school of chemistry spectroscopy workshop school of chemistry the queen’s university of belfast
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School of Chemistry
Spectroscopy Workshop
School of Chemistry
The Queen’s University of Belfast
School of Chemistry
Workshop Content
Spectroscopy overview
Ultra-violet/visible (UV-vis)
Infra-Red (IR)
Nuclear Magnetic Resonance (NMR)
Mass Spectrometry
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Spectroscopy
In spectroscopy, transitions between different energy levels within atoms and molecules are recorded and then used to give information on chemical structure.
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The range of energies that can be used for spectroscopy is very large and spans a large proportion of the electromagnetic spectrum.
VisibleX-Rays
Gamma Rays
UV IRRadio
Microwave
10- 11 10- 9 10- 7 10- 5 10- 3 10- 1 10 310
Wavelength (cm)
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In a typical experiment, the molecules or atoms start at lower energy and go to a higher energy level upon absorption of radiation of appropriate wavelength.
Ene
rgy
After
EBefore
Absorptio
n
Ene
rgy
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After
After
Before
Absorption can only occur when the energy of the radiation (calculated from the frequency or wavelength) matches the energy gap.
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rgy
After
If there are several different upper levels (and there usually are) then several transitions will be observed.
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For current purposes we look only at:
UV/visible ( highest energy)
Infra red (intermediate)
Radio frequency (lowest energy).
But in all cases :
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To record a spectrum, sweep through the appropriate range of energies and look for absorption at particular values.
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Absorption gives peaks, when these have been measured this gives the energy gaps within the sample. These can then be related to structure.
Interpretation depends on the energy range investigated.
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UV/visible Spectroscopy
Chemical compounds are coloured because they absorb visible light.
In general, even organic compounds that are colourless will absorb UV light.
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Absorption of visible light
Where has the energy that was within the photons gone to ?
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In UV/visible spectroscopy the energy of the absorbed photon is used is used to drive the molecule into an excited electronic state.
In the excitation the energy of the whole molecule increases.
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rgy
After
EBefore
Absorptio
n
Ene
rgy
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This overall change is typically due to promotion of a single electron from a lower to higher energy orbital. The energy of the transition depends on the gap between the two orbitals.
In organic compounds which have only single bonds between the atoms the excitation energy is very high- lies in deep UV.
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H
H
H
H
e.g. ethene
This excitation gives a dramatic decrease in bond order due to excitation from
Even if have a simple bond, the excitation from highest occupied to lowest unoccupied orbitals still lies in the UV.
a bonding to an anti-bonding orbital.
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If we have a highly conjugated molecule the energy separation between the orbitals is smaller.
Excitation of the electron thus has a proportionately smaller effect and requires less energy- energy gap may lie in the visible region.
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Again note that lowest energy transition may lie in visible.
But we can also excite to higher orbitals with sufficiently
energetic (UV) photons.
H
H
H
H
H
H
Orbitals of Butadiene
Bonding
Anti-bondingE
nerg
y
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With increasing conjugation, the decreasing energy gap is reflected by absorption at longer wavelengths.
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The structures of many coloured compounds show they are very extensively conjugated.
HOOCCOOH
trans-Crocetin
16,17-DimethoxyViolanthrone
O
OMe OMe
ON
NN
N
O
O H
H
NH2
Xanthopterin
beta-Carotene
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Substituents added to the compound may alter the energy of the orbitals which e- is excited from or to.
Auxochromes: substituents that alter the wavelength or intensity of the absorption due to the chromophore
ORANGE
O
O
NH2
PURPLE
O
O
NH2
OH
BLUE
O
O
NHCH3
NHCH3
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O
O
OH
O
O
O
HO O-
Changes in chemical composition can give rise to pronounced colour changes since this can dramatically alter the energies of the orbitals involved in the transitions e.g. pH indicators.
-2H+
Phenolphthalein
pinkcolourless
O
O
OH
O
O
O
HO O-
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N
N N
SO3-
CH3
CH3
N
N N+
SO3-
CH3
CH3
H
N
N N
SO3-
CH3
CH3
N
N N+
SO3-
CH3
CH3
H
Methyl orange
H+
red
orange-yellow
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Summary
Absorption of UV-vis radiation occurs via excitation of electrons from filled to unfilled orbitals i.e. they are electronic transitions.
Molecules have characteristic absorption spectra.
The absorption can lead to coloured materials.
pH Indicators use the change in colour between the acid and alkali forms of the molecules.
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IR Spectroscopy
Origin of the absorption
The spectrometer
The spectra
Organic compounds
Example problem
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Origin of IR absorptions
Atoms within a molecule are never still. They vibrate in a variety of ways (modes).
Atoms may be considered as weights connected by springs.
