Various Tools and Techniques used for

Structural Elucidation

Prof. Dr. A. V. Patil

Smt. S. S. Patil College of Pharmacy, Chopda
 INTRODUCTION
 Electromagnetic radiation is composed of electrical and magnetic
waves which oscillate on perpendicular planes. wave nature and particle nature
 The different properties of the various types of electromagnetic radiation are due to
differences in their wavelengths, and the corresponding differences in their energies:
shorter wavelengths correspond to higher energy.
 The full range of electromagnetic radiation wavelengths is
referred to as the electromagnetic spectrum.
Here is the key to molecular spectroscopy: a given molecule
will specifically absorb only those wavelengths which have
energies that correspond to the energy difference of the transition
that is occurring. Thus, if the transition involves the molecule
jumping from ground state A to excited state B, with an energy
difference of ΔE, the molecule will specifically absorb radiation
with wavelength that corresponds to ΔE, while allowing other
wavelengths to pass through unabsorbed.
By observing which wavelengths a molecule absorbs, and to what
extent it absorbs them, we can gain information about the nature
of the energetic transitions that a molecule is able to undergo, and
thus information about its structure.
 Infrared spectroscopy
 Covalent bonds in organic molecules are not rigid sticks – rather, they behave
more like springs.
At room temperature, organic molecules are always in motion, as their bonds
stretch, bend, and twist. These complex vibrations can be broken down
mathematically into individual vibrational modes.
 The energy of molecular vibration is quantized rather than continuous,
meaning that a molecule can only stretch and bend at certain 'allowed'
frequencies.
 If a molecule is exposed to electromagnetic radiation that matches the
frequency of one of its vibrational modes, it will in most cases absorb energy
from the radiation and jump to a higher vibrational energy state – what this
means is that the amplitude of the vibration will increase, but the vibrational
frequency will remain the same.
 The difference in energy between the two vibrational states is equal to the
energy associated with the wavelength of radiation that was absorbed. It turns
out that it is the infrared region of the electromagnetic spectrum which contains
frequencies corresponding to the vibrational frequencies of organic bonds.
 The power of infrared spectroscopy - that different functional groups have
different characteristic absorption frequencies.
 Some bonds absorb infrared light more strongly than others, and some bonds
do not absorb at all.
 In order for a vibrational mode to absorb infrared light, it must result in a
periodic change in the dipole moment of the molecule. Such vibrations are said
to be infrared active.
 In general, the greater the polarity of the bond, the stronger its IR
absorption.
 The carbonyl bond is very polar, and absorbs very strongly. The carbon-
carbon triple bond in most alkynes, in contrast, is much less polar, and thus a
stretching vibration does not result in a large change in the overall dipole
moment of the molecule. Alkyne groups absorb rather weakly compared to
carbonyls.
 Some kinds of vibrations are infrared inactive. The stretching vibrations of
completely symmetrical double and triple bonds, do not result in a change in
dipole moment, and therefore do not result in any absorption of light (but other
bonds and vibrational modes in these molecules do absorb IR light).
 On the horizontal axis we see IR wavelengths expressed in terms of a unit called
wavenumber (cm-1), which tells us how many waves fit into one centimeter. On
the vertical axis we see ‘% transmittance’, which tells us how strongly light
was absorbed at each frequency (100% transmittance means no absorption
occurred at that frequency).
 You will notice that there are many additional peaks in this spectrum in the
longer-wavelength 400 -1400 cm-1 region. This part of the spectrum is called the
fingerprint region. The pattern of absorbance peaks in the fingerprint region is
unique to every molecule, meaning that the data from an unknown sample can be
compared to the IR spectra of known standards in order to make a positive
identification.
 Ultraviolet and visible spectroscopy
 While interaction with infrared light causes molecules to undergo vibrational
transitions, the shorter wavelength, higher energy radiation in the UV (200-400
nm) and visible (400-700 nm) range of the electromagnetic spectrum causes
many organic molecules to undergo electronic transitions.
 It means that when the energy from UV or visible light is absorbed by a
molecule, one of its electrons jumps from a lower energy to a higher energy
molecular orbital. Electronic transitions. The molecular orbital picture consists
of one bonding MO, and a higher energy antibonding MO.
 When the molecule is in the ground state, both electrons are paired in the
lower-energy bonding orbital – this is the Highest Occupied Molecular Orbital
(HOMO). The antibonding orbital, in turn, is the Lowest Unoccupied Molecular
Orbital (LUMO). If the molecule is exposed to light of a wavelength with energy
equal to ΔE, the HOMO-LUMO energy gap, this wavelength will be absorbed
and the energy used to bump one of the electrons from the HOMO to the LUMO
– in other words, from the bonding to the antibonding orbital. This is referred as
transition.
 UV-vis spectroscopy becomes useful to most organic and biological chemists
is in the study of molecules with conjugated (pi) systems. In these groups, the
energy gap for π -π* transitions is smaller than for isolated double bonds, and
thus the wavelength absorbed is longer. Molecules or parts of molecules that
absorb light strongly in the UV-vis region are called chromophores.
 UV-vis spectroscopy becomes useful to most organic and biological chemists is
in the study of molecules with conjugated (pi) systems. Molecules or parts of
molecules that absorb light strongly in the UV-vis region are called chromophores.
 From the molecular orbital diagram, there are several possible electronic
transitions that can occur, each of a different relative energy.

