Organic Mass Spectrometry

1. Organic Mass Spectrometry Interpretation of Mass Spectra Part 3

2. The Molecular Ion • Most valuable info of the mass spectrum • Molecular mass • Elemental composition • Fragments must be consistent with it • Not always stable with EI • Be careful about over-interpretation of peak of highest m/z! • Use soft-ionization such as CI in parallel • MS Definition: • m/z of the molecular ion is the peak that contains the most abundant isotope of all the elements involved (by convention) • Won’t always be most abundant peak

3. Requirements for the Molecular Ion • Necessary but not sufficientconditions • It must be the ion of highest mass (isotope caveat) • It must be an odd-electron ion • It must be capable of yielding the most important ions in the high-mass region by loss of logicalneutral species • If candidate fails either test, it cannot be the MI • If candidate passes all tests, it may or may not be the MI

4. Odd-Electron Ions • For EI, a molecule becomes ionized by loosing one electron • It must have an unpaired electron (so it’s a radical)

5. More on Odd- & Even-Electron Ions • If you can establish the elemental composition of the ion, the rings plus double-bonds rule will show whether the ion is odd or even-electron: • Even: integer + 1/2 RPDB • Odd: integer RPDB • – CxHyNzOn : • Even or Odd? • C5H5N+ • C7H5O+

6. Even Electron Ions • Even-electron ions: • All electrons on the outer shell are fully paired • Generally more stable • Often the more abundant fragment ions CH4+⋅ → CH3+ + H⋅ • In CI, even electron ions such as MH+are formed, resulting in lower fragmentation

7. The Nitrogen Rule - I • For most elements in organic compounds, there is a relationship between mass of the most abundant isotope and the valence • Both odd or both even • N is the exception

8. The Nitrogen Rule - II • The ‘Nitrogen Rule’: If a compound contains no • (or even number of) N atoms, its molecular ion will be at an even mass number

9. The Nitrogen Rule - III • N-Rule applies to all ions • An odd-electron ion will be at an even mass number if it contains an even number of nitrogen atoms • An even-electron ion containing an even number of nitrogen atoms will appear at an odd mass number

10. Which of the following are OE+. and EE+? Which have odd and even mass? Does it agree with N-Rule? C2H4 C3H7O C4H9N C3H9 C4H8NO C7H15ClBr C3F10 C29F29 C3H9SiO Nitrogen Rule Practice

11. Which Ions Are OE vs. EE?

12. The “importance” of a peak generally increases with: Increasing intensity Increasing mass in the spectrum Increasing mass in the peak group A scarcity of even-mass ions, especially at lower m/z values, indicate an even-mass molecular weight. Relative Importance of Peaks

13. OE vs. EE • Important OE ions are less likely at low m/z • Intense even mass peaks in that region usually have an odd-number of N

14. Logical Neutral Losses I • Only a certain number of low mass neutral fragments are commonly lost in decompositions of molecular ions • Small neutral fragments lost from the molecular ion are commonly those attached by a single bond • Mass losses of 4 to 14 and 21 to 25 that give important peaks are highly unlikely - WHY?

15. Logical Neutral Losses II • The presence of an ‘important’ ion separated from the highest mass ion by an anomalous mass or elemental formula will indicate that the latter ion is not the molecular ion! • E.g., if there is an abundant ion 5 mass units below the ion of highest m/z, can that be the molecular ion? • Can the ion of highest mass (first) be the molecular ion if the following are the major ions of high mass? • C10H15O, C10H14O, C9H12O, C10H13, C8H10O • C10H14, C10H13, C9H11, C8H9, C7H8, C7H7

16. Unknown 3.4 Elemental composition A+2, A+1, O, H, A Molecule? RPDB? Even/Odd e- ions? Molecular ion? N-Rule? Neutral losses? Unknown 3.4

17. Elemental composition A+2, A+1, O, H, A Molecule? RPDB? Even/Odd e- ions? Molecular ion? N-Rule? Neutral losses? Unknown 3.5

18. Molecular Ion Abundance - I • Abundance of molecular ion depends on: • Its stability (often not in spectrum) • The amount of energy needed to ionize the molecule • There is a correlation between those properties and the structure of the molecule • The magnitude of M+. provides an indication about the structure of the molecule

19. Molecular Ion Abundance - II • In general the chemical stability of M+. parallels the stability of the molecule • M+. increases with ‘un-saturation’ and rings • M+. decreases with chain branching • Effect of MW is not as clear

20. Molecular Ion Abundance III • If less energy is needed to ionize the molecule, more molecular ions of lower internal energy (‘cool’ ions) will be formed • Intensity of the M+. will be higher • Ease of ionization increases down on a column in the periodic table or to the left in a row

21. Molecular Ion Abundance IIIa • Ease of ionization increases down on a column in the periodic table or to the left in a row

