CH 121 Organic Chemistry I
Spectroscopic Methods
Professor Dr. Tanvir Muslim
Department of Chemistry
University of Dhaka
Spectroscopic Methods: A very brief treatment of spectroscopic methods- UV, IR NMR
and Mass spectroscopy, their application in organic chemistry with reference to
identification of organic compounds.
Introduction to Spectroscopy
The Nature of Light
Electromagnetic radiation (light) exhibits both wave- like properties and particle- like
properties. Consequently, electromagnetic radiation can be viewed as a wave or as a
particle. When viewed as a wave, electromagnetic radiation consists of perpendicular
oscillating, electric and magnetic fields.
The perpendicular, oscillating, electric and magnetic fields associated with
electromagnetic radiation.
The wavelength describes the distance between adjacent peaks of an oscillating field, while
the frequency describes the number of wavelengths that pass a particular point in space per
unit time. Accordingly, a long wavelength corresponds with a small frequency, and a short
wavelength corresponds with a large frequency. This inverse relationship is summarized in
the following equation where frequency ν (nu) in hertz (Hz), and wavelength λ (lamda) in
centimeters (cm) are inversely proportional. The constant of proportionality is the speed of
light (c) , 3×1010 cm/second :
When viewed as a particle, electromagnetic radiation consists of packets of energy, called
photons. The energy of each photon is directly proportional to its frequency,
where h is Planck’s constant (h = 6.626×10−34 J·s). The range of all possible frequencies is
known as the electromagnetic spectrum, which is arbitrarily divided into several regions.
Different regions of the electromagnetic spectrum are used to probe different aspects of
molecular structure.
One of the most important tasks of organic chemistry is the determination of organic
structures. When an interesting compound is isolated from a natural source, its structure
must be completely determined before a synthesis can begin. Whenever we run a reaction,
we must determine whether the product has the desired structure. The structure of an
unwanted product must be known so the reaction conditions can be altered to favor the
desired product.
In many cases, a compound can be identified by chemical means. We find the molecular
formula by analyzing the elemental composition and determining the molecular weight. If
the compound has been characterized before, we can compare its physical properties
(melting point, boiling point, etc.) with the published values. Chemical tests can suggest the
functional groups and narrow the range of possible structures before the physical properties
are used to make an identification.
These procedures are insufficient, however, for complex compounds that have never been
synthesized and characterized. They are also impractical with compounds that are difficult
to obtain, because a relatively large sample is required to complete the elemental analysis
and all the functional group tests. We need analytical techniques that work with tiny samples
and that do not destroy the sample.
Spectroscopic techniques often meet these requirements. Absorption spectroscopy is the
measurement of the amount of light absorbed by a compound as a function of the
wavelength of light. In general, a spectrometer irradiates the sample with light, measures the
amount of light transmitted as a function of wavelength, and plots the results on a graph.
Unlike chemical tests, most spectroscopic techniques are nondestructive; that is, the sample
is not destroyed. Many different kinds of spectra can be measured with little or no loss of
sample.
We use four spectroscopic or related techniques that serve as powerful tools for structure
determination in organic chemistry:
Ultraviolet (UV) spectroscopy observes electronic transitions and provides information on
the electronic bonding in the sample.
Infrared (IR) spectroscopy observes the vibrations of bonds and provides evidence of the
functional groups present.
Nuclear magnetic resonance (NMR) spectroscopy observes the chemical environments
of the hydrogen atoms or the carbon atoms and provides evidence for the structure of the
alkyl groups and clues to the functional groups.
Mass spectrometry (MS) is not a spectroscopic technique, because it does not measure
absorption or emission of light. A mass spectrometer bombards molecules with electrons and
breaks the molecules into fragments. Analysis of the masses of the fragments gives the
molecular weight, possibly the molecular formula, and clues to the structure and functional
groups. Less than a milligram of sample is destroyed in this analysis.
These spectroscopic techniques are complementary, and they are most powerful when used
together. In many cases, an unknown compound cannot be completely identified from one
spectrum without additional information, yet the structure can be determined with
confidence using two or more different types of spectra.
