1. Created with MindGenius Business 2005® Mass Spectrometry Mass Spectrometry

2. Created with MindGenius Business 2005®

3. Mass Spectrometry Mass Spectrometry Principles Mass Spectra http://www.mrc-dunn.cam.ac.uk/facilities/mass_spectrometry.php

4. Created with MindGenius Business 2005® Principles Principles The study of ionised molecules in the gas phase Principles date back to ~ 1897 Based on accelerating ions in a vacuum Joseph J. Thompson used an early MS to discover the electron. Received the Nobel Prize in 1906 [Physics]. For a “friendly” practical introduction see: http://www.asms.org/whatisms/p1.html and following pages http://www.asms.org/whatisms/p1.html USES Molecular weight determination Structural characterisation Gas phase reactivity study Qualitative and Quantitative analysis of mixtures

5. Created with MindGenius Business 2005® Principles Principles Volatilisation Ionisation Separation Detection Sample Volatilisation Ionisation Separation Detection

6. Created with MindGenius Business 2005® Volatilisation Volatilisation Gaseous and volatile samples are readily drawn into the reservoir. Less volatile solid samples require heating. The volatile sample diffuses from the reservoir into the ionization chamber via a leak - a pin-hole restriction in a gold foil.

7. Created with MindGenius Business 2005® Ionisation (1) Ionisation (1) Electron impact or EI (most common) Sample passes through an electron beam. energy of e - beam is increased until e - is ejected from the target molecule (normally ~70eV) high energy causes substantial fragmentation M + e  [M] +. + 2e Radical cation [MOLECULAR ION] Most MS are set up to detect positive ions.

8. Created with MindGenius Business 2005® Ionisation (2) Ionisation (2) Chemical ionisation (CI) Softer than EI (used for more sensitive compounds). Sample is introduced with an excess of a carrier gas (eg NH 3 ) which is ionised by the electron beam. Lower energy means less fragmentation

9. Created with MindGenius Business 2005® Separation Separation A stable controllable magnetic field separates the ions according to their momentum. Only ions of a single mass/charge [m/z] ratio will have the trajectory to be detected. By varying the magnetic, field ions with different m/z values are focused on the detector

10. Created with MindGenius Business 2005® Detection Detection The ion current will cause emission of secondary electrons from a metal plate detector. The Faraday cup detector suppresses secondary ion formation. The -ve plate also suppresses secondary ion formation

11. Created with MindGenius Business 2005® Mass Spectra Mass Spectra Features Fragmentation patterns

12. Created with MindGenius Business 2005® Features Features After ionisation: Ejection of an electron from the parent molecule gives the molecular ion (generally M +, but depends on ionisation technique) M + fragments giving rise to other peaks Gives rise to a mass spectrum: Plotted as intensity (%) vs m/z (amu) The tallest peak is termed the base peak and is given an intensity of 100%. Other peak intensities are given relative to this

13. Created with MindGenius Business 2005® Features Features

14. Created with MindGenius Business 2005® Fragmentation patterns (1) Fragmentation patterns (1) Occurs via two major routes: [M]+.  A+ (even electron cation) + B. (radical) OR [M]+.  C+. (cation radical) + D (molecule) NB Only particles with positive charges are detected

15. Created with MindGenius Business 2005® Fragmentation patterns (2) Fragmentation patterns (2) Characteristic fragmentation patterns arise as: Weak bonds tend to break Formation of stable fragments (ions, radicals and molecules) is favoured Some molecules can form cyclic transition states

16. Created with MindGenius Business 2005® Fragmentation patterns Fragmentation patterns Alkanes Alkenes and Aromatic compounds Heteroatoms Isotopes

17. Created with MindGenius Business 2005® Alkanes (1) Alkanes (1) Carbocation is an sp 2 hybrid with an empty p orbital. Stability of the cation depends on the number of alkyl groups, due to inductive effects

18. Created with MindGenius Business 2005® Alkanes (2) Alkanes (2) Aliphatic carbon skeletons are readily cleaved at branches because it results in carbocations that are more stable

19. Created with MindGenius Business 2005® Alkanes (3) Alkanes (3) Stable fragments formed from branched alkyl chain results in less strong Molecular Ion (MI) NB Size of peak is relative

20. Created with MindGenius Business 2005® Alkenes and Aromatic compounds (1) Alkenes and Aromatic compounds (1) Cleavage occurs β to double bonds because more stable carbocations are produced due to resonance stabilisation Cyclic alkenes can undergo rearrangements Double bonds easily migrate in MS and isomers may easily be difficult to identify

21. Created with MindGenius Business 2005® Alkenes and Aromatic compounds (2) Alkenes and Aromatic compounds (2) Aromatic hydrocarbons strong molecular ion β cleavage favoured strongly by resonance stabilisation fragmentation of ring energetically disfavoured

