7 | Alcohol | -ol | Ethanol |
| 8 | Thiol | -thiol | Ethanethiol |
| 9 | Amine | -amine | Ethylamine |
| 10 | Alkene | -ene | Ethene |
| 11 | Alkyne | -yne | Ethyne |
| 12 | Ether | ether | Diethyl ether |
| 13 | Halide | halide | Chloroethane |

### Hydrocarbon Chemistry

#### Alkanes (Saturated Hydrocarbons)

- **General formula**: CₙH₂ₙ₊₂
- **Hybridization**: sp³
- **Bond angle**: 109.5°
- **Reactions**: Halogenation (radical), combustion

```
CH₄ + Cl₂ → CH₃Cl + HCl (monochlorination)
           ↓ (excess Cl₂)
    CHCl₃ → CCl₄
```

#### Alkenes (Unsaturated - C=C)

- **General formula**: CₙH₂ₙ
- **Hybridization**: sp²
- **Bond angle**: 120°
- **Reactions**: Addition, polymerization, oxidation

```
Addition Reactions:
┌─────────────────────────────────────────────────┐
│ Electrophilic Addition:                        │
│                                                 │
│   H₂C=CH₂ + HCl → CH₃-CH₂Cl                   │
│   (Markovnikov: H adds to less-substituted C)  │
│                                                 │
│   H₂C=CH₂ + H₂O → CH₃-CH₂OH (acid-catalyzed)  │
│                                                 │
│ Halogen Addition:                               │
│                                                 │
│   H₂C=CH₂ + Br₂ → Br-CH₂-CH₂-Br                │
│   (Anti addition - stereospecific)             │
│                                                 │
│ Hydroboration:                                  │
│                                                 │
│   H₂C=CH₂ + BH₃ → CH₃-CH₂-BH₂                  │
│   → H₂O₂ → CH₃-CH₂OH (Anti-Markovnikov)        │
└─────────────────────────────────────────────────┘
```

#### Alkynes (Unsaturated - C≡C)

- **General formula**: CₙH₂ₙ₊₂
- **Hybridization**: sp
- **Bond angle**: 180°
- **Reactions**: Addition, oxidation, acid-base

---

## Reaction Mechanisms

### Nucleophilic Substitution (SN1 and SN2)

|Feature|SN2|SN1|
|-------|----|----|
|**Mechanism**|Concerted, backside attack|Two-step, carbocation intermediate|
|**Stereochemistry**|Inversion (Walden inversion)|Racemization|
|**Rate law**|2nd order (depends on both)|1st order (depends on substrate)|
|**Substrate preference**|Primary > Secondary|Secondary > Tertiary|
|**Nucleophile strength**|Strong nucleophiles favored|Weak nucleophiles okay|
|**Solvent polar protic favors**|No|Yes|

```python
# Reaction kinetics conceptual model
class NucleophilicSubstitution:
    """Analyze SN1 vs SN2 reaction factors"""
    
    def predict_mechanism(self, substrate_type, nucleophile, solvent):
        """
        Predict whether SN1 or SN2 is favored
        """
        factors = {
            "substrate": {
                "methyl": "SN2 only",
                "primary": "SN2 favored",
                "secondary": "depends on conditions",
                "tertiary": "SN1 only"
            },
            "nucleophile": {
                "strong": "SN2 (if substrate allows)",
                "weak": "SN1 (if substrate allows)"
            },
            "solvent": {
                "polar_protic": "SN1 favored (solvates nucleophile)",
                "polar_aprolic": "SN2 favored (nucleophile free)"
            }
        }
        
        if substrate_type == "tertiary":
            return "SN1"
        elif substrate_type == "primary":
            return "SN2"
        else:
            return "depends on nucleophile and solvent"
    
    # Steric hindrance calculation
    def steric_hindrance_score(self, substituents):
        """Estimate relative steric hindrance"""
        hindrance = {
            "H": 0,
            "CH3": 1,
            "C2H5": 1.5,
            "iPr": 2,
            "tBu": 3
        }
        return sum(hindrance.get(s, 2) for s in substituents)
```

### Elimination Reactions (E1 and E2)

|Feature|E2|E1|
|-------|----|----|
|**Mechanism**|Concerted, anti-periplanar|Two-step, carbocation|
|**Stereochemistry**|Anti-elimination required|Racemization|
|**Base requirement**|Strong base required|Weak base okay|
|**Substrate preference**|Secondary/tertiary|Secondary/tertiary|

---

## Stereochemistry

### Chirality and Enantiomers

- **Chiral center**: Tetrahedral carbon with 4 different substituents
- **Enantiomers**: Non-superimposable mirror images
- **Optical activity**: Rotate plane-polarized light in opposite directions

### R/S Configuration Determination

```
Priority rules (Cahn-Ingold-Prelog):
1. Higher atomic number = higher priority
2. If tie, check next atoms (I > Br > Cl > S > P > F > O > N > C > H)
3. Double/triple bonds count as multiple atoms

Determination steps:
┌────────────────────────────────────────────────┐
│ 1. Assign priorities (1=highest, 4=lowest)   │
│ 2. View from side opposite lowest priority   │
│ 3. 1→2→3 clockwise = R (Rectus)              │
│ 4. 1→2→3 counterclockwise = S (Sinister)    │
└────────────────────────────────────────────────┘
```

### Geometric Isomers (E/Z)

|E|Z|
|---|---|
|Ethyl > Ethyl (trans)|Same side (cis)|
|Higher priority groups on opposite sides|Higher priority groups on same side|