Mass Spectrometry
Mass spectrometry (MS) is a technique for measuring the molecular weight, and therefore
the formula, of a molecule. Mass spectrometry differs from the other instrumental methods
It does not depend on the absorption of electromagnetic radiation but rather examines ions
produced from a molecule in the gas phase. Several techniques have been developed for
ionization in mass spectrometry. In one method, the molecule is bombarded with high-
energy electrons. If an electron having an energy of about 70 electronvolts (eV) collides
with an organic molecule, the energy transferred as a result of that collision is sufficient to
dislodge one of the molecule’s electrons.
Mass spectrometers have three basic parts:
(i) an ionization source in which sample molecules are given an electrical charge;
(ii) a mass analyzer in which ions are separated by their mass-to-charge ratio, m/z; and
(iii) a detector in which the separated ions are observed and counted. Since the number of
charges z on each ion is usually 1, the value of m/z for an ion is simply its mass, m. Masses
up to approximately 2500 atomic mass units (amu) can be analyzed with an accuracy up to
four decimal places.
Diagram of a mass spectrometer. Only positive ions are detected. The cation X + has the
lowest mass-to charge ratio and its path is deflected most by the magnet. The cation Z + has
the highest mass-to-charge ratio and its path is deflected least.
A mass spectrum is a graph that on the x-axis represents the formula weights of the
detected ions, and on the y-axis represents the abundance of each detected ion.
Formation of Ions: Electron Impact Ionization
The ions in mass spectrometry may be formed in a variety of ways. One method for
converting molecules to ions (ionization) in a mass spectrometer is to place a sample under
high vacuum and bombard it with a beam of high-energy electrons (70 eV). This method is
called electron impact (EI) ionization mass spectrometry.
The impact of the electron beam dislodges a valence electron from the gas-phase molecules,
leaving them with a +1 charge and an unshared electron. This species is called the molecular
ion (M•+). We can represent this process as follows:
The molecular ion is a radical cation because it contains both an unshared electron and a
positive charge. Using propane as an example, we can write the following equation to
represent formation of its molecular ion by electron impact ionization:
Depicting the Molecular Ion
Notice that we have written the above formula for the propane radical cation in brackets.
This is because we do not know precisely from where the electron was lost in propane. We
only know that one valence electron in propane was dislodged by the electron impact
process. However, depicting the molecular ion with a localized charge and odd electron is
sometimes useful. One possible formula representing the molecular ion from propane with a
localized charge and an odd electron is the following:
When a molecule contains oxygen, nitrogen, or a π bond, we place the odd electron and
charge at a nitrogen, oxygen, halogen, or π bond. If resonance is possible, the radical cation
may be delocalized.
The following are examples of these cases.
Fragmentation
Molecular ions formed by EI mass spectrometry are highly energetic species, and in the
case of complex molecules, a great many things can happen to them. A molecular ion can
break apart in a variety of ways, the fragments that are produced can undergo further
fragmentation, and so on. We cannot go into all of the processes that are possible, but we
can examine a few of the more important ones.
As we begin, let us keep three important principles in mind:
1. The reactions that take place in a mass spectrometer are unimolecular, that is, they do not
involve collisions between molecules or ions. This is true because the pressure is kept so
low (10-6 torr) that reactions involving bimolecular collisions do not occur.
2. We use single-barbed arrows to depict mechanisms involving single electron movements.
3. The relative ion abundances, as indicated by peak intensities, are very important. We shall
see that the appearance of certain prominent peaks in the spectrum gives us key information
about the structures of the fragments produced and about their original locations in the
molecule.
Fragmentation by Cleavage at a Single Bond
One important type of fragmentation is the simple cleavage of a single bond. With a
radical cation this cleavage can take place in at least two ways; each way produces a
cation and a radical. Only the cations are detected in a positive ion mass spectrometer.
