Name: mass spectrometry fragmentation patterns
Uploaded: 2024-04-04T10:51:33.000Z
Duration: 1 min 20 s
Channel: JoVE

In mass spectrometry, the analyte molecule gets ionized into a molecular ion with one fewer electron than the analyte molecule.
The loss of an electron weakens some bonds in the molecular ion, which subsequently fragments through pathways that lead to relatively stable, smaller species.
For example, consider the fragmentation of the pentane molecular ion. The cleavage occurs preferentially at the bond between the second and third carbon, not between the terminal and its adjacent carbon. The former yields a relatively stable carbocation.
Fragmentation generates a cation and a radical, where the arrangement of the unpaired electron results in two modes of cleavage. The cleavage that produces a stable carbocation is preferred to that generating a stable radical.
Fragmentation also occurs via the cleavage of two bonds. For example, molecular ions of alcohols yield a radical cation and a neutral molecule.
Another fragmentation pattern is the formation of resonance-stabilized carbocations, driven by the presence of pi bonds or nonbonding electrons in the analyte molecule.

mass spectrometry: molecular fragmentation overview

Mass Spectrometry: Molecular Fragmentation Overview

The ionization of a molecule into a molecular ion inside the mass spectrometer causes instability in the molecule's structure due to the loss of an electron. This eventually leads to the fragmentation or breaking of some bonds in the molecule. The fragmentation occurs predominantly at specific bonds to yield relatively stable fragments.
One type of fragmentation pattern is the cleavage of a single bond in the molecular ion. The cleavage leads to a radical and a cation. The cleavage can occur at various single bonds in the molecule, but the cleavage preferentially occurs at the positions that generate a stable carbocation and a radical. At a specific bond, the unpaired electron can be transferred to either fragment, creating two sets of products. The preferred orientation of electron transfer occurs in such a way as to generate a more stable carbocation rather than a stable radical. Consider the fragmentation pattern of pentane shown in Figure 1.
<img alt="Mass spectrometry fragmentation, diagram, molecule ion, m/z values, chemical analysis process." src="/files/ftp_upload/12298/12298-PT_Figure_1.svg" style="text-align: center; height: 375px;" data-altupdatedat="1761830439000" data-alt="Figure1" />
Figure 1. Fragmentation of the pentane molecular ion.
From the abundance of carbocations in mass spectra, as depicted in Figure 2, it is clear that the cleavage of molecular ions can occur between any two adjacent carbon atoms. However, the cleavage between two inner carbon atoms is preferred to the cleavage between the terminal and its adjacent carbon. The cleavage of inner carbons yields a relatively stable primary carbocation and primary radical. The cleavage of the bond between the terminal and its adjacent carbon yields a primary carbocation and a methyl radical or a primary radical and a methyl carbocation. If this cleavage occurs, it is via the cleavage mode that leads to a butyl carbocation and a methyl radical.
<img alt="Chromatography mass spectrometry graph, peak intensities, compound identification, analytical chemistry." src="/files/ftp_upload/12298/12298-PT_Figure_2.svg" style="text-align: center; height: 275px;" data-altupdatedat="1761830439000" data-alt="Figure2" />
Figure 2. The mass spectrum of pentane.
Another type of cleavage is the dissociation of multiple bonds to yield fragments. This type of fragmentation produces a smaller radical cation and a neutral molecule. For example, alcohols can fragment into a smaller radical cation by expelling a water molecule. Consequently, the mass spectra exhibit an M&#8722;18 peak. Figure 3 presents the schematic fragmentation of 1-heptanol.
<img alt="Chemical reaction mechanism, mass spectrometry fragmentation, showing m/z=116 to m/z=98 and m/z=18." src="/files/ftp_upload/12298/12298-PT_Figure_3.svg" style="text-align: center; height: 100px;" data-altupdatedat="1761830439000" data-alt="Figure3" />
Figure 3. Fragmentation of 1-heptanol.
The molecular mass of heptanol is 116 u, and a peak at m/z = 98 is visible in its mass spectrum, shown in Figure 4. Similarly, cycloalkenes undergo a retro-Diels&#8211;Alder reaction to expel an alkene and a smaller radical cation.
<img alt="Chromatography mass spectrum graph; chemical compound analysis; peak identification data." src="/files/ftp_upload/12298/12298-PT_Figure_4.svg" style="text-align: center; height: 275px;" data-altupdatedat="1761830439000" data-alt="Figure4" />
Figure 4. The mass spectrum of heptanol.
The third type of fragmentation is observed in molecules with unshared electrons or &#960; bonds. In molecules with lone pairs, the carbon&#8211;carbon bond next to the lone-pair-bearing atom breaks to yield a resonance-stabilized carbocation. Figure 5 depicts the fragmentation of ether as an example.
<img alt="Organic reaction mechanism diagram showing electron transfer and bond formation." src="/files/ftp_upload/12298/12298-PT_Figure_5v2.svg" style="text-align: center; height: 140px;" data-altupdatedat="1761830439000" data-alt="Figure5" />
Figure 5. Fragmentation of ethers.
The &#960; bonds in a molecular ion promote the fragmentation of the molecule to create an allylic carbocation stabilized by resonance. Figure 6 shows the fragmentation pattern of a terminal alkene.
<img alt="Radical cation formation: chemical reaction diagram, electron transfer and resonance structures." src="/files/ftp_upload/12298/12298-PT_Figure_6v2.svg" style="text-align: center; height: 120px;" data-altupdatedat="1761830439000" data-alt="Figure6" />
Figure 6. Fragmentation of alkenes.

