Mass Spectrometry Instrumentation
A mass spectrometer is composed of an inlet system (which introduces the
sample to the instrument and vaporizes the sample)
A molecular leak (which produces a steady stream of the vapor), an ionization
chamber (where a beam of high energy electrons bombards the vapor),
A mass analyzer (a series of charged plates which focuses and accelerates the
beam of ions into a curved tube with an applied magnetic field which separates the
ions by mass),
A detector (a simple counter which produces a current every time an ion strikes
it), and
A recorder (which produces the mass spectrum).
A schematic for a typical mass spectrometer is shown in Figure 1.
Figure 1. Schematic diagram of mass spectrometer.
Ionization
In mass spectrometry, a small sample of a chemical compound is vaporized,
bombarded with high energy electrons to Ionize the sample,
and the ions produced are detected based on the mass to charge ratio
(m/z) of the ions. A typical ionization process is shown in Scheme 1 for
benzamide.
Scheme 1. Ionization process in the EI mass spectrometry of benzamide.
The beam of high energy electrons in the ionization chamber remove an
electron from the molecule resulting in the formation of a molecular ion
(M+) and a second free electron.
Several different types of ions can be produced during this process. If
the compound loses only one electron, then a molecular ion (frequently
symbolized by M+), having the same mass as the original compound, is
produced .This m/z of the molecular ion gives the nominal molecular
weight of the compound. The stream of high energy electrons is
sufficiently powerful so that chemical bonds in the molecule may be
broken, producing a series of molecular fragments. These positively
charged fragments are detected by the instrument, producing the mass
spectrum. Organic chemical compounds will often fragment in very
specific ways depending upon what functional groups are present in the
molecule (see Scheme 2 for the common fragments produced by
benzamide). Analysis of the fragmentation pattern can lead to the
determination of the structure of the molecule.
Accurate Mass
In the example above involving benzamide
(C7H7NO), the molecular ion (M+) has a mass-to-
charge ratio (m/z) of 121. This value is calculated
using the most abundant isotopes of the elements
present in the molecule:
7 * 12C = 84
7 * 1H = 7
1 * 14N = 14
1 * 16O = 16
121
Nitrogen Rule
If a compound contains an even number of nitrogen atoms(or
no nitrogen atoms), Its molecular ion will appear at an even
mass number. If, however, a compound contains an odd
number of nitrogen atoms, then its molecular ion will appear at
an odd mass value. This rule is very useful for determining the
nitrogen content of an unknown compound. In the case of
benzamide (Figure 1),the molecular ion appears at m/z 121,
indicating an odd number of nitrogen atoms in the structure.
The complete mass spectrum of benzamide is given in Figure 1.
Straight Chain Alkanes
When an alkane is ionized by EI, it will lose an electron to
form a radical cation. This radical cation has the same mass as
the parent compound (minus one electron) and is the
molecular ion (M+.).
Height of parent peak decreases as the molecular mass
increases .
The most intense peaks are due to C3 and C4 ions at m/z 43
and m/z 57 resp.
The relative abundances of the formed ions depends upon
a) stability of positively charged ion (3o > 2o > 1o > methyl )
b)stability of the radical which is lost(greater the disposal of
odd electron ,greater the stability of free radical)
Mechanism of fragmentation for pentane.
The ions of m/z 57 and 43 result from the loss of methyl and ethyl
radical, respectively. The ions of m/z 29 and 15 result from the
subsequent loss of ethene from these two higher mass fragments.
In general, once a radical is lost, the subsequent losses are of
neutral molecules. This is called the even electron (EE) ion rule.
That is, once an even electron ion is formed, it fragments by
rearrangement to give other EE ions. For instance, in decane (see Figure 4): M ® [M – 15] ® [M - 15 – 28] or [M - 15- 42] or
[M - 15 – 56]. The same can be said for M - 29 ® [M - 29 – 28], etc.
This is how that characteristic EE ion series: 29, 43, 57, 71, 85
arises in hydrocarbon MS.
. Mass spectrum of pentane
Branched Alkanes
Branched alkanes tend to fragment very easily owing to the presence of
2o, 3o, and 4o carbon atoms in the structure.
When branched alkanes fragment, stable secondary and tertiary
carbocations can form.
the molecular ion is much less abundant than for straight-chain alkanes.
The most important mode of fragmentation in branched alkanes usually
occurs at the branch point.
