CHEM 235-A: Organic Chemistry Laboratory - Study Guide

CHEM 235-A: Organic Chemistry Laboratory - Study Guide

Overview of Organic Chemistry

  • Definition: Study of carbon-containing compounds.

  • Focus Areas:

    • Structure

    • Properties

    • Composition

    • Reactions

    • Synthesis

  • Importance: Essential for understanding biological systems and drug design.

Organic Synthesis

  • Definition: Construction of complex products from simple, commercially available starting materials.

  • Purpose of Synthesis:

    • Structure confirmation.

    • Access to scarce compounds.

    • Methodology development.

    • Stereochemical and mechanistic insight (Wender, 1997).

Synthesis Process of Small Organic Molecules

  1. Step 1: Reaction Set-up

  2. Step 2: Work-up and purification

  3. Step 3: Structure elucidation and analysis

Structure Elucidation

  • Key Questions About Molecular Structure:

    1. Which functional groups are present?

    • Functional Group: A specific set of atoms within a molecule that imparts characteristic physical properties and predictable chemical reactivity.

    1. What is the exact structure of the molecule?

    • Connectivity: The specific arrangement of atoms linked by covalent bonds.

    • Conformation: Different spatial orientations accessible to flexible molecules due to bond rotations and noncovalent interactions.

    • Configuration: The fixed stereochemical arrangement of atoms (stereochemistry).

Functional Groups and Their Properties

  • Physical Properties:

    • Structure & Bonding

    • Atomic & Molecular Orbitals

    • Hybridization States

    • Bond Types: σ, π

    • Geometry / 3D Structure

    • Resonance

    • Polarity

    • Electronegativity

    • Dipole Moments

    • Intermolecular Interactions:

    • Dispersion Forces

    • Dipole–Dipole Interactions

    • Hydrogen Bonding

    • Acidity / Basicity:

    • Acids: X–H (X = heteroatom)

    • Bases: X: (X = heteroatom with lone pair)

  • Chemical Reactivity:

    • Functional Groups: Specific combinations of atoms defining the reactive portion of a molecule.

    • Alkanes: Considered generally unreactive, serving as a baseline “inert” framework.

Functional Group Nomenclature

  • Functional Groups and Molecular Classifications:

    • Aldehyde: R-H / Aldehyde/Carbaldehyde

    • Alkene: R = Alkenyl (<2 groups)

    • Alkyne: R = Alkynyl

    • Ketone: R-Keto/Oxo

    • Alcohol: R-OH / Hydroxy

    • Alkyl Halide: R-X / Halo (fluoro, chloro, bromo, iodo)

    • Carboxylic Acid: R-C(O)OH / Carboxylate

    • Amine: R-NH2 / R₂NH / RN / Amino

    • Ether: R-O-R / Alkoxy

    • Nitrile: R-C≡N / Cyano

    • Nitroalkane: R-NO2 / Nitro

    • Sulfide: R-S-R' / Thioether

    • Ester: R-C(O)O-R'

    • Amide: R-C(O)N-R’ / Amido

IUPAC Nomenclature Rules

  1. Identify the Parent Chain:

    • Longest continuous carbon chain determines root name.

  2. Identify the Principal Functional Group:

    • Highest priority functional group determines suffix of the compound's name.

  3. Number the Parent Chain:

    • Number carbons from the end giving the highest priority functional group the lowest possible number.

  4. Name and Locate Substituents:

    • Name groups attached to the parent chain using prefixes, indicate positions with carbon atom numbers, and list in alphabetical order.

  5. Assemble the Name:

    • Combine substituents, parent name, and functional group suffix.

Hydrocarbons

Alkanes

  • Types:

    • Linear alkane

    • Branched alkane

    • Cyclic alkane (limited C-C rotation)

    • Bicyclic alkane (no C-C rotation)

  • Structure: Contain only C and H.

  • Molecular Formula: C$n$H${2n+2}$.

  • Hybridization: Carbon atoms are sp$^3$ hybridized.

  • Linkage: Free rotation around C-C single bonds.

  • Nomenclature Example:

    1. Methane (Me-)

    2. Ethane (Et-)
      … up to Decane.

Alkenes

  • Definition: Contain C and H, with C atoms in double bond sp$^2$ (trigonal planar geometry).

  • Nomenclature Examples:

    1. Methene

    2. Ethene
      … up to Pentene.

  • Degrees of Unsaturation Formula:
    DU=2−n+racN2+racX2DU = 2 - n + rac{N}{2} + rac{X}{2}
    where n = number of carbons, N = number of nitrogens, X = number of halogens.

Alkynes

  • Definition: Contain C atoms in a triple bond (sp hybridized, linear geometry).

  • Nomenclature Examples:

    1. Methyne

    2. Ethyne
      … up to Decyne.

Aromatic Compounds

  • Characteristics:

    • Completely conjugated pi electron systems with additional stability.

    • Planarity: All C atoms in a ring are sp$^2$ hybridized, resulting in equal bond lengths.

  • Resonance Structures: Different depictions of pi bonding electrons.

  • Electron Count Rule: Must have 4n + 2 π electrons (n = 0, 1, 2, …).

Functional Groups
Alcohols

  • Definition: Contain the hydroxy group (-OH).

  • Properties: Weak acids (pKa ~10-15) capable of forming H-bonds.

  • Nomenclature Examples:

    1. Methanol

    2. Ethanol
      … up to Butanol.

Ethers

  • Definition: Compounds with an oxygen atom linking two hydrocarbon groups.

  • Nomenclature:

    • Common naming: Phenyl Propyl Ether

    • Cyclic ethers referred to as epoxides.

Thiols & Sulfides

  • Definition: Thiols (RSH) and thioethers (R-S-R) are similar to alcohols and ethers respectively.

  • Nomenclature:

    • Thiols use suffix -thiol, thioethers identified as sulfides.

Amines

  • Properties: Basicity; N atom is sp$^3$ hybridized, undergoes inversion.

  • Nomenclature: Designated based on carbon substituents.

Aldehydes & Ketones

  • Definition: Contain a polar carbonyl group (C=O).

  • Nomenclature:

    • Aldehydes: Formaldehyde, Ethanal, etc.

    • Ketones: Designated by similar rules with chain identification.

Carboxylic Acid Derivatives

  • Characteristics: Weak acids due to hydrogen-bonding capabilities; forms dimers.

  • Nomenclature:

    • Carboxylic acids: Methanoic Acid, Ethanoic Acid, etc.

    • Esters: Identified based on R' and R groups.

Nitro Groups

  • Definition: Planar functional group where the nitrogen is sp$^2$ hybridized.

  • Resonance: NO bonds possess bond order of 1.5 due to resonance; can conjugate with alkenes or aromatic compounds.

Spectroscopy Techniques

Infrared (IR) Spectroscopy

  • Principle: Absorption of IR radiation matching bond vibrations; this frequency must equal the bond vibration frequency.

  • Application: Used for structural characterization.

Ultraviolet-Visible (UV-VIS) Spectroscopy

  • Principle: Involves electronic excitation; absorption leads to transitions between molecular orbitals (e.g., p to p* transition).

Nuclear Magnetic Resonance (NMR) Spectroscopy

  • Mechanism: External magnetic field aligns nuclear spins; radio frequency changes the vector properties of these spins.