Mass spectroscopy

Mass spectrometry (MS) is an analytical technique of displaying the spectra of

masses of the atoms or molecules comprising a sample of material. The
spectra are used to determine the elemental or isotopic signature of a sample,
the masses of particles & of molecules, & to elucidate the chemical structures
of molecules, such as peptides & other chemical compounds. Mass
spectrometry works by ionizing chemical compounds to generate charged
molecules or molecule fragments & measuring their mass-to-charge ratios. In a
typical MS procedure:
1. A sample (which may be solid, liquid, or gas) is ionized by bombarding it
with electrons. This may cause some of the sample's molecules to break
into charged fragments.
2. These ions are then separated according to their mass-to-charge ratio,
typically by accelerating them & subjecting them to an electric or magnetic
field: ions of the same mass-to-charge ratio will undergo the same amount
of deflection.The ions are separated according to their mass-to-charge
ratio. This is key step.
3. The ions are dynamically detected by some mechanism capable of
detecting energetic charged particles such as an electron multiplier.
4. The signal is processed into spectra of masses of particles of that sample.
Results are displayed as spectra of the relative abundance of detected ions
as a function of the mass-to-charge ratio.
 The atoms or molecules in the sample can be identified by correlating known
masses to identified masses or through a characteristic fragmentation pattern.
In order to measure the characteristics of individual molecules, a mass
spectrometer converts them to ions so that they can be moved about &
manipulated by external electric & magnetic fields. The three essential
functions of a mass spectrometer, & the associated components, are:
1. A small sample is ionized, to cations by loss of an electron. The Ion Source
2. The ions are sorted & separated according to their mass & charge. The
Mass Analyzer.
3. The separated ions are then measured, & results displayed on a chart. The
Detector
The ionizer converts a portion of the sample into ions. There is a wide variety
of ionization techniques, depending on the phase (solid, liquid, gas) of the
sample and the efficiency of various ionization mechanisms for the unknown
species. An extraction system removes ions from the sample, which are then
trajected through the mass analyzer & onto the detector. The differences in
masses of the fragments allows the mass analyzer to sort the ions by their
mass-to-charge ratio. The detector measures the value of an indicator quantity
and thus provides data for calculating the abundances of each ion present.
Because ions are very reactive & short-lived, their formation & manipulation
must be conducted in a vacuum. The pressure under which ions may be
handled is roughly 10-5 to 10-8 torr (less than a billionth of an atmosphere). Each
of the three tasks listed above may be accomplished in different ways. In one
common procedure, ionization is effected by a high energy beam of electrons,
& ion separation is achieved by accelerating & focusing the ions in a beam,
which is then bent by an external magnetic field. The ions are then detected
electronically & the resulting information is stored & analyzed in a computer. A
mass spectrometer operating in this fashion is outlined in the following diagram.

The heart of the spectrometer is the ion source.

Here molecules of the sample (black dots) are
bombarded by electrons (light blue lines) issuing
from a heated filament. This is called an EI
(electron-impact) source. Gases & volatile liquid
samples are allowed to leak into the ion source
from a reservoir (as shown). Non-volatile solids
and liquids may be introduced directly. Cations
formed by the electron bombardment (red dots) are pushed away by a charged
repellor plate (anions are attracted to it), & accelerated toward other electrodes,
having slits through which the ions pass as a beam. Some of these ions
fragment into smaller cations & neutral fragments. A perpendicular magnetic
field deflects the ion beam in an arc whose radius is inversely proportional to
the mass of each ion. Lighter ions are deflected more than heavier ions. By
varying the strength of the magnetic field, ions of different mass can be focused
progressively on a detector fixed at the end of a curved tube (also under a high
vacuum). When a high energy electron collides with a molecule it often ionizes
it by knocking away one of the molecular electrons (either bonding or non-
bonding). This leaves behind a molecular ion (colored red in the following
diagram). Residual energy from the collision may cause the molecular ion to
fragment into neutral pieces (colored green) and smaller fragment ions
(colored pink and orange). The molecular ion is a radical cation, but the
fragment ions may either be radical cations (pink) or carbocations (orange),
depending on the nature of the neutral fragment.