Each vibrational mode has its own resonant frequency.
symmetric stretch
asymmetric stretch
bending
CO2
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If the vibrational mode involves a change in molecular dipole moment, the vibration can be induced by absorption of a photon - it is ‘IR-active’
Appropriate energy for this is infra-red
symmetric stretch
asymmetric stretch
bending
no dipoleno dipole
change in dipole - IR active
change in dipole - IR active
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The IR spectrometer
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CO2 IR spectra
The bigger the change in dipole, the more intense the absorption
The symmetric stretch is not IR active (no change in dipole)
Wavenumber /cm-1
Stretching higher energy than bending
2800 2400 2000 1600 1200 800 4000
100
Tra
nsm
ittan
ce /%
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More complex:
IR spectra of organic compounds
20004000 3000 1500 1000
Wavenumber/cm-1
500Ethyl ethanoate (CH3COOCH2CH3)
C-O stretch
C=O bond
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But functional groups have characteristic frequencies
1000
Wavenumber / cm- 1
6501500200030004000
N H
C H
C OC Cl
O H(all types) C O
C C
C N
C C
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Four regions in the spectrum:
4000 3500 3000 2500 2000 1500 1000
O-HN-HC-Hstretching
C CC NX Y Zstretching
C CC OC N
stretchingN-Hbending
N O
other stretching, bending and combination bands:fingerprint region
Wavenumber / cm-1
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Example problem Identify two main functional groups present in the compound which gave this spectrum
(a) Explain why infrared radiation is absorbed by molecule HCl but not by molecules H2 and Cl2.(b) Explain what occurs in the HCl molecule when infrared radiation is absorbed.(c) The simplified infrared spectrum below is that of an organic compound.
(i) Identify two main functional groups on the spectrum.(ii) This compound has composition by mass C, 67.9%; H, 5.7%; N, 26.4%, and Mr of 53.
Suggest a structural formula for the compound.
4000 3600 3200 2800 2400 2000 1900 1800 1700 1600Wavenumber / cm-1
10
20
30
40
50
60
70
80
90
100
Tra
nsm
itta
nce
/ %
C-H CCCN?
C=CC=O?C=N?
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Combine this information with the following data to deduce its structure
C 67.9%H 5.7%N 26.4%
Mr 53
So, formula = C3H3N
Likely structure:
Cyanoethene
H
H
H
C N
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Summary
Absorption of IR can occur if a vibrational mode is associated with a change in dipole.
Functional groups have characteristic absorption frequencies.
In combination with other analytical data, the structure of an organic compound can often be deduced.
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NMR Spectroscopy
The Basis of NMR Spectroscopy
The Spectrometer
Chemical Shifts
Signal Intensity and Integration
Coupling Constants
Example Spectra
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Atomic nuclei behave like small bar magnets as a result of their charge and spin.
The Basis of NMR Spectroscopy
In the presence of an applied magnetic field the spin states have different energy and the magnetic moment can align with or against the applied field.
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The difference in energy between the two spin states is dependent on the external magnetic field strength.Irradiation of a sample with radio frequency energy corresponding to the spin state separation (E) will excite nuclei in the +½ state to the higher energy –½ state.
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The 1H NMR Experiment
For example, consider a water sample in a 2.3487 Texternal magnetic field irradiated by 100 MHz radiation. If the magnetic field is increase to 2.3488 T the waterprotons will at some point absorb rf energy (E) and aresonance signal will appear,
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Not all protons give resonance signals at the same field frequency. Electrons move in response to the applied field and generate a secondary magnetic field which opposes the applied field. The secondary field shields the nucleus from the applied field and nuclei in different environments resonate at different frequencies.
The Chemical Shift
The difference in resonance frequency is measured as a chemical shift, units
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Proton Chemical Shift Ranges
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The relative area of the absorption signals can providevaluable structural information. The area under a peak is proportional to the number ofa given type of nuclei in the molecule.
Signal Intensity
O
CH3
H3C
H H
MEK
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The keto-enol equilibrium ratio of 2,4-pentandione candetermined by 1H NMR spectroscopy
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Spin-Spin Coupling
The applied magnetic field experienced by a proton Ha will be modified by the local field produced by its neighbouring Hb
Ha modifies the field at Hb by aligning with or against the applied field and and gives 2 resonant frequencies for Hb (doublet)
Similarly Hb modifies the field at Ha in 3 different ways (triplet)
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Splitting pattern can provide valuable structural information Chemically equivalent protons act as a group and a peak due to n adjacent protons is split into n+1 lines, with a coupling constant J
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1H NMR Spectrum of Ethyl Acetate
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1H NMR Spectrum of 1,3-Dichloropropane
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Example ProblemGiven the formula, deduce what you can about the structure
Integration corresponds to 2H : 2H : 3H A triplet must correspond to 2 near neighbour protons
A sextet corresponds to 5 near neighbour protons Therefore CH2, CH2 and CH3 groups are present
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Solution
Connectivity can be deduced to be NO2
H
H
HH
H H
H
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NMR spectroscopy involves irradiating a sample with radio frequency radiation
Protons in different chemical environments have different chemical shifts
Protons in different environments can couple to each other with a coupling constant J
The combination of chemical shifts and coupling constants provides valuable structural information
Summary
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Mass Spectrometry
The basic principles
Applications
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What is a mass spectrometer ?
