1. Infrared Spectroscopy and Mass Spectrometry
Organic Chemistry
Second Edition
David Klein
Chapter 15
Infrared Spectroscopy and Mass Spectrometry
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Klein, Organic Chemistry 2e

2. 15.1 Introduction to Spectroscopy
Spectroscopy involves an interaction between matter and light (electromagnetic radiation)
Light can be thought of as waves of energy or packets (particles) of energy called photons
Properties of light waves include wavelength and frequency
Is wavelength directly or inversely proportional to energy? WHY?
Is frequency directly or inversely proportional to energy? WHY?
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Klein, Organic Chemistry 2e

3. 15.1 Introduction to Spectroscopy
There are many wavelengths of light that can not be observed with your eyes
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4. 15.1 Introduction to Spectroscopy
When light interacts with molecules, the effect depends on the wavelength of light used
This chapter focuses on IR spectroscopy
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5. 15.2 IR Spectroscopy
Molecular bonds can vibrate by stretching or by bending in a number of ways
This chapter will focus mostly on stretching frequencies
WHY do objects emit IR light?
WHY do some objects emit more IR radiation than others?
WHERE does that light come from?
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6. 15.2 IR Spectroscopy
Some night vision goggles can detect IR light that is emitted
IR or thermal imaging is also used to detect breast cancer
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7. 15.2 IR Spectroscopy
The energy necessary to cause vibration depends on the type of bond
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8. 15.2 IR Spectroscopy
An IR spectrophotometer irradiates a sample with all frequencies of IR light
The frequencies that are absorbed by the sample tell us the types of bonds (functional groups) that are present
How do we measure the frequencies that are absorbed?
Most commonly, samples are deposited neat on a salt (NaCl) plate. WHY is salt used?
Alternatively, the compound may be dissolved in a solvent or embedded in a KBr pellet
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Klein, Organic Chemistry 2e

9. 15.2 IR Spectroscopy Analyze the units for the wavenumber,
ν = frequency and c = the speed of light
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10. 15.2 IR Spectroscopy
A signal on the IR spectrum has three important characteristics: wavenumber, intensity, and shape
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11. 15.3 IR Signal Wavenumber
The wavenumber for a stretching vibration depends on the bond strength and the mass of the atoms bonded together
Should bonds between heavier atoms require higher or lower wavenumber IR light to stretch?
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12. 15.3 IR Signal Wavenumber
Rationalize the trends below using the wavenumber formula
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13. 15.3 IR Signal Wavenumber
The wavenumber formula and empirical observations allow us to designate regions as representing specific types of bonds
Explain the regions above
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Klein, Organic Chemistry 2e

14. 15.3 IR Signal Wavenumber
The region above 1500 cm-1 is called the diagnostic region. WHY?
The region below 1500 cm-1 is called the fingerprint region. WHY?
FINGERPRINT REGION
DIAGNOSTIC REGION
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15. 15.3 IR Signal Wavenumber
Analyze the diagnostic and fingerprint regions below
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Klein, Organic Chemistry 2e

16. 15.3 IR Signal Wavenumber
Analyze the diagnostic and fingerprint regions below
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Klein, Organic Chemistry 2e

17. 15.3 IR Signal Wavenumber Compare the IR spectra
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18. 15.3 IR Signal Wavenumber
Greater difference in masses of atoms attached, greater
the greater the wavenumber
C-H stretch ≈ 3000 cm-1
O-H stretch ≈ 3400 cm-1
Practice with conceptual checkpoint 15.1
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Klein, Organic Chemistry 2e

19. 15.3 IR Signal Wavenumber Compare the IR stretching wavenumbers below
Are the differences due to mass or bond strength?
Which bond is strongest, and WHY?
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Klein, Organic Chemistry 2e

20. 15.3 IR Signal Wavenumber
Note how the region ≈3000 cm-1 in the IR spectrum can give information about the functional groups present
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21. 15.3 IR Signal Wavenumber
Is it possible that an alkene or alkyne could give an IR spectra without any signals above 3000 cm-1?
Predict the wavenumbers that would result (if any) above 3000 cm-1 for the molecules below
Practice with conceptual checkpoint 15.2
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Klein, Organic Chemistry 2e