Scheme shows the mechanism of fragmentation for isobutane,
Notice the reduced intensity of the molecular ion (m/z 58).
Cyclic Alkanes
The fragmentation patterns of cycloalkanes may show mass
clusters in a homologous series, as for the alkanes. However,
Additionally, if the cycloalkane has a side chain, loss of that
side chain is also a favorable mode of fragmentation.
. The mass spectrum of cyclohexane has an abundant ion
of m/z 56 arising by the loss of ethylene.
the most significant mode of cleavage of the cycloalkanes
involves the loss of ethylene from the parent molecule or from
intermediate radical-ions.
This is probably due to the loss of a p-bonding electron,
leaving the carbon skeleton relatively undisturbed.
The most important fragmentation events for alkenes
involve cleavage of the allylic (favored) and vinylic
(less favored) carbon-carbon bonds.
For terminal alkenes, allylic fragmentation forms an
allylic carbocation of m/z 41.
The fragmentation mechanism for 1-butene shown in
Scheme illustrates these points. The complete mass
spectrum of 1-butene is given in Figure .
Straight Chain Alkenes
Straight Chain Alkenes
Mechanism of fragmentation for 1-butene.
Cyclic Alkenes
The mass spectra of cycloalkenes show distinct molecular ions.
It may be impossible to locate the position of a double bond
due to migration.
The mechanism of fragmentationis according to Mclafferty
rearragment for cyclic alkenes give intense peak
One noteworthy characteristic is the fragmentation of
cyclohexenes to undergo a reverse Diels-Alder reaction as
indicated in Scheme .
This rearrangement is characteristic of many isoprenoid
natural products and of tetralin derivatives, and is useful for
assigning structure and distinguishing isomers.
The complete mass spectrum of cyclohexene is
given in Figure .
Mechanism of fragmentation for cyclohexene.
Mass spectrum of cyclohexene
Alkynes
The mass spectra of alkynes are virtually identical to those of alkenes.
The molecular ion is usually more abundant, and fragmentation
parallels that of the alkenes.
Two differences are worth mentioning: terminal alkynes fragment to
form propargyl ions (m/z 39),
and can also lose the terminal (or an a-) hydrogen, yielding a strong
M - 1 ion.
These two modes of fragmentation are outlined in Scheme for 1-
butyne, and the complete mass spectrum of 1-butyne is given in
Figure .
Mechanism of fragmentation for 1-butyne
An alternative way to describe the loss of hydrogen radical from an alkyne
would involve a 1,2-hydride shift (converting a vinylic radical cation to a
more stable allylic radical cation) that subsequently loses hydrogen radical to
give the M - 1 ion. This alternate mechanism is outlined in Scheme
. Alternate mechanism of fragmentation for 1-butyne.
Aromatic Compounds
The mass spectra of most aromatic compounds show distinct
and abundant molecular ions. This is probably due to the
loss of an electron from the p system, leaving the carbon
skeleton relatively undisturbed.
When an alkyl side-chain is attached to the ring, fragmentation
usually occurs at the benzylic position, producing initially a
benzyl ion, which often rearranges to the tropylium ion (m/z 91).
However, fragmentation can also occur at the attachment
point to the ring producing the phenyl cation (m/z 77).
If the side-chain is a propyl group or larger, then the McLafferty
rearrangement is a possibility, producing a fragment of m/z 92.
Formation of a substituted tropylium ion is typical for alkyl-
substituted benzenes producing an ion of m/z 105.
Each of these possible fragmentation events is described in
Scheme .
Mechanism of fragmentation for propylbenzene.
The phenyl cation will fragment further. One route involves the loss of
acetylene yielding a fragment with formula C4H3+ (m/z 51). Another route
involves the loss of presumably an allene diradical with formula C3H2, forming
probably the simplest aromatic species of the formula C3H3+ (m/z 39), namely
the cyclopropenyl ion. Aproposed mechanism for the formation of these
fragments is given in Scheme . Note that this mechanism is
complete conjecture, and only serves as one possible explanation.
Proposed mechanism for phenyl cation fragmentation
Mass spectrum of propylbenzene
Aldehydes
The molecular ion is usually
observable, although it can be of low
relative abundance. The important a-
and b-cleavage patterns (as well as
the McLafferty rearrangement) are
illustrated in Scheme
Mechanism of fragmentation for hexanal
The complete mass spectrum of hexanal
Ketones It appears that the loss of the larger alkyl group
is favored in ketones in the a-cleavage process as
shown in Scheme .
