1. Organic Mass Spectrometry
Interpretation of Mass Spectra Part 2

2. Rings + Double Bonds
Because of the valences, the total number of rings and double bonds in a molecule of the formula CxHyNzOn will be:
Calculate: C4H10 , C6H6 , C5H5N , C7H5O
For ions, the value may end in 0.5 (‘even electron ion’)
More general case AyBnCzDx, where A = H, F, Cl, Br, I; B = O, S; C = N, P; and D = C, Si
Does not count double bonds to elements in higher valence states

3. Rings + Double Bonds Negative values arise from
Ion rearrangement
Chemical ionization
Values < -0.5 are not possible!
Must arise from
Incorrect elemental composition or
Incorrect RPDB calculation

4. Elemental Composition
Insert the experimental abundances in ‘intensity’ column
Normalize all data to set dominant peak to 100%
Find all possible A+2 elements and show their expected abundance contribution in separate columns
O will be last, may not be accurate
Assign the possible number of carbons, showing their relative contributions in columns
Assign the A elements by difference (remember bonding rules)

5. Unknowns 2.9 & 2.10 (use procedure)

6. Unknown 2.9?

7. Tips for Elemental Composition
We have assumed so far that A+1 and A+2 peaks are only from isotopes
But there could be other contributions
Other fragments
Background, impurities, noise, etc.
If identified, they can be corrected
Most of the time the calculations give you MAX number of atoms
Example: m/z 42/41 in Unknown 2.4
Next example: CH3Br
Error can go the other way, if another fragment contributes to A peak
Example: Methyl Bromide (CH3Br)

8. Methyl Bromide MS

9. Linear Supposition of Isotopic Peaks

10. More Tips for Elemental Composition
Highest mass peaks first (both in general and in each group)
Least isotopic contamination
Use highest intensity peaks
More accurate peak ratio determination

11. More Tips for Elemental Composition
Choose A peak
Peak of highest mass than contains only the most abundant isotopes (‘nonisotopic peak’).
Try the largest peak in the group; if the second largest peak is at m/z > A+2, try it instead.
Next if [A-2]/[A] > 30%, check the possible Cl/Br patterns.
Next, calculate elemental compositions for A.
If composition cannot account for other peaks, another peak is a nonisotopic peak.

12. More Tips for Elemental Composition
Use every group of peaks possible
Check the composition assignments for internal consistency
M+. has to have the most atoms of all elements
Does this hold for every group of peaks vs. the groups below?
Composition of fragments will show some consistency

13. Isotopes of Other Elements

14. Standard Interpretation Procedure
Ask questions in a logical order
Big picture questions first (e.g. which elements are present)
Avoid “blind alleys”
More detailed questions later (e.g. molecular substructures)
Put it all together at the end
Postulate a molecule that is consistent with all previous information

15. Standard Interpretation Procedure
Study all available information (spectroscopic, chemical, sample history). Give explicit directions for obtaining spectrum (better yet, do it yourself).
a) Verify the m/z assignments. Use calibrants if needed.
Using isotopic abundances (where possible) deduce the elemental composition of each peak in the spectrum; calculate rings plus double bonds.
Test molecular ion identity; must be the highest mass peak in spectrum, odd-electron ion, and give logical neutral losses. Check with CI or other soft ionization.

16. Standard Interpretation Procedure
4) Mark ‘important’ ions: odd-electron and those of highest abundance, highest mass, and/or highest in a group of peaks.
5) Study general appearance of the spectrum: molecular stability, labile bonds, etc.
6) Postulate and rank possible sub-structural assignments for:
a) Important low-mass ion series
b) Important primary neutral fragments from M.+ indicated by high-mass ions (loss of largest alkyl favored) plus those secondary fragmentations indicated by MS/MS spectra.
c) Important characteristic ions.

17. Standard Interpretation Procedure
7) Postulate molecular structures; test against a reference spectrum, against spectra of similar compounds, or against spectra predicted from mechanisms of ion decompositions
Remember to follow SIP step-by-step in order.

18. What Unusual Element Is In This Molecule?

19. From the NIST Isotope Calculator

20. From the NIST Isotope Calculator

21. Identity Tetrahydrotellurophene (C4H8Te)
R+BD = x - 1/2y + 1/2z +1 (for CxHyNzOn)
R+BD = = 1

22. Determine the Elemental Compositions

23. Unknown 2.11

24. Determine the Elemental Compositions

25. Another Mystery! What unusual element is present in this molecule?
Can you guess what the molecule is?
WF6!

26. Mass Spectrum of Tungsten

27. Mass Spectrum of Tungsten Hexafluoride

28. What is the compound? How many carbon atoms does the M+. Ion suggest?
What does the M+2 ion tell you?

29. Unknown

30. Mass Spectrum of t-Butyl Mercaptan

31. Mass Spectrum of 2-Chloro-2-methylpropane