Teory of Mass Spectrometry Taslim Ersam

Teory of Mass Spectrometry Taslim Ersam I. Fragmentation Chemistry of Ions 1. ne bond σ-cleavages: a. cleavage of C-CC C C C C b. cleavage of C-heteroatom C Z C Z 15/09/2011 1

I. Fragmentation Chemistry of Ions 1. ne bond σ-cleavages: c. α-cleavage of C-heteroatom C C Z C C Z C C Z C C Z C C Z C C Z 15/09/2011 2

D. Fragmentation Chemistry of Ions 2. Two bond σ-cleavages/rearrangements: a. Elimination of a vicinal and heteroatom: Full mechanism Abbreviated: C C Z C C Z b. Retro-Diels-Alder 15/09/2011 3

Fragmentation Chemistry of Ions 2. Two bond σ-cleavages/rearrangements: c. McLafferty Rearrangement Full mechanism Abbreviated: 3. ther types of fragmentation are less common, but in specific cases are dominant processes These include: fragmentations from rearrangement, migrations, and fragmentation of fragments 15/09/2011 4

I. Fragmentation Chemistry of Ions 4. When deducing any fragmentation scheme: The even-odd electron rule applies: thermodynamics dictates that even electron ions cannot cleave to a pair of odd electron fragments Mass losses of 14 are rare The order of carbocation/radical stability is benzyl/3 > allyl/2 > 1 > methyl > * the loss of the longest carbon chain is preferred Fragment ion stability is more important than fragment radical stability Fragmentation mechanisms should be in accord with the even-odd Fragmentation mechanisms should be in accord with the even odd electron rule 15/09/2011 5

II. Fragmentation Patterns of Groups Aside: Some nomenclature rather than explicitly itl writing out single bond cleavages each time: C C 2 2 C C3 Fragment obs. by MS Neutral fragment inferred by its loss not observed Is written as: 57 15/09/2011 6

III. Fragmentation Patterns of Groups 1. Alkanes a) Very predictable apply the lessons of the stability of carbocations (or radicals) to predict or explain the observation of the fragments b) Method of fragmentation is single bond cleavage in most cases c) This is governed by Stevenson s s Rule the fragment with the lowest ionization energy will take on the charge the other fragment will still have an unpaired electron Example: iso-butanei C 3 C 3 15/09/2011 7

4. Fragmentation Patterns of Groups 1. Alkanes Fragment Ions : n-alkanes For straight chain alkanes, a M is often observed Ions observed: clusters of peaks C n 2n1 apart from the loss of C 3, -C 2 5, -C 3 7, etc. Fragments lost: C 3, C 2 5, C 3 7, etc. In longer chains peaks at 43 and 57 are the most common 15/09/2011 8

5. Fragmentation Patterns of Groups 1. Alkanes Example MS: n-alkanes n-heptane 43 57 M 15/09/2011 9

5. Fragmentation Patterns of Groups 1. Alkanes Fragment Ions : branched alkanes Where the possibility of forming 2 and 3 carbocations is high, the molecule is susceptible to fragmentation Whereas in straight chain alkanes, a 1 carbocation is always formed, its appearance is of lowered intensity with branched structures M peaks become weak to non-existent as the size and branching of the molecule increase Peaks at 43 and 57 are the most common as these are the isopropyl and tert-butyl cations 15/09/2011 10

5. Fragmentation Patterns of Groups 1. Alkanes Example MS: branched alkanes 2,2-dimethylhexane 57 M 114 15/09/2011 11

5. Fragmentation Patterns of Groups 1. Alkanes Fragment Ions : cycloalkanes Molecular ions strong and commonly observed cleavage of the ring still gives same mass value A two-bond cleavage to form ethene (C 2 4 ) is common loss of 28 2 C C 2 C 2 n C C R 2 C C 2 Side chains are easily fragmented 12

5. Fragmentation Patterns of Groups 1. Alkanes Example MS: cycloalkanes cyclohexane M - 28 = 56 M 84 13

1. Alkanes Example MS: cycloalkanes trans-p-menthane 97 M 140 14

2. Alkenes a) The π-bond of an alkene can absorb substantial energy molecular ions are commonly observed b) After ionization, double bonds can migrate readily determination of isomers is often not possible c) Ions observed: clusters of peaks C n 2n-1 apart from -C 3 5, -C 4 7, - C 5 9 etc. at 41, 55, 69, etc. d) Terminal alkenes readily form the allyl carbocation, m/z 41 R C 2 C C 2 R 2 C C C 2 15

