2. Application of organic chemistry/synthesise/spectroscopy
Ch. 2 - 2
Satoshi Ōmura, a microbiologist collected soil samples
hunting for new antibacterial compounds (1960s)
Sent it to William Campbell to test their effect on parasites in
animals.
One species was discovered to be very effective against these
parasites i.e. Streptomyces avermictilis
The researchers began chemically modifying the compounds,
tweaking their molecular structures slightly to see if they could make
avermectin even more potent against parasites and safer for the
animals being treated.
By synthesizing thousands of similar compounds, Merck scientists
found that, with slight chemical modification, some of the avermectin
compounds displayed enhanced activity as well as safety.
Benefits of organic synthesise:
To make naturally occurring compounds which are biologically active but difficult (or impossible) to obtain
For the intellectual challenges- new problems demand new solutions and can lead to the development of new chemistry and reagents
3. Spectroscopy
Technique used to determine the structure of a compound
using the interaction of the compound and radiant energy
(radiation).
Spectrum of a compound is a plot of how much
electromagnetic radiation is adsorbed or transmitted at
each frequency and can be highly characteristic of a
compound structure.
Ch. 2 - 3
4. Physical
stimulus
Molecule response Detecting
instrument
Visual (most common)
representation, or
Spectrum
SPECTROSCOPY - Study of spectral
information
Upon irradiation with infrared light, certain bonds respond by vibrating faster. This
response can be detected and translated into a visual representation called a
spectrum.
5. Spectroscopic methods for organic
structure determination
a) Infrared Spectroscopy (IR)
● Triggers molecular vibration through irradiation with infrared
radiation
● Provides information about the presence or absence of
characteristic functional group such as C=O, C–O, O–H, COOH,
NH2 … etc.
b) Nuclear Magnetic Resonance (NMR)
• Excitation of the nucleus of atoms through radiofrequency irradiation.
• Provides extensive information about molecular structure and atom
connectivity
c) Mass Spectroscopy (MS)
● Bombardment of the sample with electrons and detection of
resulting molecular fragments for certain functional groups.
● Provides information about molecular weight, molecular mass
and formula (C4H8O2, C6H12O3 etc)
d) Ultraviolet Spectroscopy (UV)
● Promotion of electrons to higher energy levels through irradiation
of the molecule with ultraviolet light.
● Provides mostly information about the presence of double and
triple bonds (i.e. dienes, aromatics and enons)
6. Fourier Transform Infrared Spectrometer
IR irradiation Mirror splits beam
Bean passes
through sample to
detector
Signal is produced
in form of a
spectrum
• Samples are prepared in the lab either in solid (KBr, thin transparent film called KBr pellet) or
liquid form (NaCl plate)
7. AN IR SPECTRUM IN ABSORPTION MODE
• The IR spectrum is basically a plot of transmitted (or absorbed)
frequencies vs. intensity of the transmission (or absorption).
• Frequencies appear in the x-axis in units of inverse centimeters
(wavenumbers), and intensities are plotted on the y-axis in
percentage units.
The graph above shows a
spectrum in absorption mode.
8. AN IR SPECTRUM IN TRANSMISSION MODE
Ch. 2 - 8
• The graph above shows a spectrum in transmission
mode.
• This is the most commonly used representation and
the one found in most chemistry and spectroscopy
books. Therefore we will use this representation.
9. Classification of bands
Ch. 2 - 9
IR bands can be classified as strong (s), medium (m), or weak (w),
depending on their relative intensities in the infrared spectrum. A strong band
covers most of the y-axis. A medium band falls to about half of the y-axis, and
a weak band falls to about one third or less of the y-axis.
10. Infrared band shapes
Ch. 2 - 10
Infrared band shapes come in various forms. Two of the most common are
narrow (A) and broad (B). Narrow bands are thin and pointed, like a
dagger. Broad bands are wide and smoother.
A typical example of a broad band is that displayed by O-H bonds, such as
those found in alcohols and carboxylic acids.
A B
11. Ch. 2 - 11
Move back and forth as if joined by a
spring
Three atoms undergo
stretching and bending
vibrations
Vibration modes
Covalent bonds can vibrate in several modes, including stretching,
rocking, and scissoring.
