VCE Professional Development Modern Analytical Techniques; IR, NMR

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VCE Professional DevelopmentModern Analytical
TechniquesIR, NMR MS.

• Dr Chris Thompson
• December 2007
• School of Chemistry
• Monash University

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Understanding Identifying Molecular Structure

• Infrared Spectroscopy (IR)
• Nuclear Magnetic Resonance Spectroscopy (NMR)
• Mass Spectrometry (MS)
• Atomic Absorption Spectroscopy (AAS)
• Ultraviolet/Visible Spectroscopy (UV/Vis)

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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?
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Understanding Identifying Molecular Structure
IR Spectroscopy
1
1/2
(k/??
n??
2?
n???frequency
????reduced mass
k force constant
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Understanding Identifying Molecular Structure
IR Spectroscopy
Several Force Constants
Molecule k / aJÅ-2
F2 (F-F) 4.45
O2 (OO) 11.41
N2 (NN) 22.41
Note IR spectra are typically presented in units
called wavenumber, or more correctly, reciprocal
centimetres (cm-1). Increasing wavenumber
corresponds to increasing frequency.
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Understanding Identifying Molecular Structure

• IR Spectroscopy

The IR Spectrum of Ethanol
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Understanding Identifying Molecular Structure

• IR Spectroscopy

The IR Spectrum of Ethanol Tabulating IR data
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
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Understanding Identifying Molecular Structure

• IR Spectroscopy

Identifying Functional Groups
C
H
C
H
C
H
C
H
C
C
O
H
C
H
O
H
C
H
C
O
C
C
C
C
C
H
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Understanding Identifying Molecular Structure

• IR Spectroscopy

Identifying Functional Groups
N
H
O
C
C
N
H
O
C
C
C
N
O
C
O
O
R
G
O
R
R
Note Conjugation in ANY of these systems results
in a lowering of the carbonyl stretching
frequency!
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Understanding Identifying Molecular Structure

• IR Spectroscopy

The origin of broad -OH and -NH bands.
Hydrogen bonding results in lower electron
density at each oxygen, thus lowering the force
constant, k, thus lowering ( broadening) the
frequency for the mode.
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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 C3H6O. a) Identify which is an
alcohol and which is a ketone. b) Propose
molecular structures for these two molecules!
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Understanding Identifying Molecular Structure

• IR Spectroscopy

Sample Questions.
Q. The three IR spectra on the right correspond
to three different molecules all with a C3 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
4000
cm-1
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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. 1H, mI ½)
• 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.

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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.

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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.

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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 (1H) in alkanes compared to
  alkenes.

• These differences manifest in changes to the
  chemical shift.

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Understanding Identifying Molecular Structure

• NMR Spectroscopy

1H Proton NMR Spectroscopy - Chemical Shifts

• The most widely used NMR format is utilising 1H.
• 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).
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Understanding Identifying Molecular Structure

• NMR Spectroscopy

1H Proton NMR Spectroscopy - Chemical Shifts
Functional Group Functional Group Chemical Shift Functional Group 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 -NH2 0.5-3.0
Ether -OCH3 3.9 Aromatic 6.0-9.0
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Understanding Identifying Molecular Structure

• NMR Spectroscopy

1H Proton NMR Spectroscopy - Chemical Shifts
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Understanding Identifying Molecular Structure

• NMR Spectroscopy

1H Proton NMR Spectroscopy - Sample Spectra
Ethanol
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Understanding Identifying Molecular Structure

• NMR Spectroscopy

Simple Spin Coupling - "J Splitting"
Arises through the coupling of nuclei spin (1H
mI ½) with the spin a neighbouring bonding
electron, which then couples to another
neighbouring electron, and so on, finally
coupling with another nearby nucleus (1H).
Electrons also have spin - ms½
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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 2J, 3J, 4J - depending on how many
  bonds (2, 3, 4 ) the coupling occurs through.
• Basic splitting rule for I ½ nuclei of
  peaks n1 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!