2. Alkenes Example MS: alkenes cis- 2-pentene 55 M 70 15/09/2011 16

2. Alkenes Example MS: alkenes 1-hexene Take home assignment: What is M-42 and m/z 42? 41 56 M 84 15/09/2011 17

2. Alkenes Example MS: alkenes 1-pentene Take home assignment 2: What is m/z 42? M 70 18

Comparison: Alkanes vs. alkenes ctane (75 ev) M 114 m/z 85, 71, 57, 43 (base), 29 ctene (75 ev) M 112 (stronger @ 75eV than octane) m/z 83, 69, 55, 41, 29 19

2. Alkenes Fragment Ions : cycloalkenes Molecular ions strong and commonly observed cleavage of the ring still gives same mass value Retro-Diels-Alder is significant observed loss of 28 Side chains are easily fragmented 15/09/2011 20

2. Alkenes Example MS: cycloalkenes 1-methyl-1-cyclohexene 81 68 M 96 15/09/2011 21

3. Alkynes Fragment Ions a) The π-bond of an alkyne can also absorb substantial energy molecular ions are commonly observed b) For terminal alkynes, the loss of terminal hydrogen is observed (M- 1) this may occur at such intensity to be the base peak or eliminate the presence of M c) Terminal alkynes form the propargyl cation, m/z 39 (lower intensity than the allyl cation) R 2 C C C R 2 C C C 15/09/2011 22

3. Alkynes Example MS: alkynes 1-pentyne 67 39 M 68 23

3. Alkynes Example MS: alkynes 2-pentyne 53 M 68 24

4. Aromatic ydrocarbons Fragment Ions a) Very intense molecular ion peaks and little fragmentation of the ring system are observed 75 ev e - b) Where alkyl groups are attached to the ring, a favorable mode of cleavage is to lose a -radical to form the C 7 7 ion (m/z 91) c) This ion is believed to be the tropylium ion; formed from rearrangement of the benzyl cation C 3 C 2 25

4. Aromatic ydrocarbons Fragment Ions d) If a chain from the aromatic ring is sufficiently long, a McLafferty rearrangement is possible e) Substitution patterns for aromatic rings are able to be determined by MS with the exception of groups that have other ion chemistry 26

4. Aromatic ydrocarbons Example MS: aromatic hydrocarbons p-xylene m/z 91 3 C C 3 C 3 M 106 27

4. Aromatic ydrocarbons Example MS: aromatic hydrocarbons n -butylbenzene 92 91 M 134 28

5. Alcohols Fragment Ions a) Additional modes of fragmentation will cause lower M than for the corresponding alkanes 1 and 2 alcohols have a low M, 3 may be absent b) The largest alkyl group is usually lost; the mode of cleavage typically is similar for all alcohols: primary 2 C m/z 31 secondary 45 tertiary 59 29

5. Alcohols Fragment Ions c) Dehydration (M - 18) is a common mode of fragmentation importance increases with alkyl chain length (>4 carbons) 1,2-elimination occurs from hot surface of ionization chamber 1,4-elimination occurs from ionization both modes give M - 18, with the appearance and possible subsequent fragmentation of the remaining alkene d) For longer chain alcohols, a McLafferty type rearrangement can produce water and ethylene (M - 18, M - 28) R R 30

5. Alcohols Fragment Ions e) Loss of is not favored for alkanols (M 1) f) Cyclic alcohols fragment by similar pathways α-cleavage m/z 57 dehydration, 2 M - 18 15/09/2011 31 Prof Dr. Taslim Ersam

5. Alcohols Example MS: alcohols n -pentanol 42-2 70 31 M 88 32

5. Alcohols Example MS: alcohols 2-pentanol 45 M 88 33

5. Alcohols Example MS: alcohols 2-methyl-2-pentanol 59 87 M 102 34

5. Alcohols Example MS: alcohols cyclopentanol 57 M 86 35

6. Phenols Fragment Ions a) Do not fully combine observations for aromatic alcohol; treat as a unique group b) For example, loss of is observed (M 1) charge can be delocalized by ring most important for rings with EDGs c) Loss of C (extrusion) is commonly observed (M 28); Net loss of the formyl radical (C, M 29) is also observed from this process C -C - 36

