Mass spectrometry provides information about molecular structure through analysis of mass-to-charge ratios of ions produced from molecules. The most abundant ion forms the base peak in the mass spectrum. Common ionization methods like electron impact cause molecular ions to fragment, producing smaller ions. High resolution mass spectrometry can distinguish between molecules with the same nominal mass but different precise masses based on their elemental compositions. Fragmentation patterns provide additional structural information.
Mass spectrometry provides information about molecular structure through analysis of mass-to-charge ratios of ions produced from molecules. The most abundant ion forms the base peak in the mass spectrum. Common ionization methods like electron impact cause molecular ions to fragment, producing smaller ions. High resolution mass spectrometry can distinguish between molecules with the same nominal mass but different precise masses based on their elemental compositions. Fragmentation patterns provide additional structural information.
Mass spectrometry provides information about molecular structure through analysis of mass-to-charge ratios of ions produced from molecules. The most abundant ion forms the base peak in the mass spectrum. Common ionization methods like electron impact cause molecular ions to fragment, producing smaller ions. High resolution mass spectrometry can distinguish between molecules with the same nominal mass but different precise masses based on their elemental compositions. Fragmentation patterns provide additional structural information.
Mass spectrometry provides information about molecular structure through analysis of mass-to-charge ratios of ions produced from molecules. The most abundant ion forms the base peak in the mass spectrum. Common ionization methods like electron impact cause molecular ions to fragment, producing smaller ions. High resolution mass spectrometry can distinguish between molecules with the same nominal mass but different precise masses based on their elemental compositions. Fragmentation patterns provide additional structural information.
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Organic Spectroscopy
Mass Spectrometry General The mass spectrum is a plot of ion abundance versus m/e ratio (mass/charge ratio). The most abundant ion formed in the ionization chamber gives to rise the tallest peak in the mass spectrum, called the base peak.
By using one of the many ionization methods, the simple removal of an electron from a molecule yields a positively charged radical cation, known as the molecular ion and symbolized as [M]+.
After formation of molecular Ion in the ionization chamber, excess energy causes further fragmentation of the molecular ion. Various positively charged masses (and/or positively charged radical cations) show up in the spectrum.
The mass of the molecular ion can be determined to an accuracy of ± 0.0001 of a
mass unit, which yields a high resolution (hi-res) mass spectrum.
Ionization Methods The most common method of ionization involves Electron impact (EI) in which molecule is bombarded with high-energy electrons. This is the strongest ionization method which usually causes further fragmentation. Since the molecular ion gets fragmented, the molecular ion usually produces a small peak with this method. Mass Spectrum of Isobutyrophenone
O 105 (base peak) C6H5CO+
molecular weight = 148
77 C6H5+
molecular ion, M M+1
(148) Facts Concerning the Molecular Ion Peak
1. The peak must correspond to the ion of highest mass excluding the usually much smaller isotopic peaks that occur at M+1, M+2, etc.
2. To be a molecular ion, the ion must contain an odd number of electrons.
One electron is lost, forming a radical-cation.
To determine this, calculate the IHD. It must be a whole number.
Consider an ion at m/z = 112. A possible molecular formula is C6H8O2. The IHD = 3 (a whole number), so this could be the molecular ion. However, an ion at 105 could correspond to a molecular formula of C7H5O. The IHD is 5.5 (not a whole number), so this can’t be the molecular ion.
3. The ion must be capable of producing smaller, fragment ions by loss
of neutral fragments of predictable structure. The Lifetimes of Various Molecular Ions Aromatics > conjugated alkenes > alicyclic compounds> organic sulfides > unbranched hydrocarbons > mercaptans > ketones > amines > esters > ethers > carboxylic acids > branched hydrocarbons > alcohols
Therefore, alcohols produce small or non-existent molecular ions because
their lifetimes are too short. They fragment before they can be detected.
CH3CH2CH2CH2OH MW = 74
No M visible The Nitrogen Rule The nitrogen rule states that an odd number of nitrogen atoms will form a molecular ion with an odd mass number. An even number of nitrogen atoms (or none at all) will produce a molecular ion with an even mass number. This occurs because nitrogen has an odd-numbered valence.
