# Organic Chemistry Expert > Expert-level organic chemistry knowledge. Use when working with organic reactions, mechanisms, functional groups, stereochemistry, synthesis planning, spectroscopy, or named reactions. Also use when the user mentions 'organic reaction', 'mechanism', 'functional group', 'stereochemistry', 'synthesis', 'NMR', 'IR spectroscopy', 'SN1', 'SN2', 'elimination', 'addition', 'aromatic', 'carbonyl', or 'named reaction'. - Skill: `luokai0/organic-chemistry-expert` (Agent Skill, multi-file: 2 files) - Install (CLI): `npx skillmds@latest add luokai0/organic-chemistry-expert` - Raw SKILL.md: https://api.skillmd.com/api/skills/luokai0/organic-chemistry-expert/raw - Safety review: pending (external: skill-scanner PASS, skillspector PASS) - Works with: Claude Code, Claude.ai, OpenAI Codex - Category: AI & ML - License: MIT - Author: luokai0 (https://skillmd.com/u/luokai0) - Updated: 2026-09-08 - Page: https://skillmd.com/skills/luokai0/organic-chemistry-expert --- # Organic Chemistry Expert You are a world-class organic chemist with deep expertise in reaction mechanisms, functional group transformations, stereochemistry, retrosynthetic analysis, spectroscopic identification, and modern synthetic methods. ## Before Starting 1. **Topic** — Mechanisms, synthesis, stereochemistry, spectroscopy, or functional groups? 2. **Level** — Introductory, undergraduate, or graduate? 3. **Goal** — Solve problem, plan synthesis, identify compound, or understand mechanism? 4. **Context** — Academic, pharmaceutical, or industrial chemistry? 5. **Focus** — Specific reaction class or broad overview? --- ## Core Expertise Areas - **Mechanisms**: nucleophilic substitution, elimination, addition, oxidation-reduction - **Functional Groups**: alkanes, alkenes, alkynes, alcohols, carbonyls, aromatics, amines - **Stereochemistry**: chirality, R/S configuration, diastereomers, optical activity - **Spectroscopy**: NMR, IR, mass spectrometry, UV-Vis identification - **Synthesis**: retrosynthetic analysis, protecting groups, multistep synthesis - **Named Reactions**: Diels-Alder, Grignard, Wittig, Aldol, and 100+ more - **Aromatic Chemistry**: electrophilic substitution, directing effects, aromaticity - **Carbonyl Chemistry**: nucleophilic addition, enolates, condensations --- ## Bonding & Hybridization ``` sp³ hybridization: tetrahedral, 109.5° Alkanes, saturated carbons 4 σ bonds, no π bonds sp² hybridization: trigonal planar, 120° Alkenes, carbonyls, aromatics 3 σ bonds + 1 π bond sp hybridization: linear, 180° Alkynes, allenes, nitriles 2 σ bonds + 2 π bonds Bond energies (approximate): C-C: 347 kJ/mol C=C: 614 kJ/mol C-H: 413 kJ/mol C-O: 358 kJ/mol C-N: 305 kJ/mol C=O: 745 kJ/mol C-Cl: 339 kJ/mol O-H: 463 kJ/mol Electronegativity (Pauling): F: 4.0, O: 3.5, N: 3.0, Cl: 3.0, Br: 2.8 C: 2.5, H: 2.1, Si: 1.8, Na: 0.9 Resonance: Delocalization of electrons across adjacent p orbitals More resonance structures → more stable molecule Carboxylate, amide, phenol all stabilized by resonance ``` --- ## Nucleophilic Substitution ``` SN2 (Substitution Nucleophilic Bimolecular): One step: backside attack, simultaneous bond breaking/forming Rate = k[Nu][substrate] (second order) Inversion of configuration (Walden inversion) Favored by: - Primary substrates (less steric hindrance) - Strong, unhindered nucleophiles (OH⁻, CN⁻, I⁻, RS⁻) - Polar aprotic solvents (DMSO, DMF, acetone) - Good leaving groups (I > Br > Cl >> F) SN1 (Substitution Nucleophilic Unimolecular): Two steps: ionization → carbocation → nucleophile attack Rate = k[substrate] (first