5. Example MS: phenols phenol -C 66 -C 65 M 94 37

An interesting combination of functionalities: benzyl alcohols Upon ring expansion to tropylium ions, they become phenols! M 108 tropyliol - C 79 M 1, 107 tropyliol 2 77 38

7. Ethers Fragment Ions a) Slightly more intense M than for the corresponding alcohols or alkanes b) The largest alkyl group is usually lost to α-cleavage; the mode of cleavage typically is similar to alcohols: R 2 C R R 2 C R c) Cleavage of the C- bond to give carbocations is observed where favorable R C R R C R R R 39

7. Ethers Fragment Ions d) Rearrangement can occur of the following type, if α-carbon is branched: R C C C 2 R C R R e) Aromatic ethers, similar to phenols can generate the C 6 5 ion by loss of the alkyl group rather than ; this can expel C as in the phenolic degradation d R R C C 5 5 40

7. Example MS: ethers butyl methyl ether 45 M 88 41

7. Example MS: ethers anisole Mass Spectrometry Take home what is m/z 78? 77 M 108 M-28 (-C 3, -C) 65 93 42

8. Aldehydes - Fragment Ions a) Weak M for aliphatic, strong M for aromatic aldehydes b) α-cleavage is characteristic and often diagnostic for aldehydes can occur on either side of the carbonyl R R C M-1 peak R R C m/z 29 c) β-cleavage is an additional mode of fragmentation R R m/z R M - 41 can be R-subs. 43

8. Aldehydes - Fragment Ions d) McLafferty rearrangement observed if γ-s present R R m/z 44 e) Aromatic aldehydes d a-cleavages are more favorable, both to lose (M - 1) and C (M 29) C m/z R Remember: aromatic ring can be subs. 44

8. Example MS: aldehydes (aliphatic) pentanal m/z 44 C 29 M-1 85 M 86 45

8. Example MS: aldehydes (aromatic) m-tolualdehyde M-1 119 M 120 91 46

9. Ketones - Fragment Ions a) Strong M for aliphatic and aromatic ketones b) α-cleavage can occur on either side of the carbonyl the larger alkyl group is lost more often M 15, 29, 43 m/z 43, 58, 72, etc. R R 1 R C R 1 R 1 is larger than R c) β-cleavage is not as important of a fragmentation mode for ketones compared to aldehydes but sometimes observed R R 1 R R 1 47

9. Ketones - Fragment Ions d) McLafferty rearrangement observed if γ- s present if both alkyl chains are sufficiently long both can be observed R R R 1 R 1 e) Aromatic ketones α-cleavages are favorable primarily to lose R (M 15, 29 ) to form the C 6 5 C ion, which can lose C R C R m/z 105 C Remember: aromatic ring can be subs. m/z 77 15/09/2011 48 Prof Dr. Taslim Ersam

9. Ketones - Fragment Ions f) cyclic ketones degrade in a similar fashion to cycloalkanes and cycloalkanols: m/z 55 m/z 70 - C m/z 42 15/09/2011 49 Prof Dr. Taslim Ersam

9. Example MS: ketones (aliphatic) 2-pentanone 43 58 M-15 M 86 50

9. Example MS: ketones (aromatic) propiophenone C m/z 105 m/z 77 M 134 51

10. Esters - Fragment Ions a) M weak in most cases, aromatic esters give a stronger peak b) Most important α-cleavage reactions involve loss of the alkoxy- radical to leave the acylium ion R R 1 R C R 1 c) The other α-cleavage (most common with methyl esters, m/z 59) involves the loss of the alkyl group R R 1 R C R 1 52

10. Esters - Fragment Ions d) McLafferty occurs with sufficiently long esters R 1 R 1 e) Ethyl and longer (alkoxy chain) esters can undergo the McLafferty rearrangement R R 53

10. Esters - Fragment Ions f) The most common fragmentation route is to lose the alkyl group by α-cleavage, to form the C 6 5 C ion (m/z 105) R C R Can lose C to give m/z 77 54

10. Esters - Fragment Ions g) ne interesting fragmentation is shared by both benzyloxy esters and aromatic esters that have an ortho-alkyl group benzyloxy ester C C 2 ketene fragmentation ortho-alkylbenzoate ester C 2 R C C 2 R 55

