VCE Professional Development

Modern Analytical Techniques;

IR, NMR & MS.
Dr Chris Thompson
December 2007
School of Chemistry
Monash University
Understanding & Identifying
Molecular Structure
Infrared Spectroscopy (IR)
Nuclear Magnetic Resonance Spectroscopy
(NMR)
Mass Spectrometry (MS)
Atomic Absorption Spectroscopy (AAS)
Ultraviolet/Visible Spectroscopy (UV/Vis)
Understanding & Identifying Molecular Structure
IR Spectroscopy
Ball and stick figure of an
ethanol molecule. But exactly
what is the ball, and for that
matter, what is the stick? An
atom doesnt really look like
a ball, nor does a chemical
bond look like a stick, right?
n
1
2
(k/
1/2
n frequency
reduced mass
k = force constant
Understanding & Identifying Molecular Structure
IR Spectroscopy
n
1
2
(k/
1/2
Molecule k / aJ
-2

F
2
(FF) 4.45
O
2
(O=O) 11.41
N
2
(NN) 22.41
Understanding & Identifying Molecular Structure
IR Spectroscopy
Several Force Constants
Note: IR spectra are typically presented in units called
wavenumber, or more correctly, reciprocal centimetres (cm
-1
).
Increasing wavenumber corresponds to increasing frequency.
OH stretch
CH stretch
CH bend
CO stretch
OH bend CC
stretch
Understanding & Identifying Molecular Structure
IR Spectroscopy
The IR Spectrum of Ethanol
Wavenumber / cm
-1
Strength Vibrational mode
900 w C-C stretch
1080 s C-O stretch
1260 m O-H bend
1400 m C-H bend
2800-3000 s C-H stretch
3650 m O-H stretch
Understanding & Identifying Molecular Structure
IR Spectroscopy
The IR Spectrum of Ethanol;
Tabulating IR data
Understanding & Identifying Molecular Structure
IR Spectroscopy
Identifying Functional Groups
C H s t r e t c h
A L K A N E S
~ 2 8 5 0 - 2 9 5 0 c m
- 1
C H b e n d ~ 1 3 5 0 - 1 4 5 0 c m
- 1
C H
2
r o c k ~ 7 2 0 c m
- 1
C H s t r e t c h
A L K E N E S
~ 3 0 0 0 - 3 1 0 0 c m
- 1
C H b e n d ~ 8 0 0 - 1 0 0 0 c m
- 1
C s t r e t c h ~ 1 6 0 0 - 1 7 0 0 c m
- 1
C
C H s t r e t c h
A L K Y N E S
~ 3 2 5 0 - 3 3 5 0 c m
- 1
C H b e n d ~ 6 3 0 c m
- 1
C s t r e t c h ~ 2 1 0 0 c m
- 1
C
O H s t r e t c h
A L C O H O L S
~ 3 2 0 0 - 3 6 5 0 c m
- 1
O H b e n d ~ 1 3 3 0 - 1 4 2 0 c m
- 1
C s t r e t c h ~ 1 0 0 0 - 1 2 6 0 c m
- 1
O
C C s t r e t c h
A R O M A T I C S
~ 1 6 0 0 & 1 4 0 0 - 1 5 0 0 c m
- 1
C H s t r e c t h ~ 3 0 0 0 c m
- 1
Understanding & Identifying Molecular Structure
IR Spectroscopy
Identifying Functional Groups
O C s y m . s t r e t c h
E T H E R S
~ 1 0 5 0 c m
- 1
O C a s y m . s t r e t c h ~ 1 2 5 0 c m
- 1
M O L E C U L E S W I T H C A R B O N Y L G R O U P S ( C = O )
N H s t r e t c h
A M I N E S
~ 3 2 5 0 - 3 4 5 0 c m
- 1
N H b e n d ~ 1 6 0 0 - 1 6 5 0 c m
- 1
C s t r e t c h ~ 1 0 0 0 - 1 2 5 0 c m
- 1
N
C
C
C
O
R G
F u n c t i o n a l g r o u p
K e t o n e
A l d e h y d e
C a r b o x y l i c A c i d
A c i d C h l o r i d e
A c i d F l u o r i d e
- G
- H
- O H
- C l
- F
- R
~ 1 7 2 0 - 1 7 4 0
~ 1 7 5 0 - 1 7 7 0
~ 1 7 7 5 - 1 8 1 5
~ 1 8 7 0
~ 1 6 8 0 - 1 7 2 0
c m
- 1
F u n c t i o n a l g r o u p
E s t e r / L a c t o n e
A m i d e / L a c t a m
- G
- N R
- O R
~ 1 6 5 0 - 1 7 0 0
~ 1 7 3 5 - 1 7 5 0
c m
- 1
O
O R
O
R
~ 1 7 5 0 & 1 8 1 5
Note: Conjugation in ANY of these systems results in a lowering of the
carbonyl stretching frequency!
Understanding & Identifying Molecular Structure
IR Spectroscopy
The origin of broad -OH and -NH bands.
gas
liquid
Hydrogen bonding results in lower
electron density at each oxygen,
thus lowering the force constant, k,
thus lowering (& broadening) the
frequency for the mode.
H
3
C
CH
2
O
H
H
O
CH
2
H
3
C
H
O
CH
2
H
3
C
H
O
CH
2
H
3
C
H
O
CH
2
H
3
C
H
O
CH
2
H
3
C
Understanding & Identifying Molecular Structure
IR Spectroscopy
Sample Questions.
Q. The two IR spectra on the
right correspond to two
different molecules sharing
the same molecular formula;
C
3
H
6
O.
a) Identify which is an
alcohol and which is a ketone.
b) Propose molecular
structures for these two
molecules!

