Glossary

12.3 Mass Spectrometry of Some Common Functional Groups

3 min read•may 7, 2024

is a powerful tool for identifying organic compounds. It works by ionizing molecules and analyzing their . Different functional groups produce unique mass spectra, allowing chemists to determine molecular structures and compositions.

Understanding mass spectrometry helps you decode the molecular puzzle. By recognizing characteristic peaks and fragmentation patterns, you can identify functional groups, determine molecular masses, and piece together structural information about unknown compounds.

Mass Spectrometry of Common Functional Groups

Ionization and Detection Methods

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  • (EI): High-energy electrons collide with sample molecules, causing and fragmentation
  • (CI): Softer ionization technique that produces less fragmentation
  • (m/z): Measurement used to identify ions based on their mass and charge
  • : Most intense peak in the mass spectrum, representing the most stable fragment ion

Fragmentation patterns of organic compounds

    • peak (M+M^+) usually present but may have low intensity due to easy fragmentation
    • [M−OH]+[M-OH]^+ peak formed by loss of hydroxyl group (ethanol)
    • [M−H2O]+[M-H_2O]^+ peak formed by loss of water molecule via rearrangement (propanol)
    • peak (M+M^+) usually present and relatively stable compared to alcohols
    • [M−1]+[M-1]^+ peak formed by loss of hydrogen atom from nitrogen (methylamine)
    • [M−CH2NH2]+[M-CH_2NH_2]^+ peak formed by α\alpha-cleavage adjacent to nitrogen atom (ethylamine)
    • Molecular ion peak (M+M^+) usually present with characteristic
      • Chlorine: M+M^+ and [M+2]+[M+2]^+ peaks in 3:1 ratio due to 35Cl^{35}Cl and 37Cl^{37}Cl isotopes (chloroethane)
      • Bromine: M+M^+ and [M+2]+[M+2]^+ peaks in 1:1 ratio due to 79Br^{79}Br and 81Br^{81}Br isotopes (bromoethane)
    • [M−X]+[M-X]^+ peak formed by loss of halogen atom X (X = F, Cl, Br, I) (iodoethane)
  • ( and )
    • Molecular ion peak (M+M^+) usually present but may have low intensity due to easy fragmentation
    • [M−CO]+[M-CO]^+ peak formed by loss of carbon monoxide (acetone)
    • α\alpha-cleavage peaks on either side of the carbonyl group (propanal)
    • peak for aldehydes and with γ\gamma-hydrogen (2-pentanone)

Mass spectra for structural determination

  • Determine molecular mass from the molecular ion peak (M+M^+) (butanal: 72)
  • Identify functional groups based on characteristic fragmentation patterns
    • Alcohols: [M−OH]+[M-OH]^+ and [M−H2O]+[M-H_2O]^+ peaks (ethanol: 31 and 45)
    • Amines: [M−1]+[M-1]^+ and [M−CH2NH2]+[M-CH_2NH_2]^+ peaks (propylamine: 59 and 30)
    • Halides: Characteristic isotope patterns and [M−X]+[M-X]^+ peaks (chlorobutane: 92 and 57)
    • Carbonyl compounds: [M−CO]+[M-CO]^+ and α\alpha-cleavage peaks (2-butanone: 57 and 43, 29)
  • Analyze relative abundance of fragment ions to determine most stable and dominant fragments
  • Use fragmentation patterns and mass differences between peaks to propose molecular structure
  • : Represents the molecular ion and provides information about the compound's molecular weight

Nitrogen rule in molecular analysis

  • : odd number of nitrogen atoms →\rightarrow odd nominal mass, zero or even number of nitrogen atoms →\rightarrow even nominal mass
  • Determine nominal mass from molecular ion peak (M+M^+)
    1. Odd nominal mass indicates odd number of nitrogen atoms (1, 3, 5, etc.) (pyridine: 79)
    2. Even nominal mass indicates zero or even number of nitrogen atoms (0, 2, 4, etc.) (aniline: 93)
  • Use presence or absence of nitrogen atoms with other fragmentation patterns to propose molecular structure (4-aminobutanoic acid: 103, odd nominal mass, amine fragments)

Key Terms to Review (26)

