penOChem
1.
Getting Started
Introduction
Practice Times
Progress Pulse
2D Structures in Content
3D Structures in Content
Drawing 2D Structures
Drawing simple molecules
Drawing Atoms
Drawing Ions
Drawing Rings
Drawing Fused RIngs
Computer Requirements
2.
First Semester Topics
General Chemistry Review
Introduction
Electron Configurations of Atoms
QM Description of Orbitals
Practice Time - Electron Configurations
Hybridization
Closer Look at Hybridization
Strategy to Determine Hybridization
Practice Time! - Hybridization
Formal Charge
Practice Time - Formal Charge
Acids-bases
Practice Time - Acids and Bases
Hydrogen Bonding is a Verb!
Progress Pulse
Structure and Bonding
Chemical Intuition
From Quantum Mechanics to the Blackboard: The Power of Approximations
Atomic Orbitals
Electron Configurations of Atoms
Electron Configurations Tutorial
Practice Time - Structure and Bonding 1
Lewis Structures
Drawing Lewis Structures
Methane - Lewis structure
Ethane - Lewis structure
Ethene - Lewis structure
Acetone - Lewis structure
Valence Bond Theory
Valence Bond Theory Tutorial
Hybridization
sp3 Hybridization in Methane
sp2 Hybridization in Ethene
sp Hybridization in Ethyne
Polar Covalent Bonds
Formal Charge
Practice Time - Structure and Bonding 2
Curved Arrow Notation
Resonance
Resonance
Resonance Between Two Atoms
Resonance Between Three Atoms
Drawing The Resonance Hybrid
Practice Time! - Drawing Resonance Hybrids
Resonance in Conjugated Systems
Practice Time! - Resonance
Resonance - Which contributes most?
Insignificant Contributors
Electrons behave like waves
MO Theory Intro
Structural Representations
3D Structures - Tetrahedral Geometry of Methane
Condensed Structural Formulas
Drawing Tetraheral Structures on Computer
Drawing Ring Structures
Practice Time! - Structural Representations
Progress Pulse
Acids/Base and Reactions
Reactions
Reaction Arrows: What do they mean?
Thermodynamics of Reactions
Acids Intro
Practice Time! Generating a conjugate base.
Lewis Acids and Bases
pKa Scale
Practice Time! pKa's
Predicting Acid-Base Reactions from pKa
Structure and Acidity
Structure and Acidity II
Practice Time! Structure and Acidity
Curved Arrows and Reactions
Nucleophiles
Electrophiles
Practice Time! Identifying Nucleophiles and Electrophiles
Mechanisms and Arrow Pushing
Proton Transfer (Acid/Base)
Nucleophilic Attack
Loss of Leaving Group
Rearrangements
Errors in Drawing Curved Arrows
Carbocation Stability
Hyperconjugation-carbocations
Radical Reactions
Practice Time! Mechanisms and Reactions
Energy Diagrams and Reactions
Energy Diagrams
Energy Diagrams - Example 1
Constructing Transition States
Practice Time! Drawing Transition States
Practice Time! - Energy Diagrams
Progress Pulse
Introduction to Retrosynthesis
Alkanes and Cycloalkanes
Introduction to Hydrocarbons and Alkanes
Occurrence
Functional Groups
Practice Time! Functional Groups.
Structure of Alkanes - Structure of Methane
Structure of Alkanes - Structure of Ethane
Naming Alkanes
The Alkane Series
Alkyl Groups
Common Named Alkyl Groups
IUPAC Nomenclature of Alkanes
Alkane Nomenclature Tutorial
Practice Time! Naming Alkanes
Alkane Isomers
Relative Stability of Acyclic Alkanes
Physical Properties of Alkanes
Ranking Boiling Point and Solubility of Compounds
Conformations of Acyclic Alkanes
Newman and Sawhorse Projections
Torsional Strain
Hyperconjugation
Steric Strain
How to draw Newman projections
Dihedral Angles
PES Ethane
PES Butane
Practice Time! Conformations of acyclic alkanes.
