Chapter 12 Structure Determination: Mass Spectrometry and Infrared Spectroscopy

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Chapter 12Structure Determination Mass
Spectrometry and Infrared Spectroscopy
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Why this Chapter?

• Finding structures of new molecules synthesized
  is critical
• To get a good idea of the range of structural
  techniques available and how they should be used

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12.1 Mass Spectrometry of Small Molecules
Magnetic-Sector Instruments

• Measures molecular weight
• Sample vaporized and subjected to bombardment by
  electrons that remove an electron
• Creates a cation radical
• Bonds in cation radicals begin to break
  (fragment)
• Charge to mass ratio is measured

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The Mass Spectrum

• Plot mass of ions (m/z) (x-axis) versus the
  intensity of the signal (roughly corresponding to
  the number of ions) (y-axis)
• Tallest peak is base peak (100)
• Other peaks listed as the of that peak
• Peak that corresponds to the unfragmented radical
  cation is parent peak or molecular ion (M)

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Other Mass Spectral Features

• If parent ion not present due to electron
  bombardment causing breakdown, softer methods
  such as chemical ionization are used
• Peaks above the molecular weight appear as a
  result of naturally occurring heavier isotopes in
  the sample
• (M1) from 13C that is randomly present

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Interpreting Mass-Spectral Fragmentation Patterns

• The way molecular ions break down can produce
  characteristic fragments that help in
  identification
• Serves as a fingerprint for comparison with
  known materials in analysis (used in forensics)
• Positive charge goes to fragments that best can
  stabilize it

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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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12.3 Mass Spectrometry of Some Common Functional
Groups

• Alcohols
• Alcohols undergo ?-cleavage (at the bond next to
  the C-OH) as well as loss of H-OH to give CC

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Mass Spectral Cleavage of Amines

• Amines undergo ?-cleavage, generating radicals

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Fragmentation of Carbonyl Compounds

• A C-H that is three atoms away leads to an
  internal transfer of a proton to the CO, called
  the McLafferty rearrangement
• Carbonyl compounds can also undergo ? cleavage

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12.5 Spectroscopy and the Electromagnetic Spectrum

• Radiant energy is proportional to its frequency
  (cycles/s Hz) as a wave (Amplitude is its
  height)
• Different types are classified by frequency or
  wavelength ranges

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Absorption Spectra

• An organic compound exposed to electromagnetic
  radiation can absorb energy of only certain
  wavelengths (unit of energy)
• Transmits energy of other wavelengths.
• Changing wavelengths to determine which are
  absorbed and which are transmitted produces an
  absorption spectrum

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12.6 Infrared Spectroscopy

• IR region lower energy than visible light (below
  red produces heating as with a heat lamp)
• IR energy in a spectrum is usually measured as
  wavenumber (cm-1), the inverse of wavelength and
  proportional to frequency
• Specific IR absorbed by an organic molecule is
  related to its structure

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Infrared Energy Modes

• IR energy absorption corresponds to specific
  modes, corresponding to combinations of atomic
  movements, such as bending and stretching of
  bonds between groups of atoms called normal
  modes
• Corresponds to vibrations and rotations

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12.7 Interpreting Infrared Spectra

• Most functional groups absorb at about the same
  energy and intensity independent of the molecule
  they are in
• IR spectrum has lower energy region
  characteristic of molecule as a whole
  (fingerprint region)

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Figure 12.14
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Regions of the Infrared Spectrum

• 4000-2500 cm-1 N-H, C-H, O-H (stretching)
• 3300-3600 N-H, O-H
• 3000 C-H
• 2500-2000 cm-1 CºC and
• C º N (stretching)

• 2000-1500 cm-1 double bonds (stretching)
• CO 1680-1750
• CC 1640-1680 cm-1
• Below 1500 cm-1 fingerprint region

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Differences in Infrared Absorptions

• Bond stretching dominates higher energy modes
• Light objects connected to heavy objects vibrate
  fastest CH, NH, OH
• For two heavy atoms, stronger bond requires more
  energy C º C, C º N gt CC, CO, CN gt CC, CO,
  CN, Chalogen

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12.8 Infrared Spectra of Some Common Functional
Groups

• Alkanes, Alkenes, Alkynes
• C-H, C-C, CC, C º C have characteristic peaks
• absence helps rule out CC or C º C

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IR Aromatic Compounds

• Weak CH stretch at 3030 cm?1
• Weak absorptions 1660 - 2000 cm?1 range
• Medium-intensity absorptions 1450 to 1600 cm?1
• See spectrum of phenylacetylene, Figure 12.15

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IR Alcohols and Amines

• OH 3400 to 3650 cm?1
• Usually broad and intense
• NH 3300 to 3500 cm?1
• Sharper and less intense than an OH

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IR Carbonyl Compounds

• Strong, sharp CO peak 1670 to 1780 cm?1
• Exact absorption characteristic of type of
  carbonyl compound
• 1730 cm?1 in saturated aldehydes
• 1705 cm?1 in aldehydes next to double bond or
  aromatic ring

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CO in Ketones

• 1715 cm?1 in six-membered ring and acyclic
  ketones
• 1750 cm?1 in 5-membered ring ketones
• 1690 cm?1 in ketones next to a double bond or an
  aromatic ring
• CO in Esters
• 1735 cm?1 in saturated esters
• 1715 cm?1 in esters next to aromatic ring or a
  double bond

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Lets Work a Problem

• Propose structures for a compound that fits the
  following data It is an alcohol with M 88 and
  fragments at m/z 73, m/z 70, and m/z 59

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Answer

• Answer We must first decide on the the formula
  of an alcohol that could undergo this type of
  fragmentation via mass spectrometry. We know that
  an alcohol possesses an O atom (MW16), so that
  leads us to the formula C5H12O for an alcohol
  with M 88, with a structure of
• One fragmentation peak at 70 is due to the loss
  of water, and alpha cleavage can result in m/z of
  73 and 59.