The Nature of Mass Spectra

A mass spectrum will usually be presented as a vertical bar graph, in which
each bar represents an ion having a specific mass-to-charge ratio (m/z)& length
of the bar indicates relative abundance of ion. The most intense ion is assigned
an abundance of 100 & it is referred to as base peak. Most of the ions formed
in a mass spectrometer have a single charge, so the m/z value is equivalent to
mass itself. Modern mass spectrometers easily distinguish (resolve) ions
differing by only a single atomic mass unit, & thus provide completely accurate
values for the molecular mass of a compound. The highest-mass ion in a
spectrum is normally considered to be the molecular ion, & lower-mass ions are
fragments from the molecular ion, assuming sample is a single pure compound.
Atomic mass is given in terms of the unified atomic mass unit (symbol: μ) or
dalton (symbol: Da). In recent years the dalton is preffered over the unified
atomic mass unit. The dalton is classified as a "non-SI unit whose values in SI
units must be obtained experimentally". It is defined as 1/12th of rest mass of an
unbound atom of C-12 in its nuclear & electronic ground state, & has a value of
1.660538782(83)x10-27 kg. The following diagram displays the mass spectra of
three simple gaseous compounds, CO2, C3H8 & cyclopropane. The molecules
of these compounds are similar in size, CO2 & C3H8 both have a nominal mass
of 44 Da, & C3H6 has a mass of 42 Da. The molecular ion is strongest ion in the
spectra of CO2 & C3H6, & moderately strong in propane. The unit mass
resolution is readily apparent in these spectra (separation of ions having m/z =
39, 40, 41 & 42 in the cyclopropane spectrum). Even though these compounds
are very similar in size, it is a simple matter to identify them from their individual
mass spectra.
Since a molecule of CO2 is composed of only three atoms, its mass spectrum is
very simple. The molecular ion is also the base peak, & the only fragment ions
are CO (m/z=28) & O (m/z=16). The molecular ion of propane also has m/z=44,
but it is not the most abundant ion in the spectrum. Cleavage of a C-C bond
gives CH3 & C2H5 fragments, one of which is a carbocation & other a radical.
Both distributions are observed, but the larger ethyl cation (m/z=29) is the most
abundant, possibly because its size affords greater charge dispersal. A similar
bond cleavage in cyclopropane does not give two fragments, so the molecular
ion is stronger than in propane, & is in fact responsible for the base peak. Loss
of H-atom, either before or after ring opening, produces the stable allyl cation
(m/z=41). The third strongest ion in the spectrum has m/z=39 (C3H3). Its
structure is uncertain, but two possibilities are shown in the diagram. The small
m/z=39 ion in propane & the absence of a m/z=29 ion in cyclopropane are
particularly significant in distinguishing these hydrocarbons. Most stable organic
compounds have an even number of total electrons, reflecting the fact that
electrons occupy atomic and molecular orbitals in pairs. When a single electron
is removed from a molecule to give an ion, the total electron count becomes an
odd number, and we refer to such ions as radical cations. The molecular ion in
a mass spectrum is always a radical cation, but the fragment ions may either be
even-electron cations or odd-electron radical cations, depending on the neutral
fragment lost. The simplest & most common fragmentations are bond
cleavages producing a neutral radical (odd number of electrons) & a cation
having an even number of electrons. A less common fragmentation, in which an
even-electron neutral fragment is lost, produces an odd-electron radical cation
fragment ion. Fragment ions themselves may fragment further. As a rule, odd-
electron ions may fragment either to odd or even-electron ions, but even-
electron ions fragment only to other even-electron ions. The masses of
molecular & fragment ions also reflect the electron count, depending on the
number of nitrogen atoms in the species.
Ions with no nitrogen odd-electron ions even-electron ions
or an even # N atoms even-number mass odd-number mass
Ions having an odd-electron ions even-electron ions
odd # N atoms odd-number mass even-number mass
This distinction is illustrated by the follwing two examples. The unsaturated
ketone, 4-methyl-3-pentene-2-one, has no N so mass of molecular ion (m/z =
98) is an even number. Most of the fragment ions have odd-numbered masses,
& therefore are even-electron cations. Diethylmethylamine, has one N- & its
molecular mass (m/z = 87) is an odd number. A majority of the fragment ions
have even-numbered masses (ions at m/z = 30, 42, 56 & 58), & are even-
electron N cations. The weak even -electron ions at m/z=15 & 29 are due to
CH3 & C2H5 cations (no nitrogen atoms). When non-bonded electron pairs are
present in a molecule (e.g. on N or O), fragmentation pathways may sometimes
be explained by assuming missing electron is partially localized on that atom.
A few such mechanisms are shown above. Bond cleavage generates a radical
and a cation, and both fragments often share these roles, albeit unequally.
Molecular ion The ion obtained by the loss of an electron from the molecule
Base peak The most intense peak in MS, assigned 100% intensity
M+ Symbol often given to the molecular ion
Radical cation +ve charged species with an odd number of electrons
Lighter cations formed by the decomposition of the molecular
Fragment ions
ion. These often correspond to stable carbcations.
Molecular ion
•The molecular ion is the ion produced when the molecule is ionised.
•The m/z of this ion corresponds to the molecular weight of the sample.
•The molecular ion should be the heaviest ion in the mass spectra
(remembering to allow for the presence of isotopes such as 13C)
•Note that not all samples give a molecular ion.... the ion needs to be stable
enough to survive until detection.
IMPORTANT
When calculating molecular weights to match to a molecular ion one need to
use integer atomic weights.This is because relative atomic weights are based
on the natural abundance of isotopes and since MS separates the isotopes, the
peaks appear at different m/z values.
The nitrogen rule ;Organic molecules composed of C, H, O and halogens
have even molecular weights. Examples : CH4 = 16 g/mol, CH3CH3 = 30 g/mol,
CH3OH = 32 g/mol, CH3F = 34 g/mol, CH3CO2H = 60 g/mol Since N forms 3
bonds, compounds with an odd number of N atoms, have odd molecular
weights. Examples : NH3 = 17 g/mol, CH3NH2 = 31 g/mol, C5H5N = 79 g/mol
Therefore, the implication is the nitrogen rule.... "an odd molecular weight
implies the presence of an odd number of N atoms" .
This can be a useful piece of information and prompt one to look for N
containing functional groups in the IR spectrum.
Isotope patterns for -Cl & -Br ;Mass spectrometers are capable of separating
& detecting individual ions even those that only differ by a single atomic mass
unit.As a result molecules containing different isotopes can be distinguished.
This is most apparent when atoms such as bromine or chlorine are present 79Br
: 81Br, intensity 1:1 & 35Cl : 37Cl,
intensity 3:1 where peaks at "M"
and "M+2" are obtained.The
intensity ratios in the isotope
patterns are due to the natural
abundance of the isotopes."M+1"
peaks are seen due the the
presence of 13C in the sample.
The following two examples of haloalkanes mass spectra show characteristic
isotope patterns of monohalogenated molecules, these are highlighted in
the green boxes: The first MS is of 2-chloropropane.Note the isotope pattern at
78 & 80 that represent M & M+2 in a 3:1 ratio. Loss of 35Cl from 78 or 37Cl from
80 gives the base peak a m/z = 43, corresponding to the secondary propyl
cation. Note that peaks at m/z = 63 & 65 still contain Cl & therefore also show
3:1 isotope pattern. The second MS is of 1-bromopropane. Note the isotope
pattern at 122 & 124 represents M & M+2 in a 1:1 ratio. Loss of 79Br from 122
or 81Br from 124 gives base peak a m/z = 43, corresponding to propyl cation
Note that other peaks, such as those at m/z = 107 &109 still contain Br &
therefore still show
the 1:1 isotope
pattern.
Note: the isotope
patterns for
polyhalogenated
molecules (such as
having both -Cl &
-Br or with multiple -
Cl or -Br) give
different (but still
characteristic
isotope patterns).
This can also be
manifested by the
following examples.
Since molecules of
Br have only two
atoms, the spectrum
on the left will come
as a surprise if a
single atomic mass
of 80Da is assumed for Br. The five peaks in this spectrum demonstrate clearly
that natural Br consists of a nearly 50:50 mixture of isotopes having atomic
masses of 79 & 81 Da respectively. Thus, Br2 molecule may be composed of
two 79Br atoms (mass 158Da), two 81Br atoms (mass 162Da) or more probable
combination of 79Br-81Br (mass 160 Da). Fragmentation of Br2 to bromine cation
then gives rise to equal sized ion peaks at 79 & 81 Da. The center & right hand

