Structure
Determination: Mass Spectrometry and Infrared Spectroscopy
Goals
¨ After this
chapter you should be able to:
– Determine
formula of molecules based on MS
– Determine
functional groups in a molecule based on IR
– Determine
molecular structure given IR and formula.
Types
of Spectroscopy
¨ Mass
Spectrometry
– MS for size and
structure features of molecule
¨ Infrared
Spectroscopy
– IR for
Functional Group identification
¨ Ultraviolet
Spectroscopy
– UV detection of
conjugated p electrons
¨ Nuclear Magnetic
Resonance Spectroscopy
– NMR determines
carbon-hydrogen framework
Mass
Spectrometry
¨
Willard H. Bennett
¨ Born June 13,
1903 - Died Sept. 28, 1987
¨
Radio Frequency Mass Spectrometer
¨ Patent No.
2,721,271
¨ Inducted into
Inventor’s Hall of Fame 1991
Mass
Spectrometer
Basic
Features
¨ A substance is
bombarded with an electron beam having sufficient energy to fragment the
molecule.
¨ The positive fragments are accelerated in a
vacuum through a magnetic field
¨ Most carry a
unit positive charge; the value m/e is equivalent to the molecular weight of
the fragment.
¨ Self sorted on
the basis of mass-to-charge ratio.
¨ Only fragments
with proper m/z ratio hit detector.
¨ The analysis of
mass spectroscopy information involves the re-assembling of fragments, working
backwards to generate the original molecule.
Equation
of Flight
¨ Fcentripetal
= Fmagnetic
¨ mv2/r
= qvB
¨ m/q = rB/v
Terminology
¨ Mass Spectra =
Bar graph of fragments
¨ Base peak =
Tallest peak
¨ Parent peak =
Molecular ion (M+) peak
¨ M+1 = peak due
to 13C isotope (1.1% of naturally occurring carbon), and 2H
isotope (.015% of naturally occurring hydrogen).
¨ Mass Spectra =
bar graph of fragments
¨ m/e ratio = mass
to charge ratio in amu/e-
Common
Fragments
Alkane
Fragmentation
¨ Tend to eliminate
methyl radical ŕ M-15
¨
The ion
formed can expel ethene ŕ M-28
Alkane
Fragmentation
¨ Branched
hydrocarbons form more stable secondary and tertiary carbocations.
¨ These peaks will
tend to dominate the mass spectrum because they are so stable and form so readily.
Aromatic
Hydrocarbons
¨ The
fragmentation of an aromatic is somewhat complex, generating a series of peaks
having m/e = 77, 65, 63, etc.
¨ This cluster is
known as the "aromatic cluster“.
Aromatic
Hydrocarbons
¨ If the molecule
contains a benzyl unit, the major cleavage will be to generate the benzyl
carbocation, which rearranges to form the tropylium ion m/e=91.
¨ Expulsion of
acetylene from tropylium generates a characteristic m/e = 65 peak.
Aldehydes
and Ketones
¨
predominate
cleavage in aldehydes and ketones is loss of one of the side-chains to generate
the substituted oxonium ion
¨ The methyl
derivative (CH3C O+) is commonly referred to as the
"acylium ion".
Aldehydes
and Ketones
¨
Another
common fragmentation observed in carbonyl compounds (and in nitriles, etc.)
involves the expulsion of neutral ethene via a process known as the McLafferty
rearrangement
Esters,
Acids and Amides
¨
As with
aldehydes and ketones, the major cleavage observed for these compounds involves
expulsion of the "X" group, as shown below, to form the substituted
oxonium ion. For carboxylic acids and unsubstituted amides, characteristic
peaks at m/e = 45 and 44 are also often observed.
Alcohols
¨
In
addition to losing a proton and hydroxy radical, alcohols tend to lose one of
the -alkyl groups (or hydrogens) to
form the oxonium ions shown below.
Alcohols
¨ For primary
alcohols, this generates a peak at m/e = 31; secondary alcohols generate peaks
with m/e = 45, 59, 73, etc., according to substitution.
