Mass Spectrometry Part 1

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 Spectroscopy
Why bother with spectroscopy?

•Determine structure of unknown substance

•Verify purity/identity of known substance

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 Spectroscopy
What methods are commonly used?

Mass spectrometry (MS)* Infrared spectroscopy (IR)

molecular formula functional groups

Nuclear magnetic resonance (NMR) X-ray crystallography*

C/H molecular skeleton spatial position of atoms
*Not rigorously a type of spectroscopy 3
 Spectroscopy

Example: unidentified white powder H

•MS: C10H15N
N
•IR: benzene ring, secondary amine (R2NH) CH3
•NMR: has CH2-CH-CH3 CH3
•X-ray: not necessary in this case

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 Mass Spectrometry
The Mass Spectrometer

Fundamental operating principle

Determine mass by manipulating flight path of an ion in a magnetic field

Electron gun Ionization: X + e-  X+. + 2 e-

Magnet
Ionization Measure ion
m/z
m/z too
too
justlarge
small
right mass-to-charge ratio
sample (m/z)
introduction

+ -

Accelerator
plates

Detector
Detector
Detector fires
Detector
quiet
quiet

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 Isotopes
Isotopes: atoms with same number of protons and same number of electrons
but different numbers of neutrons
Aston mass spectrum of neon (1919)
•Ne empirical atomic weight = 20.2 amu
•Ne mass spectrum: predict single peak at m/z = 20.2

Results m/z relative intensity

20.2 no peak
20.0 90%
22.0 10%

Conclusions
•Neon is a mixture of isotopes
•Weighted average: (90% x 20.0 amu) + (10.0% x 22.0 amu) = 20.2 amu
•Nobel Prize in Chemistry 1922 to Aston for discovery of stable element isotopes
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 The Mass Spectrum
Example: methane CH4 + e-  CH4+. + 2 e-
m/z = (1 x 12) + (4 x 1) = 16
C H
Base peak: most abundant ion
Relative ion abundance (%)

mass-to-charge ratio (m/z)

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 The Mass Spectrum
Alternate data presentation...
m/z (amu) Relative abundance (%)
18 < 0.5 M+2 14C1H or 12C3H1H3 or...
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17 1.1 M+1 13C1H or 12C2H1H
4 3
16 100.0 M 12C1H
4
15 85.0 M-H
14 9.2 M - 2H
13 3.0 M - 3H
12 1.0 M - 4H

Molecular ion (M): intact ion of substance being analyzed

Fragment ion: formed by cleavage of one or more bonds on molecular ions

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 The Mass Spectrum
Origin of Relative Ion Abundances
M contributors M+1 contributors M+2 contributors
Natural Natural Natural
Isotope Isotope Isotope
Abundance Abundance Abundance
1H 99.9855% 2H 0.015% 3H ppm
12C 98.893 13C 1.107 14C ppm
14N 99.634 15N 0.366
16O 99.759 17O 0.037 18O 0.204
19F 100.0
32S 95.0 33S 0.76 34S 4.22
35Cl 75.77 37Cl 24.23
79Br 50.69 81Br 49.31
127I 100.0
This table will be provided on an exam. Do not memorize it. 9
 The Mass Spectrum
Relative Intensity of Molecular Ion Peaks

Imagine a sample containing 10,000 methane molecules...

Molecule # in sample m/z Relative abundance

12C1H 9889 12 + (4 x 1) = 16 100%
4

13C1H 110 13 + (4 x 1) = 17 (110/9889) x 100% = 1.1%*

4

14C1H ~1 14 + (4 x 1) = 18 (1/9889) x 100% = < 0.1%*

4

*Contributions from ions with 2H are ignored because of its very small natural abundance

CH4 mass spectrum

m/z = 16 (M; 100%), m/z = 17 (M+1; 1.1%), m/z = 18 (M+2; < 0.1%)

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 Formula from Mass Spectrum
M+1 Contributors

Comparing many mass spectra reveals M+1 intensity  ~1.1% per C in formula
•Examples: C2H6 M = 100%; M+1 = ~2.2%
C6H6 M = 100%; M+1 = ~6.6%

Working backwards gives a useful observation...

When relative contribution of M = 100% then relative abundance of M+1/1.1%

gives the approximate number of carbon atoms in the molecular formula

Other M+1 contributors

•15N (0.37%) and 33S (0.76%) should be considered
•2H (0.015%) and 17O (0.037%) can be ignored

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 Formula from Mass Spectrum
M+2 Contributors

Anything useful from intensity of M+2?