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Understanding Identifying Molecular Structure

• NMR Spectroscopy

1H Proton NMR Spectroscopy - Sample Spectra
Ethanol
3J Coupling n1 triplet
3J Coupling n1 quartet
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Understanding Identifying Molecular Structure

• NMR Spectroscopy

1H NMR - Sample Spectra CH3CHClCOOH
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Understanding Identifying Molecular Structure

• NMR Spectroscopy

Sample Question
Q. How could 1H NMR be used to distinguish
between the two following isomers?
H
C
1-nitropropane
2-nitropropane
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Understanding Identifying Molecular Structure

• NMR Spectroscopy

Sample Question
Q. How could 1H NMR be used to distinguish
between the two following isomers?
1-nitropropane
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Understanding Identifying Molecular Structure

• NMR Spectroscopy

Sample Question
Q. How could 1H NMR be used to distinguish
between the two following isomers?
H
C
2-nitropropane
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Understanding Identifying Molecular Structure

• NMR Spectroscopy

Sample Question
The three spectra on the right show the C6
hydrocarbons hexane, 1-hexene, 1-hexyne. Whi
ch spectrum belongs to which? Which of these
spectra is the only one to exhibit a singlet?
0
2
4
6
8
10
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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

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Understanding Identifying Molecular Structure

• Mass Spectrometry

Basic Principle

• 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!

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Understanding Identifying Molecular Structure

• Mass Spectrometry

The Components of a Mass Spectrometer

1. Ion Source
2. Analyser
3. Detector
4. Data Acquisition

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Understanding Identifying Molecular Structure

• Mass Spectrometry

The Components of a Mass Spectrometer
1. Ion Source
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)
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Understanding Identifying Molecular Structure

• Mass Spectrometry

The Components of a Mass Spectrometer
2. Analyser
a) Magnetic deflection
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Understanding Identifying Molecular Structure

• Mass Spectrometry

The Components of a Mass Spectrometer
2. Analyser
b) Time-of flight (TOFMS)
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Understanding Identifying Molecular Structure

• Mass Spectrometry

The Components of a Mass Spectrometer
2. Analyser
c) RF fields (ie quadrupoles)
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Understanding Identifying Molecular Structure

• Mass Spectrometry

The Components of a Mass Spectrometer
3. Detector
Faraday Cup
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Understanding Identifying Molecular Structure

• Mass Spectrometry

The Components of a Mass Spectrometer
3. Detector
Micro-channel plates
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Understanding Identifying Molecular Structure

• Mass Spectrometry

What sort of information can we get from MS?

• Molecular Mass
• Molecular Structure (fragmentation)
• Elemental composition (ICP-MS)
• Not discussed in this presentation.

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Understanding Identifying Molecular Structure

• Mass Spectrometry

What sort of information can we get from MS?

• 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.

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Understanding Identifying Molecular Structure

• Mass Spectrometry

What sort of information can we get from MS?

• 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 (CnH2n).

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Understanding Identifying Molecular Structure

• Mass Spectrometry

What sort of information can we get from MS?

1. Molecular Mass - Example Problem.

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Understanding Identifying Molecular Structure

• Mass Spectrometry

What sort of information can we get from MS?

• 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
• ? Malkene 84, ie. 84 n 12 2n 1
• n 84/(122) n 6
• ? The alkene is C6H12 - hexene.
• But is it 1-hexene, 2-hexene or 3-hexene?!?!?!?

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Understanding Identifying Molecular Structure

• Mass Spectrometry

What sort of information can we get from MS?
2. Molecular Structure - Fragmentation
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Understanding Identifying Molecular Structure

• Mass Spectrometry

What sort of information can we get from MS?

• 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!

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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!

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Understanding Identifying Molecular Structure

• Mass Spectrometry

Hyphenated techniques GC-MS
GC (Gas Chromatograph)
Excellent in separation and quantitation Poor in
identification
MS (Mass Spectrometer)
Excellent in identification and
quantitation Poor in separation
GC-MS
Excellent in separation, identification and
quantitation!
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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/soun
ds/GC-MS.mov http//www.shsu.edu/7Echm_tgc/sounds
/gcms.mov http//www.shsu.edu/7Echm_tgc/sounds/SI
M.mov
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• Now go forth and train our VCE students to be
  spectroscopy specialists!