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