1. Mass Spectrometry A key Tool for the chemist’s toolbox.
The logic is, we always want the molecular weight.
Second, we can smash out fragments that are intact structurally
These are easier to solve and relate back to the starting structure
Implication is, we don’t get the sample back; a destructive method

2. Mass Spectrometry
A primary tool for chemists from almost every discipline
Molecular Weights are fundamental to almost every structural question. Molecular weight is not ambiguous. A compound has a unique MW.
Our ability to analyze compounds on this basis, depends completely on being able to generate ions from the compound. Specifically molecular ions*, whose weight is equal to the MW of the compound, are critical.
Once produced, our analysis according to MW depends on differential mobility or acceleration of ions proportionate to the MW.
*We can usefully broaden this definition from [M]+ to embrace [M+H]+, [M-H]-, Chemical Ionization adducts, etc.

3. What’s in a Mass Spectrum?
Derived from molecular ion or higher weight fragments
Fragment Ions
[M+H]+(CI)
Or M•+ (EI)
“molecular ion”
Ion Abundance (as a %of Base peak)
Unit mass spacing
In CI, adduct ions, [M+reagent gas]+
Not usually scanned below m/z=32 (Why?)
High mass
Mass, as m/z. Z is the charge, and for doubly charged ions (often seen in macromolecules), masses show up at half their proper value

4. Molecular Ions give us the molecular mass
Dislodges an electron
Electron Impact M
-e•
2e-•
M+•
Chemical Ionization M H+
[M+H]+
Weighs one more than MW

5. Identifying Molecular Ions
Potential question; Is the largest m/z the molecular ion or is it a prominent fragment from an even heavier molecule?
Increase sample loading
In EI, can lower the beam voltage (make the M•+ less energetic, perhaps more long-lived.)
Logical interval between significant peaks and suspected M•+ . i.e. the loss of 3-14 mass units is unusual, as is loss of (except F). Loss of 33, 35, 38 also unusual. However a loss of 15, 18, 31 is good evidence for a molecular ion.
Switch to CI, vary reagent gas. Positive, negative probes. Check for CI adduct ions. e.g. C2H5+ , CH5+, C3H5+
Find MW by other method
Prepare derivative
Other compounds present may give ions that deceive us. May be more detectable. MS intensities are problematic

6. The “Nitrogen Rule”
Molecules containing atoms limited to C,H,O,N,S,X,P of even-numbered molecular weight contain either NO nitrogen or an even number of N
This is true as well for radicals as well.
Not true for pre-charged, e.g. quats, (rule inverts) or radical cations.
In the case of Chemical Ionization, where [M+H]+ is observed, need to subtract 1, then apply nitrogen rule.
Example, if we know a compound is free of nitrogen and gives an ion at m/z=201, then that peak cannot be the molecular ion.

7. ElectronImpact and ChemicalIonizationEI
Sometimes too energetic for molecular ion to survive
Rich harvest of fragment ions
“fingerprint” nature of fragment patterns lends itself to database library searches CI
Stronger, more reliable molecular ions
Fewer fragments
Can choose different reagent gasses and exploit chemistry, giving different fragmentation. e.g. NH3/ND3
Adduct ions give support to identities
Nitrogen rule works but inverted
Can do negative ion Mass Spec EI CI

8. When would you use CI, EI? EI CI
When “fingerprint” is needed for Identification by comparison screening in databases
Trace analysis
Forensics
Environmental
Total unknowns, e.g natural products
Fragment homology within a series, e.g. of natural products CI
When rapid, reliable identification of molecular ion is needed.
LC-MS
Following a synthetic chemistry route, tentative impurity ID
Biological samples, other fragile or sensitive to decomposition; Drug or other metabolite ID
When reagent gas chemistry is key, e.g. exchange D in for H
Minimize fragmentation, get most intensity in molecular ion.