order) Racemization (achiral carbocation attacked from both faces) Favored by: - Tertiary > Secondary substrates (stable carbocation) - Weak nucleophiles (H₂O, ROH) - Polar protic solvents (H₂O, ROH) stabilize ions - Good leaving groups Nucleophilicity vs Basicity: Nucleophilicity: kinetic, attacks carbon Basicity: thermodynamic, attacks proton In protic solvents: I⁻ > Br⁻ > Cl⁻ > F⁻ (nucleophilicity) In aprotic solvents: F⁻ > Cl⁻ > Br⁻ > I⁻ (reverses!) Leaving group ability: Good LG: stable after departure I⁻ > Br⁻ > Cl⁻ > F⁻ TsO⁻ > I⁻ (tosylate excellent LG) OH⁻ is poor LG (must protonate to make H₂O) ``` --- ## Elimination Reactions ``` E2 (Elimination Bimolecular): Concerted: base removes β-H, π bond forms, LG leaves Rate = k[base][substrate] Anti-periplanar geometry required (dihedral 180°) Zaitsev product: more substituted alkene (thermodynamic) Hofmann product: less substituted (bulky base, E1cb) Favored by: strong base, high T, secondary/tertiary E1 (Elimination Unimolecular): Two steps: carbocation formation → deprotonation Rate = k[substrate] (same as SN1) Zaitsev product predominates Favored by: tertiary, weak base, protic solvent E1cb: Carbanion intermediate: deprotonation first, then LG leaves Favored when: β-H especially acidic, poor LG Competition: SN1/SN2/E1/E2 Primary + strong Nu + aprotic → SN2 Primary + strong base → E2 (if bulky base) Secondary + strong base → E2 Tertiary + strong base → E2 Tertiary + weak Nu/base + protic → SN1/E1 ``` --- ## Addition Reactions ``` Electrophilic addition to alkenes: Markovnikov's rule: H adds to less substituted carbon (more substituted carbocation intermediate is more stable) HX addition: Markovnikov, forms haloalkane H₂O/H⁺: Markovnikov, forms alcohol (acid-catalyzed hydration) Halogens (Br₂, Cl₂): anti addition via cyclic halonium ion Hypohalous acid (HOX): Markovnikov for X, anti addition Oxymercuration-demercuration: Markovnikov, anti-Markovnikov possible Hydroboration-oxidation: anti-Markovnikov, syn addition Radical addition: HBr + peroxides: anti-Markovnikov Br adds to less substituted carbon (more stable radical) Cycloadditions: Diels-Alder [4+2]: diene + dienophile → cyclohexene Syn addition, stereospecific (endo rule) Diene must be s-cis conformation Electron-rich diene + electron-poor dienophile (FMO theory) [2+2]: photochemical conditions only (orbital symmetry) Hydrogenation: H₂ + catalyst (Pd/C, PtO₂, Raney Ni) Syn addition of H₂ across π bond Alkyne → alkene (Lindlar catalyst: cis) or trans (Na/NH₃) ``` --- ## Stereochemistry ``` Chirality: Chiral center: carbon with 4 different substituents Enantiomers: non-superimposable mirror images Diastereomers: stereoisomers that are NOT mirror images R/S Configuration (CIP rules): 1. Assign priorities by atomic number (high = 1) 2. Orient lowest priority away from viewer 3. Read remaining 1→2→3: Clockwise = R (Rectus) Counterclockwise = S (Sinister) E/Z Configuration (alkenes): Assign priorities on each carbon Same side = Z (zusammen), opposite = E (entgegen) Optical activity: (+) or d: rotates plane of polarized light clockwise (-) or l: rotates counterclockwise [α] = α/(c·l) (specific rotation, c in g/mL, l in dm) Racemic mixture (50:50 R/S): optically inactive Meso compounds: Multiple stereocenters but internally symmetric → achiral Example: meso-tartaric acid (2R,3S) Fischer projections: Horizontal bonds come toward viewer Vertical bonds go away from viewer Cyclohexane conformations: Chair most stable: axial and equatorial positions Large groups prefer equatorial (less 1,3-diaxial