Richard F. Daley and Sally J.

Daley
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Organic Chemistry
Chapter 9

Infrared Spectroscopy and Mass Spectrometry

9.1 Electromagnetic Radiation and Spectroscopy 9.2 Molecular Vibrations in Infrared Spectroscopy 9.3 Introduction to Interpreting Infrared Spectra 9.4 Hydrogen Bonded to sp3 Hybrid Atoms 439 9.5 Hydrogen Bonded to sp2 and sp Hybrid Atoms 9.6 CarbonHeteroatom Bonds 448 9.7 Other Bonds 452 9.8 Interpreting Infrared Spectra, Part 2 456 9.9 Mass Spectrometry 459 9.10 The Molecular Ion 463 Key Ideas from Chapter 9 467 431 434 436 443

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Copyright 1996-2005 by Richard F. Daley & Sally J. Daley All Rights Reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise, without the prior written permission of the copyright holder.

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Chapter 9

Infrared Spectroscopy and Mass Spectrometry

Chapter Outline
9.1 9.2 9.3 9.4 9.5 9.6 9.7 9.8 9.9 9.10 Electromagnetic Radiation and Spectroscopy
Background on the basis of molecular spectroscopy

Molecular Vibrations in Infrared Spectroscopy

The molecular motions that absorb energy in an infrared spectrum

Introduction to Interpreting Infrared Spectra

How to read an infrared spectrum The infrared absorptions for various hydrogens to sp3 hybridized carbon, nitrogen, and oxygen bonds Hydrogen Attached to sp2 and sp Hybrid Atoms The infrared absorptions for various hydrogens to sp2 and sp hybridized carbon, nitrogen, and oxygen bonds The infrared absorptions for various hydrogens to sp2 and sp hybridized carbon, nitrogen, and oxygen bonds

Hydrogen Attached to sp3 Hybrid Atoms

CarbonHeteroatom Bonds

Other Bonds
The infrared absorptions for various bonds not already covered in the last three sections

Interpreting Infrared Spectra, Part 2

Using an infrared spectrum to find information about an unknown compound

Mass Spectrometry
An introduction to the techniques of mass spectrometry

The Molecular Ion

Using the molecular ion in interpreting a mass spectrum

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Objectives
Understand what types of molecular motions absorb infrared energy Know the wavenumbers for the absorptions of common types of bonds in an infrared spectrum Be able to interpret significant peaks in the functional group region of an infrared spectrum Confirm, where appropriate, functional group absorptions with peaks in the fingerprint region of the spectrum Understand how mass spectrometry works and what information you can gather from the molecular ion

What a wondrous pair of spectacles is here! Shakespeare

The basis of molecular spectroscopy involves exposing the molecule to an energy source, then observing how the molecule responds to that energy.

rganic chemists frequently obtain many new compounds through laboratory syntheses and extraction from biological or environmental sources. They then need to either identify or confirm the structure of these new compounds. Before the 1950s, they had only three general methods available to obtain this information. One, they could perform an elemental analysis on the compound. Two, they could perform chemical transformations, or reactions, using the compound they wanted to identify, then observe the results. Many of these transformations were simple chemical tests that provided information rapidlyfuture chapters present many of these reactions, as they are still useful. Three, they could take physical measurements of the compounds, such as the refractive index, melting or boiling point, and density. Then they compared these measurements with the known values of previously studied compounds. Now chemists have instruments to help identify the structure of compounds. These instruments supplement, and at times replace, the chemical tests and physical property measurements. Although many methods of instrumental analysis are available, the most widely used techniques are those of molecular spectroscopy. Infrared (IR), nuclear magnetic resonance (NMR), and mass spectrometry (MS) are the most prominent of the molecular spectroscopy techniques. Subjecting a molecule to these three techniques gives sufficient

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information to allow chemists to draw accurate conclusions about the identity and structure of most molecules. This chapter considers infrared spectroscopy and mass spectrometry. By using IR spectroscopy, chemists obtain information about the vibrational motions of a molecule. Each type of molecule has its own characteristic set of stretching and bending motions. These motions respond to infrared electromagnetic radiation in specific ways. Chemists use this information to identify the functional groups contained in a molecule. Mass spectrometry helps determine the molecular formula and major groups of a molecule. Fundamentally, mass spectrometry is different from IR and NMR in that it is not based on the absorption of electromagnetic energy. MS shows how a molecule fragments when a beam of energetic electrons bombards it. The spectrometer then analyzes these fragments and plots them as the relative numbers of the various fragments versus the mass of the fragments. The chemist then examines the spectrum to obtain the molecular weight of the molecule as well as information about its structure. Chapter 10 covers NMR, which helps determine the organic skeleton of the molecule.

9.1 Electromagnetic Radiation and Spectroscopy

Before beginning the study of infrared spectroscopy, you need some background information about electromagnetic radiation and spectroscopy. Electromagnetic radiation exists in a broad range of energies. Visible light, infrared light, ultraviolet light, microwaves, and radio frequencies are different energy subdivisions of electromagnetic radiation. Electromagnetic radiation consists of discreet parcels of energy called photons. Photons have dual natures, as they possess properties of both particles and waves. Although photons at rest have no mass, each does have an amount of energy called a quantum. The following equation expresses the relationship of the energy of a photon and its wavelength. E = h In this equation, E represents the energy of the photon, h is Planck's constant (6.62 x 1034 joule/second), and is the frequency of the photon in hertz (or cycles/second). Frequency refers to the number of oscillations that a particular electromagnetic radiation wave makes per second. An oscillation is the full cycle of a wave from the crest of that wave through its trough to the crest of its next wave. Wavelength is the distance between two crests of a wave and is symbolized as .

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This equation measures the energy of a photon of a particular wavelength in joules. The relationship between the frequency of a photon and its wavelength is given by the following equation: c = Where c is the velocity, or speed, of the electromagnetic radiation. The speed of the electromagnetic radiation is the same velocity as visible light in a vacuum, which is 3.0 x 108 m/s, and is a constant. Thus, the shorter the wavelength of light, the higher the frequency and the higher the energy of the photon. Radio waves are very low energy, visible light is higher energy, and x-rays and -rays are much higher. Figure 9.1 shows the range of frequencies in the electromagnetic spectrum.

Energy Frequency ( ) in Hz 1020 1018 rays

1016

1014 Infrared 10-6 Visible

1012

1010

108

X rays Ultraviolet

Microwave Radio wave 10-2 100

10-10 10-12 10-8 Wavelength ( ) in meters

10-4

Violet
Figure 9.1. The electromagnetic spectrum.

Red

The excited state is a higher energy level than the normal, or ground, state.

Recall from Chapter 1 that electrons in atoms and molecules have different energy levels called atomic and molecular orbitals. Chapter 1 also discusses the electrons that inhabit these orbitals. When an atom absorbs electromagnetic radiation of a given energy, an electron moves from a lower energy level to a higher one; that is, it moves from its normal orbital to a higher energy orbital. Chemists call this higher energy level an excited state. The excited state of an electron is a higher energy level than its ground state, the energy level that an electron normally inhabits. The electron returns to its ground state when it loses the energy absorbed from the electromagnetic radiation. The transition of an atom from its normal state to its excited state requires the input of an exact amount of energy. If the photon

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involved has either too little energy or too much energy, then no transition occurs. Scientists say that the energy states of atoms are quantized because atoms require a specific amount of energy to move an electron from its normal state to its excited state. The following equation gives the difference in energy between the ground state (E0) and the excited state (E1) of an atom.

