1. Infrared Spectroscopy, Mass Spectrometry, and NMR Spectroscopy

2. Introduction to Spectroscopy
Spectroscopy involves an interaction between matter and light (EMR)
Light can be thought of as waves of energy or packets (particles) of energy called photons
Properties of light waves include wavelength and frequency

3. Introduction to Spectroscopy
Only a small segment of EMR spectrum is visible to us.

4. Introduction to Spectroscopy
Frequency & wavelength are inversely related: As wavelength (λ) get longer, frequency (ν) gets lower, and vice-versa (c = λν). Higher frequency = higher energy.

5. Introduction to Spectroscopy
When light interacts with molecules, the effect depends on the wavelength of light used

6. Introduction to Spectroscopy
Matter exhibits both particle-like and wave-like properties
Matter on the molecular scale exhibits quantum behavior
A molecule will only rotate or vibrate at certain rates (i.e., discrete energies)
For each different bond, vibrational energy levels are separated by gaps (quantized)
If a photon of light strikes the molecule with the exact amount of energy needed, a molecular vibration will occur
Energy is eventually released from the molecule generally in the form of heat
Infrared (IR) Light generally causes molecular vibration

7. IR Spectroscopy
Molecular bonds can vibrate by stretching or by bending in a number of ways
We can’t see IR, but we have technology that can
Some night vision goggles can detect IR light that is emitted
IR or thermal imaging is also used to detect breast cancer

8. IR Spectroscopy
The energy necessary to cause vibration depends on the type of bond

9. 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

10. IR Spectroscopy
IR energy is absorbed in some regions by bonds, but not others. The % transmittance decreases where energy is absorbed.

11. IR Spectroscopy Units for the wavenumber = inverse cm
ν = frequency and c = the speed of light
Wavenumber directly proportional to frequency: Higher frequency = higher energy=higher wavenumber

12. IR Spectroscopy
A signal on the IR spectrum has three important characteristics: wavenumber, intensity, and shape

13. IR Signal Wavenumber
The wavenumber for a stretching vibration depends on the bond strength and the mass of the atoms bonded together
Shorter, stronger bonds, and smaller atoms, absorb at higher frequencies (ergo, at longer wavenumbers)

14. IR Signal Wavenumber
The wavenumber formula and empirical observations allow us to designate regions as representing specific types of bonds
As previously noted, shorter, stronger bonds and smaller atoms have higher wavenumber

15. IR Signal Wavenumber
The region above 1500 cm-1 is called the diagnostic region, which has fewer absorptions and is easier to interpret.
The region below 1500 cm-1 is called the fingerprint region. This region contains signals from stretching and bending of most single bonds and is more difficult to interpret. However, each compound has a unique fingerprint even if signals overlap.
DIAGNOSTIC REGION
FINGERPRINT REGION

16. IR Signal Wavenumber
Compare the IR spectra

17. IR Signal Wavenumber Compare the IR stretching wavenumbers below
As s character of bond increases, orbitals get more compact, bonds get shorter and stronger, wavenumber gets larger.

18. IR Signal Wavenumber
Note how the region ≈3000 cm-1 in the IR spectrum can give information about the functional groups present

19. IR Signal Wavenumber
Tetrasubstituted alkenes and internal alkynes do not produce C-H signals in diagnostic region.
Predict the wavenumbers that would result (if any) above 3000 cm-1 for the molecules below

20. IR Signal Wavenumber
In general, conjugation of pi bonds weaken the carbonyl by increasing resonance structures, giving it more single bond character, resulting in lower wavenumber.

21. IR Signal Strength
The strength of IR signals can vary

22. IR Signal Strength
When a bond undergoes a stretching vibration, its dipole moment also oscillates
Recall the formula for dipole moment includes the distance between the partial charges,
The oscillating dipole moment creates an electrical field surrounding the bond

23. 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 (increased intensity)
NP alkenes may produce no signal

24. IR Signal Strength
Stronger signals are also observed when there are multiple bonds of the same type vibrating
Although C-H bonds are not very polar, they often give very strong signals, because there are many of them.
Because sample concentration can affect signal strength, the Intoxilyzer 5000 can be used to determine blood alcohol levels be analyzing the strength of C-H bond stretching in blood samples

25. IR Signal Shape
Some IR signals are broad, while others are very narrow
O-H stretching signals are often quite broad

26. 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
This leads to signal broadening
The O-H stretch signal will be narrow if a dilute solution of an alcohol is prepared in a solvent incapable of H-bonding

27. IR Signal Shape
In a sample with an intermediate concentration, both narrow and broad signals are observed because some –OH groups are H-bonding, and some are not.

28. 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
C.A.s produce an even broader –OH signal due to dimeric H-bonding.

29. IR Signal Shape
Primary and secondary (but not tertiary) amines exhibit N-H stretching signals.
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?

30. 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, producing two different signals

31. Analyzing an IR Spectrum
Table 15.2 (p. 701) 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

32. Analyzing an IR Spectrum
Often, the molecular structure can be identified from an IR spectra
Focus on the cm-1 (X-H) region
What can you conclude from this spectrum?

33. 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?

34. 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?

35. Intro to Mass Spectrometry
Mass spectrometry (MS) used primarily to determine molar mass and formula for a compound
A compound is vaporized and then ionized
The masses of the ions are detected and graphed
Electron impact (EI) ionization most common method for ionizing molecules
The sample is bombarded with a beam of high energy electrons (1600 kcal or 70 eV). This ejects an electron and produces a radical cation.