The ionization of a molecule into a molecular ion inside the mass spectrometer causes instability in the molecule&#39;s structure due to the loss of an ...

mass-spectrometry-molecular-fragmentation-overview

Education

JoVE Core

Analytical Chemistry

Unit 1

Principles of Mass Spectrometry

KEY TERMS AND CONCEPTS

mass spectrometry fragmentation patterns

Mass spectrometry fragmentation patterns show how a molecular ion breaks apart after ionization. When a molecule loses an electron inside the mass spectrometer, its structure becomes unstable. The ion then fragments at bonds that often produce the most stable pieces.

One common pattern is cleavage of a single bond in the molecular ion. This break forms a radical and a cation. The bond can split in more than one way, but the favored path is the one that gives the more stable carbocation rather than the more stable radical.

Pentane shows this idea clearly. Its molecular ion can break between any two adjacent carbon atoms, but cleavage between two inner carbon atoms is preferred over cleavage near the end of the chain. That inner break gives a relatively stable primary carbocation and primary radical. When the terminal bond breaks, the products can include a primary carbocation and a methyl radical, or a primary radical and a methyl carbocation. In the preferred case, the cleavage leads to a butyl carbocation and a methyl radical.

A second pattern is loss of a neutral fragment from the ion. This type of fragmentation gives a smaller radical cation plus a neutral molecule. Alcohols can lose water in this way, so their mass spectra often show an M−18 peak. For example, 1-heptanol has a molecular mass of 116 u, and its spectrum shows a peak at m/z = 98. Cycloalkenes can also follow a retro-Diels–Alder reaction to expel an alkene and leave a smaller radical cation.

A third pattern appears in molecules with lone pairs or π bonds. In compounds with lone pairs, the carbon-carbon bond next to the atom bearing the lone pair can break to form a resonance-stabilized carbocation, as seen with ethers. In molecules with π bonds, fragmentation often creates an allylic carbocation that is stabilized by resonance. A terminal alkene is a common example of this behavior.

Mass Spectrometry Fragmentation Patterns

mass spectrometry: overview

Mass Spectrometry and Molecular Identity

Mass spectrometry helps identify a compound by measuring its molecular mass and molecular formula. It does this by turning the analyte molecule into ions and then comparing ion abundance with mass-to-charge ratio. One common ionization method is electron ionization, or EI. In EI, high-energy electron beams strike analyte molecules in the gas phase. The beam removes an electron and leaves a molecular ion behind. A molecular ion is a radical cation, so it has a positive charge and an unpaired...

mass spectrometry: isotope effect

Isotope Peaks in Mass Spectra

Isotope peaks in mass spectra show how natural isotope mixtures change the signal of a molecule. Most elements occur as a mix of isotopes, which are atoms of the same element with different numbers of neutrons. Because isotopes have different masses, the same fragment can appear at more than one position in a spectrum. The mass of a molecule depends on which isotopes are present in its atoms. The size of each isotope peak also depends on how common those isotopes are in nature. Carbon is a...

Mass spectrometry fragmentation patterns show how a molecular ion breaks apart after ionization. When a molecule loses an electron inside the mass spectrometer, its structure becomes unstable. The ion then fragments at bonds that often produce the most stable pieces. One common pattern is cleavage of a single bond in the molecular ion. This break forms a radical and a cation. The bond can split in more than one way, but the favored path is the one that gives the more stable carbocation rather...

mass spectrometers

How Mass Spectrometers Sort Ions

A mass spectrometer sorts charged ions by their mass-to-charge ratio and records their relative abundance. It turns vaporized analyte molecules into ions, separates them, and then measures the signal from each type of ion. The process begins in the ionization chamber. The analyte is in the gas phase inside a vacuum, and it is struck by high-energy electrons. The electrons have about 70 eV of energy, which is enough to remove an electron from the analyte and form a molecular ion. After...

mass spectrum

Reading Peaks in a Mass Spectrum

A mass spectrum shows the charged fragments in an analyte as peaks plotted by mass-to-charge ratio, or m/z. The x-axis gives the mass of each charged fragment divided by the number of charges it carries. The y-axis shows the relative abundance of each charged species based on the signal intensity recorded at the detector. The tallest peak is called the base peak. It is assigned an abundance of 100%, and the other peaks are scaled against it. The peak from the molecular ion is called the parent...