E = E1 E0 = h
An atom absorbs energy only when the energy of the photon of electromagnetic radiation, h, equals E. Molecules consist of several different energy levels: thus, they absorb energy at several different regions of the electromagnetic spectrum. For example, transitions that involve the nonbonding and electrons in a molecule absorb radiation in the ultraviolet and visible regions of the spectrum. Vibrational energy changes take place in the infrared region while rotational energy changes occur in the microwave region. The electromagnetic spectrum is an arbitrary division of the different types of electromagnetic radiation. Table 9.1 summarizes the regions of significance to organic chemists.
Region of Spectrum Ultraviolet Visible Infrared Microwave Radiofrequency Molecular Change Electronic transitions Molecular vibrations Molecular rotations Orientation of the spin of nucleus Energy (kcal mole1) 50 to 100 5 3 x 103 Frequency (Hertz) 1014 to 1016 1012 to 1014 1010 Wavelength (cm) 106 to 104 104 to 102 1

107

107 to 109

105 to 106

Table 9.1. Selected regions of the electromagnetic spectrum used in spectroscopy. -

Because molecules absorb electromagnetic radiation in specific ways, chemists have developed instruments, called spectrometers, to measure this information. Chemists use the general term spectroscopy to describe this method. Spectrometers consist mainly of four parts: a source of electromagnetic radiation, a sample chamber, a detector for the radiation, and data handling system for the spectrum. Typical data handling systems range from a plotter to a sophisticated computer system. Figure 9.2 shows schematically how a spectrometer works. As the instrument directs electromagnetic radiation at the molecule sample, it varies the frequency of the radiation. The detector then compares that intensity with the intensity of the radiation at the source. When the sample absorbs energy, the detector senses a

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A spectrum is a plot of the intensity of electromagnetic radiation reaching the detector versus the wavelength of the radiation. Trasnsmittance is the intensity of the infrared radiation at a given wavelength of the sample in the instrument divided by the intensity with no sample present.

decrease in the intensity. It then plots the relationship between the intensity and the wavelength as a spectrum. An infrared spectrum is plotted as transmittance (the y-axis) versus wavelength (the x-axis).

Figure 9.2. Schematic diagram of a spectrometer.

Modern infrared spectrometers have a schematic that looks similar to Figure 9.2. To obtain a spectrum, first run the instrument with no sample in the beam. This blank spectrum measures spectrum of the source of the infrared radiation and any background absorptions in the atmosphere as it passes through the spectrometer. Next, place a sample in the instrument and obtain a second spectrum. The spectrometer subtracts the first spectrum from the second, thus, eliminating the effects of atmospheric components. Placing pure solvent in the instrument when obtaining the blank allows the spectrometer to subtract the spectrum of the solvent from a solution.

9.2 Molecular Vibrations in Infrared Spectroscopy

Because the atoms within a molecule move constantly, they cause bond distortion. Atoms move, or vibrate, in two general ways. They stretch, and they bend. An infrared spectrum detects changes in these molecular vibrations. Stretching vibrations produce changes in the bond length. Bending vibrations cause changes in the bond angle. Because there are a number of specific stretching or bending vibrations, these are often called stretching or bending modes. Figure 9.3 shows two stretching modes, and Figure 9.4 shows four bending modes observed in the infrared.

Molecular vibrations are the motions of atoms in molecules. Stretching and bending vibrations are the molecular vibrations observed in the IR spectrum.

Stretching: C C Antisymmetric

Symmetric

Figure 9.3. Stretching modes measured in the infrared.

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Bending: C In-Plane C

Scissoring

Rocking

Out-of-Plane Twisting Wagging

Figure 9.4. Bending modes measured in the infrared.

When a beam of light strikes a bond with a dipole moment, the oscillating electric field component of light causes the bond to vibrate by alternately stretching and compressing. The bonds vibration is analogous to a spring that either stretches or compresses when an external force is applied. As the bond vibrates in response to the changing polarity of the electric field, it absorbs energy, as shown in Figure 9.5. The frequencies at which these bonds absorb energy are in the infrared region of the spectrum.

Figure 9.5. A bond with a dipole moment is either stretched or compressed in the presence of the oscillating electric field component of light.

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Wavenumbers are the reciprocal of the wavelength in centimeters and are reported as cm1.

Molecules have many vibrational energy states. The set of vibrations belonging to each molecule is unique for that particular molecule. The molecules that make up a homologous series also have a unique set of vibrations. This uniqueness is the basis of infrared spectroscopy. By understanding the meaning of the various peaks, you can obtain information about a molecule's functional groups. Molecules absorb infrared electromagnetic radiation within the wavelength range of 2.5 to 16 m (a m is 106 meters). Most infrared spectra are reported in wavenumbers, so this range corresponds to 4000 to 625 cm1. An advantage of using wavenumbers is that they are directly proportional to energy, whereas wavelengths are inversely proportional to energy. Thus, a wavelength of 2.5 m corresponds to 4000 cm1 and is the high-energy end of the scale. A typical infrared spectrum consists of a series of absorption peaks. These peaks vary in shape and intensity in relation to the vibrational energy states of the particular molecule that you are analyzing. Intensity refers to the size of a peak. The greater the amount of radiation absorbed, the larger the size of the peak. The intensity of an absorption peak, or band, corresponds to the magnitude of the change in the dipole moment caused by the vibration of the molecule. The larger the change in the dipole moment, the more intense the absorption. For example, the stretching in a carbonyl group (C=O) increases an already large dipole moment. This stretching produces a peak of greater intensity than a peak obtained from the stretching of a C=C double bond because there is a relatively small change in the dipole moment of a C=C double bond. Because of these variations in intensity, the interpretation of an infrared spectrum requires a more careful observation of relative intensities than just simply reading numbers from tables.

9.3 Introduction to Interpreting Infrared Spectra

Each infrared spectrum consists of two parts. The first part covers the area from 4000 cm1 to about 1500 cm1 and gives information about the functional groups contained in the molecule. Of the two parts, this one is usually the easier to interpret. The second part, called the fingerprint region, covers the region from approximately 1500 cm1 to 625 cm1. Table 9.2 summarizes the characteristic infrared absorption frequencies. The types of bonds present in a molecule determine the frequencies at which the functional groups absorb the energy. Figure 9.6 summarizes Table 9.2 by diagramming these frequencies by bond type.

The fingerprint region gives information about the molecular structure of the molecule.