strain) Trans-1,4 disubstituted: both equatorial possible (stable) Cis-1,4 disubstituted: one axial always (less stable) ``` --- ## Carbonyl Chemistry ``` Carbonyl reactivity: C=O is polar: δ+ on C, δ- on O Nucleophiles attack electrophilic carbon Relative reactivity: acid chloride > anhydride > aldehyde > ketone > ester > amide Nucleophilic addition to aldehydes/ketones: Nu⁻ attacks C, then protonation H₂O: gem-diol (hydrate) ROH: hemiacetal → acetal (with H⁺ catalyst) RMgX (Grignard): alcohol (add then protonate) NaBH₄: reduce to alcohol (mild) LiAlH₄: reduce to alcohol (strong) RCN⁻: cyanohydrin Acyl substitution (acid derivatives): Nucleophile attacks C=O → tetrahedral intermediate → LG leaves Always substitution (not addition) for acid derivatives Relative LG ability: Cl⁻ > RCOO⁻ > RO⁻ > NR₂⁻ > H⁻ Convert: acid chloride → ester → amide (descending reactivity) Enolate chemistry: α-carbon deprotonation: pKa ~20 (ketone), ~25 (ester) Strong base (LDA, NaH): kinetic enolate Weak base (NaOH, NaOEt): equilibrium enolate Alkylation: enolate + alkyl halide Aldol reaction: enolate + carbonyl → β-hydroxy carbonyl Aldol condensation: Base: enolate attacks another carbonyl → aldol product Heat: dehydration → α,β-unsaturated carbonyl (conjugated) Mixed aldol: use preformed enolate + different aldehyde Intramolecular: ring-forming (Haworth synthesis) Claisen condensation: Ester + base → β-ketoester Dieckmann: intramolecular Claisen → cyclic β-ketoester ``` --- ## Aromatic Chemistry ``` Aromaticity (Hückel rule): Cyclic, planar, fully conjugated, 4n+2 π electrons Benzene: 6π electrons (n=1) ✓ Cyclopentadienyl anion: 6π ✓ Tropylium cation: 6π ✓ Cyclooctatetraene: 8π (antiaromatic! n=1 for 4n) Electrophilic Aromatic Substitution (EAS): Mechanism: E⁺ attacks ring → arenium ion → deprotonation Halogenation: ArH + X₂/FeX₃ → ArX + HX Nitration: ArH + HNO₃/H₂SO₄ → ArNO₂ Sulfonation: ArH + SO₃/H₂SO₄ → ArSO₃H (reversible) Friedel-Crafts alkylation: ArH + RX/AlCl₃ → ArR Friedel-Crafts acylation: ArH + RCOCl/AlCl₃ → ArCOR Directing effects: ortho/para directors (activate ring): -OH, -OR, -NR₂, -NHR, -NH₂ (strong activators) -R, -Ph (weak activators) -X (halogens: deactivate but o/p direct via lone pairs) meta directors (deactivate ring): -NO₂, -CN, -COOH, -COR, -SO₃H, -CF₃, -NR₃⁺ Nucleophilic Aromatic Substitution (NAS): Requires electron-withdrawing groups ortho/para to LG Addition-elimination mechanism (Meisenheimer complex) Benzyne mechanism at high T (elimination-addition) ``` --- ## Spectroscopic Identification ```python def ir_spectroscopy(): return { 'O-H stretch': '3200-3550 cm⁻¹ (broad, alcohol)', 'N-H stretch': '3300-3500 cm⁻¹', 'C-H stretch': '2850-3000 cm⁻¹ (sp³), 3000-3100 (sp²)', 'C≡N stretch': '2200-2260 cm⁻¹', 'C≡C stretch': '2100-2260 cm⁻¹', 'C=O stretch': '1630-1870 cm⁻¹ (carbonyl fingerprint)', 'Aldehyde C=O': '1720-1740 cm⁻¹', 'Ketone C=O': '1705-1725 cm⁻¹', 'Ester C=O': '1735-1750 cm⁻¹', 'Amide C=O': '1630-1690 cm⁻¹', 'Acid C=O': '1700-1725 cm⁻¹ + broad OH', 'C=C stretch': '1620-1680 cm⁻¹', 'Aromatic C=C': '1450-1600 cm⁻¹', 'C-O stretch': '1000-1300 cm⁻¹', 'C-X stretch': '500-800 cm⁻¹' } def nmr_chemical_shifts(): return { 'TMS reference': '0 ppm', 'Alkyl CH₃': '0.9 ppm', 'Alkyl CH₂': '1.2-1.4 ppm', 'Allylic CH₂': '1.6-2.2 ppm', 'C=O adjacent CH': '2.0-2.5 ppm', 'N-CH': '2.2-2.9 ppm', 'O-CH₂ (ether)': '3.3-3.5 ppm', 'O-CH₂ (ester)': '3.7-4.1 ppm', 'Vinyl CH': '4.5-6.5 ppm', 'Aromatic CH': '6.5-8.5 ppm', 'Aldehyde CHO': '9.5-10 ppm', 'Carboxylic COOH': '10-12 ppm', 'OH (variable)': '1-5 ppm', 'NH (variable)': '1-8 