Spectroscopy of Organic Compounds Prepared By Dr. Khalid Ahmad
Shadid Islamic University in Madinah Department of Chemistry
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The Identification of Organic Compounds
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Methods in General Use
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Spectroscopy The study of interaction of spectrum of light with
a substance to be analysed, for its identification (i.e qualitative
analysis) as well as determination of its amount (i.e quantitative
analysis). The Absorption of Electromagnetic Radiation and the use
of the Resulting Absorption Spectra to Study the Structure of
Organic Molecules.
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Structural Features we can address Spectroscopically Molecular
weight Chemical Formula Functional groups Skeletal Connectivity,
structural isomers Spatial-geometric arrangements, stereoisomerism,
symmetry Presence and location of chromophores Chirality issues
Some of these are more central than others. Sometimes we can stop
when the answer is fit to purpose.
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Techniques we will study in this Course NMR--looks at atoms by
means of their nuclei. Connectivity pathways, spatial arrangements
of atoms and 1:1 correspondence between signals and atoms Mass
Spec--measures molecular weight, most fundamentally useful for
unknowns. Controlable fragmentation can distinguish among rival
possibilities IR -Vibrations characteristic of bonds, particulary
for functional group identification. Excellent fingerprint
UV--reports on conjugation and multiple bonds.
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Limitations Can we ever achieve a fully secure structure?
Harrisonin Heterocycles 1976, 5, 485. J. Nat. Prod. 1997, 60,
822
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Limitations Can we ever achieve a fully secure structure? J.
Nat. Prod. 2007, 70, 412. J. Am. Chem. Soc. 2008, 130, 804
(+)-Neopeltolide
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Molecular Orbitals Molecular orbitals (MOs) are mathematical
equations that describe the regions in a molecule where there is a
high probability of finding electrons Molecular orbitals (MOs) are
essentially combinations of atomic orbitals two types exist,
bonding and antibonding orbitals Molecular orbitals (MOs) are built
up (Aufbau principle) in the same way as atomic orbitals The
following topic will help you to understand bonding
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Sigma and pi bonds: Types of Molecular Orbitals There are three
important types of molecular orbitals sigma pi n Each of these
types of orbitals will be discussed further...
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Sigma Bonds Pi Bonds 1s-2p 2p-2p symmetric to rotation about
internuclear axis not symmetric Sigma and Pi Bonds END-TO-END
OVERLAP SIDE-TO-SIDE OVERLAP
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Pi ( ) Bonds In a multiple bond, the first bond is a sigma (
bond and the second and third bonds are pi ( bonds. Pi bonds are
formed differently than sigma bonds. Non-Bonded Pairs : n.. :
n
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Visualizing MOs The hydrogen molecule Antibonding MO = region
of diminished electron density Bonding MO = enhanced region of
electron density
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MOs for the 2p Electrons The two p x orbitals combine to form
sigma bonding and antibonding MOs. The two p y orbitals and the two
p z orbitals give pi bonding and antibonding MOs.
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Molecular Orbital Diagram Bonding MOs s AOs = MOs p AOs = MOs
Antibonding MOs = higher energy and MOs
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MO diagram for He 2 + and He 2 Energy MO of He + * 1s 1s AO of
He + 1s MO of He 2 AO of He 1s AO of He 1s * 1s 1s Energy He 2 +
bond order = 1/2 He 2 bond order = 0 AO of He 1s He 2 does not
exist!
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The Electromagnetic Spectrum According to quantum mechanics,
electromagnetic radiation has a dual and seemingly contradictory
nature. Electromagnetic radiation can be described as a wave
occurring simultaneously in electrical and magnetic fields. It can
also be described as if it consisted of particles called quanta or
photons.
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The Electromagnetic Spectrum A wave is usually described in
terms of its wavelength () or its frequency (). A simple wave is
shown in Figure The distance between consecutive crests (or
troughs) is the wavelength. The number of full cycles of the wave
that pass a given point each second, as the wave moves through
space, is called the frequency and is measured in cycles per second
(cps), or hertz (Hz).
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Photon a particle of light. Electromagnetic radiation ALL
light. Visible AND invisible visible light, x-rays, gamma rays,
radio waves, microwaves, ultraviolet rays, infrared.