Ethers
¨ 
Following the
trend of alcohols, ethers will fragment, often by loss of an alkyl radical, to
form a substituted oxonium ion, as shown below for diethyl ether.
Halides
¨
Organic
halides fragment with simple expulsion of the halogen, as shown below.
¨ 35Cl/37Cl
ratio is roughly 3.08:1
¨ 79Br/81Br
ratio is 1.02:1
¨ Both chlorine
and bromine-containing compound will have two peaks, separated by two mass
units
Mass
Spectrum Practice
¨ Best one
¨ Same with a
different interface
Infrared
Spectroscopy
¨ Light in the
infrared region of the electromagnetic spectrum is absorbed by molecules
causing them to vibrate.
¨ The energy of
the absorbed light is equal to the energy of particular atoms vibrating about
their bonds.
¨ What is all this vibrating about?
The IR
Spectrum
¨ Useful Infrared
spectrum has a wavelength range from 2.5 to 15 micrometers (µ).
¨ In practice,
units proportional to frequency, (wave number in units of cm-1)
rather than wavelength, are commonly used and the region 2.5 to 15 µ corresponds to approximately 4000 to
600 cm-1.
Different
Modes of Vibration
Springs
and Things
¨ Hook’s Law
–
Frequency of vibration is proportional to the square root
of the bond strength, k, and inversely proportional to the the reduced mass m. Where m is m1m2/(m1+m2)
•
Never go there peter.
Some
Ranges for IR Absorption
¨ 3700 - 2500 cm-1:
X-H stretching (X = C, N, O, S)
¨ 2300 - 2000 cm-1:
C X stretching (X = C or N)
¨ 1900 - 1500 cm-1:
C X stretching (X = C, N, O)
¨ 1300 - 800 cm-1:
C-X stretching (X = C, N, O)
Some
Regions of IR Absorption
Identification
of Complex Spectra
¨
Since most
organic molecules have single bonds, the region below 1500 cm-1 can
become quite complex and is often referred to as the ‘fingerprint region’. This
region is unique to a compound.
Interpreting
Spectra
¨ Examine the
spectra for functional group absorptions by using an absorption table
– See page 458
Alcohols
¨ Alcohols and
amines display strong broad O-H and N-H stretching bands in the region
3400-3100 cm-1.
¨ The bands are
broadened due to hydrogen bonding and a sharp 'non-bonded' peak can often be
seen at around 3400 cm-1.
Alkene
and Alkyne
¨ Alkene and
alkyne C-H bonds display sharp stretching absorptions in the region 3100-3000
cm-1.
¨ The bands are of
medium intensity and are often obscured by other absorbances in the region
(i.e., OH).
Triple
Bonds
¨ Triple bond
stretching absorptions occur in the region 2400-2200 cm-1.
¨ Absorptions from
nitriles are generally of medium intensity and are clearly defined.
¨ Alkynes absorb
weakly in this region unless they are highly asymmetric; symmetrical alkynes do
not show absorption bands.
Carbonyl
Compounds
¨ Carbonyl
stretching bands occur in the region 1800-1700 cm-1.
¨ The bands are
generally very strong and broad.
¨ Carbonyl
compounds which are more reactive in nucleophilic addition reactions (acyl
halides, esters) are generally at higher wave number than simple ketones.
¨ Aldehydes, and
amides are the lowest, absorbing in the region 1700-1650 cm-1.
Carbon-Carbon
Double Bonds
¨ Carbon-carbon
double bond stretching occurs in the region around 1650-1600 cm-1.
¨ The bands are
generally sharp and of medium intensity.
¨ Aromatic
compounds will typically display a series of sharp bands in this region.
Carbon-Oxygen
Single Bonds
¨ Carbon-oxygen
single bonds display stretching bands in the region 1200-1100 cm-1.
¨ The bands are
generally strong and broad.
¨ However; many
other functional groups have bands in this region, which appear similar so
tread carefully.
Lots
of Practice Makes it Easy
Goals
¨ After this
chapter you should be able to:
– Determine
formula of molecules based on MS
– Determine
functional groups in a molecule based on IR
– Determine
molecular structure given IR and formula.
