Courses

Course

Organic Chemistry

Yale University

This course is the first semester of a two-semester introductory sequence in organic chemistry, designed for students with a solid foundation in chemistry and physics. The course emphasizes:

  • Current theories of structure and mechanism in organic chemistry
  • The historical development of these theories
  • The experimental observations that inform our understanding of organic chemistry

The primary goal is to cultivate a taste for original scientific inquiry and to develop the intellectual skills necessary for innovative research. Freshmen with excellent preparation in related fields are encouraged to enroll.

Course Lectures
  • How Do You Know: Divine or Human Authority vs Logic and Experiment
    How Do You Know: Divine or Human Authority vs Logic and Experiment
    J Michael McBride
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    This module introduces students to the foundational question of scientific knowledge: "How do you know?" Professor McBride discusses the limitations of divine or human authority, advocating for logic and experimental evidence as reliable sources of knowledge.

    Key historical examples illustrate these concepts:

    • The rise of modern science in the seventeenth century
    • The crucial experiment on light by Isaac Newton
    • Samuel Pepys's correspondence with Newton, emphasizing the scientific mindset

    The module sets the stage for the first half of the semester, focusing on understanding the Force Law that describes chemical bonds.

  • Force Laws, Lewis Structures and Resonance
    Force Laws, Lewis Structures and Resonance
    J Michael McBride
    Play

    In this module, Professor McBride examines the concept of force laws as they pertain to chemical bonding. He critiques existing models, such as Hooke's Law and Coulomb's Law, highlighting their inadequacy in describing chemical interactions.

    The discussion covers:

    • The development of the Morse potential as a composite force law for chemical bonding
    • G. N. Lewis's "cubic-octet" theory and shared pair model of bonding
    • Lewis-dot notation, formal charge, and the challenges of resonance in complex bonding scenarios

    This foundational understanding prepares students for more advanced topics in chemical structures.

  • Double Minima, Earnshaw's Theorem, and Plum-Puddings
    Double Minima, Earnshaw's Theorem, and Plum-Puddings
    J Michael McBride
    Play

    This module continues the exploration of Lewis structures and chemical forces, introducing students to the double-well potential of ozone and its structural equilibrium. Professor McBride discusses Earnshaw's Theorem, which delineates the limitations of inverse-square force laws in stabilizing charged particles.

    Key points of discussion include:

    • Visualization of lines of force to illustrate Earnshaw's Theorem
    • J.J. Thomson's plum-pudding model as a response to these limitations
    • The implications of Rutherford's findings regarding atomic structure and Coulomb's law

    This module emphasizes the complex nature of atomic interactions and provides a basis for understanding stability in chemical structures.

  • Coping with Smallness and Scanning Probe Microscopy
    Coping with Smallness and Scanning Probe Microscopy
    J Michael McBride
    Play

    In this lecture, the focus shifts to the practical aspects of confirming chemical bonds through visualization. Professor McBride discusses historical attempts to "see" atomic structures and the challenges involved.

    Topics covered include:

    • The work of early 20th-century charlatans claiming to see atomic details
    • Experiments by Newton and Franklin measuring small distances
    • Advancements in Scanning Probe Microscopy that allow chemists to "feel" individual molecules and atoms

    While these techniques have advanced significantly, the module highlights the ongoing challenges in directly observing chemical bonds.

  • X-Ray Diffraction
    X-Ray Diffraction
    J Michael McBride
    Play

    This module offers an in-depth look at X-ray diffraction, specifically how it applies to studying electron distributions in molecules. Professor McBride explains the underlying theory of light diffraction by charged particles.

    Key learning points include:

    • The principles of light diffraction and its relevance to molecular structure
    • How molecular patterns and crystal lattices contribute to diffraction results
    • Real-world applications demonstrated through laser light experiments

    Students gain insight into how X-ray diffraction techniques provide crucial information about molecular arrangements and interactions.

  • Seeing Bonds by Electron Difference Density
    Seeing Bonds by Electron Difference Density
    J Michael McBride
    Play

    Continuing the discussion on X-ray crystallography, this module emphasizes the relationship between diffraction patterns and electron distribution within molecules. Utilizing Franklin’s X-ray pattern of DNA, Professor McBride illustrates:

    • How diffraction patterns in reciprocal space correlate with molecular structures
    • Methods for mapping electron density, identifying bonds, and unshared electron pairs
    • The significance of anomaly in electron density, particularly in carbon-fluorine bonds

    This exploration leads to the fundamental course question: "Compared to what?" revealing the nuanced understanding of molecular bonding.