Isotopes Natural abundances Intensity M : M+2

32S : 34S 95.0 : 4.2 100 : 4.4
35Cl : 37Cl 75.8 : 24.2 100 : 31.9
79Br : 81Br 50.7 : 49.3 100 : 97.2

Conclusion: Mass spectra of molecules with S, Cl, or Br have significant M+2 peaks

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Formula from Mass Spectrum
M+2 Contributors

CH3

H C Cl C3H7Cl
CH3

C H Cl
M: 36 + 7 + 35 = 78
M+2: 36 + 7 + 37 = 80

78 80 M:M+2
abundance
~3:1

m/z
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 Formula from Mass Spectrum
M+2 Contributors

C3H7Br
Relative abundance (%)

Br

C H Br
M: 36 + 7 + 79 = 122
M+2: 36 + 7 + 81 = 124

M:M+2
122 124
abundance
~1:1

m/z
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 Identifying the Molecular Ions
Which peaks are molecular ions? Br C7H7Br
•Highest m/z not always M M: m/z = 170
•M+1 has m/z one more than m/z of M

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 Formula from Mass Spectrum
Summary of Information from Mass Spectrum

M: Reveals mass of molecule composed of lowest mass isotopes

M+1: Intensity of M+1 / 1.1% = number of carbons
M+2: Intensity reveals presence of sulfur, chlorine, and bromine

Next lecture: procedure for deriving formula from mass spectrum

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 Summary of Part 1
Spectroscopy: Study of the interaction of photons and matter
•Useful to determine molecular structure
•Types: MS*, IR, NMR, x-ray crystallography* *not really spectroscopy

MS fundamental principle: Manipulate flight path of ion in magnetic field

•Charge (z), magnetic field strength are known; ion mass (m) is determined

Isotopes: Natural abundance of isotopes controls relative abundance of ions

Molecular ion (M, M+1, M+2, etc.): Intact ion of substance being analyzed
•m/z of M = molecular mass composed of lowest mass isotopes 1H, 12C, 35Cl, etc.
•Relative abundance of M+1/1.1% gives approximate number of carbons
•M+2 reveals presence of sulfur, chlorine, or bromine

Fragment ion: From decomposition of molecular ion before reaching detector

•Analysis of fragmentation patterns not important for Chem 14C
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 Mass Spectrum  Formula  Structure
How do we derive structure from the mass spectrum?

?
CH3

 H C Cl

CH3

•Not trivial to do this directly

•Structure comes from formula; formula comes from mass spectrum

CH3

 C3H7Cl  H C Cl

CH3

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 Mass Spectrum  Formula  Structure
How do we derive formula from the mass spectrum?
•m/z and relative intensities of M, M+1, and M+2

M: m/z = 78
C2H6O3
C3H7Cl
M C5H4N
C6H6
etc.

•A few useful rules to narrow the choices

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 How Many Nitrogen Atoms?
Consider these molecules:
CH3 O
CH3
O2N NO2 H3C N
N
NH3 H2NNH2
O N N

NO2 CH3

Formula: NH3 N2H4 C7H5N3O6 C8H10N4O2

m/z (M): 17 32 227 194

Conclusion
•When m/z (M) = even, number of N in formula is even
•When m/z (M) = odd, number of N in formula is odd }The Nitrogen Rule
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 How Many Nitrogen Atoms?
A Nitrogen Rule Example

Example: Formula choices from previous mass spectrum

M: m/z = 78 m/z even

C2H6O3 even nitrogen count

C3H7Cl even nitrogen count

discarded C5H4N odd nitrogen count

C6H6 even nitrogen count

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 How Many Hydrogen Atoms?
One pi bond Two pi bonds

HC C

C6H14 C6H12 C6H10

max H for 6 C H count = max - 2 H count = max - 4

Conclusion: Each pi bond reduces max hydrogen count by two

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 How Many Hydrogen Atoms?
One ring Two rings

C6H14 C6H12 C6H10

max H for 6 C H count = max - 2 H count = max - 4

Conclusion: Each ring reduces max hydrogen count by two

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 How Many Hydrogen Atoms?
One nitrogen Two nitrogens
NH2 NH2

