Transcript 12. Structure Determination: Mass Spectrometry and

12. Structure Determination: Mass
Spectrometry and Infrared Spectroscopy
Determining the Structure of an
Organic Compound
• The analysis of the outcome of a reaction
requires that we know the full structure of
the products as well as the reactants
• In the 19th and early 20th centuries,
structures were determined by synthesis
and chemical degradation that related
compounds to each other
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Determining the Structure of an
Organic Compound
• Physical methods now permit structures to
be determined directly. We will examine:
– mass spectrometry (MS)—this chapter
– infrared (IR) spectroscopy—this chapter
– nuclear magnetic resonance spectroscopy
(NMR)—Chapter 13
– ultraviolet-visible spectroscopy (VIS)—
Chapter 14
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12.1 Mass Spectrometry (MS)
• Sample vaporized and bombarded by
energetic electrons that remove an electron,
creating a cation-radical
• Bonds in cation radicals begin to break
(fragment)
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Mass Spectrometer
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The Mass Spectrum
• Plot mass of ions (m/z) (x-axis) versus the
intensity of the signal (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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MS Examples: Methane and
Propane
• Methane produces a parent peak (m/z = 16) and
fragments of 15 and 14 (See Figure 12-2 a)
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MS Examples: Methane and
Propane
• The Mass Spectrum of propane is more
complex (Figure 12-2 b) since the molecule
can break down in several ways
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12.2 Interpreting Mass Spectra
• Molecular weight from the mass of the molecular
ion
• Double-focusing instruments provide highresolution “exact mass”
– 0.0001 atomic mass units – distinguishing specific
atoms
• Example MW “72” is ambiguous: C5H12 and
C4H8O but:
– C5H12 72.0939 amu exact mass C4H8O 72.0575 amu
exact mass
– Result from fractional mass differences of atoms 16O =
15.99491, 12C = 12.0000, 1H = 1.00783
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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
– (M+1) from 13C that is randomly present
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12.3 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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2,2-Dimethylpropane:
MM = 72 (C5H12)
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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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Hexane
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Practice Problem 12.2: methylcyclohexane
or ethylcyclopentane?
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Mass Spectral Cleavage
Reactions of Alcohols
• Alcohols undergo -cleavage (at the bond next
to the C-OH) as well as loss of H-OH to give
C=C
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Mass Spectral Cleavage of
Amines
• Amines undergo -cleavage,
generating radicals
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Fragmentation of Ketones and
Aldehydes
• A C-H that is three atoms away leads
to an internal transfer of a proton to
the C=O, called the McLafferty
rearrangement
• Carbonyl compounds can also
undergo  cleavage
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Fragmentation of Ketones and
Aldehydes
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12.5 The Electromagnetic Spectrum
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Wavelength and Frequency
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Absorption Spectra
• Organic compounds exposed to electromagnetic
radiation can absorb photons of specific
energies (wavelengths or frequencies)
• Changing wavelengths to determine which are
absorbed and which are transmitted produces an
absorption spectrum
• Energy absorbed is distributed internally in a
distinct and reproducible way (See Figure 12-11)
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Infrared Absorption Spectrum of
Ethanol
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12.6 Infrared Spectroscopy of
Organic Molecules
• IR region is lower in photon energy than visible
light (below red – produces heating as with a
heat lamp)
• 2.5  106 m to 2.5  105 m region used by
organic chemists for structural analysis
• IR energy in a spectrum is usually measured as
wavenumber (cm-1), the inverse of wavelength
and proportional to frequency:
• Wavenumber (cm-1) = 1/l(cm)
• Specific IR absorbed by organic molecule is
related to its structure
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IR region and vicinity
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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”
• Energy is characteristic of the atoms in the
group and their bonding
• Corresponds to molecular vibrations
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Infrared Energy Modes
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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
• Characteristic IR absorptions in Table
12.1 can be used to confirm the
existence of the presence of a functional
group in a molecule
• IR spectrum has lower energy region
characteristic of molecule as a whole
(“fingerprint” region)
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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 CC and C  N (stretching)
• 2000-1500 cm-1 double bonds (stretching)
– C=O 1680-1750
– C=C 1640-1680 cm-1
• Below 1500 cm-1 “fingerprint” region
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Regions of the Infrared
Spectrum
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Differences in Infrared
Absorptions
• Molecules vibrate and rotate in
normal modes, which are
combinations of motions (relates
to force constants)
• Bond stretching dominates higher
energy (frequency) modes
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Differences in Infrared
Absorptions
• Light objects connected to heavy objects
vibrate fastest (at higher frequencies): CH, N-H, O-H
• For two heavy atoms, stronger bond
requires more energy (higher frequency):
C  C, C  N > C=C, C=O, C=N > C-C, CO, C-N, C-halogen
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12.8 Infrared Spectra of
Hydrocarbons
• C-H, C-C, C=C, C  C have characteristic
peaks
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Hexane
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Alkenes
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1-Hexene
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Alkynes
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12.9 Infrared Spectra of Some
Common Functional Groups
• Spectroscopic behavior of
functional groups is discussed
in later chapters
• Brief summaries presented
here
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IR: Alcohols
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Amines
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IR: Aromatic Compounds
• Weak C–H stretch at 3030 cm1
• Weak absorptions 1660 - 2000 cm1 range
• Medium-intensity absorptions 1450 to 1600 cm1
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Phenylacetylene
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IR: Carbonyl Compounds
• Strong, sharp C=O 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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Practice problem 12.7:
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Phenylacetaldehyde
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C=O 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
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C=O 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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Chromatography: Purifying Organic
Compounds
• Chromatography : a process that separates compounds
using adsorption and elution
– Mixture is dissolved in a solvent (mobile phase) and placed into
a glass column of adsorbent material (stationary phase)
– Solvent or mixtures of solvents passed through
– Compounds adsorb to different extents and desorb differently in
response to appropriate solvent (elution)
– Purified sample in solvent is collected from end of column
– Can be done in liquid or gas mobile phase
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Principles of Liquid
Chromatography
• Stationary phase is alumina (Al2O3) or silica gel
(hydrated SiO2)
• Solvents of increasing polarity are used to elute
more and more strongly adsorbed species
• Polar species adsorb most strongly to stationary
phase
– For examples, alcohols adsorb more strongly
than alkenes
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High-Pressure (or High-Performance)
Liquid Chromatography (HPLC)
• More efficient and complete separation than
ordinary LC
• Coated silica microspheres (10-25 µm diameter)
in stationary phase
• High-pressure pumps force solvent through
tightly packed HPLC column
• Detector monitors eluting material
• Figure 12.17: HPLC analysis of a mixture of 14
pesticides, using acetonitrile/water as the mobile
phase
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HPLC of Pesticide Mixture
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Prob. 12.39: Cyclohexane or
Cyclohexene?
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Problem 12.48: Unknown
hydrocarbon
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Problem 12.49: Unknown
hydrocarbon2
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Some Useful Websites:
• Interpretation of IR spectra (CSU Stanislaus):
http://wwwchem.csustan.edu/Tutorials/INFRARED.HTM
• IR Spectroscopy Tutorial (CU Boulder):
http://orgchem.colorado.edu/hndbksupport/irtutor/tutorial.
html
• NIST Chemistry WebBook:
http://webbook.nist.gov/chemistry/
• SDBS Data Base:
http://www.aist.go.jp/RIODB/SDBS/menu-e.html
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