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 (C 7 H 7 NO), the molecular ion (M+) has a mass-tocharge ratio (m/z) of 121. This value is calculated using the most abundant isotopes of the elements present in the molecule: 7 * 12 C = 84 7 * 1 H = 7 1 * 14 N = 14 1 * 16 O = 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 C 3 and C 4 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 (3 o > 2 o > 1 o > 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 2 o, 3 o, and 4 o 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.
Straight Chain Alkenes 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 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 alkylsubstituted benzenes producing an ion of m/z 105. Each of these possible fragmentation events is described Scheme.
Mechanism of fragmentation for propylbenzene.
The phenyl cation will fragment further. One route involves the loss of acetylene yielding a fragment with formula C 4 H 3+ (m/z 51). Another route involves the loss of presumably an allene diradical with formula C 3 H 2, forming probably the simplest aromatic species of the formula C 3 H 3+ (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. Alkoxy Radical Ester Ion to Observe Formed methyl CH 3 O M - 31 ethyl CH 3 CH 2 O M - 45 propyl (and isopropyl) CH 3 CH 2 CH 2 O M - 59 phenyl C 6 H 5 O (PhO ) M - 93 benzyl C 6 H 5 CH 2 O (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 ( 35 Cl and 37 Cl in a 3:1 ratio) and bromine ( 79 Br and 81 Br 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 also lose 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.
Thiols Loss of H 2 S (analogous to dehydration of alcohols) is mainly evident in primary thiols. Just as with alcohols, cleavage on either side of the thiol carbon (a-cleavage) is the most important feature in thiol fragmentation. This will typically involve the loss of an alkyl group, and, often, it is the largest alkyl group that preferentially fragments. If the alkyl chain attached to the thiol 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 thiol sulfur leads to the loss of hydrogen sulfide from the molecule.
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
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 NO 2+ ion (m/z 46). The complete mass spectrum of 1-nitrobutane is given in Figure 35, which illustrates these points.
Mass Spectrometry Summary of Fragmentation Patterns Alkanes Alkenes Cycloalkanes Aromatics good M+ 14-amu fragments distinct M+ m/e = 27 CH 2 =CH+ m/e = 41 CH 2 =CHCH 2 + M-15, M-29, M-43, etc... strong M+ loss of alkyl M-28 loss of CH 2 =CH 2 M-15, M-29, M-43, etc... strong M+ loss of alkyl m/e = 105 C 8 H 9 + m/e = 91 C 7 H 7 + m/e = 77 C 6 H 5 + m/e = 65 (weak) C 5 H 5 +
Halides Alcohols Phenols M+ and M+2 Cl and Br m/e = 49 or 51 m/e = 93 or 95 CH 2 =Cl+ CH 2 =Br+ M-36, M-38 loss of HCl M-79, M-81 loss of Br M-127 loss of I M+ weak or absent M-15, M-29, M-43, etc... loss of alkyl m/e = 31 m/e = 45, 59, 73,... m/e = 59, 73, 87,... CH 2 =OH+ RCH=OH+ R 2 C=OH+ M-18 loss of H 2 O M-46 loss of H 2 O and CH 2 =CH 2 strong M+ strong M-1 loss of H M-28 loss of CO
M+ weak or absent Nitrogen rule Amines m/e = 30 M-15, M-29, M-43, etc... weak M+ m/e = 29 CH 2 =NH 2 + (base peak) loss of alkyl HCO+ M-29 loss of HCO M-43 loss of CH 2 =CHO Aldehydes m/e = 44, 58, 72, 86,... strong M+ M-1 McLafferty rearrangement aromatic aldehyde aromatic aldehyde loss of H
M+ intense Ketones M-15, M-29, M-43, etc... m/e = 43 m/e = 55 m/e = 42, 83 m/e = 105, 120 M+ weak but observable loss of alkyl CH 3 CO+ +CH 2 CH=C=O in cyclohexanone in aryl ketones M-17 loss of OH Carboxylic Acids M-45 loss of CO 2 H m/e = 45 CO 2 H+ m/e = 60 CH 2 C(OH) 2 + M+ large aromatic acids M-18 ortho effect
Esters M+ weak but observable methyl esters M-31 methyl esters loss of OCH 3 m/e = 59 methyl esters CO 2 CH 3 + m/e = 74 methyl esters CH 2 C(OH)OCH 3 + M+ weaker higher esters M-45, M-59, M-73, etc... loss of OR m/e = 73, 87, 101 CO 2 R+ m/e = 88, 102, 116 m/e = 61, 75, 89 m/e = 108 m/e = 105 M-32, M-46, M-60 CH 2 C(OH)OR+ RC(OH) 2 + (long alkyl ester) loss of CH 2 =C=O (benzyl, acetate) C 6 H 5 CO+ (benzoate) loss of ROH (ortho effect)