10. Example MS: esters (aliphatic) ethyl butyrate 29 71 both McLafferty (take home exercise) m/z 88 43 M 116 56

10. Example MS: esters (aliphatic) ethyl butyrate 29 71 both McLafferty (take home exercise) m/z 88 43 M 116 57

10. Example MS: esters (benzoic) methylortho-toluate 119 91 C C 2 m/z 118 M 150 58

11. Carboxylic Acids - Fragment Ions a) As with esters, M weak in most cases, aromatic acids give a stronger peak b) Most important α-cleavage reactions involve loss of the alkoxyradical to leave the acylium ion R R C c) The other α-cleavage (less common) involves the loss of the alkyl radical. Although less common, the m/z 45 peak is somewhat diagnostic for acids. R R C 59

11. Carboxylic Acids - Fragment Ions d) McLafferty occurs with sufficiently long acids m/z 60 e) aromatic acids degrade by a process similar to esters, loss of the gives the acylium ion which can lose C : C further loss of C to m/z 77 60

11. Carboxylic Acids - Fragment Ions f) As with esters, those benzoic acids with an ortho-alkyl group will lose water to give a ketene radical cation ortho-alkylbenzoic acid C 2 C C 2 61

11. Example MS: carboxylic acids (aliphatic) pentanoic acid m/z 60 M 102 62

11. Example MS: carboxylic acids (aromatic) p-toluic acid M 136 119 91 63

Summary Carbonyl Compounds For carbonyl compounds there are 4 common modes of fragmentation: A 1 & A 2 -- two α-cleavages R G C G 2 R R G R C G B -- β-cleavage g R G R G C McLafferty Rearrangement R G R G 64

Summary Carbonyl Compounds In tabular format: Aldehydes Ketones m/z of ion observed Esters Acids Amides Fragmentation ti Path G = G = R G = R G = G = N 2 A 1 α-cleavage A 2 α-cleavage -R 29 43 b 59 b 45 44 d -G 43 b 43 b 43 b 43 b 43 b B - G 43 a 57 b 73 b 59 a 58 a β-cleavage C McLafferty 44 a 58 b,c 74 b,c 60 a 59 a b = base, add other mass attached to this chain a = base, if α-carbon branched, add appropriate mass c = sufficiently i long structures can undergo on either side of C= d = if N-substituted, add appropriate mass 65

12. Amines - Fragment Ions a) Follow nitrogen rule odd M, odd # of nitrogens; nonetheless, M weak in aliphatic amines b) α-cleavage reactions are the most important fragmentations for amines; for 1 n-aliphatic amines m/z 30 is diagnostic R C N R C N c) McLafferty not often observed with amines, even with sufficiently long alkyl chains d) Loss of ammonia (M 17) is not typically observed 66

12. Amines - Fragment Ions e) Mass spectra of cyclic amines is complex and varies with ring size f) Aromatic amines have intense M g) Loss of a hydrogen atom, followed by the expulsion of CN is typical for anilines N 2 N CN h) Pyridines have similar stability (strong M, simple MS) to aromatics, expulsion of CN is similar to anilines 67

12. Example MS: amines, 1 pentylamine 30 N 2 M 87 68

12. Example MS: amines, 2 dipropylamine N 72 N M 101 69

12. Example MS: amines, 3 tripropylamine N 114 M 143 70

13. Amides - Fragment Ions a) Follow nitrogen rule odd M, odd # of nitrogens; observable M b) α-cleavage reactions afford a specific fragment of m/z 44 for primary amides R C N2 R C N 2 m/z 44 c) McLafferty observed where γ-hydrogens are present N 2 N 2 71

13. Example MS: amides butyramide C N2 44 59 N 2 M 87 72

13. Example MS: amides (aromatic) benzamide N 2 C 77 N C 2 M 121 105 73

14. Nitriles - Fragment Ions a) Follow nitrogen rule odd M, odd # of nitrogens; weak M b) Principle degradation is the loss of an -atom (M 1) from α- carbon: R 2 C C N c) Loss of CN observed (M 27) R C C N d) McLafferty observed where γ-hydrogens are present N C N 2 C C m/z 41 e) Aromatic nitriles give a strong M as the strongest peak, loss of CN is common (m/z 76) as opposed to loss of CN (m/z 77) 74

