In mass spectrometry, fragmentation is the

dissociation Dissociation, in the wide sense of the word, is an act of disuniting or separating a complex object into parts. Dissociation may also refer to: * Dissociation (chemistry), general process in which molecules or ionic compounds (complexes, or salts) ...

of energetically unstable molecular ions formed from passing the molecules in the ionization chamber of a mass spectrometer. The fragments of a molecule cause a unique pattern in the

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 pattern is useful to determine the molar weight and structural information of the unknown molecule. 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 Electron ...

(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 Tandem mass spectrometry, also known as MS/MS or MS2, is a technique in instrumental analysis where two or more mass analyzers are coupled together using an additional reaction step to increase their abilities to analyse chemical samples. A comm ...

. EISA and collision-induced dissociation (CID) among other physical events that impact ions are a part of

gas-phase ion chemistry Gas phase ion chemistry is a field of science encompassed within both chemistry and physics. It is the science that studies ions and molecules in the gas phase, most often enabled by some form of mass spectrometry. By far the most important appl ...

. 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 of selected ions in the gas phase. The selected ions (typically molecular ions or protonated ...

(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 mass analyzers are coupled together using an additional reaction step to increase their abilities to analyse chemical samples. A comm ...

(SID) using fast moving ions collision with a solid surface, laser induced dissociation which uses laser to induce the ion formation,

electron-capture dissociation Electron-capture dissociation (ECD) is a method of fragmenting gas-phase ions for structure elucidation of peptides and proteins in tandem mass spectrometry. It is one of the most widely used techniques for activation and dissociation of mass sel ...

(ECD) due to capturing of low energy electrons,

electron-transfer dissociation Electron-transfer dissociation (ETD) is a method of fragmenting multiply-charged gaseous macromolecules in a mass spectrometer between the stages of tandem mass spectrometry (MS/MS). Similar to electron-capture dissociation, ETD induces fragment ...

(ETD) through electron transfer between ions,

negative electron-transfer dissociation Tandem mass spectrometry, also known as MS/MS or MS2, is a technique in instrumental analysis where two or more mass spectrometry, mass analyzers are coupled together using an additional reaction step to increase their abilities to Analytical chem ...

(NETD),

electron-detachment dissociation Tandem mass spectrometry, also known as MS/MS or MS2, is a technique in instrumental analysis where two or more mass analyzers are coupled together using an additional reaction step to increase their abilities to analyse chemical samples. A comm ...

(EDD),

photodissociation Photodissociation, photolysis, photodecomposition, or photofragmentation is a chemical reaction in which molecules of a chemical compound are broken down by photons. It is defined as the interaction of one or more photons with one target molecule. ...

, particularly

infrared multiphoton dissociation Infrared multiple photon dissociation (IRMPD) is a technique used in mass spectrometry to fragment molecules in the gas phase usually for structural analysis of the original (parent) molecule. How it works An infrared laser is directed through ...

(IRMPD) using IR radiation for the bombardment and

blackbody infrared radiative dissociation Tandem mass spectrometry, also known as MS/MS or MS2, is a technique in instrumental analysis where two or more mass analyzers are coupled together using an additional reaction step to increase their abilities to analyse chemical samples. A com ...

(BIRD) which use IR radiation instead of laser,

higher-energy C-trap dissociation Collision-induced dissociation (CID), also known as collisionally activated dissociation (CAD), is a mass spectrometry technique to induce fragmentation of selected ions in the gas phase. The selected ions (typically molecular ions or protonate ...

(HCD), EISA, and

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

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. Homolysis (Chemistry) V

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, which 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 which ...

s, secondary and tertiary

carbocation A carbocation is an ion with a positively charged carbon atom. Among the simplest examples are the methenium , methanium and vinyl cations. Occasionally, carbocations that bear more than one positively charged carbon atom are also encountere ...

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 neutral 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 carbon atom. The term ''alcohol'' originally referred to the primary alcohol ethanol (ethyl alcohol), which is ...

ether In organic chemistry, ethers are a class of compounds that contain an ether group—an oxygen atom connected to two alkyl or aryl groups. They have the general formula , where R and R′ represent the alkyl or aryl groups. Ethers can again be c ...

ketone In organic chemistry, a ketone is a functional group with the structure R–C(=O)–R', where R and R' can be a variety of carbon-containing substituents. Ketones contain a carbonyl group –C(=O)– (which contains a carbon-oxygen double bo ...

ester In chemistry, an ester is a compound derived from an oxoacid (organic or inorganic) in which at least one hydroxyl group () is replaced by an alkoxy group (), as in the substitution reaction of a carboxylic acid and an alcohol. Glycerides ar ...

amine In chemistry, amines (, ) are compounds and functional groups that contain a basic nitrogen atom with a lone pair. Amines are formally derivatives of ammonia (), wherein one or more hydrogen atoms have been replaced by a substituen ...

alkene In organic chemistry, an alkene is a hydrocarbon containing a carbon–carbon double bond. Alkene is often used as synonym of olefin, that is, any hydrocarbon containing one or more double bonds.H. Stephen Stoker (2015): General, Organic, an ...

s, and

aromatic compound Aromatic compounds, also known as "mono- and polycyclic aromatic hydrocarbons", are organic compounds containing one or more aromatic rings. The parent member of aromatic compounds is benzene. The word "aromatic" originates from the past grouping ...

s 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 usually used more specifically to indicate that non-carbon atoms have replaced carbon in the backbone of the molecula ...

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. charged

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 Inductive cleavage, in organic chemistry, is the charge-initiated counterpoint to radical initiated alpha-cleavage. Since inductive cleavage does not require unpairing and re-pairing electrons it can occur at both radical cationic and cationic site ...

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 The McLafferty rearrangement is a reaction observed in mass spectrometry during the fragmentation or dissociation of organic molecules. It is sometimes found that a molecule containing a keto-group undergoes β-cleavage, with the gain of the γ-hyd ...

/ γ-hydrogen rearrangement. This occurs in the radical cations with unsaturated functional groups, like

aldehyde In organic chemistry, an aldehyde () is an organic compound containing a functional group with the structure . The functional group itself (without the "R" side chain) can be referred to as an aldehyde but can also be classified as a formyl grou ...

carboxylic acids In organic chemistry, a carboxylic acid is an organic acid that contains a carboxyl group () attached to an R-group. The general formula of a carboxylic acid is or , with R referring to the alkyl, alkenyl, aryl, or other group. Carboxylic ...

amide In organic chemistry, an amide, also known as an organic amide or a carboxamide, is a compound with the general formula , where R, R', and R″ represent organic groups or hydrogen atoms. The amide group is called a peptide bond when it is ...

olefin In organic chemistry, an alkene is a hydrocarbon containing a carbon–carbon double bond. Alkene is often used as synonym of olefin, that is, any hydrocarbon containing one or more double bonds.H. Stephen Stoker (2015): General, Organic, an ...

s, 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 A quinone methide is a type of conjugated organic compound that contain a cyclohexadiene with a carbonyl and an exocyclic methylidene or extended alkene unit. It is analogous to a quinone, but having one of the double bonded oxygens replaced wit ...

(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