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Bond Type CH CH CH CH CH OH OH OH NH NH CC C C C C C C CO C O C O C O C O C O C O CN CN C N NO2

Functional Group Alkane Alkene Alkyne Aldehyde Aromatic Alcohols (H-bonded) Alcohols (No H-bonds) Acid Amine Amide Alkane Alkene Aromatic Alkyne Alcohol, ether, ester Ketone Aldehyde Aryl ketone Ester Acid Amide Alkyl amine Aryl amine Nitrile Nitro

Stretching (cm1) 29702850 (s) 3080-3020 (m) 3300 (s) 2900 (m) 2700 (m) 3100-3000 (v) 3500-3300 (s, broad) 3650-3590 (v) 3000-2500 (s, broad) 3500-3300 (m) 3500-3350 (v) 1200-800(w) 1680-1620 (v) 1600-1450 (v) 2260-2100 (v) 1300-1000 (s) 1725-1705 (s) 1740-1720 (s) 1700-1680 (s) 1750-1735 (s) 1725-1700 (s) 1690-1650 (s) 1220-1050 (w) 1360-1250 (s) 2260-2100 (v) 1580-1560 (s) 1400-1380 (s)

Bending (cm1) 1470-1350 (s) 1000-675 (s)

800-675 (s) 1620-1590 (v) 1655-1510 (v)

(s) - Strong - the most intense, or largest, peaks in the spectrum. (m) - Medium - peaks that are 40 to 70% of the intensity of the strong peaks. (w) - Weak - peaks that are less than 40% of the intensity of the strong peaks. (v) - Variable - variable intensity peaks. Usually medium to weak. Table 9.2. Characteristic infrared absorption frequencies.
100

O-H, N-H, C-H Stretch

N-H Bend

C C H Bend

C C , C N Stretch C-O, C-N Bend C C, C N Stretch C-H Bend

0 4000 3000 2500 2000 1500 1300 1100 1000 900 800 700 650

Wavenumber (cm-1)

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Figure 9.6. Regions where different types of bonds absorb energy in the infrared.

To see how the structural features of individual molecules affect infrared spectra, compare the spectra of hexane (Figure 9.7a) and hexene (Figure 9.7b). The two spectra look different. For example, the peak just above 3000 cm1 present in the spectrum of hexene is absent in the hexane spectrum. This peak is characteristic of the CH stretching of an sp2 hybridized carbon. The similar peaks just below 3000 cm1 in both spectra are characteristic of the CH stretching in an sp3 hybridized carbon. The next significant difference is the peak at 1640 cm1 in hexene. This peak is characteristic of C=C double bond stretching. The peaks between 1500 and 1300 cm1, present in both spectra, are the result of CH bending on an sp3 hybridized carbon. The last difference is the peaks at 990 and 910 cm1 of the hexene spectrum. These peaks are characteristic of the bending of the CH bonds on a double bond.
100

0 4000

3000

2500

2000

15 0 0

13 0 0

110 0

10 0 0 9 0 0

800

700

650

Wavenumber (cm )

-1

(a)
100

0 4000

3000

2500

2000

15 0 0

13 0 0

110 0

10 0 0 9 0 0

800

700

650

Wavenumber (cm )

-1

(b)
Figure 9.7. Infrared spectrum of (a) hexane and (b) 1-hexene.

If you are a beginner, and you try to interpret every peak of an IR spectrum, you may find the analysis very complex and very difficult. A typical IR spectrum simply contains too much information to allow easy analysis. Frequently, even experienced chemists require

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help analyzing spectra, so they use extensive tables similar to Table 9.2 and Appendix B. Thus, the goal of this book is to help you recognize the typical peak patterns and what the main peaks indicate. This recognition allows you to rapidly identify individual functional groups. When identifying the functional groups, examine in detail the 4000 to 1500 cm1 region of the spectrum. Refer to the fingerprint region only as necessary to confirm the functional groups that you found in the 4000 to 1500 cm1 region.

9.4 Hydrogen Attached to sp3 Hybrid Atoms

The appearance of each peak in a spectrum is typical of all the compounds in that particular class of compounds. For example, the infrared spectra of hexane and hexene in Figure 9.7 both show similar peaks for sp3 CH bonds just below 3000 cm1. However, even though the spectral peaks for several compounds have a similar appearance, none are identical. Even two spectra of the same compound may look somewhat different on different instruments using different concentrations of compound. The important considerations when looking at a spectrum are the position and general appearance of the peaks, not the details of their specific shapes. The spectral fragments shown in this and the following sections are from actual spectra. Three common types of hydrogen to sp3 hybrid atom bonds in organic chemistry are hydrogen to oxygen bonds, hydrogen to nitrogen bonds, and hydrogen to carbon bonds. This section discusses the appearance of the IR peaks that arise from the stretching of these three kinds of bonds. First, examine the three types of hydrogen to oxygen, HO, bonds: alcohols, phenols, and carboxylic acids. Both alcohols and phenols produce a strong broad peak around 3500 - 3300 cm1. The first spectral fragment in Figure 9.8 shows an HO stretch peak of an alcohol involved in hydrogen bonding. On rare occasions, the HO bond is not hydrogen bonded but is a free bond. A free HO bond occurs at about 3550 cm1. The free bond peak is neither as strong nor as broad as the hydrogen bonded peak and occurs only when the alcohol is either very dilute or too sterically crowded for hydrogen bonding to occur. The center spectral fragment in Figure 9.8 shows the free HO group as it typically appears when mixed with some of the hydrogen bonded HO group. The appearance of a phenolic HO group is nearly identical with the appearance of the alcohols. The third spectral fragment in Figure 9.8 shows the HO bond of a carboxylic acid. This peak is usually broad and its specific location is hard to pin down. When you see a very broad peak, generally covering the region between 3500 and 2500 cm1, interpret it as a carboxylic acid.

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Typical OH Peaks
100

0 4000

30 0 0

2500

4000

3000

2500

4000

3000

2500

Wavenumber (cm )

-1

Hydrogen bonded Nonhydrogen bonded Alcohol Alcohol

Carboxylic acid

Figure 9.8. Comparison of different types of OH groups in the IR.

Next, examine the two functional groups with hydrogen to nitrogen, HN, bonds: amines and amides. Each of these groups contains either one or two HN bonds. The primary amide and amine peaks have similar appearances and positions, as do the secondary amide and amine peaks. Primary amides and amines produce two peaks, but the secondary amides and amines produce only one. Figure 9.9 shows these four types of HN bonds. The positions for these bonds are in the 3500 cm1 to 3300 cm1 region of the spectrum. This region is similar to the region for the HO bonds. Generally, the peaks for HN stretching are weaker than the peaks for HO stretching. The major difference between amines and amides is the strong peak for the carbonyl stretching at about 1700 cm1. Section 9.6 discusses carbonyls in more detail. This difference illustrates an important concept for interpreting infrared spectra. When identifying a peak at one location, you must confirm your identification by using any other peaks indicating that functional group.

Typical NH Peaks

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0 4000

3000

2500 4 0 0 0

3000

2500 4000

3000

2500 4000

3000

2500

Wavenumber (cm )

-1

Primary amine

Secondary amine

Primary amide

Secondary amide

Figure 9.9. Comparison of different types of NH bonds in the IR.

The last type of sp3 bond is the HC bond in saturated hydrocarbon groups. Separating the methyl (CH3), methylene (CH2), and methine (CH) groups in this region is usually very difficult. When you see a broad, often multiple, peak between 3000 and 2850 cm1, you need only note that the molecule has some type of sp3 hybrid H C bonds. In addition, HC bending appears in the range of 1470 to 1350 cm1 as a set of two or more peaks. The lower wavenumber peak increases in intensity and often splits into two or three peaks with increasing branching. Figure 9.10 shows these two regions.

