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)