C
O
C H
3
H
3
C
H
C
C
H
2
H
2
C
O H
Understanding & Identifying Molecular Structure
IR Spectroscopy
Sample Questions.
Q. The three IR spectra on the right
correspond to three different
molecules all with a C
3
carbon chain
but different degrees of unsaturation.
a) Identify which of these is propane,
propene and propyne.
b) Label each peak with the relevant
vibrational mode.
Satisfy yourself that some features
unambiguously identify some kinds
of functional groups
2000 3000 1000
cm
-1

4000
Understanding & Identifying Molecular Structure
NMR Spectroscopy
Basic Principle
Technique applying exclusively to nuclei with spin. I 0
In a magnetic field, these nuclei become non-degenerate
(differ in energy) due to differences in spin. (eg.
1
H, m
I
= )
Electromagnetic radiation, at frequencies corresponding to
the difference in energy, can resonate with some nuclei and it is
absorbed.
'Shielding' from the local chemical environment means
resonance can occur across a variety of frequencies.
Understanding & Identifying Molecular Structure
NMR Spectroscopy
Basic Principle
Therefore, these frequencies have embedded information
regarding the local chemical environment - ie. the functional
groups.
These differences are measured on a scale of chemical shift.
NMR has subsequently become one of the most powerful
techniques for determining molecular structure, now extending
to species as large as proteins.
Understanding & Identifying Molecular Structure
NMR Spectroscopy
Units - Chemical Shift (ppm)
The units for chemical shift usually appear as ppm, typically in the
range 0-10. But what does this mean?
The chemical shift is the difference in the magnitude of the precession
frequency between two nuclei with different spin "" (Hz) in a some
magnetic field "B (MHz).
Since this is dependant on the strength of the magnetic field, we often
express the chemical shift as the quotient;
B (Hz/MHz, thus ppm)
This allows us to compare chemical shift measured on different
instruments.
Understanding & Identifying Molecular Structure
NMR Spectroscopy
Shielding - What is it?
While nuclei with spin are perturbed by a magnetic field, the electrons
in the vicinity also serve to shield the nuclei to a degree.
Thus, the degree of perturbation is going to be different depending on
where the electrons are with respect to the nuclei.
For example there will be a difference between hydrogen atoms (
1
H)
in alkanes compared to alkenes.
These differences manifest in
changes to the chemical shift.
Understanding & Identifying Molecular Structure
NMR Spectroscopy
1
H Proton NMR Spectroscopy - Chemical Shifts
The most widely used NMR format is utilising
1
H.
The chemical shifts for protons with respect to different
functional groups are well known.
Note: Proton NMR is the underlying
principle for the now common medical
procedure of MRI (Magnetic Resonance
Imaging).
Understanding & Identifying Molecular Structure
NMR Spectroscopy
1
H Proton NMR Spectroscopy - Chemical Shifts
Functional Group Chemical
Shift
Functional Group Chemical
Shift
Name Structure ppm Name Structure ppm
Alkane 0-2.0 Ketone 2.0-3.0
Alkene 4.3-7.3 Aldehyde 9.0-10.0
Alkyne 2.0-3.0 Acid
-COOH
10-13.5
Alcohol
-OH
0.5-4.0* Amine
-NH
2