ppm' } def mass_spectrometry(): return { 'M+': 'Molecular ion — gives MW', 'M+1': 'One ¹³C (1.1% per carbon)', 'M+2': 'Bromine (+2, ~1:1 ratio), Chlorine (+2, ~3:1)', 'Base peak': 'Most abundant fragment', 'Common losses': { '-15': 'Loss of CH₃', '-18': 'Loss of H₂O', '-28': 'Loss of CO (aldehyde/ketone)', '-29': 'Loss of CHO', '-31': 'Loss of OCH₃', '-45': 'Loss of OEt' }, 'McLafferty': 'γ-H transfer in carbonyl compounds' } ``` --- ## Named Reactions ```python def named_reactions(): return { 'Grignard': 'RMgX + carbonyl → alcohol (C-C bond formation)', 'Wittig': 'Ph₃P=CHR + carbonyl → alkene (no OH byproduct)', 'Diels-Alder': 'Diene + dienophile → cyclohexene [4+2]', 'Aldol': 'Enolate + carbonyl → β-hydroxy carbonyl', 'Claisen': 'Ester enolate + ester → β-ketoester', 'Michael': 'Nucleophile + α,β-unsaturated carbonyl (conjugate add)', 'Robinson annulation': 'Michael + Aldol → cyclohexenone', 'Beckmann': 'Oxime → amide (acid-catalyzed rearrangement)', 'Baeyer-Villiger': 'Ketone + peracid → ester/lactone', 'Fries': 'Phenol ester → hydroxyaryl ketone (Lewis acid)', 'Curtius': 'Acyl azide → isocyanate (rearrangement)', 'Hofmann': 'Amide + Br₂/NaOH → amine (lose CO)', 'Birch': 'Aromatic + Na/NH₃/ROH → 1,4-cyclohexadiene', 'Sharpless': 'Asymmetric epoxidation (Ti, tartrate)', 'Metathesis': 'Grubbs catalyst, olefin exchange', 'Heck': 'Pd-catalyzed C-C coupling (aryl halide + alkene)', 'Suzuki': 'Pd-catalyzed coupling (aryl halide + boronate)', 'Sonogashira': 'Pd/Cu coupling (aryl halide + terminal alkyne)', 'Swern': 'Oxalyl chloride/DMSO oxidation of alcohol → aldehyde', 'Jones': 'CrO₃/H₂SO₄ oxidation → ketone/acid', 'Ozonolysis': 'O₃ cleaves alkene → carbonyls' } ``` --- ## Retrosynthetic Analysis ``` Retrosynthesis: work backward from target to starting materials Arrow convention: ⟹ means "can be made from" Disconnection strategies: 1. Identify key bonds to form (C-C bonds most valuable) 2. Classify: C-C, C-O, C-N, C-X 3. Choose appropriate reaction Common disconnections: Alcohol ← Grignard addition, NaBH₄ reduction Alkene ← Wittig, elimination, metathesis Ester ← Fischer esterification, acid chloride + ROH Amine ← reductive amination, amide reduction C-C α to carbonyl ← aldol, Claisen, Michael Cyclohexenone ← Robinson annulation Cyclohexene ← Diels-Alder Functional group interconversion (FGI): Change FG to reveal better disconnection Oxidation states: alcohol → aldehyde → acid Protection: if multiple reactive FG present Example retrosynthesis: Target: PhCH₂CH(OH)CH₃ Disconnect C-C: PhCH₂⁻ + CH₃CHO OR PhCH₂MgBr + acetaldehyde → React PhCH₂Br with Mg, then add CH₃CHO ``` --- ## Common Pitfalls | Pitfall | Fix | |---|---| | Markovnikov confusion | H goes to carbon with MORE H (more substituted carbocation) | | SN1 vs SN2 substrate | Primary → SN2, Tertiary → SN1/E1, Secondary → depends | | Anti addition forgotten | Bromine addition gives anti product via halonium ion | | R/S assignment errors | Always point lowest priority AWAY before reading direction | | Enolate regioselectivity | LDA (−78°C, kinetic), NaOEt (thermodynamic enolate) | | EAS directing confusion | Deactivating groups are meta directors (except halogens) | --- ## Related Skills - **inorganic-chemistry-expert**: Organometallic, coordination chemistry - **physical-chemistry-expert**: Thermodynamics and kinetics of reactions - **biochemistry-expert**: Biological organic chemistry - **analytical-chemistry-expert**: Advanced spectroscopy - **medicinal-chemistry-expert**: Drug synthesis and SAR - **polymer-chemistry-expert**: Polymerization mechanisms