In mass spectrometry, fragmentation is the dissociation of energetically unstable molecular ions formed from passing the molecules

mass spectrum A mass spectrum is a histogram plot of intensity vs. ''mass-to-charge ratio'' (''m/z'') in a chemical sample, usually acquired using an instrument called a ''mass spectrometer''. Not all mass spectra of a given substance are the same; for example ...

. These reactions are well documented over the decades and fragmentation patterns are useful to determine the molar weight and structural information of unknown molecules. Fragmentation that occurs in tandem mass spectrometry experiments has been a recent focus of research, because this data helps facilitate the identification of molecules. TolueneFragmentation

Mass spectrometry techniques

Fragmentation can occur in the

ion source An ion source is a device that creates atomic and molecular ions. Ion sources are used to form ions for mass spectrometers, optical emission spectrometers, particle accelerators, ion implanters and ion engines. Electron ionization Elect ...

(in-source fragmentation) where it has been used with electron ionization to help identify molecules and, recently (2020), with electrospray ionization it has been shown to provide the same benefit in facilitating molecular identification. Prior to these experiments, electrospray ionization in-source fragmentation was generally considered an undesired effect however, electrospray ionization using Enhanced In-Source Fragmentation/Annotation (EISA) has been shown to promote in-source fragmentation that creates fragment ions that are consistent with tandem mass spectrometers. Tandem mass spectrometry-generated fragmentation is typically made in the collision zone (post-source fragmentation) of a tandem mass spectrometer. EISA and collision-induced dissociation (CID) among other physical events that impact ions are a part of gas-phase ion chemistry. A few different types of mass fragmentation are

collision-induced dissociation Collision-induced dissociation (CID), also known as collisionally activated dissociation (CAD), is a mass spectrometry technique to induce fragmentation (chemistry), fragmentation of selected ions in the gas phase. The selected ions (typically m ...

(CID) through collision with neutral molecule,

surface-induced dissociation Tandem mass spectrometry, also known as MS/MS or MS2, is a technique in instrumental analysis where two or more stages of analysis using one or more mass spectrometry, mass analyzer are performed with an additional reaction step in between these ...

(SID) using fast moving ions collision with a solid surface, laser induced dissociation which uses laser to induce the ion formation, electron-capture dissociation (ECD) due to capturing of low energy electrons, electron-transfer dissociation (ETD) through electron transfer between ions, negative electron-transfer dissociation (NETD), electron-detachment dissociation (EDD), photodissociation, particularly infrared multiphoton dissociation (IRMPD) using IR radiation for the bombardment and blackbody infrared radiative dissociation (BIRD) which use IR radiation instead of laser, higher-energy C-trap dissociation (HCD), EISA, and charge remote fragmentation.

Fragmentation reactions

Fragmentation is a type of chemical dissociation, in which the removal of the electron from the molecule results in ionization. Removal of electrons from either sigma bond, pi bond or nonbonding orbitals causes the ionization. This can take place by a process of homolytic cleavage or homolysis or heterolytic cleavage or heterolysis of the bond. Relative bond energy and the ability to undergo favorable cyclic transition states affect the fragmentation process. Rules for the basic fragmentation processes are given by Stevenson's Rule. Two major categories of bond cleavage patterns are simple bond cleavage reactions and rearrangement reactions.

Simple bond cleavage reactions

Majority of organic compounds undergo simple bond cleavage reactions, in which direct cleavage of bond take place. Sigma bond cleavage, radical site-initiated fragmentation, and charge site-initiated fragmentation are few types of simple bond cleavage reactions. Sigma bond cleavage example

Sigma bond cleavage / σ-cleavage

Sigma bond cleavage is most commonly observed in molecules that can produce stable cations, such as saturated

alkane In organic chemistry, an alkane, or paraffin (a historical trivial name that also has other meanings), is an acyclic saturated hydrocarbon. In other words, an alkane consists of hydrogen and carbon atoms arranged in a tree structure in whi ...

s or secondary and tertiary

carbocation Carbocation is a general term for ions with a positively charged carbon atom. In the present-day definition given by the IUPAC, a carbocation is any even-electron cation with significant partial positive charge on a carbon atom. They are further ...

