1 organic mass spectrometry interpretation of mass spectra part 2
TRANSCRIPT
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Organic Mass Spectrometry
Interpretation of Mass Spectra Part 2
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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
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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
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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)
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Unknowns 2.9 & 2.10(use procedure)
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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
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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)
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Methyl Bromide MS
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Linear Supposition of Isotopic Peaks
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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
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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.
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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
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Isotopes of Other Elements
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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
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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.
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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.
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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.
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What Unusual Element Is In This
Molecule?
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From the NIST Isotope Calculator
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2020
From the NIST Isotope Calculator
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Identity
Tetrahydrotellurophene (C4H8Te)
– R+BD = x - 1/2y + 1/2z +1 (for CxHyNzOn)
– R+BD = 4 -4 + 1 = 1
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Determine the Elemental Compositions
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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
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Determine the Elemental Compositions
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Another Mystery!
What unusual element is present in this molecule?
Can you guess what the molecule is?
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Mass Spectrum of Tungsten
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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
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What is the compound?
How many carbon atoms does the M+. Ion suggest?
What does the M+2 ion tell you?
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Unknown
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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
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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