Fragmentation Pattern In Mass Spectrometry

 Fragmentation Pattern In Mass Spectrometry

Mass Spectrometry

In order to determine the mass-to-charge ratio (m/z) of one or more molecules in a sample, mass spectrometry is a valuable analytical instrument. The precise molecular weight of the sample's constituent parts can frequently be determined using these measures as well.

Fragmentation in mass spectrometry is the dissociation of energetically unstable molecular ions created when molecules pass through an instrument's ionization chamber. A molecule's fragments result in a distinctive pattern in the mass spectrum.

A recent study has concentrated on the fragmentation that happens during tandem mass spectrometry investigations since this information makes molecular identification easier.

Fragmentation

Fragmentation is a sort of chemical dissociation in which an electron is removed from a molecule, resulting in ionization. Ionization is brought on by the removal of electrons from sigma bonds, pi bonds, or nonbonding orbitals. This can happen by the bond's homolytic cleavage, homolysis, heterolytic cleavage, or heterolysis. The fragmentation process is influenced by relative bond energy and the capacity for advantageous cyclic transition states. Stevenson's Rule outlines the primary fragmentation mechanisms.

Simple bond cleavage reactions and rearrangement reactions are two major groups of bond cleavage patterns.

Fragmentation pattern

Fragmentation reactions

Simple reactions that cleave bonds

The majority of organic molecules proceed via simple bond cleavage reactions, which involve direct bond cleavage. Among the many different kinds of straightforward bond cleavage reactions are sigma bond cleavage, radical site-initiated fragmentation, and charge site-initiated fragmentation.

Cleavage of the sigma bond

The most frequent occurrence of sigma bond breakage is found in molecules that can create stable cations like saturated alkanes, secondary, and tertiary carbocations. When an alpha electron is taken away, this happens. As the C-C bond lengthens and deteriorates, fragmentation results. At this location, fragmentation yields both charged and neutral fragments.

Alpha Fission

Site-initiated radical fragmentation, Homolytic cleavage

Sigma bond cleavage can also occur on radical cations that are not ionized. Alcohols, ethers, ketones, esters, amines, alkenes, and aromatic compounds with a carbon linked to the ring are examples of substances where this is frequently seen. A radical on a heteroatom or an unsaturated functional group is present in the cation. The radical ion's significant propensity for electron pairing acts as the catalyst for fragmentation. When the radical and an odd electron from bonds next to the radical move to create a bond with the heteroatom or unsaturated functional group, this is known as cleavage. This cleavage, sometimes referred to as homolytic bond cleavage or -cleavage, occurs when the sigma bond breaks.

Heterolytic Cleavage

The inductive impact of the charge site in radical cations is what propels fragmentation that is triggered by the charge site. The charge-bearing atom receives electrons from the bond next to it, which causes the charge to become neutral and shift to a different location. This process is an illustration of heterolytic bond cleavage and is also known as inductive cleavage.

McLafferty Rearrangement reactions

Rearrangement reactions are fragmentation reactions that create new bonds and an intermediate structure prior to cleavage. The McLafferty rearrangement/-hydrogen rearrangement is one of the most researched rearrangement reactions. This happens when radical cations, such as ketones, aldehydes, carboxylic acids, esters, amides, olefins, and phenylalkanes, have unsaturated functional groups. The functional group will initially receive -hydrogen during this reaction, and the intermediate will then undergo -bond cleavage.  

McLafferty Rearrangement

Fragmentation Rules

1. The straight chain compound has the highest relative height of the molecular ion peak, which then falls.

2. In a homologous series, the relative height of the molecular ion peak often declines as molecular weight increases. The apparent exception is fatty esters.

3.Cleavage occurs preferentially at alkyl-substituted carbon atoms; the more substituted, the higher the likelihood of cleavage. This results from tertiary carbocations being more stable than secondary carbocations, which are more stable than primary carbocations.

Tertiary > Secondary >Primary> Methyl Group

4. The molecular ion is stabilized by double bonds, cyclic structures, and particularly aromatic (or heteroaromatic) rings, which raises the likelihood of their appearance.

5. The resonance-stabilized allylic carbocation is produced by double bonds, which favor allylic cleavage. Due to the ready migration of the double bond, this rule does not apply to simple alkenes, but it does apply to cycloalkenes.

Allylic carbon

The allylic carbon is connected to a carbon atom, which is doubly bound to another carbon atom. The allylic carbon atom is represented by the asterisk in the generic formula for allyl, which is R-CH2-CH=CH2. In contrast to the vinyl group, the allylic carbon atom is sp3 hybridised since it formed a single covalent bond with CH=CH2.

6.Alkyl side chains typically disappear from saturation rings at the bond. This is essentially an exception to branching (rule 3). The ring fragment usually retains its positive charge. A retro Diels-Alder reaction can occur in an unsaturated ring.

7. Cleavage at the bond to the ring in alkyl-substituted aromatic compounds is very likely to result in the resonance-stabilized benzyl ion or, more likely, the tropylium ion. See diagram below.

8. The charge is frequently left on the fragment containing the heteroatom, whose nonbonding electrons offer resonance stabilization, when the C-C bonds close to it break. See below in picture.

9. Cleavage is frequently accompanied by rearrangement and the removal of tiny, stable, neutral molecules such alcohols, mercaptans, olefins, water, ammonia, hydrogen cyanide, hydrogen sulphide, or carbon monoxide.

Nitrogen Rule

Any molecule (with all paired electrons) containing an odd number of nitrogen atoms will have an odd nominal mass, according to the nitrogen rule. The integer mass of an atom, ion, or molecule made up exclusively of the most stable isotope is known as the nominal mass (s).

This rule is used when molecules have only carbon, Nitrogen, Hydrogen, Oxygen, and Halogen atoms.

Here below are examples that are helpful for understanding the Nitrogen rule, you will be able to find out the molecular formula of the unknown compound by using this rule.

Compounds containing an even or odd number of nitrogen atoms their molecular weight will also be even or odd respectively. Even or no nitrogen atom in molecules means its molecular weight will be even.