  • Quantum Mechanical Kinetic Energy
    Quantum Mechanical Kinetic Energy
    J Michael McBride
    Play

    This module marks a significant transition to quantum mechanics, seeking to reconcile discrepancies observed in electron density and Lewis bonding theory. Professor McBride introduces the wave function (ψ) and its complexities.

    Key concepts discussed include:

    • The relationship between the curvature of ψ and kinetic energy
    • How positive and negative kinetic energies arise based on ψ's behavior
    • Comparative analysis of classical and quantum mechanical perspectives on bonding

    This introduction lays the groundwork for understanding chemical bonding at a more fundamental level.

  • One-Dimensional Wave Functions
    One-Dimensional Wave Functions
    J Michael McBride
    Play

    Building on the previous discussions, this module further explores the wave function by examining one-dimensional systems. Professor McBride illustrates the relationship between wave function curvature and kinetic energy, highlighting:

    • The significance of the wave function's magnitude and its relation to electron probability density
    • Allowed energies and their implications for harmonic oscillators and potential systems
    • The isotopic effects on molecular dynamics and bond characteristics

    This foundational knowledge equips students to analyze more complex multi-dimensional systems in future modules.

  • Chladni Figures and One-Electron Atoms
    Chladni Figures and One-Electron Atoms
    J Michael McBride
    Play

    This module emphasizes the transition to multi-dimensional wave functions, using solutions to Schrödinger’s equation to explain bonding in three-dimensional systems. Professor McBride discusses:

    • The significance of Chladni figures in illustrating nodal patterns and frequencies
    • The form of wave functions for hydrogen-like one-electron atoms
    • How these concepts relate to molecular structures and bonding theories

    This comprehensive understanding of wave functions is crucial for analyzing more complex molecular interactions in later modules.

  • Reality and the Orbital Approximation
    Reality and the Orbital Approximation
    J Michael McBride
    Play

    This module advances the discussion of the Schrödinger equation, focusing on multi-electron systems. Professor McBride addresses the challenges inherent in describing these systems using one-electron orbitals.

    Topics covered include:

    • The impact of nuclear charge on one-electron atom energies
    • The concept of hybridization in bonding
    • Limitations of one-electron orbital models in multi-electron systems

    This comprehensive exploration prepares students for understanding the complexities of orbital theory in organic chemistry.

  • Orbital Correction and Plum-Pudding Molecules
    Orbital Correction and Plum-Pudding Molecules
    J Michael McBride
    Play

    In this lecture, students learn about orbital correction methods that address errors in using orbitals due to electron repulsion. Professor McBride introduces:

    • The concepts of "Z-effective" and "Self Consistent Field" for correcting orbital usage
    • The relationship between molecular orbitals and J.J. Thomson's plum-pudding model
    • Analogies between molecular orbitals of CH4 and NH3 and atomic orbitals of neon

    This discussion provides insight into the fundamental principles governing molecular behavior and orbital interactions.

  • Overlap and Atom-Pair Bonds
    Overlap and Atom-Pair Bonds
    J Michael McBride
    Play

    This module focuses on the concept of overlap in atom-pair bonds. Professor McBride applies previously discussed methods to more complex molecules, introducing:

    • The idea of localized pairwise bonding between atoms
    • Formulating atom-pair molecular orbitals as the sum of atomic orbitals
    • The significance of overlap in establishing bond strength

    Using the hydrogen molecule as an example, students explore how atomic orbital sums can closely match reality, especially with hybridization.

  • Overlap and Energy-Match
    Overlap and Energy-Match
    J Michael McBride
    Play

    This module continues the discussion on covalent bonding, emphasizing the significance of both orbital overlap and energy-match. Professor McBride explains how:

    • Orbital overlap is influenced by hybridization
    • The number of shared electrons affects bond strength
    • The importance of energy mismatches in bonding interactions

    Through practical examples, students understand how quantum mechanics elucidates the factors leading to strong attractions between particles.

  • Checking Hybridization Theory with XH3
    Checking Hybridization Theory with XH3
    J Michael McBride
    Play

    This lecture applies theoretical discussions on hybridization to experimental observations in three XH3 molecules. Professor McBride explores:

    • The relationship between hybridization and molecular structure
    • The concept of "Umbrella Vibration" and its role in rehybridization
    • How strong bonds and stable atoms interact to create molecular differences

    Empirical evidence from infrared and electron spin resonance experiments reinforces the understanding of molecular structure determinants.

