Organic Chemistry Curriculum Content Outline

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1 Organic Chemistry Curriculum Content Outline CHEM 0203: Organic Structure and Reactivity 1. Structure & Bonding (Brief Review from General Chemistry) a. Ionic & Covalent Bonding b. Lewis Structures and Formal Charges c. Delocalized Electrons, Resonance Contributors, and Energy d. Atomic & Molecular Orbitals ( / * / *) and Correlation Diagrams e. Hybridization (sp 3, sp 2, sp), Molecular Geometry f. Bond & Molecular Dipoles and Physical Properties (e.g., Solubility) 2. Acid Base Chemistry a. Organic Acids & Bases and pka s b. Electronic and Structural Influences on pka c. Predicting Keq from pka s d. Relating ph, pka, and acid/conjugate base ratio (Henderson-Hasselbach Equation) 3. Organic Nomenclature a. Alkanes, Alkyl Halides, Skeletal (line) Structures, Structural Isomers b. Alkenes (cis/trans, E/Z) & Alkynes c. Ethers, Alcohols, & Amines d. Aromatic Compounds e. Aldehydes & Ketones f. Carboxylic Acids and Derivatives (Acyl Halides, Anhydrides, Esters, Amides, Nitriles) 4. Alkane and Cycloalkane Conformations a. Newman Projections b. Ethane and Butane: Conformations and Energy ( G) c. Cycloalkanes and Ring Strain d. Cyclohexane: Chair Conformations & Ring Flips e. Monosubstituted Cyclohexanes: axial vs. equatorial & Energy ( G) f. Disubstituted Cyclohexanes: cis/trans vs. ax./eq. & Energy ( G) 5. Stereochemistry a. Chirality and Enantiomers b. R/S Nomenclature & Drawing Conventions i. Perspective (Wedge & Dash) ii. Fischer Projections (optional for now) c. Optical Activity: (+/ ), [ ] D, and Enantiomeric Excess (ee) d. Diastereomers & Meso Compounds e. Separation of Enantiomers

2 6. Substitution & Elimination Reactions a. S N 1 and S N 2 Mechanisms and Stereochemistry b. E1, E2, and E1cb Mechanisms, Stereochemistry, and Regiochemistry c. Curved Arrow Formalism for Reaction Mechanisms d. Reaction Coordinate Diagrams e. Carbocation Stability & Rearrangements f. Leaving Groups: Halides, Alcohols, Ethers, Epoxides, and Sulfonate Esters, g. Converting Alcohols into Halides, Ethers, and Sulfonate Esters h. Nucleophilicity vs. Basicity i. Steric Effects ii. Electronic Effects iii. Solvent Effects i. Competition between S N 1, S N 2, E1, and E2 j. Kinetic Isotope Effects 7. Aldehydes and Ketones a. Structure and Reactivity b. Nucleophilic Addition Reactions i. Grignard Reagents ii. Hydride Reagents c. H 2 / metal and Related Reductions d. Formation of Oxygen, Sulfur, and Nitrogen Derivatives i. Hemi and Full Acetals / Ketals and Thioacetals / Thioketals ii. Imines and Enamines 8. Carboxylic Acids and Derivatives (Acyl Halides, Anhydrides, Esters, Amides, & Nitriles) a. Structure and Reactivity b. Acyl Substitution Mechanism (Nucleophilic Addition-Elimination) c. Acidic vs. Basic Hydrolysis Mechanisms d. Reactions that Interconvert Carboxylic Acids and Derivatives e. Reduction Reactions f. Cyclic Derivatives: Lactones and Lactams g. Fatty Acids, Triglycerides, and Phospholipids: Structure and Properties h. Thioesters and Phosphate Esters: Structure, Properties, and Reactivity i. Amino Acids: Structure & Properties of the 20 Naturally Occurring j. Peptides & Proteins: Structure (1º to 4º), Covalent & Non-Covalent Interactions

3 9. Reactivity to Carbonyl a. Keto-Enol Tautomerization b. Halogenation of -Carbon c. Enolate Formation (Thermodynamic vs. Kinetic) d. Enolate Alkylations e. Aldol Reaction f. Claisen Reaction g. Crossed Aldol and Claisen Reactions h. Dehydration of Aldol Products to -Unsaturated Compounds i. 1,4-Additions (aka Michael / Conjugate Additions) j. Decarboxylation of -Keto Esters 10. Carbohydrates a. Structure and Classification of Aldoses and Ketoses i. Fischer Projections (required now) ii. D and L Nomenclature iii. Reducing and Nonreducing Sugars iv. Acyclic and Cyclic Forms v. Special Importance of Glucose, Fructose, Ribose, and Deoxyribose vi. Fischer Proof of the Stereochemistry of Glucose b. Glycosides & The Anomeric Effect c. Disaccharides and Polysaccharides i. and linkages ii. Starch, Glycogen, Cellulose, and Chitin d. Cell Surfaces & Signaling 11. DNA and RNA a. Nucleoside & Nucleotide Structures: Tautomeric Forms & Base Pairing b. Double Helical DNA Structure c. RNA Secondary Structures d. Deamination of Cytosine