9. How can I tell which (EI or CI) was run?
Chemical Ionization
Adduct ions higher m/z than MH+, ,[M+C2H5]+ ,[M+C3H5]+ [M+NH4]+
Large molecular ion
Relatively few fragment ions
Electron Impact
No ions higher m/z than M•+
Smaller M•+ intensity
Rich family of fragment ions

10. The “Rule of 13” as an aid to guessing a molecular Formula
Take the Weight of ion, divide by 13
This answer is N, for (CH)N and any numerical remainder is added as H
e.g.; 92
92/13 = 7 with remainder = 1; C7H8 weighs 92. This is our candidate formula
Can evaluate other alternative candidate formulas possessing heteroatoms. For each member of the list below, replace the indicated number of CHs in the above answer
Hetero substitution
CH replacement O
CH4 P
C2H7 N
CH2 S
C2H8
O+N
C2H6
O+S C4 F
CH7 I
C10H7 Si
C2H4
Cl,Br
(use isotopes)

11. Analyzing Ion Clusters: a way to rule candidate structures in or out
Mass spectrometry “sees” all the isotopomers as distinct ions
An ion with all 12C is one mass unit different from an ion with one 13C and the rest 12C
Since the isotope distribution in nature is known* for all the elements (13C is 1.1%), the anticipated range and ratios of ions for a given formula can be predicted and calculated
Follows a binomial expansion: e.g.; for N carbon atoms
(%12C + %13C)N

12. Clusters of Ions
Spaced by unit mass
Each peak is for the same molecular formula
Different peaks because there are some molecules with 13C, 2H etc.
Especially significant for Cl, Br
The Nominal mass is m/z of the lowest member of the cluster. This is the isotopomer that has all the C’s as 12C, all protons as 1H, all N’s as 14N, etc.
m/z

13. Isotope Patterns in Ion Clusters
Here are two molecular ions of nearly the same m/z. One of them is “carbon-rich”, and has a larger number of 13C’s
The other, presumably has proportionately, more heteroatoms
C24H50 C12H22O11

14. Why is this Important?
A rule of thumb, made possible by knowing the isotopic abundance is that the number of C in a formula is given by: N=
All 12C
1 13C
C10
C100
2 13C
From this, it is clear that for large or macromolecules, there will be practically no population having all 12C or even only 113C

15. Fragmentation or B+ + A· EI [M·]+ A+ + B· (neutral)
Better carbocation wins and predominates (“Stevenson’s Rule”) CI
[M+H]+ PH+ + N (neutral)
The “Even Electron Rule” dictates that even (non-radical) ions will not fragment to give two radicals (pos• + neutral•) (CI)

16. Reading a Mass Spec from the M+• Down (EI)
Fragment
Due to loss of…
Interpretation
M+• -1
-H•
Aldehydes, tert. Alcohols, cyclic amines
M+• -2
Multiple -H•
Secondary alcohols
M+• -3
Primary alcohols
M+• -4 to -13
(doubtful)
Consider contaminants
M+• -14
CH2• , N• not good losses
M+• -15
CH3•
Available methyl groups, methylesters
M+• -16 O•
Peroxides
M+• -17
OH•
Alcohols, phenols, RCO2H
M+• -18
H2O
alcohols
M+• -19
-F•
M+• -20
-HF
M+• -21 to -25
No peaks expected
M+• -26
HCCH
M+• -27
•HC=CH2 or HCN
HCN from pyridine, anilines
M+• -28
CO or CH2=CH2
Check for McLafferty R&R

17. How Do I go about using Mass Spec Data for Unknowns?
First, get the molecular weight
Identify prime, smaller mass losses like water, etc.
Now stop. Don’t worry about the fragments till you have some candidate structures
Based on NMR, IR get some notions of structure candidates or partial structures, functional groups
Now go back to MS, predict some fragments your structure will give, calculate the molecular weights and check MS
Back and forth with other data, to corroborate or refute a possible structure.

18. Nominal Mass
Here for example is a list of the compounds in the Merck Index (9th ed) that weigh nominally, 200
Exact mass measurements can easily distinguish
These instruments (and other) can generate exhaustive lists of possible structure formulas near the exact mass value.

