FRAGMENTATION

When a molecule has been bombarded by high energy electrons in the ionization chamber of a mass spectrometer, besides losing one electron to form an ion, the molecule also absorbs some of the energy transferred in its collision with the incident electrons. This extra energy places the molecular ion may be unstable and it may lose some of its extra energy by breaking apart into fragments. If the life time of the molecular ion is greater than 10-5 seconds, a peak corresponding to the molecular ion appears in the spectrum. However, molecular ions with lifetimes less than 10-5 seconds break apart into fragments before they are accelerated with in the ionization chamber. In such cases, peaks corresponding to mass to charge ratios for these fragments appear in the mass spectrum. For a given compound, not all of the molecular ions formed by ionization have precisely the same life time, some may have shorter lifetime than others. As a result, in a spectrum one usually observes peaks corresponding to both the molecular ion and the fragments. Electron bombardment with energy 10 15 eV usually removes one electron from the molecule of the organic compound in the vapour phase. It results in the formation of molecular ion i.e. no fragmentation of the parent ion takes place. The highest occupied orbital of aromatic system and non bonding electron orbitals on oxygen and nitrogen atom readily lose one electron. An electron from double bond or triple bond is usually lost. In alkanes, the ionization of c-c sigma bonds is easier than that of C-H bonds. But if energy of bombarding electron is around 70 eV, then additional energy is consumed in fragmenting the parent ion. This results in the formation of fragment ions or the daughter ions.

GENERAL FRAGMENTATION MODES

Important fragmentation modes are described below

1. SIMPLE CLEAVAGE

This process involves homolytic or heterolytic cleavage of a single covalent bond. A) HOMOLYTIC CLEAVAGE I. Mode l This fragmentation mode operates in compounds in which a hetero atom is singly bonded to a carbon atom. A new bond is formed with the adjacent atom through the donation of the unpaired electrons and the transfer of an electron from the adjacent bond.

This is seen in case of alcohols, amines, ethers etc. E.g. Cleavage in 2 butanol

Most abundant peaks are formed by the cleavage of carbon carbon bond which is in the position to the hetero atom. II. Mode ll When a hetero atom is attached to a carbon atom by a double bond, cleavage is the preferred fragmentation mode. This type of fragmentation is shown by many compounds such as ketones, esters etc.

In ketones, significant peaks are observed due to the cleavage of carbon carbon bond which is alpha to the carbonyl group. Unsymmetrical ketones show two types of peaks since either alkyl group can be lost. The elimination of a bigger alkyl radical is preferred. In the same way, the fragmentation mode in 2

aldehydes, esters and amides leads to the cleavage of C-H, C-O, C-N bond respectively. III. Mode lll Benzylic cleavage is an energetically preferred fragmentation mode. It involves the cleavage of a carbon carbon bond which is beta to the aromatic ring. B) HETEROLYTIC CLEAVAGE Cleavage of C-X ( X = O, N, S, Cl ) bond is more difficult than that of a C - C bond. In such cleavage, the positive charge is carried by the carbon and not by the hetero atom. In case of alkyl halides, As the size of the halogen atom increases, the C X bond becomes weak. E.g. C X bond in alkyl bromides and iodides are easily broken while alkyl chlorides are less susceptible to fragmentation so that elimination of HCl occurs. In ethers, cleavage of C O bond leads to the formation of an alkyl ion rather than an alkoxy ion.

2. RETRO DIELS ALDER REACTION

The reaction is an example of multi centered fragmentation which is characteristic of cyclic olefins It involves cleavage of two bonds of a cyclic system resulting in the formation of two stable unsaturated fragments in which two new bonds are formed. This process is not accompanied by hydrogen transfer rearrangement. The charge can be carried by any one of the fragments. The more highly substituted or more conjugated fragment which has lower ionization potential carries a charge. In simple system, charge is carried by a diene.

3. HYDROGEN TRANSFER REARRANGEMENTS

The simplest rearrangement involves the transfer of a hydrogen atom from one part of the molecule to another. These processes are very common in mass spectrometry. These involve intra molecular hydrogen transfer rearrangement in aliphatic hydrocarbons and aromatic compounds. E.g. 1. Hydrogen transfers from ortho position in benzoic acid prior to fragmentation.

2. Elimination of ketene is a characteristic fragmentation mode of n-alkyl amides and o-acetate of phenols

3. In ortho substituted aromatic compounds or in cis olefins, the substituent and a hydrogen atom can come in close proximity so as to eliminate a neutral molecule.

 Such an elimination distinguishes 1) between cis and trans isomers 2) ortho substituted compound from meta and para substituted isomers. 4. Mc LAFFERTY REARRANGEMENT This arrangement involves the cleavage of a beta bond followed by a gamma hydrogen transfer. The rearrangement leads to the elimination of neutral molecules from aldehydes, ketones, amines, unsaturated compounds, substituted aromatic compounds etc. The rearrangement proceeds through a sterically hindered six membered transition state.

5.

Similarly, a large number of organic compounds, via. Ketones, amines, alcohols, esters, acids which contain a gamma hydrogen atom forms a Mc Lafferty rearrangement ion.

MASS SPECTRUM
RECORDING OF A MASS SPECTRUM
First of all, the sample is introduced into the ionization chamber very slowly to produce positive mass particles. Then the accelerating voltage V is adjusted to a high voltage to accelerate the mass particles to a high velocity. Under these conditions only particles with the lowest mass number reach the collector and are counted. The accelerating voltage V is then progressively decreased so that mass numbers reaching the collector simultaneously increase. When V becomes zero, the record of the distribution of the masses in the sample is complete and is presented as a mass spectrogram. The sequence in which the particle hit the detector follows equation which is as follows

PRESENTATION OF DATA
1. The mass spectrum is presented in terms of ion abundance vs. m/e ratio . 2. The most abundant ion formed in ionization gives rise to the tallest peak on the mass spectrum this is the base peak. Its relative intensity or abundance is taken as 100. The tallest peak comes from the most stable species.

3. All other peak intensities are relative to the base peak as a percentage.

- M/Z is a dimensionless ratio of the mass number of the given particle to the number (Z) of the charge carried by the particle. Usually the particle is singly charged and ratio is expressed as M/e. doubly charged particles are insignificant in the mass spectra of organic compounds. But the peak corresponding to stable doubly charged ions may be sometime useful. - The relative abundance of the given ions tells its intensity relative to the base peak. 4. If a molecule loses only one electron in the ionization process, a molecular ion is observed that gives its molecular weight this is designated as M+ on the spectrum or parent peak. Highest M/Z usually corresponds to the molecular ion.

5. In most cases, when a molecule loses a valence electron, bonds are broken, or the ion formed quickly fragment to lower energy ions. 6.The masses of charged ions are recorded as fragment ions by the spectrometer neutral fragments are not recorded !

DETERMINATION OF MOLECULAR MASS

1. When a M+ peak is observed it gives the molecular mass assuming that every atom is in its most abundant isotopic form - carbon is a mixture of 98.9% 12C (mass 12), 1.1% 13C (mass 13) and <0.1% 14C (mass 14) - The mass spectrometer, by its very nature would see a peak at mass 12 for atomic carbon and a M + 1 peak at 13 that would be 1.1% as high.

CONFIRMATION OF RECOGNIZED MOLECULAR PEAK

1. NITROGEN RULE This rule given by Beynon (1960) states that a molecule containing an even number of nitrogen atoms or no nitrogen has even numbered molecular mass; an odd number of nitrogen atoms require an odd numbered molecular mass. This rule holds for all compounds contains carbon, hydrogen sulphur, boron, silicon, arsenic, halogen and alkaline earths.