For interpretation purposes,the rule that “the larger
alkyl group is lost” is effective in interpretation.
Fragmentation patterns mimic those of the aldehydes.
The molecular ion is usually quite abundant.
. Mechanism of fragmentation for 2-pentanone.
Mass spectrum of 2-pentanone
For aromatic ketones, a-cleavage usually involves cleavage of the alkyl
group leaving behind an acylium ion. This is subsequently followed by a loss
of carbon monoxide from the molecule as indicated in Scheme . If the
aromatic ketone has a 3 carbon alkyl chain (or longer), then McLafferty
rearrangements (as described above for 2-pentanone) are possible.
Aromatic ketone fragmentation illustrated for acetophenone
Mass spectrum of acetophenone
Esters
The molecular ion is usually of low abundance but generally observable for
esters.
As in all carbonyl compounds, a-cleavage is an important fragmentation
process.
In general, cleaving the C-O ester bond occurs most readily leading to the
favorable loss of an alkoxy radical. Table summarizes this cleavage process
for the most common types of esters.
Table . Alkoxy Radicals formed from the most common esters.
EsterAlkoxy Radical
FormedIon to Observe
methyl CH3O· M - 31
ethyl CH3CH2O· M - 45
propyl (and
isopropyl)CH3CH2CH2O· M - 59
phenyl C6H5O· (PhO·) M - 93
benzyl C6H5CH2O· (BzO·) M - 105
Mechanism of fragmentation for methyl butyrate
Mass spectrum of methyl butyrate
Benzyl and phenyl esters undergo a rearrangement involving hydride transfer
from the a-carbon to the ester oxygen. The resulting fragments include a neutral
ketene and a charged alcohol as described in Scheme below.
Most common fragmentation involving benzyl and phenyl esters
Most common fragmentation involving benzoate and ortho substituted
benzoate esters.
Mass spectra of methyl benzoate (top) and methyl 2-aminobenzoate
Amides
The molecular ion is usually observable, and will be a good
indication of the presence of an amide (invoke the nitrogen
rule!).
An important fragmentation pattern involves a-cleavage
(breaking either bond to the carbonyl carbon) as shown in
Scheme .
Mechanism of fragmentation for butyramide.
Mass spectrum of butyramide
Carboxylic Acids
The molecular ion is often of low abundance for
carboxylic acids, but generally observable.
As is indicated in Scheme , the loss of hydroxyl
radical (leading to an M - 17 ion) is indicative of the
presence of the carboxylic acid functionality.
All the important fragmentation events for
carboxylic acids are illustrated in Scheme .
As for all other carbonyl compounds, a-cleavage,
b-cleavage, and McLafferty rearrangements rule the
day.
Mechanism of fragmentation for butyric acid
Mass spectrum of butyric acid
As was seen with esters, benzoic acids substituted with alkyl,
amino, or hydroxy substituents at the ortho position readily
dehydrate via proton transfer from the ortho substituent to
the hydroxyl group (ortho effect). Water is lost, resulting in a
major M - 18 ion in the mass spectrum. Scheme 19 outlines
this process for o-toluic acid.
The “ortho effect” fragmentation of o-toluic acid.
Mass spectrum of o-toluic acid
Amides
The molecular ion is usually observable, and
will be a good indication of the presence
of an amide (invoke the nitrogen rule!).
An important fragmentation pattern involves
a-cleavage (breaking either bond to the
carbonyl carbon) as shown in Scheme .
Mechanism of fragmentation for butyramide.
Mass spectrum of butyramide
Anhydrides
Aliphatic acid anhydrides rarely afford a molecular ion in their
mass spectra whereas aromatic anhydrides usually do.
Understanding and interpreting the mass spectra for anhydrides
is quite straight forward,
as they fragment by following the general rules set forward for all
carbonyl compounds:
a-cleavage on either side of the carbonyl carbon contributes to the major
ions observed in the mass spectrum as shown in Scheme for butyric
anhydride.
Mechanism of fragmentation for butyric anhydride
Mass spectrum of butyric anhydride
Aromatic anhydrides show evidence of the molecular ion and undergo
a similar fragmentation as seen for butyric anhydride. However, an
additional rearrangement where carbon monoxide is lost from the
molecule is evident in nearly all mass spectra of aromatic anhydrides.