  • Chemical Reactivity: SOMO, HOMO, and LUMO
    Chemical Reactivity: SOMO, HOMO, and LUMO
    J Michael McBride
    Play

    In this module, Professor McBride delves into chemical reactivity through the lens of molecular orbitals. Students learn how to evaluate reactivity based on:

    • Singly-occupied molecular orbitals (SOMOs)
    • High-energy highest occupied molecular orbitals (HOMO)
    • Low-energy lowest unoccupied molecular orbitals (LUMO)

    This approach generalizes traditional acid-base concepts and establishes criteria for assessing molecular reactivity in various contexts.

  • Recognizing Functional Groups
    Recognizing Functional Groups
    J Michael McBride
    Play

    This module continues examining the HOMO/LUMO framework by focusing on recognizing functional groups and predicting their reactivity. Professor McBride illustrates:

    • How to identify high-energy HOMOs and low-energy LUMOs
    • The reactivity of compounds such as BH3 based on their unique bonding characteristics
    • The role of MO nodes and their contributions to acidity and basicity

    The module emphasizes practical examples, including the reaction of HF as an acid with OH-, showcasing simultaneous bond-making and bond-breaking.

  • Reaction Analogies and Carbonyl Reactivity
    Reaction Analogies and Carbonyl Reactivity
    J Michael McBride
    Play

    Continuing the molecular orbital theory discussion, this module highlights analogies among diverse organic chemistry reactions. Professor McBride analyzes:

    • Acid-base reactions, SN2 substitutions, and E2 eliminations
    • The mechanisms of bond-breaking and bond-making during these reactions
    • The trajectory of carbonyl group reactivity, predicting attack patterns based on HOMO levels

    Students explore the experimental validation of these theories through Bürgi and Dunitz's analysis of crystal structures via X-ray diffraction.

  • Amide, Carboxylic Acid and Alkyl Lithium
    Amide, Carboxylic Acid and Alkyl Lithium
    J Michael McBride
    Play

    This module wraps up the first half of the semester by analyzing three key functional groups: amides, carboxylic acids, and alkyl lithiums. Professor McBride explains:

    • The role of localized atomic or pairwise orbitals in understanding these functional groups
    • The resonance phenomenon in amide groups and its significance in biological polypeptides
    • The acidity of carboxylic acids and the aggregation behavior of methyl lithium

    The discussions contextualize modern experimental and theoretical tools within the historical understanding of organic structure.

  • Oxygen and the Chemical Revolution (Beginning to 1789)
    Oxygen and the Chemical Revolution (Beginning to 1789)
    J Michael McBride
    Play

    This module introduces the historical development of organic chemistry, starting with Lavoisier, often deemed the father of modern chemistry. Key discussion points include:

    • The practice of ancient chemistry and alchemy prior to modern developments
    • Key contributions from figures like Scheele, who discovered oxygen and organic acids
    • Lavoisier's Traité Élémentaire de Chimie, which established foundational concepts in modern chemistry

    Understanding these early developments equips students with a broader context for the evolution of organic chemistry theories.

  • Rise of the Atomic Theory (1790-1805)
    Rise of the Atomic Theory (1790-1805)
    J Michael McBride
    Play

    In this module, students explore the evolution of atomic theory through the contributions of Dalton and Berzelius. The focus includes:

    • Dalton's atomic theory and its consistency with empirical laws
    • Berzelius's advancements in elemental analysis and notation
    • The confusion surrounding atomic weights and the implications of Avogadro's and Gay-Lussac's laws

    This historical perspective underscores the gradual development of analytical techniques in organic chemistry.

  • Berzelius to Liebig and Wöhler (1805-1832)
    Berzelius to Liebig and Wöhler (1805-1832)
    J Michael McBride
    Play

    This module chronicles the contributions of chemists like Berzelius, Gay-Lussac, and Davy, who advanced organic chemistry between 1805 and 1832. Key topics include:

    • New elements discovered through combustion analysis
    • Development of the theory of dualism and its implications for organic chemistry
    • Wöhler's synthesis of urea and his collaboration with Liebig on radical theory

    This exploration of early chemical theories prepares students for understanding the complexities of modern organic chemistry.

  • Radical and Type Theories (1832-1850)
    Radical and Type Theories (1832-1850)
    J Michael McBride
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    This module discusses the development of radical and type theories in organic chemistry during the 1832-1850 period. Key figures include Wöhler and Liebig, who influenced chemical understanding through:

    • Research on benzaldehyde and the concept of radicals
    • Dumas's temporary advocacy for radicals, followed by his conversion to type theory
    • The psychological and sociological factors affecting chemists during this era

    Students gain insights into how these early theories laid the groundwork for modern nomenclature and organic chemistry principles.

