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Organic Chemistry
Table of Contents
Unit 12 Overview: Mass Spec and IR Spectroscopy in Organic Chem
12.1 Mass Spectrometry of Small Molecules: Magnetic-Sector Instruments
12.2 Interpreting Mass Spectra
12.3 Mass Spectrometry of Some Common Functional Groups
12.4 Mass Spectrometry in Biological Chemistry: Time-of-Flight (TOF) Instruments
12.5 Spectroscopy and the Electromagnetic Spectrum
12.6 Infrared Spectroscopy
12.7 Interpreting Infrared Spectra
12.8 Infrared Spectra of Some Common Functional Groups

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

  • 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

Key Terms to Review (28)

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.
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.
Quadrupole mass analyzer: A quadrupole mass analyzer is a device used in mass spectrometry to separate ions of different mass-to-charge ratios by using oscillating electrical fields. It consists of four parallel rods, with each opposing rod pair being electrically connected.
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 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.
M+2 Peak: The M+2 peak in a mass spectrum refers to the peak that appears at a mass-to-charge ratio (m/z) two units higher than the molecular ion (M+) peak. This peak is caused by the presence of naturally occurring isotopes of certain elements, typically heavier isotopes, in the molecule being analyzed.
Exact Mass: Exact mass refers to the precise mass of a molecule or ion, calculated based on the masses of its constituent atoms. It is a fundamental concept in mass spectrometry, which is used to determine the molecular composition of chemical compounds.
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.
Beta Cleavage: Beta cleavage, also known as $\beta$-cleavage, is a fragmentation process that occurs during mass spectrometry analysis. It involves the breaking of a carbon-carbon bond adjacent to a carbonyl group, leading to the formation of two fragment ions.
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.
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.
Time-of-Flight: Time-of-Flight (TOF) is a fundamental concept in mass spectrometry that refers to the measurement of the time it takes for ionized molecules or atoms to travel a known distance within the mass spectrometer. This time-of-flight information is then used to calculate the mass-to-charge ratio (m/z) of the detected species, providing crucial data for analyzing the composition and structure of chemical compounds.
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.
Relative Abundance: Relative abundance refers to the proportional representation of different components within a mixture or sample, typically measured in mass spectrometry. It describes the comparative quantity or prevalence of specific ions or molecules relative to the most abundant species detected.
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.
M+1 Peak: The M+1 peak in a mass spectrum refers to the peak that appears one mass unit higher than the molecular ion peak (M+). This peak is caused by the presence of naturally occurring isotopes of the atoms that make up the molecule, typically carbon-13 and deuterium.
High-Resolution Mass Spectrometry: High-resolution mass spectrometry (HRMS) is an analytical technique that provides precise and accurate mass measurements of chemical compounds, allowing for the determination of their elemental composition with high confidence. This advanced mass spectrometry method is particularly useful in the context of interpreting mass spectra, as it enables the identification of unknown compounds and the verification of the molecular formulas of known substances.
Nominal Mass: Nominal mass is the whole number mass of an atom or molecule that corresponds to the sum of the masses of its constituent protons and neutrons. It is the mass value that is typically reported for an element or compound and is useful for quickly estimating the molecular weight of a substance.
Retro Diels-Alder: The retro Diels-Alder reaction is the reverse of the Diels-Alder cycloaddition reaction, where a cyclic compound undergoes fragmentation to form a diene and a dienophile. This process is particularly relevant in the interpretation of mass spectra, as it can lead to the formation of characteristic fragment ions.
Mass Analyzer: A mass analyzer is a critical component of a mass spectrometer that separates and sorts ions based on their mass-to-charge ratio (m/z). It is a fundamental part of the mass spectrometry technique used to identify and quantify molecules in complex samples, as seen in the topics of Interpreting Mass Spectra and Mass Spectrometry in Biological Chemistry.
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.
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.
Molecular Ion Peak: The molecular ion peak in a mass spectrum represents the molecular mass of a compound, providing crucial information about its molecular structure and composition. This term is particularly relevant in the context of mass spectrometry techniques used to analyze small molecules, as well as the interpretation of mass spectra and the spectroscopic analysis of aldehydes and ketones.
Isotope Peaks: Isotope peaks refer to the distinct signals or peaks observed in a mass spectrum that correspond to the different isotopic forms of a molecule. These peaks provide valuable information about the elemental composition and abundance of the molecule being analyzed.
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.
Characteristic Fragments: Characteristic fragments are specific patterns or ions observed in a mass spectrum that provide valuable information about the structure and identity of a molecule. These fragments are formed during the ionization and fragmentation process in mass spectrometry and can serve as fingerprints to help identify unknown compounds.
Elemental Composition: Elemental composition refers to the relative amounts of different chemical elements that make up a substance or compound. It is a fundamental property that describes the atomic-level structure and constitution of a material.
Fourier transform ion cyclotron resonance: Fourier transform ion cyclotron resonance (FT-ICR) is a powerful analytical technique used in mass spectrometry to determine the mass-to-charge ratio (m/z) of ionized molecules with high precision and resolution. It relies on the principles of ion cyclotron resonance, where ions are trapped in a strong magnetic field and their motion is used to determine their mass-to-charge ratio.