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bromine vinyl chloride methylene chloride
spectra show that Cl is also composed of two isotopes, more abundant with
mass 35Da, & minor isotope 37Da.The isotopic composition of Cl & Br is : Cl:
75.77% 35Cl & 24.23% 37Cl ; Br: 50.50% 79Br & 49.50% 81Br. Presence of Cl or
Br in a molecule or ion is easily detected by noticing the intensity ratios of ions
differing by 2Da. In case of CH2Cl2,molecular ion consists of three peaks at m/z
=84, 86 & 88Da & their diminishing intensities may be calculated from natural
abundances given above. Loss of Cl atom gives two isotopic fragment ions at
m/z=49 & 51Da, clearly incorporating a single Cl atom. F2& I2 are mono isotopic
, having masses of 19Da & 127Da respectively. Presence of halogen atoms in a
molecule or fragment ion does not change odd-even mass rules given above.
Fragmentation ; The fragmentation pattern of the spectra beside the
determination of the molar weight of an unknown compound also suitable to
give structural information, especially in combination with the calculation of
the degree of unsaturation from the molecular formula (when available). Neutral
fragments frequently lost are carbon monoxide, ethylene, water,ammonia,
and hydrogen sulfide.
fragmentations arise from:
•homolysis processes. An example is the cleavage of C-C next to a heteroatom