22. 15.3 IR Signal Wavenumber
Resonance can affect the wavenumber of a stretching signal
Consider a carbonyl that has two resonance contributors
If there were more contributors with C-O single bond character than C=O double bond character, how would that affect the wavenumber?
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Klein, Organic Chemistry 2e

23. 15.3 IR Signal Wavenumber
Use the given examples to explain HOW and WHY the conjugation and the –OR group affect resonance and thus the IR signal?
Practice with conceptual checkpoint 15.3
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Klein, Organic Chemistry 2e

24. 15.4 IR Signal Strength The strength of IR signals can vary
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25. 15.4 IR Signal Strength
The more polar the bond, the greater the opportunity for interaction between the waves of the electrical field and the IR radiation
Greater bond polarity = stronger IR signals
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26. 15.4 IR Signal Strength
Note the general strength of the C=O stretching signal vs. the C=C stretching signal
Imagine a symmetrical molecule with a completely nonpolar C=C bond: 2,3-dimethyl-2-butene
2,3-dimethyl-2-butene does not give an IR signal in the cm-1 region
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27. 15.5 IR Signal Shape
Some IR signals are broad, while others are very narrow
O-H stretching signals are often quite broad
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28. 15.5 IR Signal Shape
When possible, O-H bonds form H-bonds that weaken the O-H bond strength
The H-bonds are transient, so the sample will contain molecules with varying O-H bond strengths
Why does that cause the O-H stretch signal to be broad?
The O-H stretch signal will be narrow if a dilute solution of an alcohol is prepared in a solvent incapable of H-bonding
WHY does H-bonding affect the O-H bond strength?
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Klein, Organic Chemistry 2e

29. 15.5 IR Signal Shape
In a sample with an intermediate concentration, both narrow and broad signals are observed. WHY?
Explain the cm-1 readings for the two O-H stretching peaks
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30. 15.5 IR Signal Shape
Consider how broad the O-H stretch is for a carboxylic acid and how its wavenumber is around 3000 cm-1 rather than 3400 cm-1 for a typical O-H stretch
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31. 15.5 IR Signal Shape
H-bonding is often more pronounced in carboxylic acids, because they can forms H-bonding dimers
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32. 15.5 IR Signal Shape
For the molecule below, predict all of the stretching signals in the diagnostic region
Practice with conceptual checkpoint 15.9
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Klein, Organic Chemistry 2e

33. 15.5 IR Signal Shape
Primary and secondary amines exhibit N-H stretching signals. WHY not tertiary amines?
Because N-H bonds are capable of H-bonding, their stretching signals are often broadened
Which is generally more polar, an O-H or an N-H bond?
Do you expect N-H stretches to be strong or weak signals?
See example spectra on next slide
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Klein, Organic Chemistry 2e

34. 15.5 IR Signal Shape Klein, Organic Chemistry 2e
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35. 15.5 IR Signal Shape
The appearance of two N-H signals for the primary amine is NOT simply the result of each N-H bond giving a different signal
Instead, the two N-H bonds vibrate together in two different ways
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Klein, Organic Chemistry 2e

36. 15.5 IR Signal Shape
A single molecule can only vibrate symmetrically or asymmetrically at any given moment, so why do we see both signals at the same time?
Similarly, CH2 and CH3 groups can also vibrate as a group giving rise to multiple signals
Practice with conceptual checkpoint 15.10
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Klein, Organic Chemistry 2e

37. 15.6 Analyzing an IR Spectrum
Table 15.2 summarizes some of the key signals that help us to identify functional groups present in molecules
Often, the molecular structure can be identified from an IR spectra
Focus on the diagnostic region (above 1500 cm-1)
cm-1 – check for double bonds
cm-1 – check for triple bonds
cm-1 – check for X-H bonds
Analyze wavenumber, intensity, and shape for each signal
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Klein, Organic Chemistry 2e

38. 15.6 Analyzing an IR Spectrum
Often, the molecular structure can be identified from an IR spectra
Focus on the cm-1 (X-H) region
Practice with SkillBuilder 15.1
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Klein, Organic Chemistry 2e