The cleavage pattern for benzoic anhydride is given in Scheme .
Mechanism of fragmentation for benzoic anhydride.
Mass spectrum of benzoic anhydride
It is interesting to note that the ortho effect (as described
above for ortho substituted esters and carboxylic acids)
applies to aromatic anhydrides as well. The fragmentation
for o-toluic anhydride (given in Scheme 23) Is an example
of this general effect.
Mechanism of fragmentation for o-toluic anhydride.
spectra of o-toluic anhydride (top) and p-toluic anhydride (bottom).
Acid Halides
Acid halides afford very low abundance, if not entirely absent,
molecular ions in their mass spectra. This is true even for aromatic
acid halides. Again, as with all carbonyl compounds, a-cleavage
is a very facile process with loss of a halogen radical perhaps the
most common event. Acid chlorides can also lose HCl from the
molecule; this is not a probable event with acid bromides. Keep in
mind that the two common isotopes for chlorine (35Cl and 37Cl in a
3:1 ratio) and bromine (79Br and 81Br in a 1:1 ratio) will lead to the
production of M + 2 observed ions in the spectra. Since the
molecular ion is not abundant, the M + 2 ions are typically very
difficult to ascertain. Scheme 24 contains the common fragments
formed for butyryl chloride.
Mass spectrum of butyryl chloride
Alcohols
The molecular ion is usually of very low abundance or absent for
aliphatic alcohols. Just as with carbonyl compounds, cleavage
on either side of the alcohol carbon (a-cleavage) is the most
important feature in alcohol fragmentation. This will typically
involve the loss of an alkyl group, and, often, it is the largest alkyl
group that is preferentially lost. If the alkyl chain attached to the
alcohol carbon is at least of three carbons in length, then a process
similar to McLafferty rearrangements seen for carbonyl compounds
can take place. Transfer of a g-hydrogen to the alcohol oxygen
leads to the loss of water from the molecule. This dehydration can
be a very important indication for the presence of an alcohol
functionality. The mechanism for alcohol fragmentation is
given in Scheme for 2-pentanol.
Unlike for aliphatic alcohols, the molecular ion for phenols can
be quite abundant. Phenols can lose the elements of carbon
monoxide to give abundant fragment ions at M - 28, and can alsolose the elements of the formyl radical (HCO•) to give abundant
fragment ions at M - 29. No attempt will be made to explain this
fragmentation mechanistically. However, Figure 27 contains the
mass spectrum of phenol, which highlights the production of the
fragment ions.
ThiolsLoss of H2S (analogous to dehydration ofalcohols) is mainly evident in primary thiols.Just as with alcohols, cleavage on either sideof the thiol carbon (a-cleavage) is the mostimportant feature in thiol fragmentation. Thiswill typically involve the loss of an alkylgroup, and, often, it is the largest alkyl groupthat preferentially fragments. If the alkylchain attached to the thiol carbon is at leastof three carbons in length, then a processsimilar to McLafferty rearrangements seen forcarbonyl compounds can take place. Transferof a g-hydrogen to the thiol sulfur leads tothe loss of hydrogen sulfide from themolecule.
Mass spectrum of 1-pentanethiol
Ethers
higher abundance than the molecular ions of alcohols. Important
fragments arise from cleavage of the carbon-oxygen bond
(ipso-cleavage), cleavage of the carbon-carbon bond adjacent to
the oxygen (a-cleavage), and transfer of hydride from the
b-carbon to the ether oxygen (a rearrangement of the ion
produced from initial a-cleavage). All of these processes are
outlined in Scheme 27 for dibutyl ether.
Mechanism of fragmentation for dibutyl ether
Mass spectrum of dibutyl ether
Sulfides
. Important fragments arise from cleavage of the carbon-sulfur
bond (ipso-cleavage), cleavage of the carbon-carbon bond
adjacent to the sulfur (a-cleavage), and transfer of hydride from
the b-carbon to the sulfide sulfur (a rearrangement of the ion
produced from initial a-cleavage). All of these processes are
outlined in Scheme 28 for dibutyl sulfide.
Mechanism of fragmentation for dibutyl sulfide.
Amines
The molecular ion is of low abundance or not detectable.
