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MS Interpretation II

Fragmentation

Ionization OE+•

Electron Ionization (EI): Even-electron neutrals yield odd-electron radical cations.

M(EE) M (OE)- 1e-

+•

Electron can come from anywhere.

- 1e- (n) - 1e- (π)

- 1e- (σ)

EI

EI EI

EI

evenelectron

evenelectron

evenelectron

oddelectron

oddelectron

oddelectron

Ionization OE+•

Electron can (and does) come from anywhere.

EI- 1e- (n)- 1e- (π)

- 1e- (σ)EIEI

Ionization OE+•

Electron can (and does) come from anywhere.

EI- 1e- (n)- 1e- (π)

- 1e- (σ)EIEI

Likelihood of each of these depends on energy levels in molecular orbitals: π

σ

nπ*σ*

vacuumlevel

IEn IE

π

IEσ

mostlikely

leastlikely

Ionization OE+•

Electron can (and does) come from anywhere.

EI- 1e- (n)- 1e- (π)

- 1e- (σ)EIEI

Naturally, cannot distinguish these in mass spectrometer (all have m/z = 100).

But fragmentation patterns will be different.

Ionization EE+

CI, MALDI and ESI: Even-electron neutrals yield even-electron cations.

M(EE) + H+ MH+(EE)

Like EI, ionization may occur at multiple places.

+ +

+ H+

+ H+

Again, instrument cannot distinguish.

Fragmentation Mechanisms: EE+

• EE+ ions don't fragment to form OE+•

• Fragmentations more familiar and spectra generally less complex than OE+•

• More frequent and varied rearrangements can make interpretation more difficult

• Spectra can be more sensitive than EI to small structural changes

• Sensitivity to experimental conditions incompatible with reference libraries

Fragmentation Mechanisms: EE+

• Bond cleavage with charge migration

Fragmentation Mechanisms: EE+

• Bond cleavage with charge migration– R-OH2+ → R+ + H2O

Fragmentation Mechanisms: EE+

• Bond cleavage with charge migration– R-OH2+ → R+ + H2O

• Cleavage with cyclization and migration

Fragmentation Mechanisms: EE+

• Bond cleavage with charge migration– R-OH2+ → R+ + H2O

• Cleavage with cyclization and migration

Fragmentation Mechanisms: EE+

O

HN

O

HN

HN CR2

HN CR2+

• Bond cleavage with charge migration– R-OH2+ → R+ + H2O

• Cleavage with cyclization and migration

• Two-bond cleavage with charge retention

Fragmentation Mechanisms: EE+

O

HN

O

HN

HN CR2

HN CR2+

• Bond cleavage with charge migration– R-OH2+ → R+ + H2O

• Cleavage with cyclization and migration

• Two-bond cleavage with charge retention

Fragmentation Mechanisms: EE+

O

HN

O

HN

HN CR2

HN CR2+

H H-H2

• Bond cleavage with charge migration– R-OH2+ → R+ + H2O

• Cleavage with cyclization and migration

• Two-bond cleavage with charge retention

• Other fragmentations require MS/MS

Fragmentation Mechanisms: EE+

O

HN

O

HN

HN CR2

HN CR2+

H H-H2

Fragmentation Mechanisms in MS: OE+•

Electron Ionization: Fragmentation is always unimolecular. Two possible categories of fragmentation:

M (OE)+• A

(OE)

+•B(EE)

M (OE)+•

B • (OE)A+(EE)

+

+

parents daughters

charge migration(radical and charge part ways)

charge retention(neutral molecule is ejected)

Fragmentation Mechanisms in MS: OE+•

Electron Ionization: Fragmentation is always unimolecular. Two possible categories of fragmentation:

M (OE)+• A

(OE)

+•B(EE)

M (OE)+•

B • (OE)A+(EE)

+

+

parents daughters

charge migration(radical and charge part ways)

charge retention(neutral molecule is ejected)

Important: Only daughter ions are detected by MS instrument. Released neutrals are only inferred.

Fragmentation Mechanisms: OE•+

Fragmentation Mechanisms: OE•+

• Direct dissociation

Fragmentation Mechanisms: OE•+

• Direct dissociation– R-R' → R+ + R'•

Fragmentation Mechanisms: OE•+

• Direct dissociation– R-R' → R+ + R'•

• Cleavage adjacent to a heteroatom

Fragmentation Mechanisms: OE•+

• Direct dissociation– R-R' → R+ + R'•

• Cleavage adjacent to a heteroatom– R-CH2-Y-R' → R-CH2+ + •Y-R'

Fragmentation Mechanisms: OE•+

• Direct dissociation– R-R' → R+ + R'•

• Cleavage adjacent to a heteroatom– R-CH2-Y-R' → R-CH2+ + •Y-R'– R-CH2-Y-R' → R-CH2• + +Y-R'

