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