22. Elemental composition A+2, A+1, O, H, A Funny elements? Molecule? RPDB? Even/Odd e- ions? Molecular ion? N-Rule? Neutral losses? Unknown 3.6

23. Example Mass Spectra • • Show trends • Look for similarities to unknowns • Refer back as we discuss fragmentation mechanisms • Key to the symbols:

24. Alkanes & Branched Alkanes

25. Mechanisms of IonFragmentation Or – How Do you Break It?

26. Introduction to Ion Fragmentation Reactions • Ion abundances • Relative abundance of an ion can be an indication the structure of the fragment and its environment in the Molecule • Source: Unimolecular Ion-decomposition Reactions • Another branch of chemistry • Many close similarities to pyrolitic, photolytic, radiolytic reactions, as well to condensed-phase organic reactions • But here each reaction involves ions & often radicals under vacuum • Rearrangement reactions are possible

27. Unimolecular Decomposition Reactions - I • EI MS reactions are unimolecular (as opposed to laser ablation ionization) • M+. are made with a wide range of internal energies • “Cool” M+. will not decompose • –ABCD + e-__> ABCD+.

28. Unimolecular Decomposition Reactions - II • “Excited” or “Hot” M+. will decompose in a chain of energy-dependent reactions • Now things get interesting… • Each one with a neutral loss • Rearrangement: NO+ from (NH4) 2SO4

29. Unimolecular Decomposition Reactions - II • ABCD __> ABCD+.__> A+ + BCD. __> A. + BCD+ I__> BC+ + D. __> D. + ABC+ I__> A + BC+ __> AD+. + B=C

30. Factors that Influence Ion Abundance - I • Stability of the product ion • Electron sharing stabilization CH3-C+=O <=> CH3-C=O+ • Resonance stabilization +CH2CH-CH2 <=> CH2+CH-CH2 • Stevenson’s Rule • Cleavage of a single bond in an OE+. ABCD+. can give A+ + BCD. or A. + BCD+ • The fragment with the higher tendency to retain the unpaired electron should have the higher ionization energy (converse is true). It will be the less abundant ion in the spectrum

31. Factors that Influence Ion Abundance - II • Loss of the largest alkyl (CnH2n+1) • Exception: abundance decreases with increasing ion stability • Stability of the neutral product • A favorable product site for the unpaired electron can provide additional influence • Electronegative sites such as oxygen are favored • The neutral product can be a molecule • Small stable molecules of high ionization energy very favored: • e.g., H2, CH4, H2O, C2H4, CO, NO, CH3OH, H2S, HCl, CH2=C=O, and CO2.

32. Factors that Influence Ion Abundance - III • Entropy/Steric Effects • Dissociation favors products with less restrictive entropy requirements even if the enthalpy barrier is higher (i.e., a simple bond cleavage) • Predict the most abundant product ion in the mass spectrum of:

34. Reaction Initiation at Radical or Charged Sites • Fragmentation reactions are often (but not always, depends on energy) initiated at the favored sites for the unpaired electron or the charge • The most favored radical and charge sites in the molecular ion are assumed to arise from loss of the molecule’s electron of lowest ionization energy • Favorability: s < p < non-bonding electrons Unlike M+., charge localization is implied

35. Reaction Classifications I • The exact EI mass spectrum of a complex organic molecule can not be ‘constructed’ a priori • Instead, we want to understand the major features • (high M+., stability, rings) and how they formed

36. Reaction Classifications - II • Decompositions of odd electron ions involving single bond cleavage results in an even electron ion and a neutral radical

37. Reaction Classifications - III • Decompositions of odd electron ions involving two bond cleavage can results in an odd electron ion and a neutral species • Important for the decomposition of rings • Gives mechanistically important information

38. Reaction Classifications - IV • Decompositions of even electron ions result in another even electron ion and a neutral species. Odd electron ion formation is not energetically favorable

39. Types of Reaction Mechanisms - I • Sigma bond dissociation • Within a saturated framework single bond cleavage is favored • Ionization is from the s bond • Alkanes: R+.CR3__> R. + +CR3 • Radical site initiation (a cleavage) • Donation of an electron to form a new bond • Formation of a new bond • Loss of largest alkyl group • Two a cleavages are the means by which rings are broken R-CR2-Y+ . R __> R. + CR2=+YR

40. Types of Reaction Mechanisms - II • Charge site initiation (inductive effect) • Attraction of an electron pair results in bond cleavage • Movement of ionic site results in most stable form R-+.Y-R __> R+ + .YR • Rearrangements • New bond formation from the radical site to another atom • Subsequent reaction(s) usually required (neutrals) • Important decomposition mechanism for rings

41. Alkanes & Branched Alkanes

42. Highly Branched Alkanes & Alkenes

43. Cycloalkanes & Aromatics

44. Alcohols & Ethers

45. Ketones

46. Acids & Esters