s. This occurs when an alpha electron is removed. The C-C bond elongates and weakens causing fragmentation. Fragmentation at this site produces a charged and a radical fragment. Radical site initiated

Radical site-initiated fragmentation

Sigma bond cleavage also occurs on radical cations remote from the site of ionization. This is commonly observed in

alcohols In chemistry, an alcohol (), is a type of organic compound that carries at least one hydroxyl () functional group bound to a Saturated and unsaturated compounds, saturated carbon atom. Alcohols range from the simple, like methanol and ethanol ...

ether In organic chemistry, ethers are a class of compounds that contain an ether group, a single oxygen atom bonded to two separate carbon atoms, each part of an organyl group (e.g., alkyl or aryl). They have the general formula , where R and R� ...

ketone In organic chemistry, a ketone is an organic compound with the structure , where R and R' can be a variety of carbon-containing substituents. Ketones contain a carbonyl group (a carbon-oxygen double bond C=O). The simplest ketone is acetone ( ...

ester In chemistry, an ester is a compound derived from an acid (either organic or inorganic) in which the hydrogen atom (H) of at least one acidic hydroxyl group () of that acid is replaced by an organyl group (R). These compounds contain a distin ...

amine In chemistry, amines (, ) are organic compounds that contain carbon-nitrogen bonds. Amines are formed when one or more hydrogen atoms in ammonia are replaced by alkyl or aryl groups. The nitrogen atom in an amine possesses a lone pair of elec ...

alkene In organic chemistry, an alkene, or olefin, is a hydrocarbon containing a carbon–carbon double bond. The double bond may be internal or at the terminal position. Terminal alkenes are also known as Alpha-olefin, α-olefins. The Internationa ...

s, and aromatic compounds with a carbon attached to ring. The cation has a radical on a

heteroatom In chemistry, a heteroatom () is, strictly, any atom that is not carbon or hydrogen. Organic chemistry In practice, the term is mainly used more specifically to indicate that non-carbon atoms have replaced carbon in the backbone of the molecular ...

or an unsaturated functional group. The driving force of fragmentation is the strong tendency of the radical ion for electron pairing. Cleavage occurs when the radical and an odd electron from the bonds adjacent to the radical migrate to form a bond between the alpha carbon and either the heteroatom or the unsaturated functional group. The sigma bond breaks; hence this cleavage is also known as homolytic bond cleavage or α-cleavage.

Charge site-initiated cleavage

The driving force of charge site-initiated fragmentation is the inductive effect of the charge site in radical cations. The electrons from the bond adjacent to the charge-bearing atom migrate to that atom, neutralizing the original charge and causing it to move to a different site. This term is also called inductive cleavage and is an example of heterolytic bond cleavage.

Rearrangement reactions

Rearrangement reactions are fragmentation reactions that form new bonds producing an intermediate structure before cleavage. One of the most studied rearrangement reaction is the McLafferty rearrangement / γ-hydrogen rearrangement. This occurs in the radical cations with unsaturated functional groups, like

aldehyde In organic chemistry, an aldehyde () (lat. ''al''cohol ''dehyd''rogenatum, dehydrogenated alcohol) is an organic compound containing a functional group with the structure . The functional group itself (without the "R" side chain) can be referred ...

carboxylic acids In organic chemistry, a carboxylic acid is an organic acid that contains a carboxyl group () attached to an Substituent, R-group. The general formula of a carboxylic acid is often written as or , sometimes as with R referring to an organyl ...

amide In organic chemistry, an amide, also known as an organic amide or a carboxamide, is a chemical compound, compound with the general formula , where R, R', and R″ represent any group, typically organyl functional group, groups or hydrogen at ...

s, olefins, phenylalkanes. During this reaction, γ-hydrogen will transfer to the functional group at first and then subsequent α, β-bond cleavage of the intermediate will take place. Other rearrangement reactions include heterocyclic ring fission (HRF), benzofuran forming fission (BFF), quinone methide (QM) fission or Retro Diels-Alder (RDA).

References

External links

Fragmentation patterns in the mass spectra of organic compounds

A tutorial in small molecule identification via electrospray ionization-mass spectrometry: The practical art of structural elucidation
{{Mass spectrometry Tandem mass spectrometry