Typical sp3 CH Peaks

100

0 4000

3000

2500 1500 1300

1100

Wavenumber (cm )

-1

CH Stretching CH Bending
Figure 9.10. Typical sp3 CH bending and stretching regions. Although there are differences between the peaks for CH3, CH2, and CH groups, the signals overlap so much that they are difficult to separate.

Exercise 9.1 Choosing from these molecules, assign a molecular structure to each of the following IR spectra.

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Phenol Butanoic acid Cyclohexanol Decanamide

Triethyl amine N-Methylcyclohexanamine

Note: Do not let yourself become confused by all the peaks in these spectra. Concentrate only on the sections covered so far. As you add more fragments, more peaks will be meaningful to you. a)
T 100 r a n s m i t t a n c e 0 (%)
4000 3000 2500 2000 1500 1300 1100 1000 Wavenumber (cm1) 900 800 700 650

b)
T 100 r a n s m i t t a n c e (%)

0
4000 3000 2500 2000 1500 1300 1100 1000 Wavenumber (cm1) 900 800 700 650

c)
T 100 r a n s m i t t a n c e 0 (%)
4000 3000 2500 2000 1500 1300 1100 1000 Wavenumber (cm1) 900 800 700 650

d)

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T 100 r a n s m i t t a n c e 0 (%)
4000 3000 2500 2000 1500 1300 1100 1000 Wavenumber (cm1) 900 800 700 650

Sample solution c) This is a spectrum of decanamide. The peaks at 3300 cm1 and 3200 cm1 indicate the NH2 group, and the peak for the carbonyl stretching at 1700 cm1 confirms the presence of the amide group. The peaks between 3000 and 2850 cm1 are typical of sp3 CH stretching.

9.5 Hydrogen Attached to sp2 and sp Hybrid Atoms

Three common types of sp2 hybrid hydrogen to carbon, HC, bonds are the HC bonds in alkenes, aromatic compounds, and aldehydes. This section examines the peaks made by these bonds. Bond bending is more important than bond stretching when interpreting alkenes and aromatic compounds. The locations of the HC bending peaks between 1000 and 650 cm1 establishes the substitution patterns of the compound. Both alkenes and aromatic compounds have a medium intensity peak between 3100 and 3000 cm 1. Usually a peak closer to 3000 cm1 indicates an alkene, and a peak closer to 3100 cm1 indicates an aromatic compound. Many aromatic compounds also have a second peak about 3000 cm1. However, this peak is not always present, so use it to confirm an aromatic compound, but do not depend on it as a diagnostic for aromatics. Figure 9.11 shows typical spectra of alkenes and aromatic compounds.

Typical sp2 CH Stretching Peaks

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100

4000

3000

2500

4000

3000

Wavenumber (cm )

2500 -1

4000

3000

2500

Alkene

Aromatic

Aldehyde

Figure 9.11. The general appearance of the peaks resulting from the HC stretching of sp2 hybrid CH bonds.

An aldehyde shows two peaks: one at 2900 cm1 and another at 2700 cm1. When identifying an aldehyde group, rely mostly on the 2700 cm1 peak, as no other common functional groups have a peak at this location. Plus, the peak at 2900 cm1 often hides in the saturated CH stretching region. The third spectral fragment in Figure 9.11 shows the appearance of an aldehyde group. Peaks in the region from 1000 cm1 to 650 cm1 indicate the positions of substituents in a compound with a double bond or on an aromatic compound. The sp2 carbon hydrogen bond bending causes these peaks. Figure 9.12 shows the most common types of double bonds. A monosubstituted double bond (RCH=CH2) has two peaks: one at approximately 990 cm1 and the other at 910 cm1. A trans disubstituted double bond has a single peak at 950 cm1, and the cis disubstituted double bond has a broad peak at 720 cm1. A trisubstituted double bond has a peak at 890 cm1 and 820 cm1. The trisubstituted example in Figure 9.12 shows the two peaks with different intensities, but the relative intensity varies. Sometimes the peaks are of equal intensity, and sometimes the 820 cm1 peak is stronger, depending on the details of the structure of the compound.

Typical sp2 CH Bending Peaks

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100

100

1100 1000

900

800

700 -1

650

1100 1000

900

800

700 -1

650

Wavenumber (cm )

Wavenumber (cm )

monosubstituted
100 100

trans disubstituted

1100 1000

900

800

700 -1

650

1100 1000

900

800

700 -1

650

Wavenumber (cm )

Wavenumber (cm )

cis disubstituted

trisubstituted

Figure 9.12. Double bond patterns for HC bending of various types of double bonds.

The 900 cm1 to 675 cm1 region of the spectrum contains peaks that indicate substitutions on aromatic rings. Figure 9.13 shows the four basic substitution patterns on an aromatic compound. The first spectrum shows a monosubstituted compound with peaks at 730 and 690 cm1. Compare this spectrum with the spectrum of the meta substitution. Frequently, confusion occurs over these two, because both spectra have two peaks at about the same position. To avoid this confusion, note that a monosubstituted aromatic ring has about 40 cm1 between its two peaks, and the meta has about 75 cm1 between its two peaks. Although the positions of the peaks vary, the separations between the pairs stay the same. People also confuse the ortho and para patterns, unless they remember that the ortho appears in the range of 730 to 690 cm1, and the para is in the range of 830 to 780 cm1.

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para meta

ortho

Relative positions of ortho, meta, and para substituents on an aromatic ring.

Typical Aromatic Substitution Patterns

100 100

900

800

700 -1

650

900

800

700 -1

650

Wavenumber (cm )

Wavenumber (cm )

Monosubstituted
100

Ortho disubstituted
100

900

800

700 -1

650

900

800

700 -1

650

Wavenumber (cm )

Wavenumber (cm )

Meta disubstituted

Para disubstituted

Figure 9.13. Substitution patterns for aromatic rings.

The location of the HC stretching for a triple bond is at approximately 3300 cm1, which is nearly the same location as the HO peaks of alcohols and phenols. You can avoid confusing the two by remembering that the OH groups have a broad peak and the CH peak is sharp. Figure 9.14 shows the HC triple bond peak.

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Typical Alkyne CH Stretch

1 0 0

4000

3000

Wavenumber (cm )

2500 -1

Alkyne Figure 9.14. The HC bond of a terminal alkyne. Note that its position is nearly the same as that of the OH peaks of alcohols and phenols, but its appearance is very different.