39. 15.7 Using IR to Distinguish Between Molecules
As we have learned in previous chapters, organic chemists often carry out reactions to convert one functional group into another
IR spectroscopy can often be used to determine the success of such reactions
For the reaction below, how might IR spectroscopy be used to analyze the reaction?
Practice with SkillBuilder 15.2
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Klein, Organic Chemistry 2e

40. Klein, Organic Chemistry 2e
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41. 15.7 Using IR to Distinguish Between Molecules
For the reactions below, identify the key functional groups, and describe how IR data could be used to verify the formation of product
Is IR analysis qualitative or quantitative?
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42. Klein, Organic Chemistry 2e
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43. Klein, Organic Chemistry 2e
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44. 15.6 Analyzing an IR Spectrum
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45. Klein, Organic Chemistry 2e
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46. Klein, Organic Chemistry 2e
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47. Klein, Organic Chemistry 2e
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48. Klein, Organic Chemistry 2e
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49. 15.8 Into to Mass Spectrometry
Mass spectrometry is primarily used to determine the molar mass and formula for a compound
A compound is vaporized and then ionized
The masses of the ions are detected and graphed
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Klein, Organic Chemistry 2e

50. 15.8 Into to Mass Spectrometry
The most common method of ionizing molecules is by electron impact (EI)
The sample is bombarded with a beam of high energy electrons (1600 kcal or 70 eV)
EI usually causes an electron to be ejected from the molecule.
What is a radical cation?
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Klein, Organic Chemistry 2e

51. 15.8 Into to Mass Spectrometry
How does the mass of the radical cation compare to the original molecule?
If the radical cation remains intact, it is known as the molecular ion (M+•) or parent ion
Often, the molecular ion undergoes some type of fragmentation.
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Klein, Organic Chemistry 2e

52. 15.8 Into to Mass Spectrometry
The resulting fragments may undergo even further fragmentation
The ions are deflected by a magnetic field
Smaller mass and higher charge fragments are affected more by the magnetic field.
Neutral fragments are not detected.
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Klein, Organic Chemistry 2e

53. 15.8 Into to Mass Spectrometry
Explain the units on the x and y axes for the mass spectrum for methane
The base peak is the tallest peak in the spectrum
For methane the base peak represents the M+•
Sometimes, the M+• peak is not even observed in the spectrum, WHY?
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Klein, Organic Chemistry 2e

54. 15.8 Into to Mass Spectrometry
Peaks with a mass of less than M+• represent fragments
Subsequent H radicals can be fragmented to give the ions with a mass/charge = 12, 13 and 14
The presence of a peak representing (M+1) +• will be explained in section 15.10
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Klein, Organic Chemistry 2e

55. 15.9 Analyzing the M+• Peak
In the mass spec for benzene, the M+• peak is the base peak
The M+• peak does not easily fragment
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Klein, Organic Chemistry 2e

56. 15.9 Analyzing the M+• Peak
Like most compounds, the M+• peak for pentane is NOT the base peak
The M+• peak fragments easily
Base peak
M+.
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Klein, Organic Chemistry 2e

57. 15.9 Analyzing the M+• Peak
The first step in analyzing a mass spec is to identify the M+• peak
It will tell you the molar mass of the compound
An odd massed M+• peak MAY indicate an odd number of N atoms in the molecule
An even massed M+• peak MAY indicate an even number of N atoms or zero N atoms in the molecule
Give an alternative explanation for a M+• peak with an odd mass
Practice with conceptual checkpoint 15.19
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Klein, Organic Chemistry 2e

58. 15.10 Analyzing the (M+1)+• Peak
Recall that the (M+1)+• peak in methane was about 1% as abundant as the M+• peak
The (M+1)+• peak results from the presence of 13C in the sample.
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Klein, Organic Chemistry 2e