Conformations of Cyclic Alkanes
Cyclopropane
Cyclobutane
Cyclopentane
Cyclohexane
Drawing Chairs
Conformational Analysis
Naming Bicyclic Compounds
Stability of Cycloalkane (Combustion Analysis)
Degree of Unsaturation
Stereochemistry
Enalapril in ACE
Constitutional and Stereoisomers
Chirality or Handedness
Drawing a Molecules Mirror Image
Exploring Mirror Image Structures
Enantiomers
Drawing Enantiomers
Practice Time! Drawing Enantiomers
Identifying Chiral Centers
Practice Time! Identifying Chiral Molecules
CIP (Cahn-Ingold-Prelog) Priorities
Determining R/S Configuration
Diastereomers
Meso Compounds
Fischer Projections
Fischer Projections: Carbohydrates
Measuring Chiral Purity
Practice Time! - Determining Chiral Purity and ee
Chirality and Drugs
Chiral Synthesis
Prochirality
Converting Fischer Projections to Zig-zag Structures
Practice Time! - Assigning R/S Configurations
Alkenes and Addition Reactions
The Structure of Alkenes
Alkene Structure - Ethene
Physical Properties of Alkenes
Naming Alkenes
Health Insight - BVO (Brominated Vegetable Oil)
E/Z and CIP
Stability of Alkenes
Hyperconjugation
H-X Addition to Alkenes: Hydrohalogenation
Practice Time - Hydrohalogenation
X2 Addition to Alkenes: Halogenation
HOX addition: Halohydrins
Practice Time - Halogenation
Hydroboration/Oxidation of Alkenes: Hydration
Practice Time - Hydroboration-Oxidation
Oxymercuration-Reduction: Hydration
Practice Time - Oxymercuration/Reduction
Oxidation and Reduction in Organic Chemistry
Calculating Oxidation States of Carbon
Identifying oxidation and reduction reactions
Practice Time - Oxidation and Reduction in Organic
Oxidation
Epoxidation of Alkenes
Reduction
Capsaicin
Alkynes
Structure of Ethyne (Acetylene)
Naming Alkynes
Practice Time! - Naming Alkynes
Physical Properties of Alkynes
Preparation of Alkynes
Practice Time! - Preparation of Alkynes
H-X Addition to Alkynes
X2 Addition
Hydration
Reduction of Alkynes
Practice Time! - Addition Reactions of Alkynes
Oxidative Cleavage of Alkynes
Alkyne Acidity and Acetylide Anions
Reactions of Acetylide Anions
Retrosynthesis Revisted
Practice Time! - Multistep Synthesis Using Acetylides
Alkyl Halides and Alcohol
Naming Alkyl Halides
Naming Alcohols
Classes of Alcohols and Alkyl Halides
Practice Time! - Naming Alkyl Halides
Practice Time! - Naming Alcohols
Physical Properties of Alcohols and Alkyl Halides
Structure and Reactivity of Alcohols
Structure and Reactivity of Alkyl Halides
Preparation of Alkyl Halides and Tosylates from Alcohols
Practice Time! - Alcohols to Alkyl Halides
Preparation of Alkyl Halides from Alkenes; Allylic Bromination
Strategy for Predicting Products of Allylic Brominations
Practice Time! - Allylic Bromination
Substitutions (SN1/SN2) and Eliminations (E1/E2)
Solvents
SN1 Reaction
SN1 - Effect of Leaving Group
SN1 - Reaction Energy Diagram
SN2 Reaction
SN2 Introduction
SN2 Mechanism and Kinetics
SN2 Effect of Substrate
SN2 - Reaction Energy Diagram
SN2 Effect of Leaving Group
SN2 Effect of Solvent
SN2 Effect of Nucleophile
SN1 or SN2?
Application: Cardura (Doxazosin)
E1 Reaction
E1 Introduction
E1 Mechanism and Kinetics
E1 Effect of Substrate
E1 Regio and Stereochemistry
E2 Reaction
E2 Mechanism and Kinetics
E2 Regio and Stereochemistry
Substitution versus Elimination
E1cB Reaction
Dienes, Allylic and Benzylic systems
Allyl Cations, Anions and Radicals
Allyl and Vinyl Groups
Allylic Halogenation
SN1 and SN2 Reactions of Allylic Halides and Tosylates
Diels Alder Reaction
Endo versus Exo Attack
Electrophilic Addition - 1,2 versus 1,4
3.