0.5-3.0
Ether
-OCH
3

3.9
Aromatic
6.0-9.0
C
O
RH
2
C CH
2
R
C O
R
H
Understanding & Identifying Molecular Structure
NMR Spectroscopy
1
H Proton NMR Spectroscopy - Chemical Shifts
Understanding & Identifying Molecular Structure
NMR Spectroscopy
1
H Proton NMR Spectroscopy - Sample Spectra; Ethanol
What are these
'multiplets'?
Understanding & Identifying Molecular Structure
NMR Spectroscopy
Simple Spin Coupling - "J Splitting"
Arises through the coupling
of nuclei spin (
1
H; m
I
= )
with the spin a neighbouring
bonding electron**, which
then couples to another
neighbouring electron, and so
on, finally coupling with
another nearby nucleus (
1
H).
**Electrons also have spin -
m
s
=
Understanding & Identifying Molecular Structure
NMR Spectroscopy
Simple Spin Coupling - "J Splitting"
Often colloquially called "J splitting as the derived coupling
constant is labelled J.
Labelled
2
J,
3
J,
4
J - depending on how many bonds (2, 3, 4 )
the coupling occurs through.
Basic splitting rule for I = nuclei; # of peaks = n+1 where n
is the number of neighbouring, equivalent nuclei.

In other words, the splitting is a clue as to the chemical
structure of the local environment!
Understanding & Identifying Molecular Structure
NMR Spectroscopy
1
H Proton NMR Spectroscopy - Sample Spectra; Ethanol
3
J Coupling; n+1 = triplet
3
J Coupling;
n+1 = quartet
Understanding & Identifying Molecular Structure
NMR Spectroscopy
1
H NMR - Sample Spectra; CH
3
CHClCOOH
3
J Coupling; n+1 = doublet
3
J Coupling; n+1 = quartet
Understanding & Identifying Molecular Structure
NMR Spectroscopy
Sample Question
Q. How could
1
H NMR be used to distinguish between the two
following isomers?
H
3
C
H
2
C
C
H
2
N O
2
H
3
C
C
C H
3
H N O
2
1-nitropropane
2-nitropropane
Understanding & Identifying Molecular Structure
NMR Spectroscopy
Sample Question
Q. How could
1
H NMR be used to distinguish between the two
following isomers?
H
3
C
H
2
C
C
H
2
N O
2
1-nitropropane
1.
1. Triplet @ ~1 ppm.
2.
2. Sextet @ ~2 ppm.
3.
3. Triplet @ ~4 ppm.
Understanding & Identifying Molecular Structure
NMR Spectroscopy
Sample Question
Q. How could
1
H NMR be used to distinguish between the two
following isomers?
H
3
C
C
C H
3
H N O
2
2-nitropropane
1.
1. Doublet @ ~2 ppm.
2.
2. Septet @ ~4 ppm.
3.
3. Doublet @ ~2 ppm.
Understanding & Identifying Molecular Structure
NMR Spectroscopy
Sample Question
0 2 4 6 8 10
The three spectra on the right show the
C
6
hydrocarbons;

hexane,
1-hexene,
1-hexyne.

Which spectrum belongs to which?
Which of these spectra is the only one to
exhibit a singlet?
Understanding & Identifying Molecular Structure
Mass Spectrometry
Discovery of isotopes
Determination of molecular weights
Characterization of new elements
Qualitative and quantitative analyses
Sequence identification (proteomics)
Stable isotope labeling and enrichment
Identification of trace elements, pollutants, and
drugs
Counter-terrorism, detection of chemical agents
Understanding & Identifying Molecular Structure
Mass Spectrometry
Molecules can be ionised via a number of different
methods, meaning they are either positively or negatively
charged.
Charged particles can be manipulated by the presence of
an electric or magnetic field.
This effect is dependant on several parameters including
the mass (m) and the charge (z) of the particle.
Mass spectrometers give us information about the
molecular mass and more!
Basic Principle
Understanding & Identifying Molecular Structure
Mass Spectrometry
1. Ion Source
2. Analyser
3. Detector
4. Data Acquisition
The Components of a Mass Spectrometer
Understanding & Identifying Molecular Structure
Mass Spectrometry
1. Ion Source
The Components of a Mass Spectrometer
Atmospheric Pressure Chemical Ionisation (APCI)
Chemical Ionisation (CI)
Electron Impact (EI)
Electrospray Ionisation (ESI)
Fast Atom Bombardment (FAB)
Field Desorption / Field Ionisation (FD/FI)
Matrix Assisted Laser Desorption Ionisation (MALDI)
Thermospray Ionisation (TSP)
Understanding & Identifying Molecular Structure
Mass Spectrometry
2. Analyser
The Components of a Mass Spectrometer
a) Magnetic deflection
Understanding & Identifying Molecular Structure
Mass Spectrometry
2. Analyser
The Components of a Mass Spectrometer
b) Time-of flight (TOFMS)