Exercise 9.2 Choosing from these molecules, assign a molecular structure to each of the following IR spectra. Cycloheptene Ethynylbenzene 4-Methylaniline 3-Methylphenol p-Dichlorobenzene Iodobenzene and phenol is

(Note: aniline is aminobenzene hydroxybenzene (PhOH).) a)

T 100 r a n s m i t t a n c e 0 (%)
4000 3000 2500 2000

(PhNH2)

1500 1300 1100 1000 900 Wavenumber (cm1)

800

700

650

b)

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T 100 r a n s m i t t a n c e 0 (%)
4000 3000 2500 2000 1500 1300 1100 1000 900 Wavenumber (cm1) 800 700 650

c)
T 100 r a n s m i t t a n c e 0 (%)
4000 3000 2500 2000 1500 1300 1100 1000 900 Wavenumber (cm1) 800 700 650

d)
T r a n s m i t t a n c e (%) 100

0
4000 3000 2500 2000 1500 1300 1100 1000 900 Wavenumber (cm1) 800 700 650

Sample solution c) This spectrum is of ethynyl benzene. The diagnostic peaks are the terminal alkyne at 3300 cm1 and the pattern matching of the mono substituted aromatic ring at 800 to 700 cm1.

9.6 CarbonHeteroatom Bonds

This section discusses the three categories of carbon to heteroatom bonds: carbon to oxygen, carbon to nitrogen, and carbon to

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halogen. All three are part of various functional groups that occur in many types of organic compounds. First, examine the CO single bonds contained in alcohols, phenols, ethers, and esters. Because the peaks for each of these types of bonds are so similar, they are difficult to differentiate among. Because they occur only in the fingerprint region, they are difficult to distinguish from the peaks of other bonds that also appear there. The important CO peaks are near 1055 cm1 for primary alkyl groups, 1110 cm1 for secondary alkyl groups, 1175 cm1 for tertiary alkyl groups and 1250 cm1 for phenyl and carbonyl groups. These peaks are usually among the strongest peaks in the infrared spectra. Most carbonyl group peaks occur near 1740 cm1. As this region has few potentially confusing absorptions, a peak here definitely means a carbonyl group. However, identifying the specific type of carbonyl group from this region of the spectrum is a challenge unless you have a high-resolution spectrum. Fortunately, each carbonyl group has other absorptions that clearly tell what type of carbonyl is present. For example, in addition to the carbonyl absorption near 1740 cm1, an aldehyde has a peak at 2700 cm1. Table 9.3 lists these correlations, and Figure 9.15 shows two carbonyl absorptions.

Typical Carbonyl groups

1 0 0 1 0 0

2000

1500 -1

2000

1500 -1

Wavenumber (cm )

Wavenumber (cm )

Typical Carbonyl

Anhydride

Figure 9.15. Carbonyl group absorptions. The spectrum on the left is a typical carbonyl group. The difficulty of this scale is to see the differences in location of most carbonyls. The spectrum on the right is an acid anhydride group. It shows two carbonyl absorptions.

Type of Carbonyl Group Aldehyde Ketone Carboxylic acid

Peak position (cm1) 1725 1710 1725

Correlating peaks (cm1) Carbonyl CH 2900, 2700 None Acid OH 3000-2500

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Type of Carbonyl Group Ester

Peak position (cm1) 1740

Amide Acyl halide Acid anhydride

1640 1820 1820, 1750

Correlating peaks (cm1) Two bands of CO stretch: 1250-1175 1175-1000 1o N, 3450, 3225 2o N, 3335 Chalogen, 1000-900 CO stretch, 1250-1000

Table 9.3. Positions of the various types of carbonyl groups and correlating peaks for identification of carbonyl-containing functional groups.

A conjugated compound has double or triple bonds alternating with single bonds. Conjugation is discussed in Chapter 16, which begins on page 000.

In many molecules, the carbonyl group is adjacent to either a double or triple bond or to a phenyl group. Chemists call these molecules conjugated carbonyl compounds. This bonding affects the location of the peak by moving it about 40 to 50 cm1 away from the position listed in Table 9.3. For example, cyclohexanecarboxylic acid has a strong carbonyl peak at 1720 cm1, whereas benzoic acid has a strong carbonyl peak at 1685 cm1.
1720 cm-1 O C OH O C OH 1685 cm-1

Cyclohexanecarboxylic acid

Benzoic acid

Frequently, carbonyl groups also produce a weak absorption near 3450 cm1. This small peak, called a carbonyl overtone band, occurs at exactly twice the wavenumber of the actual carbonyl group peak. Be careful not to confuse the carbonyl overtone band with HO and HN peaks or with sp hybridized CH bonds. These absorptions are much stronger in comparison to an overtone band. Carbon to nitrogen single bonds form amines, anilines, and amides. The peaks for these bonds appear at nearly the same position as the carbon to oxygen single bond. The primary alkyl bond to nitrogen emerges at 1065 cm1, the secondary bond at 1150 cm1, and the tertiary bond at 1235 cm1. The amide peak occurs in nearly the same region as the amines. The anilines appear at 1280 cm1. Carbon to nitrogen double bonds are much less common in organic molecules than carbon to nitrogen triple bond. You can recognize nitriles by the medium intensity peak at 2250 cm1. The

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only other common functional group in this region is the alkyne triple bond discussed in the Section 9.7. Figure 9.16 shows the nitrile peak.

Typical Nitrile Peak

1 0 0

2500

2000 -1

Wavenumber (cm )

Nitrile Figure 9.16. The position of the nitrile group.

Halogen absorptions occur between 1250 and 550 cm1. However, because there are numerous absorptions within this range, identifying the specific halogen present is difficult. The most useful absorptions are the CCl stretch at 725 cm1 and the CBr stretch at 645 cm1. Aromatic chlorines appear about 1090 cm1, and aromatic bromines appear about 1030 cm1. When you suspect halogens, use mass spectrometry, not infrared spectroscopy, for identification. Exercise 9.3 Choosing from these molecules, assign a molecular structure to each of the following IR spectra. Benzonitrile Cyclohexanone a)
T 100 r a n s m i t t a n c e (%)

Heptanenitrile Methanoic acid

Cyclohexanol Cyclohexanecarboxaldehyde

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4000

3000

2500

2000

1500 1300 1100 1000 Wavenumber (cm1)

900

800

700

650

b)
T 100 r a n s m i t t a n c e (%)

0
4000 3000 2500 2000 1500 1300 1100 1000 Wavenumber (cm1) 900 800 700 650

c)
T r a n s m i t t a n c e ( %)
0 1 0 0

4000

3000

2500

2000

1500 1300 1100 1000 Wavenumber (cm1)

900

800

700

650

d)
T 100 r a n s m i t t a n c e (%)

0
4000 3000 2500 2000 1500 1300 1100 1000 Wavenumber (cm1) 900 800 700 650

Sample solution c) This spectrum is either benzonitrile or heptanenitrile. The peak at about 2200 cm1 readily identifies the compound as a nitrile. The peaks at 3000-2950 cm1 identify it as an alkane. Thus, it must be heptanenitrile.

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9.7 Other Bonds

There are a variety of additional bonds that do not fit easily into any of the categories discussed in Sections 9.4, 9.5, and 9.6. These bonds include the carbon to carbon double and triple bonds and the nitro groups. The double bonds of both the alkenes and the arenes appear within the same range in the infrared. For the alkenes this range is 1690 to 1540 cm1, with most of the simple alkenes appearing as a medium intensity peak around 1640 cm1. Arenes generally have two bands: one weak to medium peak appearing at 1600 cm1 and a stronger peak at 1500 cm1. Figure 9.17 shows typical peaks for these two absorptions.