•Rearrangement reactions, e.g. a retro Diels-Alder reaction extruding neutral

ethylene:

or the McLafferty rearrangement

•Ion-neutal complex formation. This pathway involves bond homolysis or bond
heterolysis, in which the fragments do not have enough kinetic energy to
separate and, instead, reaction with one another like an ion-molecule reaction.
Some general rules:
•A useful aid is the nitrogen rule: if the m/z ratio is an even number, the
compound contains no nitrogen or an even number of nitrogens.
•Cleavage occurs at alkyl substituted carbons reflecting the order generally
observed in carbocations.
•Double bonds and arene fragments tend to resist fragmentation.
•Allylic cations are stable and resist fragmentation.
•the even-electron rule stipulates that even-electron species (cations but not
radical ions) will not fragment into two odd-electron species but rather to
another cation and a neutral molecule.
Fragmentation reaction may be written:
The decomposition of a metastable ion of mass-to-charge ratio into an ion of
mass-to-charge ratio after electric acceleration of the metastable ion and
before magnetic deflection gives rise to a peak in the mass spectrum at an
apparent mass, . The symbol should be used to indicate the apparent
mass of the product ions giving rise to this peak. Traditionally, the peak itself
has been called a metastable peak and this should preferably be expressed as
metastable ion peak. It is nevertheless recommended that the former term
should be retained. The word metastable should never be used as a noun. Its
use as an adjective should be limited to such terms as metastable ion, where it
is used correctly, and to the special case of metastable peak discussed above.
It should never be used in such terms
as metastable reaction, metastable decomposition, metastable studies, etc. It
should be clear that the metastable ion is the ion that undergoes fragmentation;
it is not detected. When a reaction is written with an asterisk above the arrow as
shown: * this means that the reaction has been confirmed by the
observation of a metastable peak. The textual description of such a process
may be written as, for example, ( , , calcd. 18.2, obsd. 18.3) meaning
'for the fragmentation a metastable peak at 18.3 (calculated
18.2) has been observed‘.
The McLafferty rearrangement is a reaction observed in mass spectrometry. It
is sometimes found that a molecule containing a keto-group undergoes β-
cleavage, with the gain of the γ-hydrogen atom. This rearrangement may take
place by a radical or ionic mechanism. A description of the reaction was first
published by the American chemist Fred McLafferty in 1959. Rearrangement
reaction involving transfer of a hydrogen atom via a six-member transition state
to the formal radical/charge site from a carbon atom four atoms distant from the
charge/radical site (the γ-carbon); subsequent rearrangement of electron
density can lead to expulsion of an olefin molecule.
(Note: Originally applied to ketone molecular ions where the charge/radical site
is the carbonyl oxygen, but is now more widely applied.) This is an example of a
rearrangement reaction and is defined as β - cleavage with concomitant
specific transfer of a γ - hydrogen atom in a six-membered transition state in
mono-unsaturated systems, irrespective of whether the rearrangement is
formulated by a radical or by an ionic mechanism and irrespective of with which
fragment the charge stays.
 Rearangement Mechanisms in Fragmentation
The odd-electron fragment ions at m/z = 86 and 58 are the result of a
McLafferty rearrangement, involving the larger alkyl chain, and a subsequent
loss of ethene (the "double-McLafferty" rearrangement).
Alpha-cleavage leads to the m/z = 99, 71 and 43 ions. The charge is apparently
distributed over both fragments.
4-nonanone
Alpha-cleavage gives ions at m/z=57 & 85 Da. The McLafferty rearrangement
on the acid side generates a m/z=116 ion. Subsequent rearrangement on the
alcohol side generates m/z=60 and 56 ions. The m/z=103 ion is probably
C4H9CO2H2(+).