s*
s s* alkanes
p*
s p* carbonyls

p p* unsaturated cmpds.
Energy
n
n s* O, N, S, halogens

n p* carbonyls
p

12
 Mass Spectroscopy

 One of the more common types of MS techniques used in the organic

laboratory is electron ionization.
 In the ionization source, the sample molecule is bombarded by a high-energy
electron beam, which has the effect of knocking a valence electron off of the
molecule to form a radical cation.
 Because a great deal of energy is transferred by this bombardment process,
the radical cation quickly begins to break up into smaller fragments, some of
which are positively charged and some of which are neutral. The neutral
fragments are either adsorbed onto the walls of the chamber or are removed by
a vacuum source.
 In the mass analyzer component, the positively charged fragments and any
remaining unfragmented molecular ions are accelerated down a tube by an
electric field.
 Nuclear Magnetic Resonance

 The extent of magnetic properties of the substances can be determined by

placing the substance in magnetic field. Interaction of oscillating magnetic field of
the radiation with chemical species when placed in radio waves.
 The quantity of energy involved in radio waves is too small to excite, vibrate, or
rotate an atom of a molecule. But this energy is sufficient to affect the nucleus of
the atoms of molecule. Therefore, the nucleus of atoms in a molecule on absorbing
radio waves may suffer in nuclear energy.
 The magnetic properties depend on the nuclear spin and spin quantum number.
 The spining nucleus (I > 0) acts as tiny magnet. When such nucleus placed in
applied in magnetic field, magnetic interaction takes place and magnetic energy
levels are created. So the transition between magnetic energy levels of nucleus of
molecule arise.
 Precessional frequency and resonance frequency.
 When frequency of radio frequency equals the Precessional frequency of the
spining nucleus in an appiled magnetic field the absorption of radio frequency
radiation by the nucleus takes place and transitions occure.
 Information in a NMR Spectra

Observable Name Quantitative Information

Peak position Chemical shifts (d) d(ppm) = uobs –uref/uref (Hz) chemical (electronic)
environment of nucleus

Peak Splitting Coupling Constant (J) Hz peak separation neighboring nuclei

(intensity ratios) (torsion angles)

Peak Intensity Integral unitless (ratio) nuclear count (ratio)

relative height of integral curve T1 dependent

Peak Shape Line width Du = 1/pT2 molecular motion

peak half-height chemical exchange
uncertainty principal
uncertainty in energy
Interpretation of NMR spectra: NMR spectrum of a substance gives very
valuable information about its molecular structure. This information is
gathered as follows:

1. The number of signals in the PMR spectrum tells us how many kinds’ protons in
different chemical environments are present in the structure under examinations.

2. The positions of signals tells us about the electronic environment of each kind of
proton.

3. The intensities of different signals tell us about the relative number of protons of
different kinds.

4. The splitting of signals tell us about the environments of the absorbing proton
with respect to the environments of the neighbouring protons.