Second Semester Topics
Arenes and Aromaticity
Common Named Arenes
Nomenclature
Practice Time - Common Named Arenes
Stability of Aromatics
Aromaticity H5P
Benzenes MO's
Huckel's 4n+2 Rule
Frosts Circle
Aromatic Ions
Aromatic Heterocycles
Reactions of Arenes
Electrophilic Aromatic Substitution
EAS-Halogenation
EAS-Nitration
Practice Time - Synthesis of Aniline
EAS-Alkylation
Practice Time - Friedel Crafts Alkylation
EAS-Acylation
Practice Time - Synthesis of Alkyl Arenes
EAS-Sulfonation
Practice Time - EAS
Donation and Withdrawal of Electrons
Regiochemistry in EAS
Practice Time - Directing Group Effects
Synthesizing Disubstituted Benzenes: Effects of Substituents on Rate and Orientation
Steric Considerations
Strategies for Synthesizing Disubstituted Benzenes
NAS - Addition/Elimination
NAS - Elimination/Addition - Benzyne
Alcohols and Phenols
Naming Alcohols
Structure and Properties of Alcohols
Acidity of Alcohols and Phenols
Preparation of Alcohols
Reduction of Aldehydes and Ketones
Addition of Grignard and OrganoLithiums
Practice Time - Preparation of Alcohols
Reductions in Organic Chemistry
Reactions of Alcohols
Review Rxns. of Alcohols
Oxidation of Alcohols
Practice Time - Reactions of Alcohols
Protection of Alcohols
Ethers and Epoxides
Intro and Occurrence
Crown Ethers and Cryptands
Preparation of Ethers
Reactions of Ethers
Practice Time - Ethers
Preparation of Epoxides
Reactions of Epoxides - Acidic Ring Opening
Practice Time - Acidic Ring Opening
Reactions of Epoxides - Nucleophilic Ring Opening
Practice Time - Nucleophilic Ring opening
Application - Epoxidation in Reboxetine Synthesis
Application - Nucleophilic Epoxide Ring Opening in Crixivan Synthesis
Physical Properties of Ethers and Epoxides
Naming Ethers and Epoxides
Aldehydes and Ketones
Naming Aldehydes and Ketones
Physical Properties of Ketones and Aldehydes
Practice Time - Naming Aldehydes/Ketones
Nucleophilic addition
Addition of Water - Gem Diols
Practice Time - Hydration of Ketones and Aldehydes
Addition of Alcohols - Hemiacetals and Acetals
Acetal Protecting Groups
Hemiacetals in Carbohydrates
Practice Time - Hemiacetals and Acetals
Addition of Amines - Imines
Addition of Amines - Enamines
Practice Time - Imines and Enamines
Application - Imatinab Enamine Synthesis
Addition of CN - Cyanohydrins
Practice Time - Cyanohydrins
Application - Isentress Synthesis
Addition of Ylides - Wittig Reaction
Practice Time - Wittig Olefination
Structure of Ketones and Aldehydes
Carboxylic Acids and Derivatives
Introduction to Carboxylic Acids
Naming Carboxylic Acids
Acidity of Carboxylic Acids
Practice Time - Carboxylic Acid Naming and Acidity
Preparation of Carboxylic Acids
Reactions of Carboxylic Acids
Nucleophilic Acyl Substitution
Mechanism of Acyl Substitution
Leaving Groups
Electrophilicity of Carboxylic Acids Derivatives.