19. Example, m/z’s for 157 Clearly, some are not realistic!
molar mass: 157
Formula M+1 M+2 MM e/o dbr
HN2O e 1.5
HN10O e 5.5
H3N3O o 1
H3N o 5
H5N4O e 0.5
H7N5O o 0
CHO e 1.5
CHN8O e 5.5
CH3NO o 1
CH3N9O o 5
CH5N2O e 0.5
CH5N e 4.5
CH7N3O o 0
C2HN6O e 5.5
C2H3N7O o 5
C2H5O e 0.5
C2H5N8O e 4.5
C2H7NO o 0
C2H7N o 4
C3HN4O e 5.5
C3H3N5O o 5
C3H5N6O e 4.5
C3H7N7O o 4
C3H9N e 3.5
C4HN2O e 5.5
C4H3N3O o 5
C4H5N4O e 4.5
C4H7N5O o 4
C4H9N6O e 3.5
C4H11N o 3
C5HO e 5.5
C5H3NO o 5
C5H5N2O e 4.5
C5H7N3O o 4
C5H9N4O e 3.5
C5H11N5O o 3
C5H13N e 2.5
C6HN e 9.5
C6H5O e 4.5
C6H7NO o 4
C6H9N2O e 3.5
C6H11N3O o 3
C6H13N4O e 2.5
C6H15N o 2
C7HN4O e 9.5
C7H3N o 9
C7H9O e 3.5
C7H11NO o 3
C7H13N2O e 2.5
C7H15N3O o 2
C7H17N e 1.5
C8HN2O e 9.5
C8H3N3O o 9
C8H5N e 8.5
C8H13O e 2.5
C8H15NO o 2
C8H17N2O e 1.5
C8H19N o 1
C9HO e 9.5
C9H3NO o 9
C9H5N2O e 8.5
C9H7N o 8
C9H17O e 1.5
C9H19NO o 1
C9H21N e 0.5
C10H5O e 8.5
C10H7NO o 8
C10H9N e 7.5
C10H21O e 0.5
C10H23N o 0
C11H9O e 7.5
C11H11N o 7
C12H e 6.5
C13H e 13.5
Clearly, some are not realistic!

20. Calculated mass distributions
IMASS for Mac OSX
Version 1.0 (v2A15)
© , Urs Roethlisberger,
Isotopic Element Massesand Atomic Weights:Lide, D.R., Ed., CRC Handbook of Chemistry and Physics,74th Ed., CRC Press, Boca Raton FL,(1993)
Isotope Distribution:Rockwood, A. L., Van Orden, S. L.,Smith, R. D.,Anal. Chem. , 67, 2699, (1995)
•iMass is freeware.
•Contact:

21. Fragment Ions
The Game is, to rationalize these in terms of the structure
Identify as many as possible, in terms of the parent structure
Generally, simply derived from the molecular ion
Or, in a simple fashion from a significant higher mw fragment.
Simply, here means, ions don’t fly apart, split out neutrals and then recombine.
Fragments will make chemical sense
A good approach is the “rule of 13” to write down a molecular formula for an ion of interest.
Especially in EI, we only identify major fragments

22. Chemical Ionization Fragmentation
Loss of neutral molecules, small stable, from MH+
Loss of neutrals from protonated fragments
Subsequent reprotonation after a loss
Typically there is no ring cleavage (needs radical) or two bond scissions.
Depends highly on ion chemistry specifically acid-base (proton affinities)

23. Some popular cleavages
Cleave at a branch point. Loss of radical or other neutral to provide a more stable cation C H 3 + .
Obs. in Mass Spec
neutral
Cleave  to a heteroatom (capable of supporting positive charge) R O :
Obs. in Mass Spec
Resonance stabilized
neutral +
Note the use of “half arrow” for one-electron movements. e.g homolytic cleavage

24. Some examples Primary alcohols, m/z=31 CH2=OH+
Primary amines, m/z=30 CH2=NH2+

25. Commonly encountered Electron-Impact fragmentsH O + 29 C H 2 + 43 H + 77 + 91 N C H 2 + 92

26. McLafferty Rearrangements
Radical cations localized on keto-type oxygen give  cleavage
The mechanism limits this to EI fragmentation
Needs a H atom on a  sp3 carbon
Ketones, esters, carboxylic acids all give McLafferty products O + H R2 R1 • O + H • R1 R2 ••
Loss of neutral alkene
Note the use here, of the “half arrow” to represent “1-electron flow”
The new radical cation is stabilized by resonance

