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

Clear History

09-13-2024

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