Chemistry - lecture 5 - Carbon Compounds and Isomerisation

Learning Outcomes

  1. Describe and visualize organic structures using agreed conventions.

  2. Identify and characterize hydrocarbon frameworks in organic molecules.

  3. Classify structures by their isomerism and identify stereochemical centers.

  4. Provide an overview of lipids and their properties.

  5. Suggested further reading: Organic Chemistry by Jonathan Clayden, Nick Greeves, and Stuart Warren.

Definition of Organic Chemistry

  • Chemistry of Living Things: Initially defined as the chemistry pertaining to living organisms.

  • Chemistry of Carbon Compounds: Focuses on molecules primarily based on carbon, often with a hydrogen framework and additional heteroatoms (O, N, S).

  • Examples of Organic Molecules: Vitamin C, Vanillin, Amoxicillin.

Hydrocarbon Frameworks and Functional Groups

  • Core Concept: Organic compounds are built on hydrocarbon frameworks where carbon serves as the main skeleton and heteroatoms are embedded.

  • Functional groups: specific combinations and geometries of heteroatoms.

  • Small number of common and stable functional groups.

  • Hydrocarbon Chains: Can be linear or branched; functional groups add chemical variety to these frameworks.

Drawing Organic Molecules

Guidelines for Structure Drawing

  1. Zig-Zag Representation: Chains are depicted in a zig-zag manner aiming to reproduce actual geometry.

  2. Omission of Hydrogen Atoms: Do not display attached hydrogen atoms or C-H bonds unless necessary for clarity.

  3. Vertex Representation: Each vertex in the chain structure represents a carbon atom.

  • Rules 2 and 3 only apply if there is no important reason to show them (i.e not involved in reactions).

  • H atoms are implicit.

Carbon Chains

  • Definition: Chains of hydrocarbons linked by single bonds are termed alkanes.

  • Names and Structures:

    • Number of Carbon Atoms: 1 (Methane), 2 (Ethane), 3 (Propane), 4 (Butane), 5 (Pentane), 6 (Hexane), etc.

    • Alkanes can exist as branched or linear structures.

Properties of Alkanes

  • Boiling Points: Influenced by van der Waals forces, stronger in larger alkanes.

    • Low boiling point.

  • Isomer Count: Increases with branching as carbon chain lengthens.

  • Reactivity: Generally weakly reactive; higher pKa values (above 50).

  • Alkanes can bond to an organic molecule by replacing a C-H bond.

Unsaturated Hydrocarbons

  • Alkenes and Alkynes:

    • Alkenes: Contain at least one C=C double bond; slightly more reactive than alkanes.

    • Alkynes: Contain at least one C≡C triple bond; rarer and more reactive than alkenes.

Aryl Groups

  • Definition: Derived from aromatic rings, including phenyl, m-tolyl, and benzyl groups.

Functional Groups

  • Definition: Combinations of heteroatoms (mostly O, N, S, and P) that determine the chemical behavior of organic molecules.

IUPAC Naming Rules

  • Overview: Complex rules governing the naming of organic compounds; often best visualized as molecular structures.

  • Example: Cholecalciferol (Vitamin D3) has a complex IUPAC name but can be represented structurally.

Basic Naming Conventions

  1. Identify the hydrocarbon framework.

  2. Determine substituents and functional groups.

  3. Assign positions to substituents using the lowest numbers possible.

  • Examples of Functional Group Indicators: Alcohol (-ol), Aldehyde (-al).

Isomerism

  • Isomers: molecules with identical molecular formulas but distinct 3-D structures.

Constitutional Isomers

  • Definition: Same atoms connected in different ways.

Stereoisomers

  • Definition: Identical bonding patterns but differing spatial arrangements.

  • Core Concepts:

    • Cis-Trans Isomers: Form from inability to rotate around bonds, creating distinct isomers.

      • Common for double bonds and rings.

      • Changes dipole.

    • Atropisomers: Result from restricted rotation around single bonds due to steric hindrance.

Chirality and Optical Activity

  • Chirality: if molecules cannot be superimposed on the mirror image through translations, rotations, and bond rotations.

  • Chiral Centres: Type of stereocentre with 4 different substitutes.

    • Stereocentres: points in molecules that exhibit chirality.

Enantiomers

  • Characteristics: Non-superimposable mirror images that rotate polarized light in opposite directions.

  • Chemical properties are identical in non-chiral environments.

  • D/L and R/S nomenclature describes stereochemistry of compounds, particularly important in biological systems.

Importance of Chirality

  • Thalidomide Case: One enantiomer is therapeutic while the other causes adverse effects.

Fischer projection

  • Mainly used for carbohydrates and designed to assign stereochemistry and identify enantiomers.

  • Bonds represented by lines and each intersection is a chiral centre.

  • Carbon chain is shown vertically.

D/L labels

  • Refer to the orientation of the final hydroxyl (OH-) or amine (-NH2) group on the carbon chain

  • Right = D and left = L

Diastereomer

  • Stereoisomers that are not mirror images of each other,

  • Only differ in some chiral centres.

Tautomerism

  • Based on a reaction between a hydroxyl group and the aldehyde/ketone in a carbohydrates.

  • Creates a new stereocentre.

  • Ring-chain tautomerism: process where many sugars form a cyclin configuration by prototropy (i.e. the relocation of a single H-atom)

  • Keto-enol tautomerism: ketone - carbonyl group that is not next to other functional groups and enol - hydroxyl group that is adjacent to a C-C double bond.