Q.4. (b) Recognition of molecular ion and its role in structure determination
Ans.4. (b)Recognition of molecular ion The molecular formula is usually the most important piece of information which one drives from the mass spectrum of an organic compound. Thus it becomes very necessary to identify the molecular ion. The ion cluster which appears at highest m/z value most likely represents the molecular ion with its attendant M+1, M+2 peaks, etc. often, the molecular ions of at least 20 per cent of the organic compounds. E.g. Alcohols, Amines decompose very rapidly so as to either escape detection (In a routine 70 eV spectrum) or may be very weak. One, therefore, applies the following tests to detect the molecular ion from the EI mass spectra, i.e., the spectra which are routinely obtained via electro impact.
1. Intensity of Molecular Ion Peak: The intensity of the molecular ion peak in a mass spectrum depends on the type of the compound.The abundant molecular ions are given by aryl amines, nitrites, fluorides and chlorides. In case no side chain of C2 or longer is present, the aromatic hydrocarbons and heteroatom compounds give strong molecular ion peaks (e.g., in toluene). An extremely weak molecular ion peak or its absence indicates highly branched molecules, when the molecular ion fragments completely before detection.
2. Index of Hydrogen Deficiency: The ion has to be an odd-electron ion, because the molecular ion is produced by loss of one electron from the neutral molecule, the converse however, is not true since there may well be odd-electron ions other than the molecular ion in the spectrum, arising from rearrangement reactions. When the elemental composition of the ion can be determined, the index of hydrogen deficiency (the sum of multiple bonds and ring systems) may be used to know if the ion is an odd-electron ion. The index of hydrogen deficiency is the number of pairs of hydrogen atoms which must be removed from the saturated open-chain formula (eg, CnH2n+2 for alkanes) to give the observed molecular formula. The index of hydrogen deficiency is then the sum of the number of rings, the no. of double bonds and twice the no. of triple bonds. For a molecule IyIInIIIzIVx, the index of hydrogen deficiency = x-y/2 + z/2 + 1
Where I = any monovalent atom
II = O, S or any other divalent atom
III = N, P or any other trivalent atom
IV = C, Si or any other tetravalent atom
Eg, Thiophen, C4H4S has an index of hydrogen deficiency of (4 - 4/2 + 1) = 3
3. Nitrogen Rule: Nitrogen rule states that the compounds containing an even number of nitrogen atoms (zero in an even no.) will give a molecular ion with an even mass number. For e.g., the following compounds give their molecular ions at even mass numbers: CH4 (m/z = 16); CH3OH (m/z = 32); CClF3 (m/z = 104). An odd no. of nitrogen atoms causes the molecular ion to be at odd mass no., e.g., NH3 (m/z = 17); C2H5NH2 (m/z = 45).It is important to note that this relationship applies to all ions and not only to the molecular ion. In other words, therefore the nitrogen rule may be stated as: an odd electron ion will be at an even mass no. if it contains an even no. of nitrogen atoms. In the same way, an even electron ion with an even no. of nitrogen atoms will appear at an odd mass no. (M+ is an odd electron ion).
4. Detection of molecular ion: That an ion is indeed the molecular ion may be known by inspecting the fragment ion peaks in the vicinity of the ion. Mass losses of between 3 & 15 and between 20 & 26 are very unlikely, and if they are observed would suggest that the putative molecular ion is in fact a fragment ion. On the other hand, losses of H. (M-1 peak) and CH3.(M-15 peak), i.e., losses of 1 and 15 mass units are commonly observed for molecular ions of common organic compounds. Similarly the presences of an M-18 peak (loss of water) or an M-31 peak (loss of OCH3 from methyl esters) again confirm the molecular ion peak.
5. Chemical Ionization (CI) Technique- Location of Molecular Ion: In addition to electron impact (EI method), one can obtain and locate the molecular ion for compounds which give very weak or non-existent molecular ions. The chemical ionization (CI) technique is very promising and often the EI and CI mass spectra are recorded routinely as these are complimentary. The chemical ionization (CI) method is thus also used for volatile compounds which can help to locate the molecular ion via [M+1]+peak with little fragmentation. In CI method the organic compound RH is introduced along with a carrier gas such as methane (other carrier gases are isobutene and ammonia). The initially formed primary ions from methane like CH4++, CH3+, etc. react with methane to yield secondary ions, e.g.,
In an acid base type reaction, a secondary ion like CH5+ is an energetic proton transfer reagent which reacts with the organic compound R-H to give RH2+.
6. Field Desorption (FD) Technique: The ionization methods described so far, EI and CI are limited to volatile samples. Field desorption (FD) or desorption ionization (DI) remove this limitation and allow the mass spectra to be recorded for samples in the condensed phase and provide a means to ionize non-volatile samples with high molecular weight. Thus by this method stable molecular ions are obtained from a sample of low volatility which is deposited directly on the anode of a pair of electrodes. The intense electric field brings about ionization and desorption as well. Molecular and quasimolecular ions are formed (e.g., from carbohydrates) with insufficient internal energyfor extensive fragmentation.
7. Fast Atom Bombardment (FAB): Polar molecules such as peptides are analysed by dissolving the compound in a high boiling viscous solvent e.g., glycerol. A drop is placed on a metal sheet and the ionization is achieved by the high energy beam of xenon atoms. The role of the solvent is to promote the ionization and diffusion of fresh sample to the surface. The molecular ion itself is not normally seen, but adduct ions like [M+H]+ are prominent (due to ion, molecule interactions similar to CI technique).
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