CHE 275: Mass Spectrometry and Infrared Spectroscopy Overview

Organic Chemistry I - Chapter 12: Mass Spectrometry & Infrared Spectroscopy

Organic Structure Determination

• Understanding the properties and reactivity of an organic molecule necessitates knowledge of its structure.

• Structure determination is essential for:

  • New compounds isolated from natural sources.

  • Confirmation of structures of molecules synthesized in the lab.

• Prior to the mid-20th century, chemical methods for structure determination were employed, which were often difficult and time-consuming.

Historical Examples of Structure Determination

• D-glucose (1891)

  • Structural representation: O OH HO OH OH HO

• Morphine (1925)

  • Structural representation: O HO HO N Me

• Strychnine (1948)

  • Structural representation: N O N H H O

Common Spectroscopic Methods

1. Mass Spectrometry (MS)

   • Chapter 12: Determines molecular weight; aids in deriving chemical formula.

2. Infrared Spectroscopy (IR)

   • Chapter 12: Identifies functional groups present in the molecule.

3. Nuclear Magnetic Resonance (NMR)

   • Chapter 13: Provides information on C-H framework of the molecule.

4. Ultraviolet Spectroscopy (UV-Vis)

   • Chapter 14: Useful for understanding extended series of π bonds (conjugation).

Mass Spectrometry General Principles

Mass Spectrometer Function

• Converts molecules to ions.

• Separates ions based on their mass-to-charge (m/z) ratio.

  • For most ions, since z = 1, m/z corresponds to the mass of the ion.

• Quantifies the number of each ion formed over a given time period.

  • Provides:

  • Molecular weight leading to the identification of the chemical formula.

  • Fragmentation data for understanding molecular structure.

Example: Propane Ionization

• Mass spectrum shows various m/z peaks:

  • m/z = 44

  • m/z = 29

  • m/z = 43

  • m/z = 28

  • m/z = 15

Mass Spectrometry Spectrum Terminology

• Parent Ion:

  • Also known as the molecular ion, represented as [M]•+ (a radical cation).

• Base Peak:

  • The tallest peak in the spectrum, assigned 100% intensity; all other peaks are shown as a percentage of this intensity.

  • Example: Mass spectrum of hexane (C(H3CH2CH2CH2CH2CH3)) shows:

  • Molecular Weight (MW) = 86.

Distinguishing Between Similar Compounds

• Molecular weight is a critical data point in x.

  • Distinction examples:

  • Hexane (MW = 86)

  • 1-Hexene (MW = 84)

  • 1-Hexyne (MW = 82)

  • Ambiguous molecular weight (e.g., 72) could correspond to multiple compounds (C(5H{12}) or C(4H8O))

  • Development of high-resolution instruments enhanced molecular identification capabilities, able to resolve differences in mass within 0.0001 atomic mass units.

High-Resolution Mass Spectrometry

• Provides exact mass due to precision of analysis.

  • Example isotope mass calculations:

  • 16O = 15.99491

  • 12C = 12.0000

  • 1H = 1.00783

  • Molecular weights calculated with high accuracy:

  • C(5H_{12}) = 72.0939 amu

  • C(4H_8O) = 72.0575 amu.

Complexity of Mass Spectra

• Mass spectral patterns are typically complex; parent ion usually not the base peak.

  • Hexane: [M+] appears at m/z = 86; base peak at m/z = 57.

• Small peaks (M+1) arise from isotopes: e.g., presence of 13C or 2H can lead to additional peaks in the spectrum.

Relative Abundance of Isotopes

• The presence of isotopes can affect the mass spectrum appearance.

• Common isotopic abundance of elements:

  • 12C (100% abundance)

  • 1H (100% abundance)

  • 14N (0.2% abundance)

  • 16O (3.35% abundance)

  • Relative intensities vary with isotopes of elements like Cl and Br, which show M and M+2 peaks in their mass spectra due to isotopic compositions.

Fragmentation in Mass Spectrometry

Ionization Process

• Electron impact ionization leads to fragmentation as follows:

  1. An electron is knocked out of the valence shell (ionization).

  2. Significant translational energy is imparted, allowing bonds in the molecule to absorb energy, prompting spontaneous cleavage.

  • Resulting fragmentation produces smaller molecular species, often yielding a complex mass spectrum with multiple peaks corresponding to positively charged ions.

Example of Fragmentation in 2,2-Dimethylpropane

• Fragile structure leads to easy fragmentation with [M+] not observed.

Analyzing Structures via Fragmentation Patterns

• MS can differentiate between compounds that share molecular formulas (e.g., C(7H_{14})).

  • Unique mass spectra can serve as “fingerprints” helping identify substances in forensic analysis and environmental testing.

• Comparison of fragmentation patterns to known database entries aids in substance identification.

Specific Fragmentation Patterns for Functional Groups

• Alcohols

  • Undergo fragmentation pathways via both alpha cleavage and dehydration (removal of water, m/z = M-18).

• Amines

  • Exhibit characteristic alpha-cleavage that may indicate nitrogen presence within the molecular structure.

  • The Nitrogen Rule:

  • An molecular ion with an odd mass indicates an odd number of nitrogen atoms; an even mass corresponds to either zero or an even number of nitrogen atoms.

Carbonyl Derivatives Fragmentation

• Aldehydes and Ketones

  • Alpha cleavage yields resonance-stabilized acyl cations and neutral radicals.

  • Structures with hydrogens on carbons three atoms away can undergo McLafferty rearrangement.

Special Trends in Isotope Peaks for Halogens

• Chlorine

  • Occurs as two isotopes (35Cl and 37Cl), in a 3:1 ratio.

• Bromine

  • Occurs as two isotopes (79Br and 81Br) in nearly equal amounts (1:1 ratio).

• Result: Compounds with these halogens exhibit recognizable M and M+2 peaks, confirming their presence in the mass spectrum.

Relative Intensities of Isotope Peaks for Halides

• Chloroethane (C(2H_5Cl))

  • Mass spectrum exhibits M (64) and M+2 peaks.

• Bromohexane (C(6H_{13}Br))

  • Shows similar behavior with respect to M and M+2 peaks due to bromine isotopes in the structure.

Summary Table of Isotope Peaks for Halides

• Comparative patterns of M, M+2, M+4, etc., for compounds with bromine and chlorine isotopes.