Understanding & Identifying Molecular Structure
Mass Spectrometry
2. Analyser
The Components of a Mass Spectrometer
c) RF fields (ie quadrupoles)
Understanding & Identifying Molecular Structure
Mass Spectrometry
3. Detector
The Components of a Mass Spectrometer
Faraday Cup
Understanding & Identifying Molecular Structure
Mass Spectrometry
3. Detector
The Components of a Mass Spectrometer
Micro-channel
plates
Understanding & Identifying Molecular Structure
Mass Spectrometry
1. Molecular Mass
2. Molecular Structure
(fragmentation)
3. Elemental composition
(ICP-MS)*
*Not discussed in this presentation.
What sort of information can we get from MS?
Understanding & Identifying Molecular Structure
Mass Spectrometry
1.Molecular Mass
* A molecule is ionised, preferably with a known charge.
* Charged particles (ions) experience a force when in the
presence of an electric or magnetic field.
* Using the appropriate algebraics of specific analysers, the
behaviour of the particle in the field can be used to
determine mass-to-charge ratio (m/z), thus indirectly the
molecular mass.
* The charge, z, is usually = 1.
What sort of information can we get from MS?
Understanding & Identifying Molecular Structure
Mass Spectrometry
1. Molecular Mass - Example Problem.
Q. IR & NMR data suggest an unknown molecule to be an
alkene, however the molecular formula is not known. How
can MS solve this problem?
A. The molecular mass can unambiguously be determined
using MS, which can in turn be used to determine (n) for
the molecular formula of the alkene (C
n
H
2n
).
What sort of information can we get from MS?
Understanding & Identifying Molecular Structure
Mass Spectrometry
1. Molecular Mass - Example Problem.
What sort of information can we get from MS?
C
n
H
2n
n = ?
84
57
41
27
69
Understanding & Identifying Molecular Structure
Mass Spectrometry
1. Molecular Mass - Example Problem.
* The molecular ion is almost always the peak with the
largest m/z value.
* (Remember, MS measures m/z, but usually z = 1.)
* So in this case, the molecular ion is 84
* M
alkene
= 84, ie. 84 = n 12 + 2n 1
n = 84/(12+2) n = 6
* The alkene is C
6
H
12
- hexene.
* But is it 1-hexene, 2-hexene or 3-hexene?!?!?!?

What sort of information can we get from MS?
Understanding & Identifying Molecular Structure
Mass Spectrometry
2. Molecular Structure - Fragmentation
What sort of information can we get from MS?
C
n
H
2n
n = ?
84
57
41
27
69
Understanding & Identifying Molecular Structure
Mass Spectrometry
2. Molecular Structure
- Fragmentation
- Subtle differences in
fragmentation patterns can be
explained by the fragmentation
mechanisms
- Of course NMR can also be
used to differentiate between
these structural isomers!

What sort of information can we get from MS?
Understanding & Identifying Molecular Structure
Mass Spectrometry
Hyphenated techniques; GC-MS
* GC-MS & LC-MS ARE high resolution separation
techniques, capable of detecting trace concentrations of
most compounds; drugs, explosives, herbicides &
pesticides, secondary metabolites
- No inherent identification ability
* Mass spectrometry is an identification technique capable
of producing a unique 'fingerprint for any given compound.
- Poor at compound separation
* IN UNISON, THESE TWO TECHNIQUES FORM AN
EXTREMELY POWERFUL FORENSIC TOOL!

Understanding & Identifying Molecular Structure
Mass Spectrometry
Hyphenated techniques; GC-MS
Excellent in separation and quantitation
Poor in identification
Excellent in identification and quantitation
Poor in separation
Excellent in separation, identification and quantitation!
MS (Mass Spectrometer)
GC (Gas Chromatograph)
Understanding & Identifying Molecular Structure
Mass Spectrometry
Online GC-MS Tutorial
Website:
http://www.shsu.edu/~chm_tgc/sounds/sound.html

Namely:
http://www.shsu.edu/%7Echm_tgc/sounds/GC-MS.mov
http://www.shsu.edu/%7Echm_tgc/sounds/gcms.mov
http://www.shsu.edu/%7Echm_tgc/sounds/SIM.mov
Now go forth and train our
VCE students to be
spectroscopy specialists!