Examples: C6H5CH2NH2 MW = 107
H2NCH2CH2NH2 MW = 60 Determining Possible Molecular Formulas from the Molecular Ion: Rule of 13
• Rule of Thirteen: Based upon the assumption that CnHn
and its mass of 13 is present in most organic compounds. • Divide the molecular ion by 13. This gives a value for n and any remainder (R) = additional H’s. • For a M+ = 106, n = 8(106/13) with a R of 2. A possible molecular formula for this ion is C8H8+2 = C8H10 • For each CH there are heteroatom equivalents. Rule of 13 Heteroatom Equivalents Element CH Element CH Equivalent Equivalent 1H C 31P C2H7 12 16O CH4 32S C2H8 14N CH2 16O32S C4 16O14N C2H6 35Cl C2H11 19F CH7 79Br C6H7 28Si C2H4 127I C10H7 Candidate molecular formulas for M+. = 108
108/13 = 8, R = 4 C8H12
O = CH4; therefore, C8H12 – CH4 + O = C7H8O
or C8H12 – 2(CH4) + 2O = C6H4O2
or C8H12 – C6H7 + Br = C2H5Br
Calculate three candidate molecular formulas for C10H18.
When an odd amu M+. is seen, suspect one nitrogen or an odd multiple. Candidate molecular formulas for a M+. = 121 are:
121/13 = 9, R = 4 C9H13; IHD = 3.5 so it can’t be M+.
O = CH4; N = CH2
or C9H13 – CH2 + N = C8H11N; IHD = 3, so it may be M+.
or C9H13 – 2(CH2) + 2N = C7H9N2; IHD = 4.5 so it can’t be M+.
or C9H13 – 3(CH2) + 3N = C6H7N3; IHD = 5, so it may be M+.
or C9H13 – (CH2) – (CH4) + N + O = C7H7NO IHD = 5,
so it may be M+. Determining the Molecular Formula from the Molecular Ion: Isotope Ratio Data In this method, the relative intensities of the peaks due to the molecular ion and related isotopic peaks are examined. Advantage: • Does not require an expensive high-res MS instrument. Disadvantages: • Isotopic peaks may be difficult to locate. • Useless when the molecular ion peak is very weak or does not appear.
3-pentanone Relative Abundances of Common Elements and Their isotopes
Relative Relative Relative
Element Isotope Abun- Isotope Abun- Isotope Abun- dance dance dance
Carbon 12C 100 13C 1.08
Hydrogen 1H 100 2H 0.016
Nitrogen 14N 100 15N 0.38
Oxygen 16O 100 17O 0.04 18O 0.20
Sulfur 32S 100 33S 0.78 34S 4.40
Chlorine 35Cl 100 37Cl 32.5
Bromine 79Br 100 81Br 98.0
Example: 3-pentanone, C5H10O %(M + 1) = 100 (M + 1)/M = 1.08 x # C atoms + 0.016 x # H atoms + 0.04 x # O atoms = 1.08 x 5 + 0.016 x 10 + 0.04 x 1= 5.60 Actual spectrum: [1% (M +1)/17.4% (M)] x 100 = 5.75 Relative Intensities of Isotope Peaks for Bromine and Chlorine
194 Determining the Molecular Formula from the Molecular Ion: High Resolution MS (HRMS) Using low resolution (LR) MS, you could not distinguish between the following molecular formulas, each of which has a mass of 60:
C3H8O = (3 x 12) + (8 x 1) + 16 = 60
C2H8N2 = (2 x 12) + (8 x 1) + (2 x 14) = 60
C2H4O2 = (2 x 12) + (4 x 1) + (2 x 16) = 60
CH4N2O = 12 + (4 x 1) + (2 x 14) + 16 = 60
However, they can be distinguished using HRMS.
