CHAPTER 3

3. STRUCTURE ELUCIDATION AND MOLECULAR

SPECTROSCOPY
3.1. Combustion analysis
• With an unknown organic substance, the identification
protocol should start by performing qualitative (and
quantitative, if possible) elemental analysis of the
constituent elements, thus determining the nature of
the elements present in the molecule and the
proportion in which they occur.

• Quantitative analysis usually involves the combustion

of given weight of the substance, determining
chromatographically (or gravimetrically) the amount
and nature of the gases formed in the combustion.

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• Instrument of the next slide that measures C, H, N,
and S in a single operation.

• First, a 2-mg sample is accurately weighed and

sealed in a tin or silver capsule. The analyzer is
swept with He gas that has been treated to remove
traces of O2, H2O, and CO2.
• At the start of a run, a measured excess of O2 is
added to the He stream. Then the capsule is
dropped into a preheated ceramic crucible, where
the capsule melts and sample is rapidly oxidized.

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• C,H,N,S elemental analyzer uses gas chromatography
with thermal conductivity detection to measure N2, CO2,
H2O, and SO2 combustion products.
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• Products pass through hot WO3 oxidation catalyst
to complete the combustion of C to CO2. In the next
zone, metallic Cu at 850° C reduces SO3 to SO2 and
removes excess O2:

• The mixture of CO2, H2O, N2, and SO2 is separated by gas

chromatography, and each component is measured with a
thermal conductivity detector. Alternatively, CO2, H2O, and
SO2 can be measured by infrared absorbance.
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 Determination of Empirical Formulas from mass of
element
• Determining a Compound’s Empirical Formula from the
Masses of its Elements

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 3.2. Molecular weight and molecular formula
• Mass spectrometry technique is relevant for the
characterization of organic substances and consists of the
ionization of a sample and later study of the fragmentation
in different ions.
• The most common method of ionization involves electron
impact (EI). Collision of a molecule M with an electron e is
followed by electron ejection that yields an odd-electron
positively charged cation radical [M]+. of the same mass
as the initial molecule M.

• The cation radical produced is known as the molecular ion,

and its mass gives a direct measure of the molecular weight
of a substance.

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Determination of molecular formulas Cont..
• Molecular formulas are derived by comparing the compound’s
molecular or molar mass to its empirical formula mass.
• Molecular mass, for example, is often derived from the mass
spectrum of the compound. Molar mass can be measured by a
number of experimental methods.
So generally
• For any empirical formula AxBy, the molecular formula is
determined by multiplying it to whole number n, Where n is ratio

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Example Cont..
• A compound whose empirical formula is determined to be CH2O. If
the compound’s molecular mass is determined to be 180 amu by
Mass spectrometry, what is the molecular formula of the compound?
Solution
• First find molecular mass of the empirical formula CH2O, it is 30
(12C+2H+16O). Then find the whole number n
n = molecular mass/empirical formula mass= 180/30=6
• Then molecular formula is (CH2O)n= (CH2O)6= C6H12O6
Activity
Determination of the Molecular Formula for Nicotine
• Nicotine, an alkaloid in the nightshade family of plants that is
mainly responsible for the addictive nature of cigarettes, contains
74.02% C, 8.710% H, and 17.27% N. If 40.57 g of nicotine contains
0.2500 mol nicotine, what is the molecular formula?
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 3.3. Ozonization

• Ozonization involves breaking of an alkene to two

carbonyl compounds. The site of cleavage shows the
position of the double bond in the former compound.

• Example1, consider unsymmetrical alkene undergoing

ozonization.

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• If you know what carbonyl compounds are formed by
ozonolysis, you can mentally work backward to deduce
the structure of the alkene.
• For example, if ozonolysis of an alkene followed by a
work-up under reducing conditions forms acetone and
butanal as products, you can conclude that the alkene
was 2-methyl-2-hexene.

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• The following products were obtained from
ozonolysis of a diene followed by work-up under
reducing conditions. Give the structure of the diene.

• SOLUTION The five-carbon dicarbonyl compound

indicates that the diene must contain five carbons
flanked by two double bonds.

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• One of the carbonyl compounds obtained from
ozonolysis has one carbon atom, and the other has
three carbon atoms.
• Therefore, one carbon has to be added to one end
of the diene, and three carbons have to be added to
the other end.

Q: What is the ozonolysis product of the following

under reduced condition?

answer

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 3.4. Molecular spectroscopy
• Spectroscopy is the study of the interaction
between matter and electromagnetic
radiation—radiant energy that displays the
properties of both particles and waves.
• Several different spectrophotometric techniques are
used to identify compounds. Each employs a
different type of electromagnetic radiation. We will
start here by looking at
 ultraviolet and visible (UV/Vis) spectroscopy &
 infrared (IR) spectroscopy.

