Demystifying Organic Chemistry

De-Mystifying Organic Chemistry : De-Mystifying Organic Chemistry Part I, Presentation A David A. Jeffrey, Ph.D.

Your Background : Your Background You really should have…. Passing grades in General Chemistry, first semester Reasonable 3-D/visual skills Good study habits/methods Good organizational skills/habits Good ‘conceptual learning’ skills….rote memorization won’t work Not critical but it helps….. Passing grade in Biology, first semester Bio-health science related interests/career goals

Tips for Success : Tips for Success Don’t worry what your friend’s cousin’s brother in med school says Challenging…but not impossible Practice, practice, practice! Work problems Use the model kit Work in small study groups Learn to recognize problem types ‘‘Rule of Three’ Reasonable schedule/time commitment Don’t fall behind! DON’T MEMORIZE….UNDERSTAND

Benefits : Benefits Highly relevant content for the health sciences professional: Aspiring M.D.’s Aspiring Pharm.D.’s Aspiring research scientists Pharmacology Biochemistry Molecular Biology Bacteriology Virology Materials science Semi-conductors Develop invaluable intellectual problem-solving tools and skills Enhance acceptance rate to professional and graduate programs

Course Elements and Sequence : Course Elements and Sequence Three Parts Part I: The Toolkit Structural ochem Part II: Organic Reactivity Functional Groups! As the predictable reactive part of an organic molecule As an organizing element Rxn mechanism Predicting rxns Part III: Synthesis

Part I: The Toolkit : Part I: The Toolkit Miscellaneous definitions, methods, e-counting, simple structures, general chemistry review Necessary foundation Tied together in Part II, Reactivity

Part I: The Toolkit : Part I: The Toolkit Lewis structures! Valence Bond Theory (VBT) Octet rule Formal charges Resonance Isomers Condensed and skeletal structure shortcuts Orbital Hybridization and VSEPR Molecular shape Shape determines bio activity

Part I: The Toolkit : Part I: The Toolkit Acids and Bases Most rxn mechanisms……acid/base catalyzed Identify Bronsted-Lowry acid, base, conjugate base, conjugate acid pKa’s General chemistry review Estimating Five structural features Intro to organic functional groups and chemical classes… ..alkanes

Part I: The Toolkit : Part I: The Toolkit Alkanes Introduction to organic nomenclature Our first two rxns Combustion ! Most important commercial/industrial process Transportation: automobiles, trucks, trains, aircraft, ships…. Environmental considerations….global warming? Reduction of raw carbon materials Radical halogenation Intro to rxn mechanism Intro to reactive intermediates

Part I: The Toolkit : Part I: The Toolkit Stereochemistry Chiral centers Absolute vs Relative Stereochemistry Enantiomers and diastereomers

Part I: Toolkit : Part I: Toolkit Enantiomers Identical except for Optical rotation Behavior in chiral environment….in biological systems Rat feeding expt: L- and D-Ala Properties Non-superimposable mirror images Inversion of all chiral centers Testing re-orientation # even/odd exchanges R/S

Toolkit : Toolkit Diastereomers 2n rule < 2n for meso Cis/trans for cyclics Special topics Other chiral atoms Non-atom based chirality….helical twists DNA! Resolution

Toolkit : Toolkit Conformational Analysis Torsional angle (dihedral) Acyclic…..ethane, propane, butane Newman projections Staggered vs eclipsed Energy profiles Cyclic….cyclohexanes Chair vs boat Two chair forms Axial, equatorial Cis/trans

END OF PART I, PRESENTATION A : END OF PART I, PRESENTATION A In Presentation B Examples Structures Simple reactions Problems