36. Into to Mass Spectrometry
If the radical cation remains intact, it is known as the molecular ion (M+•) or parent ion
Often, the molecular ion is unstable and may undergo further fragmentation where 1 fragment carries the unpaired electron and the other fragment carries the charge.
This process can generate many carbocation fragments

37. Into to Mass Spectrometry
The resulting fragments are then accelerated, and charged ions are deflected by a magnetic field into a detector
Radicals not detected
Smaller mass and higher charge fragments are affected more by the magnetic field.
Cations separated by mass-to-charge ratio (m/z), and usually have a charge of +1.

38. 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 (100% relative abundance)
The base peak isn’t always the same as the parent ion (M+•)
Sometimes, the M+• peak is not even observed in the spectrum, WHY?

39. 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

40. Into to Mass Spectrometry
Mass spec is a relatively sensitive analytical method
Many organic compounds can be identified
Pharmaceutical: drug discovery and drug metabolism, reaction monitoring
Biotech: amino acid sequencing, analysis of macromolecules
Clinical: neonatal screening, hemoglobin analysis
Environmental: drug testing, water quality, food contamination testing
Geological: evaluating oil composition
Forensic: Explosive detection
Many More

41. Analyzing the M+• Peak
In the mass spec for benzene, the M+• peak is the base peak
The M+• peak does not easily fragment for this compound

42. Analyzing the M+• Peak
Like most compounds, the M+• peak for pentane is NOT the base peak
The M+• peak fragments easily

43. 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

44. 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 isotope in the sample.

45. Analyzing the (M+1)+• Peak
The natural abundance of 13C is ~1.1%. For every 100 molecules of CH4, ~1.1% contain 13C. For every 100 molecules of decane (10 C), ~11% contain 13C.
Comparing the heights of the (M+1)+• peak and the M+• peak can allow you to estimate how many carbons are in the molecule, based on isotopic abundance of C.
𝑅𝑒𝑙. 𝐴𝑏𝑢𝑛𝑑𝑎𝑛𝑐𝑒 𝑜𝑓 𝑀+1 +• 𝑅𝑒𝑙. 𝐴𝑏𝑢𝑛𝑑𝑎𝑛𝑐𝑒 𝑀 +• ×100=𝑋%
𝑋% 1.1% =𝑁𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝐶

46. Analyzing the (M+2)+• Peak
Chlorine has two abundant isotopes
35Cl=76% and 37Cl=24%
Molecules with chlorine often have strong (M+2)+• peaks

47. Analyzing the (M+2)+• Peak
79Br=51% and 81Br=49%, so molecules with bromine often have equally strong (M)+• and (M+2)+• peaks

48. Analyzing the Fragments
A thorough analysis of the molecular fragments can often yield structural information
Consider pentane
Remember, MS only detects charged fragments

49. Analyzing the Fragments
WHAT type of fragmenting is responsible for the “groupings” of peaks observed?

50. Analyzing the Fragments
In general, fragmentation will be more prevalent when more stable fragments (ions and radicals) are produced
Correlate the relative stability of the fragments here with their abundances on the previous slide

51. 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
Tertiary carbocations more stable than secondary, etc. Should be evident in spectrum.

52. Analyzing the Fragments
Alcohols generally undergo two main types of fragmentation: alpha cleavage and dehydration
M-18 produced due to loss of water

53. Analyzing the Fragments
Amines generally undergo alpha cleavage
Carbonyls generally undergo McLafferty rearrangement when H is present on gamma C

54. High Resolution Mass Spec
High Resolution MS allows m/z to be measured up to 4 decimal places
Masses generally not whole number integers
1 proton = amu and 1 neutron = amu
One 12C atom = exactly amu, because amu scale based on mass of 12C
All atoms other than 12C will have a mass in amu that can be measured to 4 decimal places by a high-resolution mass spec instrument

55. High Resolution Mass Spec
Using the exact masses and natural abundances for each element, high-res is better for distinguishing between compounds with nearly identical molar masses, when molecular ion is observed.

56. GC/MS MS is suited for the identification of pure substances
However, MS instruments are often connected to a gas chromatograph so mixtures can be separated and analyzed

57. High Resolution Mass Spec
GC-MS gives two main forms of information
GC-MS is a great technique for detecting compounds such as drugs in solutions such as blood or urine
The chromatogram gives the retention time
The Mass Spectrogram (low-res or high-res)

58. 1MS of Large Biomolecules
To be analyzed by EI mass spec, substances generally must be vaporized prior to ionization
Until recently (last 30 years), compounds that decompose before they vaporize could not be analyzed
In Electrospray ionization (ESI), a high-voltage needle sprays a liquid solution of an analyte into a vacuum causing ionization
ESI is a “softer” ionizing technique.

59. 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
Analysis of a molecule’s formula can yield a list of possible structures, and indicate degrees of unsaturation
Alkanes follow the formula below, because they are saturated
Adding 1 degree of unsaturation decreases the number of H atoms by two = 1 unit on the hydrogen deficiency index (HDI)
CnH2n+2

60. 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?
A non-carbonyl oxygen does not affect the HDI.

61. 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?
You can also use the formula below

62. 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