Fragmentation Mechanisms: OE•+

• Direct dissociation– R-R' → R+ + R'•

• Cleavage adjacent to a heteroatom– R-CH2-Y-R' → R-CH2+ + •Y-R'– R-CH2-Y-R' → R-CH2• + +Y-R'

• α-Cleavage

Fragmentation Mechanisms: OE•+

• Direct dissociation– R-R' → R+ + R'•

• Cleavage adjacent to a heteroatom– R-CH2-Y-R' → R-CH2+ + •Y-R'– R-CH2-Y-R' → R-CH2• + +Y-R'

• α-Cleavage– R-CH2-Y-R' → R• + CH2=Y-R'+

Fragmentation Mechanisms: OE•+

• Direct dissociation– R-R' → R+ + R'•

• Cleavage adjacent to a heteroatom– R-CH2-Y-R' → R-CH2+ + •Y-R'– R-CH2-Y-R' → R-CH2• + +Y-R'

• α-Cleavage– R-CH2-Y-R' → R• + CH2=Y-R'+

– R-CH2-Y-R' → R+ + •CH2-Y-R'

Fragmentation Mechanisms: OE•+

• Direct dissociation– R-R' → R+ + R'•

• Cleavage adjacent to a heteroatom– R-CH2-Y-R' → R-CH2+ + •Y-R'– R-CH2-Y-R' → R-CH2• + +Y-R'

• α-Cleavage– R-CH2-Y-R' → R• + CH2=Y-R'+

– R-CH2-Y-R' → R+ + •CH2-Y-R'• Two-bond cleavage

Fragmentation Mechanisms: OE•+

• Direct dissociation– R-R' → R+ + R'•

• Cleavage adjacent to a heteroatom– R-CH2-Y-R' → R-CH2+ + •Y-R'– R-CH2-Y-R' → R-CH2• + +Y-R'

• α-Cleavage– R-CH2-Y-R' → R• + CH2=Y-R'+

– R-CH2-Y-R' → R+ + •CH2-Y-R'• Two-bond cleavage

– Retro Diels-Alder

Fragmentation Mechanisms: OE•+

• Direct dissociation– R-R' → R+ + R'•

• Cleavage adjacent to a heteroatom– R-CH2-Y-R' → R-CH2+ + •Y-R'– R-CH2-Y-R' → R-CH2• + +Y-R'

• α-Cleavage– R-CH2-Y-R' → R• + CH2=Y-R'+

– R-CH2-Y-R' → R+ + •CH2-Y-R'• Two-bond cleavage

– Retro Diels-Alder• Rearrangement

Fragmentation Mechanisms: OE•+

• Direct dissociation– R-R' → R+ + R'•

• Cleavage adjacent to a heteroatom– R-CH2-Y-R' → R-CH2+ + •Y-R'– R-CH2-Y-R' → R-CH2• + +Y-R'

• α-Cleavage– R-CH2-Y-R' → R• + CH2=Y-R'+

– R-CH2-Y-R' → R+ + •CH2-Y-R'• Two-bond cleavage

– Retro Diels-Alder• Rearrangement

– McLafferty Rearrangement

Fragmentation Mechanisms in MS:Direct Cleavage

(electron can come from any bond)

Fragmentation

+ ++ +

EI

(one-electron bond can break either way)

+

+

+ +

+

+ +

Fragmentation Mechanisms in MS:Direct Cleavage

(electron can come from any bond)

Fragmentation

+ ++ +

EI

(one-electron bond can break either way)

+

+

++

+

+

+ +

15

1571

7143

43

57

29

Fragmentation Mechanisms in MS

+

+

++

+ +

15

1571

7143

43

57

29

m/z

Rel

ativ

e A

bund

ance

+

+

Fragmentation Mechanisms in MS

+

+

++

+ +

15

1571

7143

43

57

29

What governs which ions are predominant?

+

+

Fragmentation Mechanisms in MS

+

+

++

+ +

15

1571

7143

43

57

29

What governs which ions are predominant?

1. Most ionizeable type of electrons. Here, all electron sources are σ bonds.

+

+

Fragmentation Mechanisms in MS

+

+

++

+ +

15

1571

7143

43

57

29

What governs which ions are predominant?

1. Most ionizeable type of electrons. Here, all electron sources are σ bonds.

2. Combination of most stable cation and radical. (Actually, this addresses most ionizeable bond within type.)

Here, secondary cation/radical combination favored over primary.

+

+

Fragmentation Mechanisms in MS

+

+

++

+ +

15

1571

7143

43

57

29

What governs which ions are predominant?

1. Most ionizeable type of electrons. Here, all electron sources are σ bonds.

2. Combination of most stable cation and radical. (Actually, this addresses most ionizeable bond within type.)

Here, secondary cation/radical combination favored over primary.

+

+

Fragmentation Mechanisms in MS

+

+

++

+ +

15

1571

7143

43

57

29

What governs which ions are predominant?