Alcohols: Alcohols are organic compounds containing a hydroxyl (-OH) functional group attached to a saturated carbon atom. They are widely used in various chemical reactions and have diverse applications in industry, medicine, and everyday life.
Aldehydes: Aldehydes are a class of organic compounds characterized by the presence of a carbonyl group (C=O) with a hydrogen atom attached to the carbon. They are important intermediates in many chemical reactions and have a wide range of applications in various industries, from pharmaceuticals to fragrances.
Alkyl halides: Alkyl halides are organic compounds in which one or more hydrogen atoms in an alkane (saturated hydrocarbon) have been replaced by a halogen atom such as fluorine, chlorine, bromine, or iodine. They are a type of functional group characterized by the presence of a carbon-halogen bond.
Alpha Cleavage: Alpha cleavage, also known as $\alpha$-cleavage, is a fragmentation process that occurs during mass spectrometry analysis. It involves the breaking of a carbon-carbon bond adjacent to (or $\alpha$ to) a functional group, leading to the formation of characteristic fragment ions that provide valuable information about the structure of the analyzed compound.
Amines: Amines are a class of organic compounds derived from ammonia (NH3) by the replacement of one or more hydrogen atoms with alkyl or aryl groups. They are characterized by the presence of a nitrogen atom with a lone pair of electrons, giving them basic properties and the ability to act as nucleophiles in chemical reactions.
Base peak: The base peak is the most intense peak in a mass spectrum, representing the ion that is the most abundantly produced during mass spectrometry. It serves as a reference point with its intensity set at 100% for comparing other peaks in the spectrum.
Base Peak: The base peak is the most intense or tallest peak in a mass spectrum, representing the fragment ion with the greatest abundance. It is a crucial feature in interpreting mass spectra and understanding the fragmentation patterns of molecules.
Carbonyl Compounds: Carbonyl compounds are a class of organic compounds that contain a carbon-oxygen double bond (C=O), known as the carbonyl group. This functional group is found in a variety of important molecules, including aldehydes, ketones, carboxylic acids, esters, and amides, which are all integral to many organic chemistry topics and reactions.
Chemical Ionization: Chemical ionization is a soft ionization technique used in mass spectrometry to generate molecular ions from analyte molecules. Unlike the more energetic electron ionization method, chemical ionization produces less fragmentation, allowing for the detection of intact molecular ions and providing information about the molecular weight of the analyte.
Electron Impact: Electron impact, also known as electron ionization, is a technique used in mass spectrometry to generate ions from neutral molecules. It involves bombarding the sample with a beam of high-energy electrons, which causes the molecules to lose one or more electrons, resulting in the formation of positively charged ions.
Enamines: Enamines are organic compounds formed by the reaction between a secondary amine and an aldehyde or ketone, characterized by the presence of a nitrogen atom connected to a carbon-carbon double bond. They are the result of nucleophilic addition of amines to carbonyl compounds followed by dehydration.
Fragmentation Patterns: Fragmentation patterns refer to the characteristic ways in which molecules break apart when subjected to the ionization process in mass spectrometry. These unique fragmentation patterns provide valuable information about the structure and composition of the analyzed compounds, allowing for their identification and characterization.
Halides: Halides are compounds formed by the chemical combination of a halogen element (fluorine, chlorine, bromine, iodine, or astatine) with a more electropositive element or group. They are an important class of compounds that play a significant role in organic chemistry, particularly in the context of SN1 reactions and mass spectrometry analysis.
Ionization: Ionization is the process by which an atom or molecule loses or gains one or more electrons, resulting in the formation of an ion. This process is fundamental to understanding the interpretation of mass spectra and the mass spectrometry of various functional groups.
Isotope Patterns: Isotope patterns refer to the distinct distributions of peaks observed in a mass spectrum that correspond to the naturally occurring isotopes of a particular element within a molecule. These patterns provide valuable information about the elemental composition and molecular structure of the analyte being analyzed.
Ketones: Ketones are organic compounds characterized by a carbonyl group (C=O) bonded to two other carbon atoms within the molecule. They are formed by the oxidation of secondary alcohols.
Ketones: Ketones are a class of organic compounds containing a carbonyl group (C=O) bonded to two alkyl or aryl groups. They are characterized by the presence of a carbonyl carbon flanked by two carbon atoms. Ketones are important in various organic chemistry topics, including chirality, oxidation reactions, mass spectrometry, infrared spectroscopy, and NMR spectroscopy.
Mass Spectrometry: Mass spectrometry is an analytical technique that measures the mass-to-charge ratio of ions to identify and quantify the chemical composition of a sample. It provides detailed information about the molecular structure and fragmentation patterns of compounds, making it a powerful tool in organic chemistry and various other fields.
Mass spectrometry (MS): Mass spectrometry is an analytical technique used in organic chemistry to determine the mass-to-charge ratio of ions. It helps identify the composition of a sample by generating ions and measuring their mass and charge.
Mass-to-Charge Ratio: The mass-to-charge ratio, often denoted as m/z, is a fundamental concept in mass spectrometry that describes the ratio of the mass of an ion to its electric charge. This ratio is a crucial parameter that allows for the identification and analysis of molecules based on their unique mass and charge characteristics.
McLafferty rearrangement: The McLafferty rearrangement is a reaction observed in mass spectrometry where a molecule undergoes fragmentation, transferring a hydrogen atom to form a double bond, resulting in a neutral and an ionized fragment. This process aids in identifying the structure of organic compounds by analyzing the resulting mass spectrum.
McLafferty Rearrangement: The McLafferty rearrangement is a type of fragmentation reaction that occurs during mass spectrometry analysis, particularly for organic compounds containing carbonyl groups. It involves the rearrangement of a molecule's structure to form a stable ion, which provides valuable information about the compound's structure.
Molecular ion: A molecular ion is a molecule that has gained or lost an electron, resulting in a charged entity. In the context of mass spectrometry, it's often the starting point for fragmentation processes that help identify the structure of the molecule.
Molecular Ion: The molecular ion, also known as the parent ion, is the intact, positively charged molecule that is formed during the ionization process in mass spectrometry. It represents the molecular weight of the analyte and is the starting point for further fragmentation and analysis.
Nitrogen Rule: The nitrogen rule is a principle used in mass spectrometry to determine the number of nitrogen atoms present in an organic compound based on the molecular ion peak and the isotopic peak pattern. It is a crucial concept in interpreting mass spectra, understanding the mass spectrometry of common functional groups, and analyzing the spectroscopy of amines.
Parent Peak: The parent peak in mass spectrometry refers to the signal corresponding to the molecular ion, which represents the intact, unfragmented molecule being analyzed. It is the peak with the highest mass-to-charge ratio (m/z) and provides information about the molecular weight of the compound.
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