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Chapter 12 Structure Determination: Mass Spectrometry and Infrared Spectroscopy

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Title: Chapter 12 Structure Determination: Mass Spectrometry and Infrared Spectroscopy


1
Chapter 12Structure Determination Mass
Spectrometry and Infrared Spectroscopy
2
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

3
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

4
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)

5
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

6
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

7
Mass Spectral Fragmentation of Hexane
  • Hexane (m/z 86 for parent) has peaks at m/z
    71, 57, 43, 29

8
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

9
Mass Spectral Cleavage of Amines
  • Amines undergo ?-cleavage, generating radicals

10
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

11
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

12
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

13
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

14
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

15
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)

16
Figure 12.14
17
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

18
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

19
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

20
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

21
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

22
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

23
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

24
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

25
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.
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