Typical sp2 CarbonCarbon Stretching Peaks

1 0 0 1 0 0

2000

1500 -1

2000

Wavenumber (cm )

Wavenumber (cm )

1500 1200 -1

Alkene

Aromatic

Figure 9.17. The bond absorptions for both the alkene and the aromatic C=C bond appear at similar locations.

The only two common absorptions in the 2500 to 2000 cm1 range are the carbon to nitrogen triple bond of the nitriles (discussed in Section 9.6) and the carbon to carbon triple bond of the alkynes. A monosubstituted alkyne (R C C H) appears as a medium peak at 2130 cm1, and a disubstituted alkyne (R C C R) appears at 2220 cm1. The disubstituted alkyne is usually a very weak peak. It is so weak, in fact, that it is often nonexistent. Figure 9.18 illustrates the alkyne carboncarbon stretching peaks.

Typical sp Carbon-Carbon Stretching Peak

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1 0 0

2500

2000

2500 -1

2000

Wavenumber (cm )

Terminal Alkyne

Internal Alkyne

Figure 9.18. The alkyne bond appears in nearly the same region as the nitrile. They are the only two common absorptions that appear in the 2500 to 2000 cm1 range of the infrared. Most of the time, the internal alkyne is very weak.

The last functional group in this section is the nitro group (NO2). Usually, the nitro group bonds to an aromatic ring. Although nitro groups do form alkyl nitrates, they are uncommon. The aromatic nitro groups occur at 1500 and 1380 cm1. They also have a peak commonly found at 740 cm1 that is easy to confuse with the aromatic substitution patterns.

Typical Nitro Group Peaks

1 0 0

2000

1500

Wavenumber (cm )

1300 -1

Nitro group Figure 9.19. Two strong absorptions, one at 1500 and the other at 1380 cm1, characterize the aromatic nitro group.

Exercise 9.4 Choosing from these molecules, assign a molecular structure to each of the following IR spectra. trans-3-Hexene cis-2-Pentene 3-Hexyne

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1,7-Octadiyne a)
T 100 r a n s m i t t a n c e 0 (%)
4000 3000 2500 2000

4-Methylnitrobenzene

3-Buten-2-ol

1500 1300 1100 1000 Wavenumber (cm1)

900

800

700

650

b)
T 100 r a n s m i t t a n c e 0 (%)
4000 3000 2500 2000 1500 1300 1100 1000 Wavenumber (cm1) 900 800 700 650

c)
T 100 r a n s m i t t a n c e 0 (%)
4000 3000 2500 2000 1500 1300 1100 1000 Wavenumber (cm1) 900 800 700 650

d)

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T 100 r a n s m i t t a n c e 0 (%)
4000 3000 2500 2000 1500 1300 1100 1000 Wavenumber (cm1) 900 800 700 650

Sample solution d) This spectrum is of cis-2-pentene. The peaks just above 3000 cm1 and at about 1650 cm1 indicate the double bond. The peak at about 700 cm1 indicates the cis double bonds.

9.8 Interpreting Infrared Spectra, Part 2

There are so many possible peaks in an infrared spectrum that interpreting them all is sometimes very challenging. The purpose of this section is to reduce that challenge. As noted earlier, an infrared spectrum consists of two sections: the functional group region from 4000 to 1500 cm1 and the fingerprint region from 1500 to 625 cm1. The functional group region breaks down further into three categories. 1) In the 3700 to 2700 cm1 region, bonds involving hydrogen appear. 2) Between 2500 and 2000 cm1 is the triple bond and nitrile region. 3) From 1800 to 1500 cm1 is the double bond and carbonyl group region. When interpreting a spectrum, first identify all the peaks of at least medium intensity in the functional group region. Then, if necessary, confirm your identifications in the fingerprint region. Identifying all the peaks in the fingerprint region is usually difficult. Table 9.4 lists some important correlations between the functional group region and the fingerprint region for alcohols and amines. Functional group Functional group region (cm1) Alcohol (OH) Amine (RNH2) (R2NH) 3350 (s, broad) 3400,3200 (m) 3200 (m) Fingerprint region (cm1) (CO or CN) o 1 2o 3o Ar 1055 1110 1175 1250 1065 1150 1235 1280

Table 9.4. Correlations between the functional group and fingerprint regions of the infrared spectrum for alcohols and amines.

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The best way to learn how to interpret infrared spectra is to work through a couple of examples. Consider the spectrum in Figure 9.20. Look first at the functional group region. In that region there is a broad weak peak at 3400 cm1, a group of peaks between 3000 and 2700 cm1 and a strong peak about 1700 cm1. You must identify these peaks to pin down the compounds class.
T 100 r a n s m i t t a n c e 0 (%)
4000 3000 2500 2000 1500 1300 1100 1000 Wavenumber (cm1) 900 800 700 650

Figure 9.20. The first infrared spectrum example analyzed in this section.

See Table 9.3 on page 000.

The peak at 3400 cm1 is similar in appearance to the OH peak of an alcohol but is much too weak to be one. However, the 3400 cm1 peak may be an overtone band for the strong 1700 cm1 peak which indicates a carbonyl group. The complex region between 3000 and 2850 cm1 matches the range of an alkyl group. Table 9.3 shows that an aldehyde has a pair of peaks at 2900 and 2700 cm1. Remember that the alkane region (3000 to 2850 cm1) often obscures the 2900 cm1 peak, so check the 2700 cm1 region. The 2700 cm1 peak is clear. Because there is little else at 2700 cm1, the compound is an aldehyde. Without further data, you cannot determine that the actual spectrum is of propanal. Now consider the second spectrum as shown in Figure 9.21. It contains a large broad peak about 3350 cm1, a small peak around 3100 cm1, two peaks just below 3000 cm1 and another about 1580 cm1. The 3350 cm1 peak is almost identical in appearance and location to that of an OH group. The small peak at 3100 cm1 suggests an aromatic compound, and the peak at 1580 cm1 confirms it. The peaks just below 3000 cm1 indicate that the compound contains alkyl groups.

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T 100 r a n s m i t t a n c e (%)

0
4000 3000 2500 2000 1500 1300 1100 1000 Wavenumber (cm1) 900 800 700 650

Figure 9.21. The infrared spectrum for the second solved exercise analyzed in this section.

At this point you have enough information to know that the compound is either an alkyl-substituted phenol or a phenyl substituted alcohol. To determine which, examine the fingerprint region. The strong broad peak just above 1200 cm1 and the lack of any strong peaks between 1200 and 1000 cm1 indicate that the compound is a phenol. The strong peaks around 800 and 700 cm1 are characteristic of a meta substituted aromatic ring. Thus, this spectrum is of a meta-alkylphenol, although the exact alkyl group is difficult to determine. The spectrum is of 3-tert-butylphenol. Exercise 9.5 Determine the functional groups and make structural generalizations for the compounds shown in the following spectra. a)
T 100 r a n s m i t t a n c e (%)

0
4000 3000 2500 2000 1500 1300 1100 1000 Wavenumber (cm1) 900 800 700 650

b)

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T 100 r a n s m i t t a n c e 0 (%)
4000 3000 2500 2000 1500 1300 1100 1000 Wavenumber (cm1) 900 800 700 650

c)
T 100 r a n s m i t t a n c e (%)

0
4000 3000 2500 2000 1500 1300 1100 1000 Wavenumber (cm1) 900 800 700 650

d)
T 100 r a n s m i t t a n c e (%)

0
4000 3000 2500 2000 1500 1300 1100 1000 Wavenumber (cm1) 900 800 700 650

Sample solution d) This compound has only alkyl groups above 1500 cm1. The only other obvious peak is at 1100 cm1. This peak indicates a CO bond, so the compound is an ether.

