Mass spectroscopy (advanced spectral analysis)

mass spectroscopy

1. Mass spectrometry Submitted To- Submitted By- Dr. Rakesh Kumar Marwaha Mayank Mehendiratta Associate Professor 1114 Department Of Pharmaceutical Sciences M.pharm-2 nd sem. M.D.U. Rohtak

2. Introduction It is the most accurate method for determining the molecular mass of compound. In this technique, molecules are bombarded with a beam of energetic electron. Molecules get converted into highly charged positively charge ion which is called molecular ion or parent ion. Parent ion further break into smaller ion called as daughter ion. Formed ions are separated according to their charge to mass ratio on applying magnetic field.

3. TERMS & DEFINITION METASTABLE ION- The ion that have sufficient energy to fragment some time after leaving the ion source but before arriving at the detector. Consider M1 is the parent ion m1+ is the daughter ion and this daughter ion formed reach the detector region and recorded as m1+ . If the above mentioned process just before reaching the detector then ion formed is metastable ion. Metastable ion are rarely formed and they form broad peaks in the spectra.

4. Isotopic peaks- Isotopes are the compounds which have the same atomic number but different mass number. Ex- hydrogen, carbon. Many elements have natural isotopes. For ex- Chlorine with mass no -37 in addition to chlorine-35. Presence of isotopes readily produce isotopic ion accompanied by molecular ion and fragment ion peak. Isotopic peaks are less intense.

5. Ring rule If the molecular formula of a compound is known the number of unsaturation can be calculated by RING RULE. According to this rule, the number of unsaturated sites ‘R’ is equal to number of rings in the molecule plus the number of double bond plus twice the number of triple bond. Molecular formula C w H X N Y O Z may be stated as- R=W+1+Y-X/2 Applying ring rule of benzene W=6 R=6 Y=0 Z=0 Thus R=6+1-3=4 Thus, Benzene has 1 ring and 3 double bonds.

6. Example- Diethyl Ether R=4+1-5=0 It shows that it has no rings as well as no double bond.

7. General rules for mass fragmenTATION In mass spectrometry,  fragmentation  is the  dissociation  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 . 1. The relative height of the molecular ion peak is greatest for the straight chain compound and decreases as the degree of branching increases. 2. The relative height of the molecular ion peak usually decreases with increasing molecular weight in a homologous series. Fatty esters appear to be an exception. If we compare the peak of octane and butane molecular peak of octane is less intense than butane.

8. 3. Cleavage is favoured at alkyl-substituted carbon atoms; the more substituted, the more likely is cleavage. This is a consequence of the increased stability of a tertiary carbocation over a secondary, which in turn is more stable than a primary. 4. Double bond, cyclic structure, and especially aromatic (or heteroaromatic ) rings stabilize the molecular ion and thus increase the probability of its appearance.

9. Double bonds favour allylic cleavage and give the resonance-stabilized allylic carbocation. This rule does not hold for simple alkenes because of the ready migration of the double bond, but it does hold for cycloalkenes .

10. Saturated rings tends to lose alkyl side chains at α bond. This is merely a special case of branching (rule 3). The positive charge tends to stay with the ring fragment. Unsaturated ring can undergo a retro Diels- Alder reaction.

11. In alkyl-substituted aromatic compounds, cleavage is very probable at the bond β to the ring, giving the resonance-stabilized benzyl ion or, more likely, the tropylium ion.

12.  Cleavage is often associated with elimination of small, stable, neutral molecule, such as carbon monoxide, olefins, water, ammonia, hydrogen sulphide, hydrogen cyanide, mercaptans , ketene, or alcohols, often with rearrangement .   The C-C bonds next to a heteroatom are frequently cleaved, leaving the charge on the fragment containing the heteroatom whose nonbonding electrons provide resonance stabilization .

13. Mc lafferty rearrangement In this rearrangement, Gamma hydrogen atom which is 3 atom away from radical cation is transferred to charged site via 6 membered transition state with concurrent cleavage of sigma bond between alpha and beta carbon.

14. Note- This rearrangement is shown by only compounds pie- electron,non bonding on hetero atom and gamma hydrogen.

15. FRAGMENTATION PATTERN ALKANES- For a straight-chain, or “normal,” alkane, a peak corresponding to the molecular ion can be observed as in the mass spectra of butane and octane. As the carbon skeleton becomes more highly branched, the intensity of the molecular ion peak decreases. Straight-chain alkanes have fragments that are always primary carbocations . Since these ions are rather unstable, fragmentation is not favoured. IF you compare the mass spectrum of butane with that of isobutane . The molecular ion peak in isobutane is much less intense than that in butane.

16. MASS SPECTRUM OF BUTANE

17. MASS SPECTRUM OF OCTANE

18. MASS SPECTRUM OF ISOBUTANE

19. ALCOHOLS - The intensity of the molecular ion peak in the mass spectrum of a primary or secondary alcohol is usually rather low, and the molecular ion peak is often entirely absent in the mass spectrum of a tertiary alcohol. The number of fragmentation modes in alcohol depend upon whether it is primary,secondary or tertiary alcohol. Common fragmentations of alcohols are α-cleavage adjacent to the hydroxyl group and dehydration. The mass spectrum of straight-chain pentanol isomers, 1-pentanol, 2-pentanol and 3-pentanol all exhibit very weak molecular ion peaks at m / z = 88, while the molecular ion in the mass spectrum of the tertiary alcohol 2-methyl-2-butanol is entirely absent .

20. Mass Spectrum of Pentan-2-ol Mass spectrum of Pentan-3-ol

21. A second common mode of fragmentation involves dehydration. The importance of dehydration increases as the chain length of the alcohol increases. While the fragment ion peak resulting from dehydration ( m / z = 70) is very intense in the mass spectrum of 1-pentanol, it is quite weak in the other pentanol isomers. Dehydration may occur by either thermal dehydration prior to ionization or by fragmentation of the molecular ion . Thermal dehydration is a 1,2 - elimination of water. If the alcohol molecules reach the ion source intact, however, dehydration of the molecular ion can still occur, but in this case it is a 1,4-elimination of water via a cyclic mechanism:

22. Amines - in the case of aliphatic amines, the molecular ion peak may be very weak or even absent . The most intense peak in the mass spectrum of an aliphatic amine arises from α-cleavage. When there is a choice of R groups to be lost through this process, the largest R group is lost preferentially .

23. ALDEHYDES- The molecular ion peak of an aliphatic aldehyde is usually observable, although at times it may be fairly weak. Principal modes of fragmentation include α-cleavage and β-cleavage. If the carbon chain attached to the carbonyl group contains at least three carbons, McLafferty rearrangement is also commonly observed . Beta-cleavage

24. Ketones - The mass spectra of ketones show an intense molecular ion peak. Loss of the alkyl groups attached to the carbonyl group is one of the most important fragmentation processes. The pattern of fragmentation is similar to that of aldehydes. Loss of alkyl groups by means of α-cleavage is an important mode of fragmentation.

25. REFERENCES Spectrometric Identification of Organic compounds-Robert M Silverstein, Sixthedition , John Wiley& Sons, 2004.