  • Valence Theory and Constitutional Structure (1858)
    Valence Theory and Constitutional Structure (1858)
    J Michael McBride
    Play

    This module highlights the transition to valence theory and molecular structure in 1858. Chemists Couper and Kekulé introduced new concepts based on:

    • The tetravalence and self-linking properties of carbon
    • Valence structures, which explained isomerism and led to new nomenclature
    • The evolution of notation and molecular models still relevant today

    This foundational understanding of valence theory significantly shaped the development of modern organic chemistry.

  • Determining Chemical Structure by Isomer Counting (1869)
    Determining Chemical Structure by Isomer Counting (1869)
    J Michael McBride
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    This module examines the logical system developed by Wilhelm Körner for determining chemical structure through isomer counting in 1869. Key points include:

    • The innovative methods Körner used to deduce the structure of benzene and its derivatives
    • The significance of proving the equivalence of hydrogen positions in benzene
    • The resistance to Körner's ideas due to geographical and authoritative barriers

    Students learn about the critical thinking and logical approaches that shaped early organic chemistry.

  • Models in 3D Space (1869-1877); Optical Isomers
    Models in 3D Space (1869-1877); Optical Isomers
    J Michael McBride
    Play

    This module discusses the contributions of chemists in the late 19th century to understanding molecular structures in 3D space. Key topics include:

    • The rise of stereochemistry and the concept of chirality, with insights from Paternó and van't Hoff
    • The prediction of chiral molecules based on optical activity and isomerism
    • Pasteur's work on separating racemic acid into its enantiomers

    Students gain insights into the significance of spatial arrangements in chemical structures and the evolution of stereochemical concepts.

  • Van't Hoff's Tetrahedral Carbon and Chirality
    Van't Hoff's Tetrahedral Carbon and Chirality
    J Michael McBride
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    This module focuses on van't Hoff's tetrahedral carbon model and its implications for understanding chirality. Key discussions include:

    • The significance of stereogenic centers in optical isomers
    • Predictions of chiral allenes, which remained undiscovered for decades
    • Symmetry operations and their influence on molecular behavior

    Students learn about the foundational role of stereochemistry in organic chemistry and its impact on molecular design.

  • Communicating Molecular Structure in Diagrams and Words
    Communicating Molecular Structure in Diagrams and Words
    J Michael McBride
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    This module emphasizes the importance of consistent communication in molecular structure through diagrams and nomenclature. Key points include:

    • The necessity of clear notation to avoid ambiguity in molecular constitution
    • The significance of Fischer projections in understanding sugar configurations
    • The implications of ambiguous diagrams in legal disputes over pharmaceuticals

    Students learn about the essential role of standardized nomenclature in the field of organic chemistry.

  • Stereochemical Nomenclature; Racemization and Resolution
    Stereochemical Nomenclature; Racemization and Resolution
    J Michael McBride
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    This module covers stereochemical nomenclature, focusing on the evolution from Fischer's convention to the CIP scheme. Professor McBride discusses:

    • The determination of atomic arrangements in configurational isomers
    • The processes of racemization and epimerization for interconversion
    • Resolution schemes for separating pure enantiomers from racemic mixtures

    Students gain insights into the intricacies of stereochemical nomenclature and its relevance in organic chemistry.

  • Preparing Single Enantiomers and the Mechanism of Optical Rotation
    Preparing Single Enantiomers and the Mechanism of Optical Rotation
    J Michael McBride
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    This module highlights the synthesis of single enantiomers and the mechanisms of optical rotation. Guest lecturer Professor Laurence Barron discusses:

    • The biological resolution of enantiomers and the synthesis of omeprazole
    • The principles behind chiral molecules' interaction with polarized light
    • The complexities involved in predicting net optical rotation

    Students learn about the practical implications of chirality in pharmaceuticals and the challenges of measuring optical properties.

  • Esomeprazole as an Example of Drug Testing and Usage
    Esomeprazole as an Example of Drug Testing and Usage
    J Michael McBride
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    This module focuses on drug testing and usage using esomeprazole as a case study. Discussions include:

    • The chemical mode of action and its insensitivity to stereochemistry
    • The design and significance of clinical trials for chiral switches
    • Insights from a clinician's perspective on the drug approval process

    This exploration highlights the intersection of chemistry and clinical practice in evaluating pharmaceuticals.