59. 15.10 Analyzing the (M+1)+• Peak
For every 100 molecules of decane, what percentage of them are made of exclusively 12C atoms?
Comparing the heights of the (M+1)+• peak and the M+• peak can allow you to estimate how many carbons are in the molecule.
The natural abundance of deuterium is 0.015%. Will that affect the mass spec analysis?
Practice with SkillBuilder 15.3
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Klein, Organic Chemistry 2e

60. 15.11 Analyzing the (M+2)+• Peak
Chlorine has two abundant isotopes
35Cl=76% and 37Cl=24%
Molecules with chlorine often have strong (M+2)+• peaks
WHY is it sometimes difficult to be absolutely sure which peak is the (M)+• peak?
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Klein, Organic Chemistry 2e

61. 15.11 Analyzing the (M+2)+• Peak
79Br=51% and 81Br=49%, so molecules with bromine often have equally strong (M)+• and (M+2)+• peaks
Practice with conceptual checkpoints and 15.24
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Klein, Organic Chemistry 2e

62. 15.12 Analyzing the Fragments
A thorough analysis of the molecular fragments can often yield structural information
Consider pentane
Remember, MS only detects charged fragments
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Klein, Organic Chemistry 2e

63. 15.12 Analyzing the Fragments
WHAT type of fragmenting is responsible for the “groupings” of peaks observed?
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Klein, Organic Chemistry 2e

64. 15.12 Analyzing the Fragments
In general, fragmentation will be more prevalent when more stable fragments are produced
Correlate the relative stability of the fragments here with their abundances on the previous slide
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Klein, Organic Chemistry 2e

65. 15.12 Analyzing the Fragments
Consider the fragmentation below
All possible fragmentations are generally observed under the high energy conditions employed in EI-MS
If you can predict the most abundant fragments and match them to the spectra, it can help you in your identification
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Klein, Organic Chemistry 2e

66. 15.12 Analyzing the Fragments
Alcohols generally undergo two main types of fragmentation: alpha cleavage and dehydration
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67. 15.12 Analyzing the Fragments
Amines generally undergo alpha cleavage
Carbonyls generally undergo McLafferty rearrangement
Practice with conceptual checkpoints
15.25 – 15.28
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Klein, Organic Chemistry 2e

68. 15.16 Degrees of Unsaturation
Mass spec can often be used to determine the formula for an organic compound
IR can often determine the functional groups present
Careful analysis of a molecule’s formula can yield a list of possible structures
Alkanes follow the formula below, because they are saturated
Verify the formula by drawing some isomers of pentane
CnH2n+2
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Klein, Organic Chemistry 2e

69. 15.16 Degrees of Unsaturation
Notice that the general formula for the compound,
CnH2n+2, changes when a double or triple bond is present
Adding a degree of unsaturation decreases the number of H atoms by two
How many degrees of unsaturation are there in cyclopentane?
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Klein, Organic Chemistry 2e

70. 15.16 Degrees of Unsaturation
Consider the isomers of C4H6
How many degrees of unsaturation are there?
1 degree of unsaturation = 1 unit on the hydrogen deficiency index (HDI)
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Klein, Organic Chemistry 2e

71. 15.16 Degrees of Unsaturation
For the HDI scale, a halogen is treated as if it were a hydrogen atom
How many degrees of unsaturation are there in C5H9Br?
An oxygen does not affect the HDI. WHY?
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Klein, Organic Chemistry 2e

72. 15.16 Degrees of Unsaturation
For the HDI scale, a nitrogen increases the number of expected hydrogen atoms by ONE
How many degrees of unsaturation are there in C5H8BrN?
Forget this formula below (you can use if you want)
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Klein, Organic Chemistry 2e

73. 15.16 Degrees of Unsaturation
NOTrogen for Nitrogen
Halogen
0xygen (the O is a zero)
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Klein, Organic Chemistry 2e

74. 15.16 Degrees of Unsaturation
Calculating the HDI can be very useful. For example, if HDI=0, the molecule can NOT have any rings, double bonds, or triple bonds
Propose a structure for a molecule with the formula C7H12O. The molecule has the following IR peaks
A strong peak at 1687 cm-1
NO IR peaks above 3000 cm-1
Practice with SkillBuilder 15.4
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Klein, Organic Chemistry 2e