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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

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12.1 Mass Spectrometry of Small Molecules: Magnetic-Sector Instruments

Citation:

Mass spectrometry is a powerful tool for analyzing molecules. It breaks compounds into charged fragments and measures their mass-to-charge ratios. This process helps identify unknown substances and determine molecular structures.

Understanding mass spectrometry is crucial for organic chemists. It provides valuable information about molecular weights, elemental composition, and structural features of compounds. Let's explore the key components and principles of this essential analytical technique.

Mass Spectrometry Fundamentals

Parts of a mass spectrometer

  • Ionization source converts sample molecules into gaseous ions using methods like electron ionization (EI) or chemical ionization (CI)
  • Mass analyzer separates ions based on their mass-to-charge ratio ($m/z$) using techniques such as magnetic-sector, quadrupole, or time-of-flight analyzers
  • Detector records the relative abundance of each ion using an electron multiplier or Faraday cup and generates a mass spectrum plot with $m/z$ on the x-axis and relative abundance on the y-axis

Electron-impact ionization vs magnetic-sector analyzers

  • Electron-impact ionization (EI) vaporizes the sample and bombards it with high-energy electrons (typically 70 eV), causing ionization and fragmentation of molecules, producing singly charged positive ions ($M^{+•}$) and fragment ions with reproducible fragmentation patterns that aid in compound identification
    • The efficiency of this process, known as ionization efficiency, affects the intensity of peaks in the mass spectrum
  • Magnetic-sector mass analyzer accelerates ions through a magnetic field, which deflects ions based on their $m/z$ ratio, with lighter ions deflecting more than heavier ions and ions with the same $m/z$ following the same path, allowing for high resolution and accurate mass measurements by varying the magnetic field strength to allow different $m/z$ ratios to reach the detector
    • The strength of the magnetic field directly impacts the resolution and sensitivity of the instrument

Interpretation of mass spectra

  • Molecular ion peak ($M^{+•}$) represents the unfragmented, singly charged molecular ion, has the highest $m/z$ value in the spectrum, provides the molecular mass of the compound, and may be absent or have low intensity for molecules that readily fragment
  • Base peak is the most intense peak in the mass spectrum, assigned a relative abundance of 100%, with other peaks reported as a percentage of the base peak intensity
  • Fragment peaks result from the dissociation of the molecular ion, provide structural information about the molecule, and include common fragmentations such as:
    1. Loss of neutral molecules (H2O, CO, NH3)
    2. Cleavage of carbon-carbon bonds
    3. Cleavage adjacent to heteroatoms (N, O, S)
  • Fragmentation patterns can be used to deduce the structure of the compound

Advanced Mass Spectrometry Concepts

  • Mass resolution refers to the ability of the instrument to distinguish between ions with similar $m/z$ values, which is crucial for accurate mass determination and structural elucidation
  • Isotope peaks appear in mass spectra due to the natural abundance of isotopes, providing additional information about the elemental composition of the molecule
  • Mass calibration ensures the accuracy of $m/z$ measurements by using known reference compounds to adjust the instrument's mass scale

Key Terms to Review (29)