3.4.1. Ultraviolet and Visible Spectroscopy

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 UV and Vis light cause only two kinds of electronic
transition: Symmetry:
allowed
transition

Forbidden transition:
lone pair orthogonal to 
system

• Only organic compounds with p electrons can produce

UV/Vis spectra.
• A visible spectrum is obtained if visible light is absorbed.
• A UV spectrum is obtained if UV light is absorbed. 17
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A chromophore is the part of a molecule that
absorbs UV or visible light

Allowed

Forbidden

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• Comparison of the π→π* and the n→π*
transitions. The n→π* transition requires less
energy because the nonbonding (n) electrons
are higher in energy than the bonding π
electrons

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 The Beer–Lambert Law
e = ~10,000 M–1cm–1,
A=ecl Allowed

e = <100 M–1cm–1,
Forbidden
A = log(I0/I)
c = concentration of substance in solution
l = length of the cell in cm
e = molar absorptivity, a measure of the
probability of the transition
The molar absorptivity of a compound is a constant that is
characteristic of the compound at a particular wavelength
and solvent
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 Effect of Conjugation on lmax

The lmax and e values increase as the number of

conjugated double bonds increases

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If a compound has enough conjugated double bonds, it
will absorb visible light (lmax >400 nm), and the
compound will be colored

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An auxochrome is a substituent in a chromophore that
alters the lmax and the intensity of the absorption:

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The Visible Spectrum and Color

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Spectroscopy and the Electromagnetic Spectrum
Spectroscopy is the study of the interaction of matter and
electromagnetic radiation

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 Vibrational Transitions
Observed in IR Spectroscopy

Functional groups
stretch at different
frequencies, and IR
spectroscopy is
used to identify
functional groups

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Infrared transitions require a bond dipole to occur:

   
h
C H C H
Higher Energy
Vibrational State

The more polar the bond, the more intense the absorptions:

The intensity of an absorption band also depends on

the number of bonds responsible for the absorption
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 Influence of symmetry on IR activity of the alkene
stretch:

1-butene — infrared active

2,3-dimethyl-2-butene — infrared inactive
2,3-dimethyl-2-heptene — infrared active, but very weak absorption band

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 The Vibrating Bond as a
Quantized Harmonic Oscillator
Quantum levels for a
stretching vibration: Ball-and-spring model:

Fundamental transition: o  1
Overtone: o  2

Overtones are twice the

frequency of the fundamental
transition and are always weak

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The approximate wavenumber of an absorption can be
calculated from Hooke’s law:

1 K
v
2c Reduced Mass 
M 1M 2
M1  M 2

 = wavenumber
c = speed of light
K = force constant
M1 and M2 = masses of atoms

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Hooke’s law predicts that lighter atoms will vibrate at a
higher frequency than heavy atoms:

C—H ~3000 cm–1

C—D ~2200 cm–1
C—O ~1100 cm–1
C—Cl ~700 cm–1

Increasing the s character of a bond (higher K value)

increases the stretching frequency:

sp
sp2
sp3

sp2 35
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Note the influence of mass and s character on stretching frequency:

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 An Infrared Spectrum
The functional group The fingerprint
region (4000–1400 cm–1) region (1400–600 cm–1)

High energy Low energy

The functional group is used to determine the functional group
present. The fingerprint region is used for structure elucidation
by spectral comparison.
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Functional group regions: Both Fingerprint regions: Compounds
compounds are alcohols are different alcohols

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The exact position of the absorption band depends on
electron delocalization, the electronic effect of
neighboring substituents, and hydrogen bonding:

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 Carbonyl
overtone

Esters have a carbonyl and a C—O stretch Ketones have only a carbonyl stretch

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Putting an atom other than carbon next to the carbonyl
group causes the position of the carbonyl absorption
band to shift:

The predominant effect of the nitrogen of an amide is

electron donation by resonance

The predominant effect of the oxygen of an ester is

inductive electron withdrawal 41
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The position of a C—O absorption varies because of
resonance release in acids and esters:

~1050 cm–1

~1050 cm–1

~1250 cm–1

~1250 cm–1 and 1050 cm–1

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Acids are readily distinguished from alcohols

Higher-frequency
Broad C─O stretch
OH stretch
C═O stretch

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The position and the breadth of the O—H absorption
band depend on the concentration of the solution

It is easier to stretch an O—H bond if it is hydrogen

bonded

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The strength of a
C—H bond
depends on the
hybridization
of the carbon

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Examine the absorption bands in the vicinity of 3000 cm–1

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 Benzene in-plane and
out-of-plane C—H bends
Benzene ring:
• Sharp absorption bands at ~1600 cm–1 and 1500–1430 cm–1.
• Overtones at 1700–1900 cm–1 for the in-plane and out-of-
plane benzene C—H bends.
• The benzene overtones in the diagnostic region are readily
recognized.
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Stretch of C—H Bond in an Aldehyde

The stretch of the C—H bond of an aldehyde shows one

absorption band at ~2820 cm–1 and another one at ~2720
cm–1
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Identifying a functional group by the bending vibrations:

• Primary amine: two N—H stretches at 3350 cm–1.

• Amine: N—H bend.
• ―Isopropyl split‖ at 1380 cm–1 indicates the presence of
an isopropyl group.

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 Analyzing Infrared Spectra
The position, intensity, and shape of an absorption band
are helpful in identifying functional groups

The absence of absorption bands can be useful in

identifying a compound in IR spectroscopy

Bonds in molecules lacking dipole moments will not be

detected

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wavenumber (cm–1) assignment
3075 sp2 CH
2950 sp3 CH
1650 and 890 a terminal alkene with two substituents
absence of bands has less than four adjacent CH2 groups
1500–1430 and 720
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wavenumber (cm–1) assignment
3050 sp2 CH
2810 and 2730 an aldehyde
1600 and 1460 benzene ring
1700 a partial single-bond
character carbonyl
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wavenumber (cm–1) assignment
3300 OH group
2950 sp3 CH
2100 alkyne

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wavenumber (cm–1) assignment
3300 N—H
2950 sp3 CH
1660 amide carbonyl
1560 N—H Bend

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wavenumber (cm–1) assignment
>3000 sp2 CH
<3000 sp3 CH
1605 and 1500 a benzene ring
1720 a ketone carbonyl
1380 a methyl group
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