14. Example MS: nitriles propionitrile M-1 54 -C N M 55 75

14. Example MS: nitriles valeronitrile (pentanenitrile) N C N C 2 C 43 m/z 41 54 N C M 83 76

15. Nitro - Fragment Ions a) Follow nitrogen rule odd M, odd # of nitrogens; M almost never observed, unless aromatic b) Principle degradation is loss of N (m/z 30) and N 2 (m/z 46) R N R N m/z 46 R N R N R N R N m/z 30 77

15. Nitro - Fragment Ions c) Aromatic nitro groups show these peaks as well as the fragments of the loss of all or parts of the nitro group N 2 N C m/z 93 m/z 65 N 2 N 2 C 4 3 C C m/z 77 m/z 51 78

15. Example MS: nitro 1-nitropropane N 2 43 N 30 N 2 46 M 89 79

15. Example MS: nitro (aromatic) p-nitrotoluene N 2 91 M 137 C 5 5 m/z 107 80

16. alogens - Fragment Ions a) alogenated compounds often give good M b) Fluoro- and iodo-compounds do not have appreciable contribution from isotopes c) Chloro- and bromo-compounds are unique in that they will show strong M2 peaks for the contribution of higher isotopes d) For chlorinated compounds, the ratio of M to M2 is about 3:1 e) For brominated compounds, the ratio of M to M2 is 1:1 f) An appreciable M4, 6, peak is indicative of a combination of these two halogens use appropriate guide to discern number of each 81

16. alogens - Fragment Ions g) Principle fragmentation mode is to lose halogen atom, leaving a carbocation the intensity of the peak will increase with cation stability R X R X h) Leaving group ability contributes to the loss of halogen most strongly for -I and -Br less so for -Cl, and least for F i) Loss of X is the second most common mode of fragmentation ti here the conjugate basicity of the halogen contributes (F > Cl > Br > I) R C C X R C C 2 X 82

16. alogens - Fragment Ions j) Less often, α-cleavage will occur: R C X R 2 C X k) For longer chain halides, the expulsion of a >δ carbon chain as the radical is observed R X X R l) Aromatic halides give stronger M, and typically lose the halogen atom to form C 6 5 83

16. Example MS: chlorine 1-chloropropane Cl 43 2 C Cl m/z 49, 51 M2 M 78 84

16. Example MS: chlorine p-chlorotoluene Cl 91 M 126 M2 85

16. Example MS: bromine 1-bromobutane Br 57 M 136 M2 2 C Br 86

16. Example MS: bromine p-bromotoluene Br 91 M2 M 170 87

16. Example MS: multiple bromines 3,4-dibromotoluene Br Br 90 Br Br 169, 171 M2 M4 M 248 88

16. Example MS: iodine iodobenzene M 204 I 77 89

F. Approach to analyzing a mass spectrum 1. As with IR, get a general feel for the spectrum before you analyze anything is it simple, complex, groups of peaks, etc. 2. Squeeze everything you can out of the M peak that you can (once you have confirmed it is the M ) Strong or Weak? Isotopes? M1? M2, 4, Apply the Nitrogen rule Apply the Rule of Thirteen to generate possible formulas (you can quickly dispose of possibilities based on the absence of isotopic i peaks or the inference of the nitrogen rule) Use the DI from the Rule of Thirteen to further reduce the possibilities Is there an M-1 peak? 90

F. Approach to analyzing a mass spectrum 3. Squeeze everything you can out of the base peak What ions could give this peak? (m/z 43 doesn t help much) What was lost from M to give this peak? When considering the base peak initially, only think of the most common cleavages for each group 4. Look for the loss of small neutral molecules from M 2 C=C 2, C C, 2, R, CN, X 5. Now consider the possible diagnostic peaks on the spectrum (e.g.: 29, 30, 31, 45, 59, 77, 91, 105 etc.) 6. Lastly, once you have a hypothetical molecule that explains the data, see if you can verify it by use of other less intense peaks on the spectrum not 100% necessary (or accurate) but if this step works it can add to the confidence level l 91

End of material Schedule: Workshops: Friday ct. 28 th, Monday ct. 31 st, Wednesday Nov. 2 nd (if needed). Exam: Monday, November 7 th (5 PM?); take home portion given out Friday, November 4 th, due Wednesday, November 9 th. NMR material will begin Friday November 4 th. We will have lecture on Monday, November 7 th (NMR)! What s left: Two NMR exams one in class, one take-home Final are left 100, 100 and 125 pts. 92