butylpentanoate
The loss of a methyl radical generates the base peak at m/z=95 Da. The
m/z=81 & 67 ions are smaller homologues of this ion (14 mass units less).
Cyclohexene compounds undergo a retro-Diel-Alder rearrangement to give
diene and alkene fragments. The charge may reside on either fragment, with
the larger usually predominating. In this case both ions are relatively strong
(m/z=54 & 56).

4,4-dimethylcyclohexene
Molecular formula and index of Hydrogen deficiency (IHD) ; There is no
simple way of predicting how many isomers a given molecular formula will
yield, (it can range from one to many). Structures are different if they cannot
be superimposed upon one another. Keep in mind that there is rotation about
all single bonds not involved in a ring, but not about double bonds. Because all
of the formulas that you will be dealing with are based on the C atom, it may be
useful to review the ways that C can bond to itself and to other atoms. We will
limit ourselves, for now, to the C atom with four bonds. Below are the possible
combinations of C having a total of four bonds.

In a hydrocarbon where all the C atoms have only single bonds & no rings are
involved, the compound would have the maximum number of H atoms. If any of
the bonds are replaced with double or triple bonds, or if rings are involved,
there would be a “deficiency” of H atoms. By calculating the index of hydrogen
deficiency (IHD), we can tell from the molecular formula whether& how many
multiple bonds & rings are involved. IHD is also called Degree of Unstaturation.
This will help cut down the possibilities one has to consider in trying to come up
with all the isomers of a given formula. Here is a summary of how the index of
hydrogen deficiency (IHD) works.A double bond and ring each counts as one
IHD.A triple bond counts as two IHD.
Hydrocarbons (CxHy): IHD = (2x + 2 - y)/2 (where x and y stand for # of C and
H respectively.)
Example 1 ; IHD for C2H4 is (2(2) + 2 - 4)/2 = 1
This means it can have either one double bond or one ring. It cannot have a
triple bond. Since you cannot form a ring with only two C’s, it must have a
double bond.
Example 2 ; IHD for C4H6 is (2(4) + 2 - 6)/2 = 2
This means it can have either one double bond and a ring such as or two
double bonds such as CH2=CH−CH=CH2 or CH2=C=CH−CH3 or two
rings , or one triple bond, such as CH3C≡CCH3.
Compounds Containing Elements Other than C and H
•O and S atoms do not affect the IHD.
•Halogens (F, Cl, Br, I) are treated like H atoms (CH2Cl2 has the same IHD as
CH4).
•For each N, add one to the number of C and one to the number H (CH5N is
treated as C2H6. CH4N2O is treated as C3H6 by adding 2 to # of C & 2 to # of H).
•Do not forget that when double bonds & rings are involved, geometric
isomers are possible.
 Index of Hydrogen Deficiency (IHD) — a Way to Get Useful Information
from a Molecular Formula ; A fairly simple calculation based on the molecular
formula of a molecule gives information about total number of pi bonds &/or
rings that are present in molecule. The method can't tell the difference between
pi bonds & rings; it only gives the total. It involves noting number of hydrogens
in the molecular formula, & comparing that number with the number that would
be present in an acyclic saturated hydrocarbon having the same number of C-
atoms. Consider the following series of molecules, all having 5 carbon atoms:
molecular general
name structure formula formula
pentane CH3 CH2 CH2 CH2 CH3 C5H1 2 Cn H2n+2 (acyclic alkane)

1-pentene CH3 CH2 CH2 CH CH2 C5H1 0 Cn H2n (acyclic monoalkene)