9.9 Mass Spectrometry

Mass spectrometry (MS) is different from infrared spectroscopy (IR) in that it does not analyze the selective absorption of electromagnetic radiation by the various energy levels of a molecule.

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A radical-cation is a species with a positive charge and an unpaired electron. The molecular ion is the molecule minus an electron. The molecular ion is sometimes called the parent ion.

Chemists use mass spectra in addition to IR and NMR spectra (Chapter 10) to gain information about the structure of molecules. To produce a mass spectrum, the spectrometer bombards the molecule with a beam of high-energy electrons. As this beam of electrons collides with the molecule, it breaks the molecule into a series of ions. The spectrometer then records the masses of these ions on the spectrum. As high-energy electrons from the mass spectrometer collide with a molecule, an electron is knocked out of the molecule. This process produces a radical-cation called the molecular ion.
B + A

A B

2e

Because the ionization process has a large excess of energy the molecular ion is unstable, so it breaks into a number of other species: other radical-cations, carbocations, radicals, and various uncharged species.
A B A B A A + B + B

The high-energy electrons can knock any electron from the molecule; thus, fragmenting the molecule in many possible ways. Within each type of molecule, however, certain electrons knock out more readily than others. The fragmentation pattern of fragments from a particular molecule is characteristic for that molecule. The pattern also contains fragments that are common with other molecules that contain the same functional groups. Figure 9.22 shows a schematic diagram of a mass spectrometer. To use a mass spectrometer, inject a sample into the injection chamber. Vapors from this sample then leak in a small stream from the injection chamber into the high vacuum chamber. Because the instrument is so sensitive, it requires only a very small amount of sample for a spectrum. As this stream of sample, or neutral molecules, passes along the chamber, a beam of high-energy electrons strikes it, changing it and fragmenting it into positive ions and neutral particles. Next, a series of negatively charged focusing plates accelerate and focus, or direct, these positive ions into the magnetic field. Any radicals or uncharged particles are unaffected by the magnetic field and are unobserved by the spectrometer.

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Po s i t i v e I o n s E l e c t r o n Be a m Ne u t r a l Mo l e c u l e s M a g n e t Po l e Fi l a m e n t

Fo c u si n g Pl a t e s Re p e l l e r P l a t e M a g n e t Po l e T o Va c u u m Pu m p De t e c t o r Sl i t s I o n Co l l e c t o r Re c o r d e r

Am p l i f i e r

Figure 9.22. Schematic diagram of a simple mass spectrometer.

In response to the magnetic field, the positively charged ions move in a curved pathway. For a given magnetic field, the radius of the curved path of each particular ion is proportional to the mass-tocharge (m/z) ratio of that ion. The larger the mass-to-charge ratio, the larger the radius of the pathway. The smaller the mass-to-charge ratio, the smaller the radius of the pathway. The charge of each ion is usually one, so the factor of consideration for each ion is its mass, or size. Beyond the magnetic field in the mass spectrometer is a collector slit. The collector slit allows only the ions with a pathway of a certain radius to pass through it. By varying either the magnetic field strength or the accelerating potential of the focusing plates, the radius of the path the ions follow changes. Whether the magnetic field strength of the accelerating potential is changed depends on the particular instrument. This process selectively focuses the ions of the various m/z ratios on the ion detector slit allowing the detector (usually called the ion collector) to count each differently sized ion. The amplifier then amplifies that count and feeds that signal into the recorder, which plots the number of ions, or ion current, vs. m/z of the ions. The abscissa of the plot is the mass-to-charge ratio, and the ordinate is the relative intensity, or the number of ions, in the sample. Figure 9.23 is the mass spectrum of acetone (2-propanone). An analysis of the mass spectrum of acetone shows the processes that occur in mass spectrometry.

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1 0 0

I n t e n s i t y

O
8 0

CH3CCH3
6 0 4 0

2 0

0 2 0 4 0 6 0 8 0 1 0 0 1 2 0 1 4 0 1 6 0 1 8 0

m/z
Figure 9.23. The mass spectrum of acetone.

In the first step of the process, the beam of high-energy electrons knocks an electron from the molecule. With acetone that electron is usually one of the nonbonding electrons from the oxygen. The result is a radical cation, or the molecular ion. The peak representing the molecular ion is important in that it gives the molecular weight of the molecule.
O O

e
CH3 H3C CH3

H3C

The base peak is the most abundant ion in the MS.

Because the radical-cation is unstable, it fragments, or breaks apart, into a series of smaller ions. The molecular ion of acetone is present in the spectrum as a peak with about 50% of the intensity, or height, of the highest peak and a m/z of 58. Keep in mind that not all molecules show a molecular ion on their spectrum. In some cases the molecular ion is so unstable that it completely fragments before it reaches the collector slit. Each line represents an individual fragment ion. The most abundant ion gives the peak with the highest intensity in the spectrum. This peak is called the base peak. The mass spectrometer always assigns the base peak the value of 100 and all other peaks their value proportional to the base peak. For acetone the base peak has a m/z of 43. When you compare this with the molecular ion, which has a m/z of 58, you see a loss of 15 mass units. A methyl group has a mass of 15. Thus, the major fragmentation pathway in acetone is the loss of a methyl group.

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O C H3C CH3 C O

+ CH3

H3C

This fragmentation forms an acylium ion, shown in its most stable resonance form, and a methyl radical. The methyl radical is not positively charged, so it does not appear in the spectrum. The other peaks shown in the spectrum are minor peaks that result from a variety of more complex fragmentation pathways. Exercise 9.6 One of the following mass spectra is of 2-pentanone and the other is of 3-pentanone. Match the appropriate spectrum with the appropriate compound. Justify your choices.

100

I n t e n s i t y

80 60 40 20 0 20 40 60 80 100 120 140 160 180

m /z
100

I n t e n s i t y

80 60 40 20 0 20 40 60 80 100 120 140 160 180

m /z

9.10 The Molecular Ion

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From an MS, chemists determine the structure of the fragments represented by the peaks, then assemble these fragments into the structure of the molecule. However, this task is complex and beyond the scope of this book. For you, the beginning organic chemist, the most useful information that you can gather from an MS is from the peaks representing the molecular ion and its isotopes. You can learn the molecular weight of the compound, and you can tell if the compound contains certain elements, such as nitrogen or a halogen. Notice that the mass spectrum in Figure 9.23 and Exercise 9.6 each have a small peak to the right of the peak representing the molecular ion. These peaks, which occur at m/z 59 and m/z 87, respectively, arise from the presence of isotopes of hydrogen, carbon, and oxygen. Most elements have more than one isotope, with the various isotopes present in varying amounts. The heavier isotopes give rise to the small peaks at a higher mass than the molecular ion peak. A peak that is one mass unit heavier than the molecular ion is called the M+1 peak. A peak that is two mass units heavier is called the M+2 peak. Table 9.5 contains a list of elements common to organic compounds, their isotopic masses, and the ratio of each isotope in a naturally occurring sample of that element. Thus, you can see how each isotope contributes to the M+1 and M+2 peaks.
Most Common Isotopes Mass % 2 0.016 13 1.1 15 0.4 17 0.04 33 0.8 -----------------

Element H C N O S F Cl Br I

Mass 1 12 14 16 32 19 35 79 127

% 100.0 98.9 99.6 99.8 95.0 100.0 75.5 50.5 100.0

Mass ------18 34 --37 81 ---

% ------0.2 4.2 --24.5 49.5 ---

Table 9.5. Natural isotopic abundance of some common elements in organic molecules.