A mass spectrometer is an instrument which produces charged particles (ions) from chemical substances under analysis.
It then uses magnetic and/or electric fields to separate those ions and to measure their mass.
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Mass Spectrometer Schematic
IonSource
Mass Analyzer
IonDetector
Inlet DataSystem
VacuumPumps
SampleIntroduction
DataOutput
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Ion Generation
~70 Volts
+
_
+_
e- e-e-
++ ++++
_
Electron Collector (Trap)
Repeller
ExtractionPlate
Filament
To Analyzer
Inlet
Electrons
NeutralMolecules Positive Ions
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The magnetic field exerts a force on these fast-moving ions and causes them to move in a
circular path, the radius of which is dependent upon their mass to charge ratio
(m/z) and speed.
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Magnetic Mass Separation
ion not detectedm/z too large
ion not detected m/z too small
Correct m/z ratioion detected
IonSource
Detector
S
N
Electromagnet
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Applications
- Chemical analysis (Chemical Research)
- Environmental analysis - Analysis of petroleum products
- Trace metals
- Biological materials
Mass spectrometers are used for all kinds of chemical analyses:
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How is mass spectral information used?
If a beam of electrons is directed through water vapour in the source of a mass spectrometer, some of the electrons will hit water molecules and knock off an electron, producing charged ions from the water:
H2O + 1 (fast) electron [H2O]+ + 2 electrons
Let us use water (H2O) as an example.
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Electron impact on a water molecule
Some of the collisions between water molecules and electrons will be so hard that the water molecules will be broken into fragments. For water, those fragments will be [OH]+, O+, and H+ with the following masses:
1 = H+
16 = O+
17 = [OH]+
18 = [H2O]+
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Mass Spectrum of Water
RelativeAbundance
Mass(mass-to-charge ratio)
1
17
16
18 [H2O]+
[OH]+
O+H+
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Examples
Alcohols
Pentan-3-ol
CH3CH2
OH
H
CH2CH3
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CH3CH2
OH
H
CH2CH3
59
m/z(parent ion) = 88
An alcohol's molecular ion is small or non-existent. Cleavage of the C-C bond next to the oxygen usually occurs. A loss of H2O may occur as in the spectra below.
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Alkanes
Hexane
CH3 CH2
CH2
CH2
CH2
CH3
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m/z(parent ion) = 86
CH3 CH2
CH2
CH2
CH2
CH3
15 43 71
5729
Molecular ion peaks are present, possibly with low intensity.The fragmentation pattern contains clusters of peaks 14 mass units apart (which represent loss of (CH2)n CH3).
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Aromatics
Naphthalene
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Molecular ion peaks are strong due to the stable structure.
10080
60
40
200
mass / charge (m/z)
rela
tiv
e a
bu
nd
an
ce128
100806040200 120 140
m/z(parent ion) = 128
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Esters
Ethylethanoate
CH3
O
O CH2CH3
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Fragments appear due to bond cleavage next to C=O (alkoxy group loss, -OR) and hydrogen rearrangements.
10080
60
40
200
100806040200mass / charge (m/z)
rela
tiv
e a
bu
nd
an
ce
-OCH2CH3
-C2H3
43
45 8861
CH3
O
O CH2CH3
61
43 45
HH
m/z(parent ion) = 88
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Halo-organics
Chloroethene
H
H
H
Cl
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Isotopes are shown by mass spectrometry
The natural abundance of each isotope gives characteristic fragmentation
e.g. 35Cl:37Cl is in a 3:1 ratio therefore the peaks containing Cl are in a 3:1 ratio and separated by 2 mass units
27
m/z(parent ion) = 62/64
H
H
H
Cl 64
62
3537
100
80
60
40
20
030 40 50 60
H2C = CH-Cl27
26
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Mass spectrometry involves the ionisation of molecules and atoms.
The mass spectrometer measures the mass to charge ratio.
On ionisation the molecule can break up giving fragments of different m/z ratios .
Each molecule has a characteristic fragmentation pattern which can be used to identify the molecule.
Summary