mass spectrum: interpretation

Decoding Molecular Ions in Mass Spectra

Mass spectra help scientists identify an unknown compound by finding the molecular ion peak. The molecular ion peak shows the mass of the intact molecule, but it is often weak or missing because high-energy electron beams cause strong fragmentation. When that happens, a soft-energy electron beam can be used to scan the spectrum and improve the molecular ion signal. Other ionization methods can also give a stronger molecular ion peak. Chemical ionization, field ionization, and desorption...

mass analyzers: overview

Mass Analyzers and Ion Separation

Mass analyzers separate ions by their mass-to-charge ratio, or m/z, in a mass spectrometer. After a sample is vaporized in the ionization chamber, it is hit with a high-energy electron beam. This creates a radical cation and also produces neutral molecules, radicals, and cations. Negatively charged accelerator plates then push the cations into the mass analyzer, where they are sent on to the detector. Several mass analyzer designs are commonly used. These include magnetic sector,...

mass analyzers: common types

Quadrupole, TOF, and Ion Trap Analyzers

Quadrupole, time-of-flight, and ion trap mass analyzers each separate ions in a different way. They are common tools in mass spectrometry and help sort ions by their mass-to-charge ratio, or m/z. A quadrupole mass analyzer uses four cylindrical metal rods arranged in a diamond shape. The rods carry a direct current, or DC, voltage and a radio-frequency AC voltage. Ion motion depends on the field strength, so only ions with a certain m/z resonate and reach the detector at that setting. This...

high-resolution mass spectrometry (hrms)

Mass Accuracy in HRMS Analysis

High-resolution mass spectrometry separates ions by very small differences in mass. This matters because atomic masses are not always exact whole numbers, even though they are often rounded for simple calculations. Atomic mass is usually estimated by adding the masses of protons and neutrons. In reality, the proton and neutron do not have exactly the same mass. That creates small differences when atomic masses are compared to the simplest hydrogen atom. Helium, for example, is made of 2...

mass spectrometry: complex analysis

Hyphenated Mass Spectrometry Methods

Mass spectrometry can be paired with separation methods to study complex mixtures. This combination is called a hyphenated method. It helps when a pure mass spectrum is too hard to read because a mixture causes too much fragmentation and too many overlapping signals. GC-MS is one common hyphenated method. GC stands for gas chromatography, which separates volatile, thermally stable compounds in narrow capillary columns before they enter the mass spectrometer. This approach is widely used in...

tandem mass spectrometry

MS/MS Scan Modes and Fragment Ions

Tandem mass spectrometry uses two or more mass analyzers in series to improve selectivity and lower chemical noise during analyte detection. A set of analyzers separated by an interaction cell lets the instrument break ions apart and study the fragment ions that form. Fragmentation happens in the interaction cell and can be caused in several ways. Collision-induced dissociation, or CID, uses inert gases such as nitrogen, argon, or helium. Other methods include surface-induced dissociation...

gas chromatography&ndash;mass spectrometry (gc&ndash;ms)

How GC-MS Separates and Identifies Compounds

Gas chromatography-mass spectrometry (GC-MS) separates compounds in a mixture and then identifies them. A gas chromatograph first splits the mixture into its parts. A mass spectrometer then analyzes each part on its own to determine molecular masses and molecular structures. The gas chromatograph uses a long, narrow capillary column. The inner wall of the column has a polysiloxane coating. This coating serves as the stationary phase. It has a high boiling point, low viscosity, and low polarity.

inductively coupled plasma&#8211;mass spectrometry (icp&#8211;ms): overview

inductively-coupled-plasmamass-spectrometry-icpms-overview

ICP-MS Sample Ionization and Detection

ICP-MS uses an inductively coupled plasma torch to turn samples into ions for mass analysis. Solid samples are first dissolved and volatilized before they enter the hot argon plasma. Solution samples are nebulized, which means they are converted into a fine spray, and then passed through the same plasma. Inside the plasma, the analytes break apart. Their atoms become positively charged ions, along with some molecular species. These positive ions are sent to the mass spectrometer, where they...

inductively coupled plasma-mass spectrometry (icp-ms): interferences

inductively-coupled-plasma-mass-spectrometry-icp-ms-interferences

ICP-MS Signal Interference Sources and Fixes

Inductively coupled plasma-mass spectrometry (ICP-MS) is a sensitive method for elemental analysis, but its spectra can be affected by interferences. These interferences can make the mass signal less accurate, even when the instrument is working well. Spectroscopic interferences happen when ions in the plasma have the same mass-to-charge ratio, or m/z, as the analyte ion. This group includes isobaric interferences, polyatomic ion interferences, and refractory oxide ion interferences. Isobaric...

key terms and concepts

Learn how molecular ions fragment in mass spectrometry, including single-bond cleavage, water loss from alcohols, and resonance-stabilized products.

Mass Spectrometry Fragmentation Patterns | JoVE K12

analytical chemistry

JoVE Core Analytical Chemistry simplifies complex chemical principles by breaking them down into clear, engaging animations, making topics from SI Units to NMR spectroscopy more accessible and straightforward. Additionally, the scientist-in-action videos highlight the application of these concepts in real-world research conducted in laboratories globally.

Mass Spectrometry Fragmentation Patterns

Description

Transcript

Tags