### Conformational Analysis

```
Butane (CH₃-CH₂-CH₂-CH₃) Newman projections:

Anti (staggered)      Gauche (staggered)     Eclipsed
    H                    CH₃                  H
  /   \                /   \                /   \
 H     H              H     H               H     CH₃
  \   /                \   /                \   /
   C-C                  C-C                   C-C
  /   \                /   \                /   \
CH₃    H              CH₃    H              CH₃    H

Energy: 0 kcal/mol      ~0.9 kcal/mol       ~3.6 kcal/mol
```

---

## Synthesis Planning

### Retrosynthetic Analysis

```python
class Retrosynthesis:
    """Simplified retrosynthetic analysis framework"""
    
    # Common transformations
    TRANSFORMATIONS = {
        "alcohol": {
            "from_alkene": ["hydroboration", "oxymercuration", "acid-catalyzed hydration"],
            "from_carbonyl": ["reduction (NaBH₄, LiAlH₄)", "Grignard addition"],
            "from_ester": ["reduction (DIBAL-H)"]
        },
        "alkene": {
            "from_alkyl_halide": ["elimination (E2/E1)"],
            "from_diol": ["pinacol rearrangement"],
            "from_alkyne": ["partial reduction (H₂/Pd, Lindlar)"]
        },
        "carbonyl": {
            "from_alcohol": ["oxidation (PCC, Jones)"],
            "from_alkene": ["ozonolysis"],
            "from_alkyne": ["hydration (HgSO₄)"]
        },
        "carboxylic_acid": {
            "from_alcohol": ["strong oxidation"],
            "from_ester": ["hydrolysis (acid or base)"],
            "from_nitrile": ["hydrolysis"]
        }
    }
    
    # Synthesis planning
    def plan_synthesis(self, target_functional_group, available_starting_materials):
        """Suggest synthetic route"""
        return self.TRANSFORMATIONS.get(target_functional_group, {})
```

### Common Named Reactions

|Reaction|Name|Key Feature|
|--------|-----|-----------|
|Oxidation|Jones oxidation|PCC for primary → aldehyde|
|Reduction|NaBH₄ reduction|Selective for aldehydes/ketones|
|Grignard|Grignard reaction|Forms C-C bonds|
|Wittig|Wittig reaction|Alkenes from carbonyls|
|Diels-Alder|[4+2] cycloaddition|Stereospecific|
|Heck|Heck coupling|Pd-catalyzed vinylation|
|Suzuki|Suzuki coupling|Boron-carbon coupling|

---

## Molecular Orbital Theory

### Frontier Molecular Orbital (FMO) Analysis

```
HOMO-LUMO Interactions:

Nucleophile (HOMO) → Electrophile (LUMO)
        or
Electrophile (HOMO) → Nucleophile (LUMO)

Orbital symmetry rules govern reaction feasibility:
- Thermally allowed: Symmetry-allowed reactions
- Photochemical: Different symmetry requirements

Conjugation effects:
- Allylic system: 3 p-orbitals → 3 MOs
  - ψ1 (bonding): Both electrons
  - ψ2 (nonbonding): 1 electron
  - ψ3 (antibonding): Empty
  
- Diene: 4 p-orbitals → 4 MOs
  - ψ1, ψ2 (bonding): Filled
  - ψ3*, ψ4* (antibonding): Empty
```

### Pericyclic Reactions

|Reaction|Type|Mechanism|
|--------|-----|--------|
|Diels-Alder|[4+2] cycloaddition|Thermally allowed|
|Electrocyclic ring closure|(4n) electrons, conrotatory|Thermally allowed|
|Electrocyclic ring closure|(4n+2) electrons, disrotatory|Thermally allowed|
|Claisen rearrangement|[3,3]-sigmatropic|Thermally allowed|

---

## Spectroscopic Methods

### IR Spectroscopy (Functional Group Identification)

|Region (cm⁻¹)|Bond|Functional Group|
|-------------|-----|-----------------|
|3600-3200|O-H stretch|Alcohol (broad), carboxylic acid (very broad)|
|3300-2500|O-H stretch|Carboxylic acid (very broad)|
|3300-2100|C≡N stretch|Nitrile|
|3000-2850|C-H stretch (sp³)|Alkanes|
|3100-3000|C-H stretch (sp²)|Alkenes, aromatics|
|3300|C-H stretch (sp)|Alkyne|
|1750-1700|C=O stretch|Carbonyl compounds|
|1700-1650|C=C stretch|Alkenes|

### NMR Chemical Shifts (¹H)

|Protons|δ (ppm)|Notes|
|--------|--------|------|
|CH₃-|~0.9|Aliphatic methyl|
|-CH₂-|~1.3|Methylene|
|CH-|~1.5|Methine|
|=CH-|~5-6|Vinyl|
|≡CH-|~2-3|Acetylenic|
|Ar-H~|7-8|Aromatic|
|-OH|variable (1-5)|Exchangeable|
|-NH|variable (1-3)|Exchangeable|
|R-CHO|~9-10|Aldehyde|

---

## Common Errors to Avoid

1. **Confusing SN1/SN2 mechanisms** — Always consider substrate structure, nucleophile, and solvent together
2. **Ignoring stereochemistry** — Label chiral centers and specify R/S in products
3. **Forgetting regiochemistry** — Markovnikov vs. anti-Markovnikov matters
4. **Incorrect IUPAC naming** — Follow latest nomenclature rules systematically
5. **Over-relying on memorization** — Understand mechanisms to predict products
6. **Skipping protonation states** — Consider pKa in acid-base reactions
7. **Ignoring steric effects** — Bulky groups affect reactivity significantly
8. **Not considering competing reactions** — Elimination vs. substitution, etc.