22. Created with MindGenius Business 2005® Alkenes and Aromatic compounds (3) Alkenes and Aromatic compounds (3) Aromatic hydrocarbons Characteristic m/z = 91 and 65 from tropylium ion and breakdown product. Alkynes – strong MI, similar to alkenes, cleave at β site

23. Created with MindGenius Business 2005® Heteroatoms (1) Heteroatoms (1) Cleavage may occur α, β or γ to heteroatoms depending on the functional groups involved. BEWARE: α to the carbonyl is β to the heteroatom! a) α cleavage promoted by electronegativity eg ethers

24. Created with MindGenius Business 2005® Heteroatoms (2) Heteroatoms (2) b) β cleavage – promoted by resonance stabilisation eg Carbonyl group NB the most stable carbocation will be found in greatest abundance

25. Created with MindGenius Business 2005® Heteroatoms (3) Heteroatoms (3) c) McLafferty rearrangements give γ cleavage (β to carbonyl) occurs with carbonyl containing compounds depends on six membered transition state (i) Ketones, and carboxylic acids 1º carboxylic acids give a characteristic peak at m/z = 60

26. Created with MindGenius Business 2005® Heteroatoms (4) Heteroatoms (4) ii) Carboxylic esters Can undergo two types of McLafferty rearrangement

27. Created with MindGenius Business 2005® Heteroatoms Heteroatoms Oxygen heteroatoms Nitrogen heteroatoms Halogen heteratoms

28. Created with MindGenius Business 2005® Oxygen heteroatoms Oxygen heteroatoms GroupFormulaMI α βγOther AlcoholsR-OHWeak or absent Yes*Main*H 2 O Elimination AldehydesRCHOweakNoacylium ion McLafferty KetonesRCOR’StrongNoacylium ion McLafferty Carboxylic Esters RCOOR’WeakNot really acylium ion McLafferty Carboxylic Acids RCOOHWeakNot really Mostly McLafferty EthersROR’Fairly weak Yes Rearrang- ements

29. Created with MindGenius Business 2005® Nitrogen heteroatoms Nitrogen heteroatoms Weak or absent MI iminium ion (like acylium) gives most intense peak may also undergo cyclic rearrangements. Nitrogen rule: Compounds with an odd number of nitrogens have an odd molecular weight. eg NH 3 MW = 17; CH 3 CH 2 NH 2 MW = 45; NH 2 CH 2 CH 2 NH 2 MW = 60

30. Created with MindGenius Business 2005® Halogen heteroatoms Halogen heteroatoms MI is strongest for Iodides less so for Bromides etc. More branched halides have weaker MIs. Cl and Br Isotopes give visible patterns Fragmentation may include (in order of likelihood): a) Loss of halogen b) Loss of HX c) β cleavage (as for oxygen) – loss of CH 2 X d) Rearrangements

31. Created with MindGenius Business 2005® Isotopes (1) Isotopes (1) It is important to use the correct method to calculate molecular weight for MS. Average atomic masses take into account the different abundances of isotopes. Need to use exact mass for MS. CARBON 1.1% of naturally occurring carbon is 13 C: gives 1% abundance m/z = 17 signal (M+H) + in spectrum of Methane. HALOGENS Significant amounts of different isotopes, visible patterns within spectrum.

32. Created with MindGenius Business 2005® Isotopes (2) Isotopes (2) Chlorine: Average Atomic weight = 35.453 Isotope 35 Cl 37 Cl Atomic weight 3537 Abundance75.824.2 Ratio ~31 Relative abundance M M+2

33. Created with MindGenius Business 2005® Isotopes (3) Isotopes (3) Bromine: Average atomic weight = 79.904 Isotope 79 Br 81 Br Atomic weight 7981 Abundance50.649.4 Ratio ~11 Relative abundance MM+2 m/z Isotopic pattern for one bromine atom Relative abundance M M+2 M+4 eg CH 3 Br Mass: 50% CH 3 79 Br = 94 50% CH 3 81 Br = 96 CH 2 Br 2 Mass: 25 % CH 2 79 Br 79 Br = 172 25 % CH 2 79 Br 81 Br = 174 25 % CH 2 81 Br 79 Br = 174 25 % CH 2 81 Br 81 Br = 176 Isotopic pattern for one bromine atom

34. Created with MindGenius Business 2005® Characteristic signals in MS Functional groupCharacteristic m/z Alkanes29, 43, 57, 71, 85 AlkenesIons resulting from β cleavage Amines30, 44, 58, 72 Benzene65, 77, 91 HalidesIsotope peaks, loss of X and HX Carbonyl, Ester, AcidAcylium ions and Mclafferty rearrangement products common