1. Most ionizeable type of electrons. Here, all electron sources are σ bonds.

2. Combination of most stable cation and radical. (Actually, this addresses most ionizeable bond within type.)

Here, secondary cation/radical combination favored over primary.

3. In charge separation, cation stability is more important than radical stability. Here, masses 71, 43 favored over 15, 57.

+

+

Fragmentation Mechanisms in MS

+

+

++

+ +

15

1571

7143

43

57

29

What governs which ions are predominant?

1. Most ionizeable type of electrons. Here, all electron sources are σ bonds.

2. Combination of most stable cation and radical. (Actually, this addresses most ionizeable bond within type.)

Here, secondary cation/radical combination favored over primary.

3. In charge separation, cation stability is more important than radical stability. Here, masses 71, 43 favored over 15, 57.

+

+

Fragmentation Mechanisms in MS

+

+

++

+ +

15

1571

7143

43

57

29

m/z

Rel

ativ

e A

bund

ance

+

+

Fragmentation Mechanisms in MS:Direct Cleavage

Fragmentation Mechanisms in MS:Direct Cleavage

Fragmentation Mechanisms in MS:Direct Cleavage

++

+ +

57

71

Fragmentation Mechanisms in MS:Direct Cleavage

++

+ +

57

71

+ +43

Further fragmentation is common.

Fragmentation Mechanisms in MS:α-Cleavage

56+

+ +41

t-butyl ethyl ether

O

102

Heteroatoms: Induced vs. Alpha Cleavage

t-butyl ethyl ether

O

102

Heteroatoms: Induced vs. Alpha Cleavage

O Oi

57

57

t-butyl ethyl ether

O

102

Heteroatoms: Induced vs. Alpha Cleavage

CH3•O

HO

O

87

5987

59

O Oi

57

57

2-butyl ethyl ether

O

102

2-butyl ethyl ether

O

102

iOO +

57

57

2-butyl ethyl ether

O

102

OO +

H

HO

73

45

α

45

73

iOO +

57

57

2-butyl ethyl ether

O

10287

59

OO +

H

HO

73

45

α

45

73

iOO +

57

57

Competition: i vs α Cleavage

Competition: i vs α Cleavage

• Induced cleavage is favored for larger heteroatoms

Competition: i vs α Cleavage

• Induced cleavage is favored for larger heteroatoms

• α-cleavage is favored for electron donating substituents

Competition: i vs α Cleavage

• Induced cleavage is favored for larger heteroatoms

• α-cleavage is favored for electron donating substituents

• Br,Cl < R•,π bond,S,O < N

SH

butanethiol

90

41

SH

butanethiol

90

41

47

SHSH +47

SH

butanethiol

90

41 57

SH+SH57

47

SHSH +47

SH

butanethiol

90

41 57

SH+SH57

47

SHSH +47

Both α- and i- cleavage are observed here

butylamine

NH2

73

butylamine

NH2

73

NH2NH2 +

30

30

butylamine

NH2

73

NH2NH2 +

30

30

α-cleavage dominates spectrum here

OE+• Fragments

OE+• Fragments

• Odd electron fragments are less common, especially at low mass

OE+• Fragments

• Odd electron fragments are less common, especially at low mass

– Even mass ions at low mass likely contain N

OE+• Fragments

• Odd electron fragments are less common, especially at low mass

– Even mass ions at low mass likely contain N

• These fragments arise from two-bond cleavages, or rearrangements

OE+• Fragments

• Odd electron fragments are less common, especially at low mass

– Even mass ions at low mass likely contain N

• These fragments arise from two-bond cleavages, or rearrangements

• Even mass OE+• fragments are important ions, as they can be highly sensitive to structural changes

2-hexanone

O

85 10071

2-hexanone

O

85 10071

O O

43

43

2-hexanone

O

85 10071

O O

43

43

HO

HO

HO

HO

5858

2-hexanone

O

85 10071

O O

43

43

HO

HO

HO

HO

5858

OE+• Product isfrom McLaffertyrearrangement

100

43

29

85

O

2-methyl 3-pentanone

100

43

29

85

O

2-methyl 3-pentanone

5757

71

OO+

OO

+

71

100

43

29

85

O

2-methyl 3-pentanone

McLafferty rearrangement is precluded here

No major OE+•

5757

71

OO+

OO

+

71

158

158

104

+

104

158

104

+

104

Charge stays with styrene fragment in this case

158

143

158

143

130

+

130

158

143

130

+

130

Charge stays with phenylbutadiene

OO

192177

136

12193

109

177

192159149135

Match the spectrum to the structure

192177

136

121

93

109

OO

- 136

Retro Diels-Alder reaction is observed

177

192159149

135

OO

O

- •CH3

XRetro Diels-Alder reaction is not observed

Aromatization via substitution dominates the spectrum

177

164

150

150

150122

119119

11891

91

77

105

O OEt O OMe O OMe

Match the Structure to the Spectrum

HO O

O

77

105

122

O OEt

O

119

91

O OMe

O

O

91119

118

O OMe