(The radicals, because they are not charged, are not detected.) With the molecular ion
obtained from propane by loss of one carbon–carbon σ bonding electron, for example, two
possible modes of cleavage are
These two modes of cleavage do not take place at equal rates, however. Although the relative
abundance of cations produced by such a cleavage is influenced by the stability of both the
carbocation and the radical, the carbocation’s stability is more important. In the spectrum of
propane shown earlier, the peak at m/z 29 (CH 3CH2+ ) is the most intense peak; the peak at
m/z 15 (CH3+ ) has a relative abundance of only 5.6%. This reflects the greater stability of
CH3CH2+ as compared to CH3+.
When drawing mechanism arrows to show cleavage reactions it is convenient to choose a
localized representation of the radical cation, as we have done above for propane. (When
showing only an equation for the cleavage and not a mechanism, however, we would use
the convention of brackets around the formula with the odd electron and charge shown
outside.) Fragmentation equations for propane would be written in the following way (note
the use of single-barbed arrows):
Fragmentation of Longer Chain and Branched Alkanes
The mass spectrum of hexane shown in Fig. illustrates the kind of fragmentation that a
longer chain alkane can undergo. Here we see a reasonably abundant molecular ion at m/z 86
accompanied by a small M•++1 peak. There is also a smaller peak at m/z 71 (M• +−15)
corresponding to the loss of •CH3, and the base peak is at m/z 57 (M • +−29) corresponding to
the loss of •CH2CH3. The other prominent peaks are at m/z 43 (M• +−43) and m/z 29 (M•+
−57), corresponding to the loss of •CH2CH2CH3 and •CH2CH2CH2CH3, respectively. The
important fragmentations are just the ones we would expect:
Chain branching increases the likelihood of cleavage at a branch point because a more
stable carbocation can result. When we compare the mass spectrum of 2-methylbutane
(Fig.) with the spectrum of hexane, we see a much more intense peak at M• +−15.
Loss of a methyl radical from the molecular ion of 2-methylbutane can give a secondary
carbocation:
whereas with hexane loss of a methyl radical can yield only a primary carbocation.
With neopentane (Fig.), this effect is even more dramatic. Loss of a methyl radical by the
molecular ion produces a tertiary carbocation, and this reaction takes place so readily that
virtually none of the molecular ions survive long enough to be detected:
Fragmentation to Form Resonance-Stabilized Cations
Carbocations stabilized by resonance are usually prominent in mass spectra. Several ways
that resonance-stabilized carbocations can be produced are outlined in the following list.
These examples begin by illustrating the likely sites for initial ionization (π and nonbonding
electrons), as well.
1. Alkenes ionize and frequently undergo fragmentations that yield resonance-stabilized
allylic cations:
2. Carbon–carbon bonds next to an atom with an unshared electron pair usually break
readily because the resulting carbocation is resonance stabilized:
3. Carbon–carbon bonds next to the carbonyl group of an aldehyde or ketone break readily
because resonance-stabilized ions called acylium ions are produced:
4. Alkyl-substituted benzenes ionize by loss of a p electron and undergo loss of a hydrogen
atom or methyl group to yield the relatively stable tropylium ion. This fragmentation gives a
prominent peak (sometimes the base peak) at m/z 91:
5. Monosubstituted benzenes with other than alkyl groups also ionize by loss of a π electron
and then lose their substituent to yield a phenyl cation with m/z 77:
Fragmentation by Cleavage of Two Bonds
Many peaks in mass spectra can be explained by fragmentation reactions that involve the
breaking of two covalent bonds. When a radical cation undergoes this type of
fragmentation, the products are a new radical cation and a neutral molecule. Some
important examples, starting from the initial radical cation, are the following:
1. Alcohols frequently show a prominent peak at M• +−18. This corresponds to the loss of a
molecule of water:
which can also be written as
2. Cycloalkenes can undergo a retro-Diels–Alder reaction that produces an alkene and an
alkadienyl radical cation:
which can also be written as
3. Carbonyl compounds with a hydrogen on their g carbon undergo a fragmentation called
the McLafferty rearrangement.