Isotope peaks give you information about the molecular formula of the compound. They help you determine what elements are present and in what ratio. To determine the exact ratio, however, you must precisely determine the relative intensity of the molecular ion peak and the M+1 and M+2 peaks. As you see in Table 9.5, the various elements occur in specific ratios, so by understanding these ratios and the patterns of their occurrences, you can gain this information. Compounds with a number of carbon, hydrogen, nitrogen, or oxygen atoms have isotope peaks at one, two, or more mass units above the mass calculated from the molecular formula and the masses of the most common isotopes. The intensity of the M+1 peak increases

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with increasing numbers of carbon, hydrogen, and nitrogen atoms. The intensity of the M+2 peak increases with increasing numbers of oxygen atoms. The M+2 peak also increases with increasing numbers of carbons and hydrogens because of the higher probability of having molecules with both 13C and 2H. The M+2 peak gives you the information needed to identify a molecule that contains chlorine, bromine, or sulfur. Here is how it works. Chlorine has two isotopes, 35Cl and 37Cl, with a ratio of nearly 3:1. In a sample of a molecule containing chlorine, three-fourths of the molecules contain 35Cl and one-fourth contain 37Cl. Every molecular fragment in the mass spectrum that contains chlorine actually appears as a pair of peaks separated by two mass units as shown in the spectrum of methyl chloride in Figure 9.24. The molecular ion, which is CH335Cl, appears at m/z 50. The isotope peak, which is CH337Cl, appears at m/z 52. The peak at m/z 50 is roughly three times the size of the peak at m/z 52, reflecting the 3:1 abundance of the two isotopes in nature. This pattern is typical for the peaks in an MS of a molecule that contains a single chlorine atom.
1 0 0

I n t e n s i t y

8 0

CH3Cl

6 0

4 0

2 0

0 2 0 4 0 6 0 8 0 1 0 0 1 2 0 1 4 0 1 6 0 1 8 0

m/z
Figure 9.24. The mass spectrum of methyl chloride.

Bromine, like chlorine, has two isotopes (79Br and 81Br). The bromine isotopes give rise to a different pattern of peaks in an MS, however, because 79Br and 81Br occur in a nearly 1:1 ratio. As a result, the mass spectrum of methyl bromide in Figure 9.25 shows every bromine-containing ion as a pair of peaks of about the same intensity separated by two mass units. The peak for CH379Br is at m/z 94, and the peak for CH381Br is at m/z 96.

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1 0 0

I n t e n s i t y

8 0

CH3Br
6 0 4 0

2 0

0 2 0 4 0 6 0 8 0 1 0 0 1 2 0 1 4 0 1 6 0 1 8 0

m/z
Figure 9.25. The mass spectrum of methyl bromide.

Exercise 9.7 There are no peaks at m/z 35 and 37 in the MS of methyl chloride (Figure 9.24) that would correspond to the Cl ion, but the Br ion does appear at m/z 79 and 81 in the MS of methyl bromide (Figure 9.25). Explain. To make the best use of an MS, you must be able to readily recognize the molecular ion peak. The following generalities may help you. The molecular ion is, with the exception of the M+1 and M+2 peaks, the highest mass peak in the spectrum. That is, the molecular ion peak appears furthermost to the right. However, molecules with bromine, chlorine, and sulfur produce peaks that are potentially confusing because each of these elements gives a more intense M+2 peak in relation to the molecular ion peak than do other elements. With sulfur-containing molecules, the M+2 peak is less obvious than with bromine or chlorine. For all organic compounds, except those with an odd number of nitrogen atoms, the molecular ion peak has an even mass. Thus, if you have an even mass peak, at the appropriate position, with most of the lower mass peaks being odd masses, the even mass peak is the molecular ion. Conversely, if you have an odd mass peak with most of the lower mass peaks being even, an odd number of nitrogens are present in the molecule. The molecular ions in alcohols and amines are not generally very stable. Frequently, they undergo a reaction and lose a small molecule. In the case of alcohols, the small molecule is water. Thus, the mass spectra for these alcohols and amines may not show any visible molecular ion peak. For example, the mass spectrum of tertbutyl alcohol (see Figure 9.26) shows no molecular ion peak at all, and the mass spectrum of 1-butanamine (see Figure 9.27) shows only a very weak molecular ion peak.

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(CH3)3COH
1 0 0

(CH3)2C

CH2

+ H2O

I n t e n s i t y

8 0

(CH3)3COH

6 0

4 0

Missing the parent ion

2 0

0 2 0 4 0 6 0 8 0 1 0 0 1 2 0 1 4 0 1 6 0 1 8 0

m/z
Figure 9.26. The MS of tert-butyl alcohol. The molecular ion is expected at m/z 74 but is absent from this spectrum.
1 0 0

I n t e n s i t y

8 0

CH3CH2CH2CH2NH2

6 0

4 0

Parent ion

2 0

0 2 0 4 0 6 0 8 0 1 0 0 1 2 0 1 4 0 1 6 0 1 8 0

m/z
Figure 9.27. The MS of 1-butanamine. The molecular ion is very weak.

Key Ideas from Chapter 9

Molecular spectroscopy involves irradiating a molecule with electromagnetic energy, then observing how that molecule responds to the energy. A molecule must absorb a specific amount, a quantum, of energy to move from its ground state to an excited state. The energy absorbed by a molecule excites its molecular vibrations. The energy absorbed give rise to the infrared

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spectrum. The molecular vibrations are the stretching and bending of the bonds of the molecule.

Small differences in molecular structure, which occurs in hybridization and functional groups, produce very different infrared spectra. Each infrared spectrum includes two regions: the functional group region and the fingerprint region. When interpreting a spectrum, analyze all the peaks in the functional group region. Then analyze the peaks in the fingerprint region as required to confirm your analysis of the functional group region. A mass spectrum is the record of the relative abundance of a series of ions that form when a molecule collides with a highenergy electron. The collision between a molecule and an electron causes the molecule to lose an electron; thus, becoming a radical-cation. The radical-cation then fragments into a series of cations and free radicals. Within a sample of a given compound, the number of molecules that follow a particular fragmentation pathway depends on the stability of the ions and radicals produced. Because the mass spectrometer records the exact masses of the various ions, the spectrum shows peaks for the different isotopes of the various elements in a molecule. This is particularly important for the identification of Br, Cl, and S in an organic compound.

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