The most useful bands in an infrared spectrum correspond to stretching
frequencies, and those will be the ones we’ll focus on.
12. Infrared of active bonds
Ch. 2 - 12
Not all covalent bonds display bands in the IR spectrum. Only polar
bonds do so. These are referred to as IR active.
The intensity of the bands depends on the magnitude of the dipole
moment associated with the bond in question:
Strongly polar bonds such as carbonyl groups (C=O) produce strong bands.
Medium polarity bonds and asymmetric bonds produce medium bands.
Weakly polar bond and symmetric bonds produce weak or non observable
bands.
13. IR absorption ranges
Ch. 2 - 13
According to Hooke's law :
The vibrational frequency is inversely proportional to the mass of the atoms attached to
the bond. The lighter the atom the higher the frequency.
The vibrational frequency is proportional to the strength of the bond.
The stronger the bond the higher the frequency.
15. • You need to examine each region in detail and make a few notes. Think of common
functional groups and try find features that will allow you to quickly identify possible
molecules.
• Do NOT focus on the fingerprint region as there are MANY bands there and it is difficult
to use. e.g. in the hydrogen region OH and NH are usually broad bands, but they have
different shapes.
• Also, 3000 cm-1 is the dividing point between sp2 and sp3-bonded hydrogen, i.e. a band
at 3055cm-1 is sp2, but 2995cm-1 is sp3.
• In the triple bond region the two most common functional groups are alkyne and nitrile –
where can you find these absorption bands in the spectrum?
• Where do you find double bonds, carbonyls, aromatics, etc. Make your own list of
important features in the IR spectrum.
• Use a correlation table for reference which is available in any organic
chemistry text book
Some tips for interpretation of IR
16. Ch. 2 - 16
Characteristic IR absorptions
Intensity: s = strong, m = medium, w = weak, v = variable
Group Freq. Range (cm-1) Intensity
Alkyl
C–H (stretching) 2853–2962 (m–s)
Alkenyl
C–H (stretching)
C=H (stretching)
cis-RCH=CHR
trans-RCH=CHR
3010–3095
1620–1680
675–730
960–975
(m)
(v)
(s)
(s)
Alkynyl
≡C–H (stretching)
C≡C (stretching)
~3300
2100–2260
(s)
(v)
17. Ch. 2 - 17
Characteristic IR absorptions
Intensity: s = strong, m = medium, w = weak, v = variable
Group Freq. Range (cm-1) Intensity
Aromatic
Ar–H (stretching)
- monosubstituted
- o-disubstituted
- m-disubstituted
- p-disubstituted
~3300
690–710
730–770
735–770
680–725
750–810
800–860
(v)
(very s)
(very s)
(s)
(s)
(very s)
(very s)
18. Ch. 2 - 18
Characteristic IR absorptions
Intensity: s = strong, m = medium, w = weak, v = variable
Group Freq. Range (cm-1) Intensity
Alcohols, Phenols & Carboxylic Acids
O–H (stretching)
- alcohols & phenols
(dilute solutions)
- alcohols & phenols
(hydrogen bonded)
- carboxylic acids
(hydrogen bonded)
3590–3650
3200–3550
2500–3000
(sharp, v)
(broad, s)
(broad, v)
19. Ch. 2 - 19
Characteristic IR absorptions
Intensity: s = strong, m = medium, w = weak, v = variable
Group Freq. Range (cm-1) Intensity
Aldehydes, Ketones, Esters, Carboxylic Acids, Amides
C=O (stretching)
Aldehydes
Ketones
Esters
Carboxylic Acids
Amides
1630–1780
1690–1740
1680–1750
1735–1750
1710–1780
1630–1690
(s)
(s)
(s)
(s)
(s)
(s)
Amines
N–H 3300–3500 (m)
Nitriles
C≡N 2220–2260 (m)
20. Its your turn
A compound with the molecular formula C4H4O2 has a strong
adsorption near 3300 cm-1, 2800-3000 cm-1 region, a strong
absorbance peak near 2200 cm-1. It also has a strong broad
absorbance in the 2500-3600 cm-1 region and a strong peak in the
1710-1780 cm-1 region. Propose a possible structure for the
compound.
Ch. 2 - 20
