11
Organic Mass Spectrometry
Interpretation of Mass Spectra Part 2
22
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
33
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
44
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)
55
Unknowns 2.9 & 2.10(use procedure)
66
Unknown 2.9?
(m a in lib ) 2H-In d e n -2-o n e , 1,3-d ih yd ro -20 30 40 50 60 70 80 90 100 110 120 130 140
0
50
100
27 3139
42 46
51
5763
78
82 85 89 97
104
115
132O
77
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)
88
Methyl Bromide MS
99
Linear Supposition of Isotopic Peaks
1010
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
1111
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.
1212
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
1313
Isotopes of Other Elements
1414
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
1515
Standard Interpretation
Procedure1) 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.
2) Using isotopic abundances (where possible) deduce the elemental composition of each peak in the spectrum; calculate rings plus double bonds.
3) 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.
1616
Standard Interpretation
Procedure4) 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.
1717
Standard Interpretation
Procedure7) 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.
1818
What Unusual Element Is In This
Molecule?
1919
From the NIST Isotope Calculator
2020
From the NIST Isotope Calculator
2121
Identity
Tetrahydrotellurophene (C4H8Te)
– R+BD = x - 1/2y + 1/2z +1 (for CxHyNzOn)
– R+BD = 4 -4 + 1 = 1
2222
Determine the Elemental Compositions
2323
Unknown 2.11
(m a in lib ) Silic o n te tra flu o rid e10 20 30 40 50 60 70 80 90 100 110 120
0
50
100
14 19 28 33 43 47 66
85
104
SiF
F
F
F
2424
Determine the Elemental Compositions
2525
Another Mystery!
What unusual element is present in this molecule?
Can you guess what the molecule is?
2626
Mass Spectrum of Tungsten
2727
Mass Spectrum of Tungsten
Hexafluoride
(m a in lib ) Tu n g ste n h e xa flu o rid e110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310
0
50
100
110 120 130 139 186 203222 241 260
279
F
W
F
F
F
F
F
2828
What is the compound?
How many carbon atoms does the M+. Ion suggest?
What does the M+2 ion tell you?
2929
Unknown
3030
Mass Spectrum of t-Butyl Mercaptan
(m a in lib ) 2-Pro p a n e th io l, 2-m e th yl-10 20 30 40 50 60 70 80 90 100
0
50
100
15
27
29
30 34
39
41
47 55
57
5962 68 71
75
76 85
90
92
SH
3131
Mass Spectrum of 2-Chloro-2-
methylpropane
(m a in lib ) Pro p a n e , 2-c h lo ro -2-m e th yl-10 20 30 40 50 60 70 80 90 100
0
50
100
15
29
30
39
41
43 49 56
57
61 64 73
77
79
C l