CH2
cyclopentane CH2 CH2 C5H1 0 Cn H2n (monocyclic alkane)
CH2 CH2
CH2
cyclopentene CH2 CH C5H8 Cn H2n-2 (monocyclic monoalkene)
CH2 CH
1-pentyne CH3 CH2 CH2 C CH C5H8 Cn H2n-2 (acyclic monoalkyne)
Notice that introducing either a pi bond or a ring reduces the number of
hydrogens by two. An alkyne, with two pi bonds, has the same effect as two
double bonds, 2 rings, or a ring and a double bond. This regular trend in
hydrogen loss can be taken advantage of to calculate the total number of pi
bonds and/or rings from a molecular formula. This number is called the Index
of Hydrogen Deficiency (IHD).
Calculating IHD for hydrocarbons (contain C and H only)
Step 1. Start by noting the actual number of hydrogens in the molecular
formula. Call this number Hact.
Step 2. Calculate the number of hydrogens that would be present for an acyclic
saturated hydrocarbon (alkane) having the same number of carbons. Call this
number Hsat. It will always equal twice the number of carbons plus 2, or Hsat =
2C + 2.
Step 3. Calculate IHD as follows: IHD = Hsat – Hact (2C + 2) – H act
=
2 2
Example: for the molecular formula C10H16,

Hs at – Hact (2C + 2) – H act (2x10 + 2) – 16 22 – 16

IHD = = = = = 3
2 2 2 2

Therefore,C10H16 has a total of 3 pi bonds &/or rings. You can't tell how many of
each.
Calculating IHD for molecules containing O, N. or halogens
The presence of heteroatoms in a molecule may or may not make a difference
in how one calculates Hsat. Consider first the effect of oxygen. Ethane is C2H6,
ethanol is C2H6O and dimethyl ether is also C2H6O. Notice that the presence of
oxygen has no effect on the number of H's found in the molecules. Now
consider ethylamine (CH3CH2-NH2 = C2H7N) or dimethylamine (CH3-NH-CH3 =
C2H7N). Notice that the presence of one N increases the number of hydrogens
by 1. Finally, consider chloroethane (CH3CH2-Cl = C2H5Cl). Notice that the
presence of one halogen reduced the number of hydrogens by 1. In all of these
cases, the molecules are saturated and contain no rings.
In summary, the presence of oxygen has no effect on the calculation of Hsat,
but it must be reduced by 1 for each halogen present, and increased by 1 for
each nitrogen. The formula for calculating Hsat for the general case is then given
as follows, where X is the number of halogens in the molecule, and N is the
number of nitrogens. Hsat = (2C + 2) – X + N . As an exercise, calculate IHD for
C7H10ClN3O3. If you have done it correctly, you will find that IHD = 4, which
means a total of 4 rings and/or pi bonds. Any rings may or may not contain the
N or O, and pi bonds may be between two carbons (C=C, CC), carbon and
oxygen (C=O), carbon and nitrogen (C=N, CN), two nitrogens (N=N), or
nitrogen and oxygen (N=O). You can't tell from the IHD alone.
Practice problems
Calculate the IHD for each of the following and see whether it corresponds to
the structure shown.

a) b) CH3CHCHCH2CHCH2

d)