4 CHEM 0204: Organic Synthesis and Spectroscopy 1. Mass Spectrometry a. Mass Spectrum and m/z Ratio b. Fragmentation and Molecular Ion Peaks c. Isotope Patterns d. Fragmentation Patterns for Common Functional Groups e. GC-MS 2. UV-Vis Spectroscopy a. Spectroscopy and the Electromagnetic Spectrum b. Chromophores, Visible Spectrum, and Color c. HOMO-LUMO Gap d. Beer-Lambert Law e. Effect of Conjugation on max and Molar Absorptivity ( ) f. Uses of UV-Vis Spectroscopy 3. IR Spectroscopy a. IR spectrum and Units (cm -1 ) b. Origin of IR Absorptions (bends and stretches) c. Characteristic IR Bands d. Fingerprint Region e. Interpretation of IR Spectra 4. NMR Spectroscopy a. The NMR Effect ( 1 H and 13 C) b. Chemical Shifts and the NMR Scale (, ppm) c. Equivalent Atoms & Number of Signals d. Diamagnetic Anisotropy & Characteristic 1 H NMR Chemical Shifts e. Integration of 1 H NMR Spectra f. Splitting of 1 H NMR Signals i. Simple Patterns: (N+1) Rule ii. Doublet of Doublets iii. More Complex Patterns g. Chemical Exchange of O H and N H signals h. Interpretation of 1 H NMR Spectra i. 13 C NMR Spectroscopy i. Number of Signals ii. Characteristic 13 C NMR Chemical Shifts iii. Interpretation of 13 C NMR Spectra j. Magnetic Resonance Imaging (MRI) k. Combined Spectral Interpretation Problems

5 5. Radical Reactions a. Structure & Stability of Radicals b. Chlorination and Bromination of Alkanes c. Chain Propagation Mechanisms d. Reactivity-Selectivity Principle e. Allylic and Benzylic Halogenations f. Utility for S N 1 / S N 2 and E1 / E2 Reactions 6. Alkene Addition Reactions a. Electrophilic Addition Reactions i. Carbocation Mechanisms: H-X, H 2 O/H +, ROH/H + ii. Anti-Additions: X 2, X 2 / H 2 O iii. Syn-Additions: BH 3, H 2 /metal, RCO 3 H b. Markovnikov s Rule c. Carbocation Rearrangements d. Stereoselective vs. Stereospecific Reactions e. Radical Additions to Alkenes (HBr / peroxides) f. Ozonolysis g. Dihydroxylations and Related Oxidations h. Heck Coupling 7. Alkyne Reactions a. Electrophilic Addition Reactions (similar to alkenes) b. Partial Reductions (H 2 / Lindlar; Na/NH 3 (liq)) c. Alkyne Acidity and S N 2 Reactions d. Sonogashira coupling e. Multistep Organic Synthesis 8. Aromaticity and The Diels-Alder Reaction a. Aromaticity (4n+2) and Anti-Aromaticity (4n) b. Molecular Orbital Description of Stability c. Diels-Alder Reaction i. HOMO-LUMO interactions ii. Regiochemistry iii. Steroechemistry iv. Synthesis of Bicyclic Compounds

6 9. Reactions of Benzene and Substituted Benzenes a. Electrophilic Aromatic Substitutions i. Halogenation ii. Nitration & Sulfonation iii. Friedel-Crafts Alkylation & Acylation b. Substituent Effects i. Reactivity ii. pka of Aromatic Acids iii. Regiochemistry of Products (o/p vs. m directors) c. Reactions at the Benzylic Position d. Arenediazomium Salts in Synthesis e. Benzyne: Structure & Reactions f. Nucleophilic Aromatic Substitutions g. Cross-Coupling Reactions (Stille, Suzuki, etc.) h. Hetereocycles 10. Carbonyl Chemistry in Synthesis a. Oxidations of Alcohols b. Protecting Groups c. Baeyer-Villiger Oxidation d. Gabriel Synthesis of Amines e. Strecker Synthesis of Amino Acids f. Reductive Amination g. Wittig Reaction h. 1,3-dicarbonyl Compounds i. Robinson Annulation 11. Special Topics in Organic Synthesis a. Total Synthesis of Natural Products b. Other Content at Instructor s Discretion