27. Important example of McLafferty R&R+•
m/z = 60
Seen for primary carboxylic acids

28. Non-Sequential Losses
M+-CH3CO
M+-CH3
MW=152

29. Hydrocarbons Weak [M•]+ Intense CnH2n+1
Good 43 m/z = C3H7 protonated cyclopropane
57 m/z = C4H9+
71 m/z = C5H11
Hydrocarbon chains characterized by successive losses of m/z=14 (clusters)

30. Cleavage  to C=O groups+ : + : . O + O
neutral +
Prominent for ketones :
CH3C=O+ m/z=43 O :
Obs. in mass spec. Acylium ions are resonance-stabilized

31. Example
M+• -45, loss of ethoxy radical

32. Example
M+• -43; also tropylium ion

33. Cleave  to Heteroatoms like O, N
neutral R + • : : R O . . : O + +
Observed in Mass Spec provided that a good stabilized carbocation can form
Heterolytic cleavage

34. Rearrangements and fragmentations to give good CarbocationsH + 2
Benzylic cation (stabilized including “tropylium” ion m/z=91
Good cleavage  to aromatic rings C + C H H 2 + H C C H 2 C H +

35. Example
Tropylium ion
Bromine pattern

36. Carboxylic acids
H present?; can give McLafferty R&R to alkene plus CH2=C(OH)(OH)•+ at m/z=60
Loss of water, especially in CI
Loss of 44 is loss of CO2
m/z=45 suggests OC–OH+

37. Amines N -R• R Cyclic amines will lose adjacent H•, form iminium ion+
-R• N R
Cyclic amines will lose adjacent H•, form iminium ion
In CI, NH+ can eliminate adjacent alkene, reprotonate

38. Silyl Ethers Loss of CH3• from Si Loss of R• in  cleavage
Loss of •CR3 then CH3• to (CH3)2Si=OH+ m/z=75
Total loss of carbinol to (CH3)3Si+ m/z=73

39. H transfer in heterosubstituted Anisoles+
Loss of CH2O
Extra H transfer mediated by adjacent heteroatom O R H H H +•

40. Nitroaromatics m/z= 93 Loss of •N=O
(this can form from lots of different origins)
Loss of •N=O N + O• O
Loss of CO
Aromatic!
m/z=65
Good test for aryloxy

41. Sulfur Compounds
Fortunately there is an [M+2]+ of 4% for the natural abundance of 34S. This is diagnostic for S vs 2x16O
Aliphatic thiols can split out H2S, [M-34]
Alpha cleavage at carbon bearing the sulfur in thiols, thioethers, similar to ethers, etc.
-R• R •

42. The “retro Diels-Alder” Cleavage
Cyclohexenes, with favorable 6-membered transition state. Can include heteroatoms (N,O, driven by keto-enol like stability. + •
Observed!
Typically you see both.
More stable cation will predominate
Also works for hetero-substituted (e.g. make enol)
Both EI (shown) and in Chemical Ionization. (protonated molecular ion, cleave, then reprotonation

43. An Example from Terpenoid Chemistry+ • + + •
12-Oleanene
m/z 204

44. A good example for Retro Diels Alder fragmentation
EI Mass Spectrum + + +
4-terpineol
MW 154
mz 86
mz 68

45. Double bonds can isomerize
-cleavage following double bond migration
MW=396
m/z118
136-water
m/z136
C9H12O+

46. Mass Spectral “shifts”
Note highly conserved regions; series of related compounds
Losses down to ions common in series.
Variation can not influence the fragmentation or introduce new fragmentation, e.g. internal fission not possible for homologs

47. Using the Information in Ion Clusters--Halogens
The paired appearance flags the ions as to the number of halogens
Fragment ions with the same halogen count preserve the pattern
35Cl
79Br
81Br2 81Br1
81Br
37Cl
CH3Cl
One chlorine
CHCl3
Three chlorines
CH3Br
One bromine
CHBr3
Three bromines

48. Great Websites http://medlib.med.utah.edu/masspec/elcomp.htm
Calculate potential molecular formulas from m/z
(neutrals only)
Wizard calculates both odd, even electron species based on m/z
The same folks provide a online wizard for calculating ion clusters (isotope patterns) from a suggested formula.
Free search of name, formulas