NH2
CH3

N H3C N
N CH3

CH3

C6H14 C6H15N C6H16N2

max H for 6 C H count = max + 1 H count = max + 2

Conclusion:
•Each nitrogen increases max H count by one
•For C carbons and N nitrogens, max number of H = 2C + N + 2
The Hydrogen Rule
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 Mass Spectrum  Formula

Procedure
•Chem 14C atoms: H C N O F S Cl Br I
•M = molecular weight (lowest mass isotopes)
•M+1: gives carbon count
•M+2: presence of S, Cl, or Br
•No mass spec indicator for F, I Assume absent unless otherwise specified
•Accounts for all atoms except O, N, and H
•MW - mass due to C, S, Cl, Br, F, and I = mass due to O, N, and H
•Systematically vary O and N to get formula candidates
•Trim candidate list with nitrogen rule and hydrogen rule

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 Mass Spectrum Formula
Example #1

m/z Molecular ion Relative abundance Conclusions

102 M 100% Mass (lowest isotopes) = 102
Given information

Even number of nitrogens

103 M+1 6.9% 6.9 / 1.1 = 6.3 Six carbons*

104 M+2 0.38% < 4% so no S, Cl, or Br

Oxygen?

*Rounding: 6.00 to 6.33 = 6; 6.34 to 6.66 = 6 or 7; 6.67 to 7.00 = 7

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 Mass Spectrum Formula
Example #1
Mass (M) - mass (C, S, Cl, Br, F, and I) = mass (N, O, and H)
102 - C6 = 102 - (6 x 12) = 30 amu for N, O, and H

Oxygens Nitrogens 30 - O - N = H Formula Notes

0 0 30 - 0 - 0 = 30 C6H30 Violates hydrogen rule

1 0 30 - 16 - 0 = 14 C6H14O Reasonable

2 0 30 - 32 - 0 = -2 C6H-2O2 Not possible

0 2* 30 - 0 - 28 = 2 C6H2N2 Reasonable
*Nitrogen rule!

•Other data (functional groups from IR, NMR integration, etc.) further trims the list
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 Mass Spectrum Formula
Example #2

m/z Molecular ion Relative abundance Conclusions

157 M 100% Mass (lowest isotopes) = 157
Odd number of nitrogens

158 M+1 9.39% 9.39 / 1.1 = 8.5

Eight or nine carbons

159 M+2 34% One Cl; no S or Br

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 Mass Spectrum Formula
Example #2
Try eight carbons: M - C8 - Cl = 157 - (8 x 12) - 35 = 26 amu for O, N, and H

Oxygens Nitrogens 26 - O - N = H Formula Notes

0 1* 26 - 0 - 14 = 12 C8H12ClN Reasonable
*Nitrogen rule!

Not enough amu available for one oxygen/one nitrogen or no oxygen/three nitrogens

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 Mass Spectrum Formula
Example #2
Try nine carbons: M - C9 - Cl = 157 - (9 x 12) - 35 = 14 amu for O, N, and H

Oxygens Nitrogens 14 - O - N = H Formula Notes

0 1* 14 - 0 - 14 = 0 C9ClN Reasonable
*Nitrogen rule!

Not enough amu available for any other combination.

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 Formula Structure

What does the formula reveal about molecular structure?

Functional groups
•Absent atoms may eliminate some functional groups
•Example: C7H9N has no oxygen-containing functional groups

Pi bonds and rings

•Recall from previous: one pi bond or one ring reduces max H count by two
•Each two H less than max H count = double bond equivalent (DBE)
•If formula has less than full H count, molecule must contain one pi bond or ring

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 Formula Structure
Calculating DBE
DBE may be calculated from molecular formula:

hydrogens and halogens nitrogens

DBE = C - H + N + 1
2 2
carbons

•One DBE = one ring or one pi bond

•Two DBE = two pi bonds, two rings, or one of each
•Four DBE = possible benzene ring

Example DBE = C - (H/2) + (N/2) + 1 Four pi bonds and/or ring

C8H10ClN = 8 - [(10+1)/2] + (1/2) + 1 Possible benzene ring
=4

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 Formula Structure
Common Math Errors

Small math errors can have devastating effects!

•No calculators on exams

Avoid these common spectroscopy problem math errors:

•Divide by 1.1  divide by 1.0
•DBE cannot be a fraction
•DBE cannot be negative

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