When observable, its odd mass (when an odd number
of nitrogens is present) is a good indication of the presence
of an amine (nitrogen rule). Important fragments arise from
cleavage of the carbon-carbon or carbon-hydrogen bond
adjacent to the nitrogen (a-cleavage), and hydrogen transfer
from the b-hydrogen to the nitrogen. These processes are
outlined in Scheme 29 for dipropyl amine. If two or more alkyl
groups of different length are attached to the alpha carbons,
then loss of the largest alkyl group is preferred.
Mechanism of fragmentation for dipropyl
amine.
Nitriles
The molecular ion is usually of too low an abundance to be
observed. However, the loss of hydrogen radical (via an a-cleavage
process) will almost always produce an observable ion. For nitriles
then, the M - 1 ion is usually more prominent than the M+. As for
the carbonyl compounds, McLafferty rearrangement involving
transfer of a g-hydrogen to the nitrile N occurs readily for nitriles
containing four or more carbons in an n-alkyl chain. The
fragmentation events described for nitriles are given in Scheme
for pentanenitrile.
Nitro Compounds
The molecular ion for aliphatic nitro compounds is seldom
observed. The mass spectrum observed for aliphatic nitro
compounds is usually due to the fragmentation of the alkyl
portion of the molecule.However, there are two fragment
ions that are indicative of the nitro group: one is NO+ ion
(m/z 30), and another is the NO2+ ion (m/z 46). The complete
mass spectrum of 1-nitrobutane is given in Figure 35, which
illustrates these points.
Mass SpectrometrySummary of Fragmentation Patterns
Alkanesgood M+
14-amu fragments
Alkenes
distinct M+
m/e = 27 CH2=CH+
m/e = 41 CH2=CHCH2+
M-15, M-29, M-43,
etc...loss of alkyl
Cycloalkanes
strong M+
M-28 loss of CH2=CH2
M-15, M-29, M-43,
etc...loss of alkyl
Aromatics
strong M+
m/e = 105 C8H9+
m/e = 91 C7H7+
m/e = 77 C6H5+
m/e = 65 (weak) C5H5+
Halides
M+ and M+2 Cl and Br
m/e = 49 or 51 CH2=Cl+
m/e = 93 or 95 CH2=Br+
M-36, M-38 loss of HCl
M-79, M-81 loss of Br·
M-127 loss of I·
Alcohols
M+ weak or absent
M-15, M-29, M-43,
etc...loss of alkyl
m/e = 31 CH2=OH+
m/e = 45, 59, 73, ... RCH=OH+
m/e = 59, 73, 87, ... R2C=OH+
M-18 loss of H2O
M-46loss of H2O and
CH2=CH2
Phenolsstrong M+
strong M-1 loss of H·
M-28 loss of CO
Amines
M+ weak or absent Nitrogen rule
m/e = 30 CH2=NH2+ (base peak)
M-15, M-29, M-43, etc... loss of alkyl
Aldehydes
weak M+
m/e = 29 HCO+
M-29 loss of HCO
M-43 loss of CH2=CHO
m/e = 44, 58, 72, 86, ...McLafferty
rearrangement
strong M+ aromatic aldehyde
M-1aromatic aldehyde loss
of H·
Ketones
M+ intense
M-15, M-29, M-43, etc... loss of alkyl
m/e = 43 CH3CO+
m/e = 55 +CH2CH=C=O
m/e = 42, 83 in cyclohexanone
m/e = 105, 120 in aryl ketones
Carboxylic
Acids
M+ weak but observable
M-17 loss of OH
M-45 loss of CO2H
m/e = 45 CO2H+
m/e = 60 ·CH2C(OH)2+
M+ large aromatic acids
M-18 ortho effect
Esters
M+ weak but observable methyl esters
M-31methyl esters loss of
OCH3
m/e = 59 methyl esters CO2CH3+
m/e = 74methyl esters
CH2C(OH)OCH3+
M+ weaker higher esters
M-45, M-59, M-73, etc... loss of OR
m/e = 73, 87, 101 CO2R+
m/e = 88, 102, 116 ·CH2C(OH)OR+
m/e = 61, 75, 89RC(OH)2+ (long alkyl
ester)
m/e = 108loss of CH2=C=O (benzyl,
acetate)
m/e = 105 C6H5CO+ (benzoate)
M-32, M-46, M-60 loss of ROH (ortho effect)