c)
e) CH3C≡CCOCH3

Answers
a) IHD = 3 ; b) IHD = 2 ; c) IHD = 5 ; d) IHD = 1 ; e) IHD = 3
Q1; An organic compound (A) is composed of carbon, hydrogen and nitrogen,
with carbon constituting over 60% of the mass. It shows a molecular ion at
m/z=112 amu in the mass spectrum.
1. Write a plausible Molecular Formula for compound A: C6 H12 N2
2. How many Rings + Double Bonds must be present in compound A? (2
rings and/or double bonds)
Q2;Another compound, B, composed only of carbon, hydrogen and oxygen,
also shows a molecular ion at m/z=112 amu.
3. Write a plausible Molecular Formula for compound B, assuming it has three
double bonds and no rings. C6H8O2
Q3;Compound C is composed only of carbon, hydrogen and oxygen, and
shows a molecular ion at m/z=180 amu. Carbon accounts for 60% of the
molecular mass.
4. Write a plausible Molecular Formula for compound C. C H O
5. How many Rings + Double Bonds must be present in compound C?
C9 H8 O4; This is Aspirin ; 6 rings and/or double bonds
Fragmentation Patterns of Different Organic Compounds ; The
fragmentation of molecular ions into an assortment of fragment ions is a mixed
blessing. The nature of fragments often provides a clue to molecular structure,
but if molecular ion has a lifetime of less than a few microseconds it will not
survive long enough to be observed. Without molecular ion peak as reference,
the difficulty of interpreting a mass spectrum increases markedly. Most organic
compounds give mass spectra that include a molecular ion. Among simple
organic compounds, most stable molecular ions are those from aromatic rings,
other conjugated pi-electron systems & cycloalkanes. Alcohols, ethers & highly
branched alkanes generally show greatest tendency toward fragmentation.
Fragmentation Patterns of Aliphatic Hydrocarbons The mass spectrum of
dodecane (on next page) illustrates the behavior of an unbranched alkane.
Since there are no heteroatoms in this molecule, there are no non-bonding
valence shell electrons. So, the
radical cation character of the
molecular ion (m/z = 170) is
delocalized over all the covalent
bonds. Fragmentation of C-C
bonds occurs because they are
usually weaker than C-H bonds &
this produces mixture of alkyl
radicals & alkyl carbocations. The
positive charge commonly resides on smaller fragment, so one see a
homologous series of hexyl (m/z=85), pentyl (m/z = 71), butyl (m/z = 57), propyl
(m/z =43), ethyl (m/z =29) & methyl (m/z=15) cations. These are accompanied
by set of corresponding alkenyl carbocations (e.g. m/z =55,41 & 27) formed by
loss of 2H. All significant fragment ions in this spectrum are even-electron
ions.In most alkane spectra propyl & butyl ions are most abundant.
The mass apectra of three different saturated hydrocarbons are displayed
below. Two are isomeric hexanes & third is cyclohexane. Comments regarding
the fragmentation patterns are presented in the box to the right of each
spectrum. Ions are sometimes characterized by loss of a specific neutral
fragment from the molecular ion,e.g. a M-15 ion is identified as loss of a methyl
group. Odd-electron ions, including the molecular ion, are colored orange when
marked. Even-electron ions are colored magenta. The three examples are
hydrocarbons having no functional groups are;
Hexane shows same fragmentation pattern as other unbranched alkanes.
Thus, alkyl carbocations at m/z=15, 29, 43 & 57 Da provide the dominant peaks
in the spectrum. The m/z=57 butyl cation (M-29) is the base peak, and the
m/z=43 and 29 ions are also abundant. Chain branching influences the
fragmentation of isomeric hexane. The molecular ion at m/z=86 is weaker than
that for hexane itself & M-15 ion at m/z=71 is stronger. The m/z=57 ion is
almost absent . An isopropyl cation (m/z=43) is very strong,& corresponding
propene radical-cation at m/z=42 (colored orange), produced by loss of
propane, gives the base peak. Molecular ion at m/z=84 is stronger than acyclic
compounds. The base peak at m/z=56 is produced by loss of ethene, so it is an
odd-electron ion (colored orange). The alkenyl cations at m/z=41 & 27 are
stronger than alkyl cations (m/z=43 & 29). The loss of methyl (m/z=69), & a
small m/z=15 ion obviously require some hydrogen rearrangements.
The MS of a typical hydrocarbon, n-decane is shown below.

