12.2 Interpreting Mass Spectra

Mass spectrometry is a powerful tool for identifying molecules and understanding their structures. It works by ionizing compounds, then measuring the mass-to-charge ratios of the resulting fragments. This technique provides crucial information about molecular mass, elemental composition, and structural features.

The molecular ion peak and fragmentation patterns are key to interpreting mass spectra. By analyzing these, chemists can deduce a compound's formula and structure. High-resolution mass spectrometry takes this further, offering precise mass measurements that can distinguish between similar molecules.

Mass Spectrometry

Molecular ion peak identification

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• Molecular ion peak ($M^+$ or $M^{•+}$) represents the intact, unfragmented molecule ionized by removing one electron
  • Highest m/z peak in the spectrum corresponds to the molecular ion
  • Indicates the molecular mass and provides information about the molecular formula of the compound
• Isotope peaks appear at M+1 and M+2 due to the presence of naturally occurring isotopes in the molecule
  • $^{13}C$ isotope contributes to the M+1 peak intensity (about 1.1% per carbon atom)
  • $^{37}Cl$, $^{81}Br$, and $^{34}S$ isotopes contribute to the M+2 peak intensity (chlorine 32%, bromine 98%, sulfur 4.4%)
• Molecular formula can be determined by considering the molecular mass and isotope patterns
  • Elements commonly found in organic compounds include C, H, N, O, S, P, and halogens (F, Cl, Br, I)
  • Use the nitrogen rule: odd molecular mass indicates an odd number of nitrogen atoms, while even molecular mass suggests an even number or absence of nitrogen atoms

Mass spectra fragmentation patterns

• Fragmentation occurs when the molecule absorbs energy from the ionization source, leading to bond cleavage and the formation of smaller charged fragments
  • Fragmentation patterns provide structural information about the molecule
  • Fragments are represented as peaks at lower m/z values relative to the molecular ion
• Common fragmentation patterns include:
  • Alpha cleavage: loss of a side chain or substituent attached to a heteroatom or functional group ($CH_3$, $C_2H_5$, etc.)
  • Beta cleavage: cleavage of a bond beta to a heteroatom or functional group, often resulting in the formation of a stable cation (alkene, carbonyl, etc.)
  • Retro Diels-Alder: cleavage of a six-membered ring into two fragments, typically observed in compounds containing cyclohexene or related structures
  • McLafferty rearrangement: migration of a hydrogen atom to a carbonyl group followed by beta cleavage, resulting in the formation of an alkene and an enol radical cation
• Characteristic fragments can indicate the presence of specific functional groups in the molecule
  • m/z 31 suggests a methoxy group ($OCH_3$), m/z 45 suggests an ethoxy group ($OC_2H_5$), and m/z 77 suggests a phenyl group ($C_6H_5$)
  • Other examples include m/z 29 for ethyl ($C_2H_5$), m/z 43 for propyl ($C_3H_7$), and m/z 91 for benzyl ($C_7H_7$)
• The base peak represents the most intense peak in the mass spectrum, with a relative abundance of 100%

High-resolution mass spectrometry analysis

• High-resolution mass spectrometry (HRMS) provides accurate mass measurements to four or more decimal places
  • Allows differentiation between compounds with similar nominal masses but different elemental compositions
  • Commonly used techniques include Fourier transform ion cyclotron resonance (FT-ICR) and time-of-flight (TOF) mass spectrometry
• Exact mass represents the precise mass calculated using the actual atomic masses of the isotopes in the molecule
  • Differs from nominal mass, which is an integer mass based on the sum of the mass numbers of the constituent atoms
  • Example: nominal mass of benzene ($C_6H_6$) is 78, while its exact mass is 78.0469
• Elemental composition can be determined by comparing the measured exact mass to the calculated exact masses of possible formulas
  • HRMS data helps identify the correct molecular formula among several possibilities with the same nominal mass
  • Example: $C_3H_8O$ (propanol) and $C_4H_8$ (butene) have the same nominal mass of 56 but different exact masses (60.0575 and 56.0626, respectively)
• HRMS can distinguish between isomers, which have the same molecular formula but different structures
  • Isomers exhibit unique fragmentation patterns due to their distinct structural features
  • Example: butanol isomers (n-butanol, sec-butanol, isobutanol, and tert-butanol) can be differentiated based on their HRMS fragmentation patterns

Ionization and Mass Analysis

• Ionization methods in mass spectrometry include electron impact (EI) and chemical ionization (CI)
  • EI involves bombarding molecules with high-energy electrons, causing extensive fragmentation
  • CI is a softer ionization technique that produces less fragmentation, often yielding a stronger molecular ion peak
• The mass analyzer separates ions based on their mass-to-charge ratio
  • Different types of mass analyzers include quadrupole, time-of-flight, and magnetic sector
• Relative abundance in mass spectra represents the intensity of each peak relative to the base peak