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.
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.
Parent peak: In mass spectrometry, the parent peak represents the highest mass-to-charge ratio (m/z) peak in a spectrum, corresponding to the unfragmented molecule. This peak helps in determining the molecular weight of the sample being analyzed.
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.
Analyzer: An analyzer is a critical component in mass spectrometry, responsible for separating and detecting the different ionized molecules based on their mass-to-charge ratio. It is a central part of the magnetic-sector instruments used in the analysis of small molecules, as described in Chapter 12.1 on Mass Spectrometry of Small Molecules.
Detector: A detector is a device or component in an analytical instrument that senses and responds to the presence of a specific substance or signal, converting it into a measurable output that can be interpreted and analyzed. Detectors play a crucial role in mass spectrometry techniques, such as magnetic-sector and time-of-flight instruments, by detecting and quantifying the ions generated during the analysis process.
Magnetic-sector instruments: Magnetic-sector instruments are a type of mass spectrometer that use a magnetic field to separate and analyze ions based on their mass-to-charge ratio. These instruments are commonly used in the study of small molecules, as described in the context of Chapter 12.1: Mass Spectrometry of Small Molecules.
Ion Source: An ion source is a device used in mass spectrometry to generate gaseous ions from a sample. It is a critical component that converts the analyte molecules into charged particles that can then be separated and detected by the mass analyzer.
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.
Fragment Ions: Fragment ions are charged species that are formed when a molecule undergoes fragmentation during the ionization process in a mass spectrometer. These smaller ionic fragments provide valuable information about the structure and composition of the original molecule, which is crucial in the analysis of small molecules using magnetic-sector mass spectrometry instruments.
Magnetic-sector mass analyzer: A magnetic-sector mass analyzer is a type of mass spectrometry instrument used to separate and detect ions based on their mass-to-charge ratio. It utilizes a strong magnetic field to bend the trajectory of charged particles, allowing for the separation and identification of different molecular species.
Mass Calibration: Mass calibration is the process of ensuring the accuracy of mass measurements in mass spectrometry, particularly in magnetic-sector instruments. It involves the use of reference compounds with known masses to calibrate the mass scale of the instrument, allowing for precise identification and quantification of analytes in a sample.
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.
Magnetic Field Strength: Magnetic field strength is a measure of the force exerted by a magnetic field on a magnetic object or particle. It is a fundamental concept in various fields, including mass spectrometry, nuclear magnetic resonance (NMR) spectroscopy, and the study of chemical shifts.
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 Ionization: Electron-impact ionization is a process used in mass spectrometry to generate ions from neutral analyte molecules. It involves bombarding the sample with high-energy electrons, causing the molecules to lose electrons and become positively charged ions that can then be detected and analyzed by the mass spectrometer.
Electron Multiplier: An electron multiplier is a device used in mass spectrometry, particularly in magnetic-sector instruments, to amplify and detect the weak ion signals produced during the analysis of small molecules. It serves as a highly sensitive detector that can amplify the signal by several orders of magnitude, enabling the detection of even trace amounts of analytes.
Faraday Cup: A Faraday cup is a device used in mass spectrometry to measure the current of charged particles, such as ions, that strike its surface. It is an essential component in magnetic-sector mass spectrometers, which are discussed in the context of 12.1 Mass Spectrometry of Small Molecules.
Mass Spectrum: A mass spectrum is a graphical representation of the relative abundance of different ions produced from a sample in a mass spectrometer. It provides information about the molecular structure and composition of a compound by displaying the masses and relative intensities of the ionized fragments.
Electron Ionization: Electron ionization (EI) is an ionization technique used in mass spectrometry to generate gas-phase ions from small organic molecules. It involves bombarding the sample with a beam of high-energy electrons, which causes the molecules to lose an electron and become positively charged ions.
Quadrupole: A quadrupole is a type of mass analyzer used in mass spectrometry instruments, particularly in the context of 12.1 Mass Spectrometry of Small Molecules: Magnetic-Sector Instruments. It consists of four parallel metal rods that create an oscillating electric field, which is used to selectively filter and separate ions based on their mass-to-charge ratio.
Time-of-flight analyzers: Time-of-flight analyzers are a type of mass spectrometry instrument that measures the time it takes for ionized molecules to travel a fixed distance in a vacuum, which is directly proportional to the mass-to-charge ratio of the ions. This information is then used to determine the molecular weights of the sample components.
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.
Mass Resolution: Mass resolution is a measure of the ability of a mass spectrometer to distinguish between ions of slightly different masses. It is a critical parameter that determines the instrument's capacity to separate and accurately identify individual components in a complex mixture.
Ionization Efficiency: Ionization efficiency refers to the ability of a mass spectrometry technique to effectively convert analyte molecules into gaseous ions that can be detected and analyzed. It is a critical parameter in the performance of mass spectrometry instruments, particularly in the context of magnetic-sector instruments used for the analysis of small molecules.
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.