In addition to these reactions, we frequently find peaks in mass spectra that result from the
elimination of other small stable neutral molecules, for example, H 2, NH3, CO, HCN, H2S,
alcohols, and alkenes.
Isotopes in Mass Spectra
All naturally occurring molecules contain isotopic forms of the atoms that comprise them.
The proportion of each isotope is determined by its natural abundance. The peaks in a mass
spectrum will show the presence of isotopes in a given sample.
13
C and 12C About 1.1% of all carbon atoms are the 13C isotope. This means that in the mass
spectrum of methane, for example, where the formula weight for most methane molecules is
16 atomic mass units, there would also be a small peak at m/z 17 next to the peak at m/z 16.
About 98.9% of the methane molecules in the sample will contain 12C, and the other 1.1%
will contain 13C. Figure shows the mass spectrum for a sample of methane (m/z 16), in
which a small m/z 17 peak can be seen for the M•++1 ion.
Mass spectrum for
methane.
For molecules with more than one carbon, the intensity of the M• ++1 peak taken in proportion
to the M•+ peak can be used as an approximation of the number of carbon atoms in the
molecule. This is because there is a 1.1% chance that each carbon in the molecule could be a
13
C isotope. However, in large molecules the (M• ++1)/ M•+ ratio is altered by the existence of
other isotopes with a nominal mass one unit larger than their most abundant form, such as for
2
H, 17O, and so on. Therefore, for large molecules the (M• ++1)/ M•+ ratio cannot be used
reliably as an indication of the number of carbons.
35
Cl and 37Cl; 79Br and 81Br Some elements that are common in organic molecules have
isotopes that differ by two atomic mass units. These include 16O and 18O, 32S and 34S, 35Cl and
37
Cl, and 79Br and 81Br. It is particularly easy to identify the presence of chlorine or bromine
using mass spectrometry because the isotopes of chlorine and bromine are relatively
abundant.
•The natural abundance of 35Cl is 75.5% and that of 37Cl is 24.5%.
•In the mass spectrum for a sample containing chlorine, we would expect to find peaks
separated by two mass units, in an approximately 3 : 1 (75.5% : 24.5%) ratio for the
molecular ion or any fragments that contain chlorine.
(a) The mass spectrum of
chlorobenzene. Note the
approximately 3 : 1 intensity ratio
of peaks at m/z 112 and 114 due
to the presence of 35Cl and 37Cl.
(b) The mass spectrum of
bromomethylbenzene. Note the
1 : 1 intensity ratio of peaks at
m/z 170 and 172 due to the
presence of 79Br and 81Br.
Figure a shows the mass spectrum of chlorobenzene. The peaks at m/z 112 and m/z 114 in
approximately a 3 : 1 intensity ratio are a clear indication that chlorine atoms are present.
An m/z 77 peak for the phenyl cation fragment is evident, as well.
•The natural abundance of 79Br is 51.5%, and that of 81Br is 49.5%.
•In the mass spectrum for a sample containing bromine we would expect to find peaks
separated by two mass units in an approximately 1 : 1 ratio (49.5% : 51.5%). Figure b
shows the mass spectrum of bromomethylbenzene. The peaks at m/z 170 and m/z 172 in an
approximately 1 : 1 intensity ratio are a clear indication that bromine is present. Note that
the base peak is m/z 91, most likely representing a tropylium cation.
If two bromine or chlorine atoms are present in a molecule, then an M + 4 peak will
appear in addition to the M•++2 and M•+ peaks. In a molecule containing two bromine
atoms, for example, the intensity of the M+D + 4 peak due to two 81Br atoms present in
one molecule is the same as the M+D peak for two 79Br atoms in one molecule. But the
probability of having one 79Br and one 81Br is double when two bromines are present
(because either bromine atom could be either isotope). Thus, the ratio of intensities for the
M•+, M•++2, and M•++4 peaks will be 1 : 2 : 1 when two bromine atoms are present.