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All electromagnetic radiation travels through a vacuum at the
same velocity. This velocity (), called the velocity of light, is
2.99792458 x 10 8 s -1 and relates to wavelength and frequency as c
= The energy of a quantum of electromagnetic energy is directly
related to its frequency: E= h Where h = Plancks constant, 6.63 x
10 -34 J s, = frequency (Hz) The higher the frequency () of
radiation, the greater is its energy. Since =c/, the energy of
electromagnetic radiation is inversely proportional to its
wavelength: E= hc/ where c = velocity of light The shorter the
wavelength () of radiation, the greater is its energy. The
Electromagnetic Spectrum
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Types of Spectroscopy Different regions of the electromagnetic
spectrum are used to probe different aspects of molecular
structure
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Electromagnetic Spectrum When UV-visible spectra interacts with
substance, absorption of light by substance causes the energy
content of the molecules (or atoms) to increase. The total
potential energy of a molecule generally is represented as the sum
of its electronic, vibrational, and rotational energies: E total =
E electronic + E vibrational + E rotational The amount of energy a
molecule possesses in each form is not a continuum but a series of
discrete levels or states. The differences in energy among the
different states are in the order: E electronic > E vibrational
> E rotational
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Electromagnetic spectrum
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UV-VIS spectrophotometer
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UVVis Spectrophotometers A UVVis spectrophotometer measures the
amount of light absorbed by a sample at each wavelength of the UV
and visible regions of the electromagnetic spectrum. log(I 0 /I) =
A, nm 200700 I0I0 I0I0 I0I0 I0I0 I
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29 A.Instrumentation Two sources are required to scan the
entire UV-VIS band: Deuterium lamp covers the UV 200-330 Tungsten
lamp covers 330-700 As with the dispersive IR, the lamps illuminate
the entire band of UV or visible light; the monochromator (grating
or prism) gradually changes the small bands of radiation sent to
the beam splitter The beam splitter sends a separate band to a cell
containing the sample solution and a reference solution The
detector measures the difference between the transmitted light
through the sample (I) vs. the incident light (I 0 ) and sends this
information to the recorder UV-Vis Spectroscopy Instrumentation and
Spectra
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30 B.Instrumentation Sample Handling Solvents must be
transparent in the region to be observed; the wavelength where a
solvent is no longer transparent is referred to as the cutoff Since
spectra are only obtained up to 200 nm, solvents typically only
need to lack conjugated systems or carbonyls Common solvents and
cutoffs: acetonitrile 190 chloroform240 cyclohexane195
1,4-dioxane215 95% ethanol205 n-hexane201 methanol205 isooctane195
water190 UV-Vis Spectroscopy Instrumentation and Spectra
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Additionally solvents must preserve the fine structure (where
it is actually observed in UV!) where possible H-bonding further
complicates the effect of vibrational and rotational energy levels
on electronic transitions, dipole-dipole interacts less so The more
non-polar the solvent, the better (this is not always possible)
UV-Vis Spectroscopy Instrumentation and Spectra
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C.The Spectrum 1.The x-axis of the spectrum is in wavelength;
200-350 nm for UV, 200-700 for UV-VIS determinations 2.Due to the
lack of any fine structure, spectra are rarely shown in their raw
form, rather, the peak maxima are simply reported as a numerical
list of lamda max values or max max = 206 nm 252 317 376
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The y-axis of the spectrum is in absorbance, A From the
spectrometers point of view, absorbance is the inverse of
transmittance: A = log 10 (I 0 /I) From an experimental point of
view, three other considerations must be made: i.a longer path
length, l through the sample will cause more UV light to be
absorbed linear effect ii.the greater the concentration, c of the
sample, the more UV light will be absorbed linear effect iii.some
electronic transitions are more effective at the absorption of
photon than others molar absorptivity, this may vary by orders of
magnitude UV-Vis Spectroscopy Instrumentation and Spectra C.The
Spectrum
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Sample containers, usually called cells or cuvettes must have
windows that are transparent in the spectral region of interest.
There are few types of cuvettes: - quartz or fused silica -
silicate glass - crystalline sodium chloride quartz or fused silica
- required for UV and may be used in visible region silicate glass
- cheaper compared to quartz. Used in UV crystalline sodium
chloride - used in IR cuvette 34 UV-Vis Spectroscopy Sample Holder
cuvette
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REGIONSOURCESAMPLE HOLDER DETECTOR UltravioletDeuterium
lampQuartz/fused silica Phototube, PM tube, diode array
VisibleTungsten lampGlass/quartzPhototube, PM tube, diode array
InfraredNernst glower (rare earth oxides or silicon carbide
glowers) Salt crystals e.g. crystalline sodium chloride
Thermocouples, bolometers Types of source, sample holder and
detector for various EM region 35
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Beers law e.g. 2,5-Dimethyl-2,4-hexadiene max (methanol) 242.5
nm ( = 13,100) 2014 by John Wiley & Sons, Inc. All rights
reserved. Example: UV absorption spectrum of
2,5-dimethyl-2,4-hexadiene in methanol at a concentration of 5.95 x
10 -5 M in a 1.0 cm A=absorbance =molar absorptivity
c=concentration =path length A= x c x A c x or =
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Transmittance I0I0 I b
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Path length / cm 00.20.40.60.81.0 %T 100502512.56.253.125
Absorbance 00.30.60.91.21.5
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External Standard and the Calibration Curve
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QUANTIZED MO ENERGEY LEVELS FOUND IN ORGANIC MOLECULES