Precise Masses of Some Common Elements Element Atomic Weight Isotope Mass Hydrogen 1.0097 1H 1.00783 2H 2.01410 Carbon 12.01115 12C 12.0000 13C 13.00336 Nitrogen 14.0067 14N 14.0031 15N Using precise masses: 15.0001 Oxygen 15.9994 16O 15.9949 C3H8O = 60.05754 17O 16.9991 18O 17.9992 C2H8N2 = 60.06884 Fluorine 18.9984 19F 18.9984 Silicon 28.086 28Si 27.9769 C2H4O2 = 60.02112 29Si 28.9765 30Si 29.9738 CH4N2O = 60.03242 Phosphorus 30.974 31P 30.9738 Sulfur 32.064 32S 31.9721 33S 32.9715 34S 33.9679 Chlorine 35.453 35Cl 34.9689 37Cl 36.9659 Bromine 79.909 79Br 78.9183 81Br 80.9163 Iodine 126.904 127I 126.9045 Fragmentation Patterns Most common: one-bond cleavage to produce an odd-electron neutral fragment, (radical, which is not detected) and an even-electron carbocation. Ease of frag- mentation to form cations follows the scheme below:
Fragmentation Patterns (cont.) Two-bond cleavage: The odd-electron molecular ion produces an odd-electron fragment ion and an even-electron neutral fragment (not detected).
Not detected
McLafferty Rearrangement
+ + H R O R O H + H3C O H3C O 71 CH3 H3C C CH2CH3 MW = 86 Cleavage at branch points CH3
57
57
71 -cleavage to hetero atoms 87 43 MW = 102 H3C O CH3
CH3 CH3 cleavage to hetero atoms
CH3-CH=OH+
43 87 91
-cleavage to aromatic ring MW = 134
91
92 (from McLafferty Rearrangement)
CH2 43
Cleavage to carbonyl groups O
MW = 86 H3C CH3
43 60 O McLafferty rearrangement OH carboxylic acids
OH 60 CH2 C OH 74 McLafferty rearrangement O esters MW = 102 CH3 O
OH CH2 C OCH3
74 Hexane C6H14 MW = 86.18 Molecular ion peaks are present, possibly with low intensity. The fragmentation pattern contains clusters of peaks 14 mass units apart (which represent loss of (CH2)nCH3). 3-Pentanol C5H12O MW = 88.15
An alcohol's molecular ion is small or non-existent.
Cleavage of the C-C bond next to the oxygen usually occurs. A loss of H2O may occur as in the spectrum below. 3-Phenyl-2-propenal C9H8O MW = 132.16
Cleavage of bonds next to the carboxyl group
results in the loss of hydrogen (molecular ion less 1) or the loss of CHO (molecular ion less 29). 3-Methylbutyramide C5H11NO MW = 101.15
Primary amides show a base peak
due to the McLafferty rearrangement. n-Butylamine C4H11N MW = 73.13 Molecular ion peak is an odd number. Alpha-cleavage dominates aliphatic amines. n-Methylbenzylamine C8H11N MW = 121.18 Another example is a secondary amine shown below. Again, the molecular ion peak is an odd number. The base peak is from the C-C cleavage adjacent to the C-N bond. Naphthalene C10H8 MW = 128.17 Molecular ion peaks are strong due to the stable structure. 2-Butenoic acid C4H6O2 MW = 86.09 In short chain acids, peaks due to the loss of OH (molecular ion less 17) and COOH (molecular ion less 45) are prominent due to cleavage of bonds next to C=O. Fragments appear due to bond cleavage next to C=O (alkoxy group loss, -OR) and hydrogen rearrangements.
oxygen atom (C-C bond next to the oxygen). 1-Bromopropane C3H7Br MW = 123.00
The presence of chlorine or bromine atoms is
usually recognizable from isotopic peaks. 4-Heptanone C7H14O MW = 114.19
Major fragmentation peaks result from cleavage
of the C-C bonds adjacent to the carbonyl. Which structure supports the following mass spectrum?
MW = 100 MW = 100 MW = 114
MW = 100 MW = 86 Which structure supports the following mass spectrum? NH2 NH2 NH MW = 101 MW = 87 MW = 87
NH2
NH2
MW = 87 MW = 73 Which structure supports the following mass spectrum?
O O O
O O O MW = 116 MW = 130 MW = 116 O O O O MW = 116 MW = 102 An unknown compound has the mass spectrum shown below. The IR spectrum shows peaks in the 3100-3030 and the 2979-2879 cm-1 ranges and a strong absorption at 1688 cm-1. Suggest a structure consistent with this data. An unknown compound has the mass spectrum shown below. The IR spectrum shows peaks in the 2963-2861 cm-1 range and a strong absorption at 1718 cm-1. Suggest a structure consistent with this data.