Practice Time - Acyl Subsitution
Carboxylic Acids
Acid Halides
Anhydrides
Esters
Amides
Practice Time - Reactions of Carboxylic Acid Derivatives
Application: Cardura (Doxazosin) Amidation Step
Enols and Enolates
Introduction to Enols
Tautomerization
Reactions of Enols
Practice Time - Enols and Tautomerism
Intro to Enolates
Reactions of Enolates
Alpha Halogenation of Ketones and Aldehydes
Direct Alkylation of Enolates
Acetoacetic Ester Synthesis
Malonic Ester Synthesis
Practice Time - Alkylation of Enolates
Condensation Reactions
Aldol Reaction
Crossed Aldol
Aldol Dehydration (Elimination)
Claisen Condensation
Micheal Addition
Robinson Annulation
Robinson Annulation - Micheal Addition
Robinson Annulation - Aldol Condensation
4.
NMR, IR, UV and MS
Spectroscopy
HNMR
Nuclear Spin
Interpreting
Chemical Shift
Practice Time! - Chemical Shift
Equivalency
Indentifying Homotopic, Enantiotopic and Diastereotopic Protons
Practice Time! - Equivalency
Intensity of Signals
Spin Spin Splitting
Practice Time! - Spin-Spin Splitting
Primer on ¹³C NMR Spectroscopy
Alkanes
Alkynes
Alcohols
Alkenes
Coupling in Cis/Trans Alkenes
Ketones
HNMR Practice 1
HNMR Practice 2
HNMR Practice 3
HNMR Practice 4
Exchangeable Protons and Deuterium Exchange
IR - Infrared Spectroscopy
Introduction to Infrared (IR) Spectroscopy
Methane Vibrations
Characteristic IR Absorptions
Intensity of IR Absorptions
The Position of Absorption Bands
The Shape of Absorption Bands
Inactive Vibrations
Interpreting IR Spectra
Discerning Ortho, Meta and Para substituted Benzenes
UV - Ultraviolet Spectroscopy
Intro to UV Spectroscopy
Mass Spectrometry
Intro to MS
MS Fragmentation
Interpreting MS
5.
The Alchemy of Drug Development
Ivermectin: From Merck Innovation to Global Health Impact
The Fen-Phen Fix: A Weight Loss Dream Turned Heartbreak
The Asymmetry of Harm: Thalidomide and the Power of Molecular Shape
Semaglutide (Ozempic): From Lizard Spit to a Once-Weekly Wonder
From Cocaine to Novocain: The Development of Safer Local Anesthesia
The Crixivan Saga: A Targeted Strike Against HIV
The story of Merck’s COX-2 inhibitor, Vioxx (rofecoxib)
The Accidental Aphrodisiac: The Story of Viagra
THC: A Double-Edged Sword with Potential Neuroprotective Properties?
Ritonavir Near Disaster and Polymorphism
6.
General Chemistry
General Chemistry Lab
Lab Equipment Guide
Vernier Calipers
Strategy for Balancing Chemical Reactions
Calculator Tips for Chemistry
Significant Figures
Practice Time! Significant Figures
Spreadsheets - Getting Started
Spreadsheets - Charts and Trend lines
Standard Deviation
Standard Deviation Calculations
Factor Labels
Practice Time! - Factor Labels
Limiting Reagent Problem
Percent Composition
Molar Mass Calculation
Average Atomic Mass
Empirical Formula
Practice time! Empirical and Molecular Formulae
Initial Rate Analysis
Practice Time! Initial Rate Analysis
Solving Equilibrium Problems with ICE
Practice Time! Equilibrium ICE Tables
Le Chatelier's
Practice Time! Le Chatelier's Principle
7.
Organic Chemistry Lab
Flash Chromatography
TLC
Distillation Setup
8.
Question Of The Day
9.
Tools and Reference
2D Editor
3D Model Kit
Periodic Table
pKa Values
Named Reactions
Luche Reaction (Reduction)
Negishi Coupling
Birch Reduction
Buchwald -Hartwig Amination
Suzuki Cross-Coupling
Sandmeyer Reaction
Mitsunobu Reaction
Staudinger Reaction (Reduction)
Sonogashira Coupling
Ullmann Reaction
Stille Coupling
Ritter Reaction
Rosenmund Reduction
Reagents
Heterocycles
Sig Fig Calculator
Molar Mass Calculator
Degree of Unsaturation Calculator
Newman Projection Tool
Bond Dissociation Energies
Fischer to Zigzag
Chromatograph Simulator
TLC Simulator
2D Editor (Copy)
10.
