Structure Determination: Mass Spectrometry and Infrared Spectroscopy

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Structure Determination Mass Spectrometry and
Infrared Spectroscopy
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Topics to discuss

• What is Spectroscopy?
• Mass Spectrometry
• What is it?
• How does it work and why is it useful?
• How to interpret a mass spectrum
• Common Fragments in MS
• IR Spectroscopy
• What is it?
• Why is it useful?
• How to interpret an IR spectrum
• Common IR absorptions
• Using Spectroscopy to Identify a Molecule

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Intro to Spectroscopy

• Q What is Spectroscopy?
• Q How does it work?

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Intro to Spectroscopy

• Q Why do we need it?
• Q How many kinds are there?

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Mass Spectrometry (MS)

• Q What is it?

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Mass Spectrometry (MS)

• Q How does it work, and why is it useful?

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The Mass Spectrum

• Q What is a mass spectrum?
• Q What is important?

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How to interpret a MS

• The way molecular ions break down can produce

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Mass Spectral Fragmentation of Hexane

• Hexane (m/z 86 for parent) has peaks at m/z
  71, 57, 43, 29

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Mass-Spectral Behavior of Some Common Functional
Groups

• Functional groups cause
• Alcohols, amines, ketones and aldehydes are all
  functional groups that

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Common Fragments in Alcohol MS
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Common Fragments in Amines MS
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Common Fragments in Ketones/Aldehydes MS
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Spectroscopy of the Electromagnetic Spectrum

• Radiant energy is proportional to
• Different types are classified by

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Absorption Spectra

• Organic compound exposed to electromagnetic
  radiation can
• Changing wavelengths to determine
• Energy absorbed is distributed

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Infrared Spectroscopy (IR)

• Q What is it?
• Q Why is it useful?

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Infrared Spectroscopy (IR)

• Q How does it work?

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Infrared Spectroscopy (IR)

• Q What is an IR spectrum?

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Interpreting Infrared Spectra

• Most functional groups absorb at
• In this example, the peak is centered at
  1750cm-1. Whenever we see a peak at 1750cm-1, we
  know that it represents

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Interpreting Infrared Spectra

• Different functional groups will yield different
  absorption spectra which arise from differences
  in
• In IR spectroscopy, various functional groups
  vibrate at unique frequencies, resulting in
• Thus, we can use the wavelength of absorption to
  determine

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Regions of the Infrared Spectrum

• 4000-2500 cm-1 N-H, C-H, O-H (stretching)
• 2500-2000 cm-1 CC and CN (stretching)

• 2000-1500 cm-1 double bonds (stretching)
• Below 1500 cm-1 fingerprint region

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Infrared Spectra of Hydrocarbons

• C-H, C-C, CC, CºC have characteristic peaks

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Infrared Spectra of Some Common Functional Groups

• Learn the most common ones. With all others, you
  can use a IR frequency correlation table.
• Most common in organic compounds
• sp2 C-H stretch
• sp3 C-H stretch
• CC stretch
• C-O stretch
• CO stretch
• O-H stretch

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IR Alcohols and Amines

• OH 3400 to 3650 cm?1
• NH 3300 to 3500 cm?1

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IR Aromatic Compounds

• Weak CH stretch at
• Weak absorptions in
• Medium-intensity absorptions at

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IR Carbonyl Compounds

• Strong, sharp CO peak at
• Exact absorption characteristic of type of
  carbonyl compound

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CO in Ketones

• 1715 cm?1 in
• 1750 cm?1 in
• 1690 cm?1 in

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CO in Esters

• 1735 cm?1 in
• 1715 cm?1 in

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Using Spectroscopy to Identify a Molecule

• 1. Recall the type of information that each
  spectrum provides
• 2. Use the spectra to verify and refute the
  existence of structural features
• 3. Piece together the structural info to arrive
  at a possible answer.
• 4. Cross check your answer with each spectrum to
  verify it.

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A Combined Spectral Problem

• Typically, you will be provided with the
  molecular formula of an unknown compound and
  different types of spectra to use to determine
  the structure of an unknown.
• The key is to learn an approach to these types of
  problems which works best for you, and use the
  same systematic approach every time.

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A Combined Spectral Problem

• First step should always be

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A Combined Spectral Problem

• Next, look quickly at the IR spectrum.
• Notice the broad peak centered at 3400cm-1.

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A Combined Spectral Problem

• Now, look at the mass spectrum.

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A Combined Spectral Problem
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A Combined Spectral Problem

• Now that we have figured out this piece, we only
  need to find two more carbons.
• There are two possible ways to do this

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A Combined Spectral Problem

• We already know the fragmentation pattern shown
  is likely in both.
• In the bottom structure, we would also expect to
  see loss of a methyl group

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A Combined Spectral Problem

• We should now try to verify that it is the top
  structure.
• Remember that we have
• So, we have now cross checked our answer with the
  spectra provided to verify it.

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Summary

• What is Spectroscopy?
• Mass Spectrometry
• What is it?
• How does it work and why is it useful?
• How to interpret a mass spectrum
• Common Fragments in MS
• IR Spectroscopy
• What is it?
• Why is it useful?
• How to interpret an IR spectrum
• Common IR absorptions
• Using Spectroscopy to Identify a Molecule