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Molecular Structure & Chemical Reactivity

A series of webcasts that explain contemporary models of molecular structure and chemical reactivity.

Jeffrey Moore

on 9 July 2011

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Transcript of Molecular Structure & Chemical Reactivity

Structure Reactivity The Elements of Organic Chemistry Atomic Trends & The Periodic Table Electron Configuration & The Origins of the Octet Rule Electron Pairs & Electron Pair Domains Period 2 Atoms The Eleven Octet Configurations Geometry Depends on the Number of Electron Pair Domains http://webcsd.ccdc.cam.ac.uk/teaching_database_demo.php Calculating Formal Charge Period 2 Building Blocks Exceptions to the Octet Rule The Building Blocks of Organic Chemistry Atom Connectedness Lewis Structures from Crystallographic Models Common Functional Groups Drawing Conventions Functional Groups http://www.chemaxon.com/anim/marvin/sketch_atom/explimplhyd.html http://www.chemaxon.com/anim/marvin/sketch_groups/expand_ungroup.html http://www.chemaxon.com/marvin/sketch/index.php IUPAC Organic Nomenclature Atom Classification Schemes Common Hydrocarbon Fragments Molecular Models Models & Lingo http://chem.sis.nlm.nih.gov/chemidplus/ Stereoisomers Stereochemistry Stereoisomer Classification https://netfiles.uiuc.edu/jsmoore/www/Jmolpages/stereochemistry/enantiomers.html https://netfiles.uiuc.edu/jsmoore/www/Jmolpages/stereochemistry/cistranschex.html https://netfiles.uiuc.edu/jsmoore/www/Jmolpages/stereochemistry/enantiomers.html https://netfiles.uiuc.edu/jsmoore/www/Jmolpages/stereochemistry/example1.html Chiral vs. Achiral Objects http://symmetry.otterbein.edu/tutorial/reflection.html The Stereocenter https://netfiles.uiuc.edu/jsmoore/www/Jmolpages/stereochemistry/fischer.html Structures Having More Than One Stereocenter Examples:http://www.chem.ucalgary.ca/courses/351/Carey5th/Ch07/ch7-2-4.html https://netfiles.uiuc.edu/jsmoore/www/Jmolpages/stereochemistry/example2.html https://netfiles.uiuc.edu/jsmoore/www/Jmolpages/stereochemistry/example3.html https://netfiles.uiuc.edu/jsmoore/www/Jmolpages/stereochemistry/configuration.html ACE Organic: http://aceorganic.pearsoncmg.com/lite/login.jsp Curved Arrows and Resonance Contributors Use the mechanism calculator to imitate what you see here:
http://aceorganic.pearsoncmg.com/epoch-plugin/public/mechmarvin.jsp The Rules of Resonance Resonance Practical Guidelines for Generating Resonance Contributors Common Mistakes Made in Drawing Resonance Contributors The Significance of Resonance Contributors The Molecular Orbital Model Shortcomings of the Lewis Model Electrostatics, Electron Density Distributions & Chemical Bonding Orbitals Are Represented as Isosurfaces The Orbitron Web Site
http://winter.group.shef.ac.uk/orbitron/ Wavefunctions Are Additive A Representation of LCAO Linear Combination of Atomic Orbitals The Orbitron Web Site
http://winter.group.shef.ac.uk/orbitron/ LCAO in Practice Sigma MOs http://butane.chem.illinois.edu/jsmoore/Jmol/SHEET1.html Disallowed Combinations http://butane.chem.illinois.edu/jsmoore/Jmol/SHEET1.html Pi MOs 10 Unique AO Combinations Trends in Orbital Energies MO Diagrams, Energy & Orbital Interactions MO Diagram of Fluorine MO Diagram of Carbon Monoxide Beyond Pairwise Combinations Interpreting the CO MO Diagram Nucleophiles, Electrophiles & the CO MO Diagram The Molecular Orbital Diagram of Carbon Monoxide http://www.stolaf.edu/people/hansonr/jmol/mo/ Hybrid Atomic Orbitals Hybridization MOs from Hybrid AOs Frontier Orbitals Filled Empty Orbital Interactions Curved Arrows & Frontier Orbitals Generalized Sigma & Pi Interactions Frontier Orbitals & Resonance Atoms in Molecules
are in Motion 3D Views to Represent
Conformation Molecular Structure,
Energy & Reactivity Anti & Gauche Conformational States Stereoisomers and the Time Scale of Interconversion Conformation http://www.chemaxon.com/marvin/sketch/index.php http://www.chem.fsu.edu/schwartz/CybermodelsJmol/jmolPages/JmolViewer2.html https://netfiles.uiuc.edu/jsmoore/www/Jmolpages/conformation/ConfViews.html http://www.chem.fsu.edu/schwartz/CybermodelsJmol/jmolPages/JmolViewer2.html http://www.chemaxon.com/marvin/sketch/index.php Cycloalkanes The Conformations
of Cycloalkanes Exploring the Conformations of Some Cycloalkanes The Conformations
of Cyclohexane The Cyclohexane Ring-Flip
A Minimum Energy Pathway Mono and Disubstituted
Cyclohexanes Reference: "Estimation of heats of formation of organic compounds by additivity methods," Chem. Rev. (1993) 93, 2419-2438. http://www.chemaxon.com/marvin/sketch/index.php http://www.chemaxon.com/marvin/sketch/index.php http://www.chem.ucalgary.ca/courses/351/Carey5th/Ch03/ch3-06.html http://www.chem.ucalgary.ca/courses/351/Carey5th/Ch03/ch3-06.html http://wetche.cmbi.ru.nl/organic/cyclohexane/jm/mecyc.html http://www.chemaxon.com/marvin/sketch/index.php The Proton Transfer [pt] Step and General Principles of Reactivity Nucleophiles & Electrophiles The Proton Transfer [pt] Step The Reaction Coordinate Diagram Transition State Structures The Proton Transfer Step on a Reaction Coordinate Diagram https://netfiles.uiuc.edu/jsmoore/www/09fa/notes/chem232fa09_packet.pdf Get the Notes! this is a 60 Mb pdf file Reactivity Concepts Structure-Reactivity Relationships Bond Energy Changes Nucleophiles & Reactivity Electrophiles & Reactivity Recognizing Acids & Bases Tools for Estimating pKa Acid-Base Equilibria The Mechanism Calculator Acidic & Basic Reagents Conventions Used in Writing Organic Reactions Acids & Bases in Organic Chemistry Substitution at sp3 Carbon Classes of Reactions Examples of Substitution Reactions [SN2] [AN] [DN] & Substitution Mechanisms [SN1] vs. [SN2] Substitution and the Electrophile Substitution and the Nucleophile Elimination at sp3 Alkene Stability Trends [E2], [DE] & [Ebeta] Steps The [E2] Mechanism The [E1] Mechanism Exceptions to Elimination Regiochemistry
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