The molecular ion is seen as a small peak at m/z = 142. C10H22 = (10 x 12) +
(22 x 1) = 142 g/mol Notice the series ions detected that correspond to
fragments that differ by 14 mass units, formed by the cleavage of the bonds
between the different -CH2- units
Toluene example ;The mass spectrum for toluene has around 30 signals.
Several peaks can be rationalized in this fragmentation pattern.
The presence of a functional group, particularly one having a heteroatom Y
with non-bonding valence electrons (Y = N, O, S, X etc.), can dramatically alter
the fragmentation pattern of a compound. This influence is thought to occur
because of a "localization" of the radical cation component of the molecular ion
on heteroatom. After all, it is easier to remove (ionize) a non-bonding electron
than one that is part of a covalent bond. By localizing the reactive moiety,
certain fragmentation processes will be favored. These are summarized in the
following diagram, where the green shaded box at top displays examples of
such "localized“molecular ions. The first two fragmentation paths lead to even-
electron ions, & elimination (path #3) gives an odd-electron ion. Note the use of
different curved
arrows to show
single electron
shifts compared
with electron pair
shifts.The charge
distributions
shown above are
common, but for
each cleavage
process the
charge may
sometimes be carried by the other (neutral) species, & both fragment ions are
observed. Of the three cleavage reactions described. here, alpha-cleavage is
generally favored for N-,O-,& S-compounds. Indeed, in the previously displayed
spectra of 4-methyl-3-pentene-2-one & N,N-diethylmethylamine major
fragment ions come from α-cleavages.
Pentanal displays a set of ions with alkyl chain (
m/z =57, 43, 41, 29 & 27). The molecular ion at
m/z=86 is very weak, as is M-1 ion at m/z =85
(aldehydes show fragment ions involving loss of
groups attached to carbonyl function). Thus, m/z
= 29 ion is probably due to both ethyl & HCO
cations. Odd-electron rearrangement ions are
observed at m/z=58 (possibly loss of CO) & 44
(rearrangement involving loss of propene).
The molecular ion at m/z=86 is more abundant
than aldehyde spectrum. Loss of carbonyl
substituents by alpha-fragmentation include: loss
of methyl (M-15 at m/z=71) & loss of a propyl
radical (M-43 at m/z=43). These comprise the
most prominent fragment ions.
The molecular ion at m/z=86 is about as strong
as in 2-pentanone. Because of the symmetry,
ethyl groups are only carbonyl substituents that
can be lost by an alpha-fragmentation. The
strongest fragment ions are found at m/z=57 loss
of an ethyl group) and m/z=29 (an ethyl cation).
 The molecular ion in mass spectrum of
ethyl acetate is weak. The base peak results
from an alpha-fragmentation of ethoxyl radical
to give an m/z=43 ion. Alpha-cleavage to an
M-15 ion is very weak. The loss of water to
generate odd-electron ion at m/z=70 is
curious. Small CH3 & C2H5 ions are found at
m/z=15 & 29.
The isomeric ester, methyl propanoate, has
a more abundant molecular ion than ethyl
acetate. The alpha fragmentation of methoxyl
radical generates strong m/z=57 ion. Alpha-
fragmentation of ethyl group leads to both m/z
= 59 & 29. A smaller methyl peak is also seen.
The stability of dimethylformamide (DMF)
is evident in the abundance of its molecular
ion (m/z=73), which is also the base peak. A
small M-15 peak is observed, but the second
most abundant ion is loss of HCO by an
alpha-cleavage (m/z=44). Other ions at
m/z=42, 30 & 28 are probably derived from
the m/z=44 ion.
In 1-pentanol there are two significant odd-
electron fragment ions, one at m/z=70 (loss of
water), & other at m/z=42 (loss of water and
ethene). The fragment ion at m/z=55 is due to
a methyl radical loss from m/z=70 ion. The
m/z=31 ion may be a protonated formaldehyde
ion, formed by alpha-fragmentation.
3-Pentanol shows three significant
fragment ions. Alpha-fragmentation (loss of an
ethyl radical) forms the m/z=59 base peak.
Loss of water from this gives a m/z=41
fragment, and loss of ethene from m/z=59
gives a m/z=31 fragment.
The molecular ion (m/z=90) is strong, &
the presence of sulfur is indicated by a larger
than usual M+2 (m/z=92) peak. This is true for
m/z=75 & 47 peaks as well. Loss of methyl &
ethyl radicals generate ions at m/z=75 & 61.
The odd-electron rearrangement ion at m/z=62
results from loss of ethene. m/z=47 may be
formed from m/z=62 by loss of methyl radical.
The MS of benzyl alcohol is shown below

The molecular ion is seen at m/z = 108. Note the small peaks at 109 and 110
which correspond to the presence of small amounts of 13C in the sample
(which has about 1% natural abundance).
Fragmentation via loss of 17 (-OH) gives a common fragment seen for alkyl
benzenes at m/z = 91. Loss of 31 (-CH2OH) from the molecular ion gives 77
corresponding to the phenyl cation.
 The mass spectrum of1-aminopentane is
simple, thanks to the directive influence of
nitrogen. Alpha-fragmentation generates the
m/z=30 even-electron cation, which is the only
significant fragment ion. The molecular ion
(m/z=87) is rather weak.
The mass spectrum of 3-aminopentane
is only slightly more complex than is isomer
above. The molecular ion is very weak, and
alpha-fragmentation again provides the base
peak (m/z=58). Loss of ammonia from this ion
generates the m/z=41 ion.
The cyclic 20 amine, piperidine, has a
complex mass spectrum. The molecular ion at
m/z=85 is relatively strong. Alpha-fragmentation
of H-gives the M-1 base peak. Because of the
ring, alpha-fragmentation of a C-group does not
result in a change of mass. This ring-opened
cation-radical may then lose ethyl radical or
ethene to give respectively m/z=56 & 57 ions.
Loss of an allyl radical from ring-opened
molecular ion would produce the m/z=44 ion.
Mass Spectrum