Organic Chemistry I: Spectrometry & Spectroscopy Notes

Introduction to Spectroscopy

• Spectroscopy: technique to determine the structure of a compound.
• Most techniques are nondestructive, meaning they destroy little or no sample.
• Absorption spectroscopy measures the amount of light absorbed by a sample as a function of wavelength.

Types of Analytical Tools

• Mass Spectrometry (MS):
  • Fragments molecules and measures their mass.
  • Can provide the molecular weight and identify functional groups.
• Infrared (IR) Spectroscopy:
  • Measures bond vibrations in a molecule.
  • Used to determine the presence of functional groups.
• Nuclear Magnetic Resonance (NMR) Spectroscopy:
  • Analyzes hydrogen and carbon environments in a molecule for structural information.
• Ultraviolet (UV) Spectroscopy:
  • Uses electronic transitions to identify bonding patterns (conjugation).

Mass Spectrometry (MS)

• MS provides molecular weight and formula from a small sample size.
• Destructive technique; sample cannot be recovered.
• Ionization occurs via a beam of high-energy electrons that break the molecule and form a radical cation (positive charge, unpaired electron).

Electron Impact Ionization

• Bonds broken during ionization generate various positive fragments detectable in MS.
• Example: molecular mass = 30.

Components of Mass Spectrometer

• Consists of insulators, electron ion source, flight tube, and detector.
• Ions of different mass are separated in a magnetic field based on their mass-to-charge ratio (m/z).

The Mass Spectrum

• The tallest peak is the base peak, assigned an abundance of 100%.
• The molecular ion peak (M+) indicates the molecular weight of the original molecule.

Gas Chromatography–Mass Spectrometry (GC–MS)

• Separates mixture into components, which are then analyzed by mass spectrometry as they exit the column.

High-Resolution Mass Spectrometry (HRMS)

• Accurate mass measurements (1 part in 20,000).
• Can distinguish among molecules with nearly identical masses through precise measurement.

Masses of Common Isotopes

• Carbon (12C): 12.000000 amu
• Hydrogen (¹H): 1.007825 amu
• Oxygen (16O): 15.994914 amu
• Nitrogen (14N): 14.003050 amu

Isotopic Abundance

• Carbon shows a M+ and small M+1 peak due to ¹³C's presence in 1.1% abundance.
• Bromine (50.5% 79Br and 49.5% 81Br) shows equal-height M+ and M+2 peaks due to isotopic distribution.
• Chlorine (75.5% 35Cl and 24.5% 37Cl) results in M+ being three times higher than M+2.

The Nitrogen Rule

• Hydrocarbons containing only C, H, and O have even molecular ion mass.
• An odd mass indicates at least one nitrogen atom.

Infrared (IR) Spectroscopy

• Frequency (n): complete wave cycles per second.
• Wavelength (λ): distance between two peaks or troughs of a wave.
• Frequency and wavelength are inversely proportional via the equation: c =
  u imes eta (where c is the speed of light).
• Photon energy expressed by: $E = h <br /> u$ (where h is Planck's constant).

The Infrared Region

• Wavelength range: $2.5 imes 10^{-4}$ to $25 imes 10^{-4}$ cm, typical units are in wavenumbers (cm⁻¹).

Bond Vibrations

• Bonds vibrate when stretched or compressed.
• A relationship exists where frequency decreases with increased atomic mass and increases with bond energy.

Molecular Vibrations

• Nonlinear molecules with n atoms have $3n - 6$ fundamental vibrational modes; water has 3 modes.

IR Absorptions and Functional Groups

• Unique IR absorption bands identify functional groups.
• Stronger bonds correlate with higher absorption frequencies (e.g., C=C bonds absorb at 1660 cm⁻¹).
• The fingerprint region (600 to 1400 cm⁻¹) has complex vibrations unique to molecules.

Carbon-Carbon Bond Stretching Frequencies

• C-C: 1200 cm⁻¹, C=C (isolated): 1645 cm⁻¹.
• Conjugation lowers frequency (e.g., cyclohexene at 1640-1680 cm⁻¹).

Carbon-Hydrogen Stretching

• More s character leads to stronger C—H bonds; sp bonds (stronger) > sp² > sp³.

Functional Group IR Spectra

• Alkanes: C—H stretching between 2800 and 3000 cm⁻¹, only show linear vibrational patterns.
• Alkenes: Key absorption at 1642 cm⁻¹ (C=C) and 3080 cm⁻¹ (unsaturated stretch).
• Alcohols: Broad O—H stretching around 3300 cm⁻¹ due to hydrogen bonding interactions.
• Amines: Broad N—H stretching around 3300 cm⁻¹; 1° amines show two peaks due to symmetric/asymmetric stretching.
• Carbonyl Compounds (C=O): Strong absorption near 1710 cm⁻¹.
• Carboxylic Acids: Broad O—H absorption; presence of two peaks (C=O and O—H) confirms identity.

Summary of IR Absorptions

Strengths and Limitations of IR Spectroscopy

• Cannot independently determine a structure; ambiguity in signals exists.
• Absence of a signal definitively indicates the absence of a functional group.
• Comparative analysis with known samples confirms identity of compounds.