Tutorials
Reaction Mechanisms (introduction)
Factor Labels
Acetylides and Synthesis
Drawing Cyclohexane Chair Structures
Drawing Lewis Structures
Aromaticity Tutorial
Common Named Aromatics (Crossword Puzzle)
Functional Groups (Flashcards)
Characteristic Reactions of Functional Groups
Alkyl and Alkenyl Groups
Valence Bond Theory
Alkane Nomenclature
11.
Special Topics
Acyl Transfer Reagents and Catalysts
Asymmetric Synthesis
Introduction
How to Obtain Enantio Pure Compounds?
Chiral Pool Synthesis
Dynamic Kinetic Resolution (DKR)
Kinetic Resolution
Resolution
Resolution
Resolution/Racemization
General Principles
Why Asymmetric Synthesis?
Single Asymmetric Induction
Double Asymmetric Induction
Kinetic versus Thermodynamic Control
Inter and Intraligand Asymmetric Induction
Assessing Chiral Purity
Substitutions
1,2 and 1,4 Additions
Cram's Rule - Open Chain Model
Cram's Rule - Cyclic Model
Felkin Ahn JSMol
Felkin Ahn JSMol 2
Felkin-Anh Model
Prelog's Rule
The Burgi-Dunitz Trajectory
Aldol and Micheal Additions
Zimmerman-Traxler Model
Zimmerman-Traxler TS1
Reductions and Hydroborations
Chiral Organoboranes
Chiral Transition Metal Catalysts
Crystallization-Induced Asymmetric Transformation (CIAT)
Oxidations
Sharpless Epoxidation
Jacobsen epoxidation
Sharpless asymmetric dihydroxylation
Cycloadditions
Curtin-Hammett Principle
Organocatalysis
Double Stereodifferentiation
Complex Induced Proximity Effect (CIPE)
Applications of Organometallic Chemistry
Introduction to Drug Development
Process Chemistry
Privileged Structures
Process Development
Kinetic Isotope Effects
Harmonic Oscillator
Morse Potential
KIE Theory
KIE Examples
Organometallic Chemistry
History
Introduction
18 Electron Guideline
18 Electron Practice Problems
Ligand Types
Carbonyl Ligands
Phosphine Ligands
Cyclopentadienyl Ligands
Halide Ligands
Ammonia Ligands
Hydride Ligands
Nitrosyl Ligands
Ethylenediamine
Benzene Ligands
Water Ligands
Organometallic Reactions
Ligand Substitution
β-Hydride Elimination
Migratory Insertion
β-Hydride Elimination
Nucleophilic Addition to Coordinated Ligands
Applications of Organometallic Chemistry
Organometallic Reactions
Ligand Substitution
Ligand Substitution questions
Oxidative Addition
Reductive Elimination
Migratory Insertion
β - Hydride Elimination
Nucleophilic Addition to Coordinated Ligands
Simmons-Smith Cyclopropanation
Cross-Coupling Reactions
Stille Coupling
Suzuki Coupling
Kumada Coupling
Negishi Coupling
Suzuki Coupling
Pericyclic Reactions
Introduction
Hückel Versus Möbius Aromaticity
Hückel Aromaticity
Möbius Aromaticity
Transition State Aromaticity Approach
Cycloaddition Example
Electrocyclic Example
Hydride Shift Example
1,5-Hydride Shift Transition State Animation
Cycloadditions
Overview
Approaches to Analyze Cycloaddition Reactions
Practice Time!
Test OOC
Practice Time!
Orbitals Animation
Electrocyclic Reactions
Overview
Approaches to Analyze an Electrocyclic Reaction
Electrocyclization of Hexa-2,4-diene Animation
Endo versus Exo Attack
Sigmatropic Rearrangments
Hydride Shifts
Alkyl Shifts
Cope Rearrangement
Claisen Rearrangement
OxyCope Rearrangements
Practice Problems
Clear History
OpenOChem Learn
Special Topics
Asymmetric Synthesis
How to Obtain Enantio Pure Compounds?
Resolution/Racemization
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Resolution/Racemization
Resolution