  • Preparing Single Enantiomers and Conformational Energy
    Preparing Single Enantiomers and Conformational Energy
    J Michael McBride
    Play

    This module concludes with a discussion on the production of single enantiomers and the implications of conformational energy. Key topics include:

    • Methods for producing single enantiomers and their legal implications
    • The complexities of conformational isomerism and its energy considerations
    • The relationship between energies, equilibrium, and rate constants in conformations

    This discussion underscores the significance of energies in understanding molecular behavior and stability.

  • Stereotopicity and Baeyer Strain Theory
    Stereotopicity and Baeyer Strain Theory
    J Michael McBride
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    This module examines stereotopicity and Baeyer strain theory, addressing the relationship between rotational barriers and molecular reactivity. Key discussions include:

    • The ongoing debate about ethane's rotational barrier and its implications
    • Analyzing stereotopicity in enzyme reactions for constitutionally equivalent groups
    • Baeyer's theory on strain-induced reactivity and its historical context

    Students learn about the complexities of molecular structure and how strain affects chemical behavior.

  • Conformational Energy and Molecular Mechanics
    Conformational Energy and Molecular Mechanics
    J Michael McBride
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    This module explores conformational energy and molecular mechanics, emphasizing the utility of molecular mechanics in estimating energies. Key points include:

    • Drawing idealized chair structures for cyclohexane and visualizing interconversions
    • Quantitative considerations of conformational energies across various alkanes
    • How empirical schemes assign strain to specific sources like bond stretching and van der Waals forces

    Students develop a deeper understanding of molecular mechanics and its role in predicting molecular stability.

  • Sharpless Oxidation Catalysts and the Conformation of Cycloalkanes
    Sharpless Oxidation Catalysts and the Conformation of Cycloalkanes
    J Michael McBride
    Play

    This module features Professor Barry Sharpless discussing titanium-based catalysts for stereoselective oxidation, sharing insights into the mechanisms involved. Key topics include:

    • The Nobel-prizewinning development of these catalysts and their applications
    • The relevance of conformational energy in cyclic alkanes
    • How molecular mechanics aids in understanding stereochemical outcomes

    Students learn about the connection between conformational analysis and practical applications in organic synthesis.

  • Understanding Molecular Structure and Energy through Standard Bonds
    Understanding Molecular Structure and Energy through Standard Bonds
    J Michael McBride
    Play

    This module emphasizes the understanding of molecular structure and energy through standard bonds. Key discussions include:

    • Analysis of bond distances using the Cambridge Structural Database
    • The inadequacy of early attempts to predict heats of combustion based on composition
    • Group- or bond-additivity schemes for understanding heats of formation

    Students learn how experimental measurements of bond energies contribute to a comprehensive understanding of molecular stability and reactivity.

  • Bond Energies / Bond Enthalpies
    Bond Energies / Bond Enthalpies
    Sylvia Ceyer
    Play

    In this module, Professor Sylvia Ceyer discusses bond enthalpy and the thermodynamics of chemical reactions. Key topics include:

    • The definition of heat of formation and its role in enthalpy changes
    • Hess's Law and its applications in predicting enthalpy changes
    • The concepts of Gibbs free energy and entropy in spontaneous reactions

    Students gain insights into how thermodynamic principles govern chemical processes and the importance of energy conservation.

  • Bond Energies, the Boltzmann Factor and Entropy
    Bond Energies, the Boltzmann Factor and Entropy
    J Michael McBride
    Play

    This module discusses bond energies and their statistical mechanics implications. Professor Ceyer focuses on:

    • The determination of bond dissociation energies through classic experiments
    • Average bond energies and their utility in understanding equilibrium
    • The Boltzmann factor and its influence on energy arrangements and disorder

    This exploration highlights the connection between statistical mechanics and chemical equilibrium, illustrating the importance of disorder in chemical systems.

  • Potential Energy Surfaces, Transition State Theory and Reaction Mechanism
    Potential Energy Surfaces, Transition State Theory and Reaction Mechanism
    J Michael McBride
    Play

    This module introduces potential energy surfaces and transition state theory as frameworks for understanding reaction mechanisms. Key discussions include:

    • The statistical basis of the law of mass action in chemical reactions
    • Developing potential energy surfaces for polyatomic systems
    • The application of Eyring theory to predict reaction rates

    Students learn how these concepts provide insights into reaction dynamics and the factors influencing reaction rates.

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