Topic 11: Measurement and data processing

Nature of science: Making quantitative measurements with replicates to ensure reliability-precision,

accuracy, systematic, and random errors must be interpreted through replication. (3.2, 3.4)

11.1 Uncertainties and errors in measurement and results

Understandings

Essential idea: All measurement has a limit of precision and accuracy, and this must be taken into
account when evaluating experimental results.

Qualitative data includes all non-numerical information obtained from observations not from
measurement

Quantitative data are obtained from measurements, and are always associated with random
errors/uncertainties, determined by the apparatus, and by human limitations such as reaction times.

Propagation of random errors in data processing shows the impact of the uncertainties on the final
result.

Experimental design and procedure usually lead to systematic errors in measurement, which cause a
deviation in a particular direction.

Repeat trials and measurements will reduce random errors, but not systematic errors.

Applications and skills

Distinction between random errors and systematic errors.

Record uncertainties in all measurements as a range (±) to an appropriate precision.

Discussion of ways to reduce uncertainties in an experiment.

Propagation of uncertainties in processed data, including the use of percentage uncertainties.

Discussion of systematic errors in all experimental work, their impact on the results and how they
can be reduced.

Estimation of whether a particular source of error is likely to have a major or minor effect on the
final result.

Calculation of percentage error when the experimental result can be compared with a theoretical or
accepted result.

Distinction between accuracy and precision in evaluating results.

Guidance

The number of significant figures in a result is based on the figures given in the data. When adding or
subtracting, the final answer should be given to the least number of decimal places. When
multiplying or dividing the final answer is given to the least number of significant figures.

Note that the data value must be recorded to the same precision as the random error.

SI units should be used throughout the programme

International-mindedness
As a result of collaboration between seven international organizations, including IUPAC, the
International Standards Organization (ISO) published the Guide to the Expression of Uncertainty in
Measurement in 1995. This has been widely adopted in most countries and has been translated into
several languages.
Theory of knowledge
Science has been described as a self-correcting and communal public endeavour.
To what extent do these characteristics also apply to the other areas of knowledge?

Utilization:
Crash of the Mars Climate Orbiter spacecraft.
Original results from CERN regarding the speed of neutrinos were flawed.
Syllabus and cross-curricular links
Option D.1-drug trials
Aims
Aim 6: The distinction and different roles of Class A and Class B glassware could be explored.
Aim 8: Consider the moral obligations of scientists to communicate the full extent of their data,
including experimental uncertainties. The "cold fusion" case of Fleischmann and Pons in the 1990s is
an example of when this was not fulfilled.

11.2 Graphical techniques

Understandings

Essential idea: Graphs are a visual representation of trends in data.

Graphical techniques are an effective means of communicating the effect of an independent variable
on a dependent variable, and can lead to determination of physical quantities.

Sketched graphs have labelled but unscaled axes, and are used to show qualitative trends, such as
variables that are proportional or inversely proportional.

Drawn graphs have labelled and scaled axes, and are used in quantitative measurements

Applications and skills

Drawing graphs of experimental results including the correct choice of axes and scale.

Interpretation of graphs in terms of the relationships of dependent and independent variables.

Production and interpretation of best-fit lines or curves through data points, including an
assessment of when it can and cannot be considered as a linear function.

Calculation of quantities from graphs by measuring slope (gradient) and intercept, including
appropriate units.

International-mindedness
Charts and graphs, which largely transcend language barriers, can facilitate communication between
scientists worldwide.
Theory of knowledge
Graphs are a visual representation of data, and so use sense perception as a way of knowing.
To what extent does their interpretation also rely on the other ways of knowing, such as language
and reason?
Utilization:
Graphical representations of data are widely used in diverse areas such as population, finance and
climate modelling.
Interpretation of these statistical trends can often lead to predictions, and so underpins the setting
of government policies in many areas such as health and education.
Syllabus and cross-curricular links
Topic 1.3-gas volume, temperature, pressure graphs
Topic 6.1-Maxwell-Boltzmann frequency distribution; concentration-time and rate-concentration
graphs
Topic 16.2-Arrhenius plot to determine activation energy
Topic 18.3-titration curves
Option B.7-enzyme kinetics
Option C.5-greenhouse effect; carbon dioxide concentration and global temperatures
Option C.7-first order/decay graph

Aims
Aim 7: Graph-plotting software may be used, including the use of spreadsheets and the derivation of
best-fit lines and gradients.

I
11.3 Spectroscopic identification of organic compounds
Nature of science: Improvements in instrumentation-mass spectrometry, proton nuclear magnetic
resonance and infrared spectroscopy have made identification and structural determination of
compounds routine. (1.8) Models are developed to explain certain phenomena that may not be
observable-for example, spectra are based on the bond vibration model. (1.10)
Understandings

Essential idea: Analytical techniques can be used to determine the structure of a compound, analyse
the composition of a substance or determine the purity of a compound. Spectroscopic techniques
are used in the structural identification of organic and inorganic compounds.

The degree of unsaturation or index of hydrogen deficiency (IHD) can be used to determine from a
molecular formula the number of rings or multiple bonds in a molecule

Mass spectrometry (MS), proton nuclear magnetic resonance spectroscopy (1H NMR) and infrared
spectroscopy (IR) are techniques that can be used to help identify compounds and to determine
their structure.

Applications and skills

Determination of the IHD from a molecular formula.

Deduction of information about the structural features of a compound from percentage composition
data, MS, 1H NMR or IR.
Guidance

The electromagnetic spectrum (EMS) is given in the data booklet in section 3. The regions employed
for each technique should be understood.

The operating principles are not required for any of these methods.

The data booklet contains characteristic ranges for IR absorptions (section 26), 1H NMR data (section
27) and specific MS fragments (section 28). For 1H NMR, only the ability to deduce the number of
different hydrogen (proton) environments and the relative numbers of hydrogen atoms in each
environment is required. Integration traces should be covered but splitting patterns are not required.

International-mindedness
Monitoring and analysis of toxins and xenobiotics in the environment is a continuous endeavour that
involves collaboration between scientists in different countries.
Theory of knowledge
Electromagnetic waves can transmit information beyond that of our sense perceptions. What are
the limitations of sense perception as a way of knowing?
Utilization:
IR spectroscopy is used in heat sensors and remote sensing in physics.
Protons in water molecules within human cells can be detected by magnetic resonance imaging
(MRI), giving a three-dimensional view of organs in the human body.
Syllabus and cross-curricular links
Topic 1.2-determination of the empirical formula from percentage composition data or from other
experimental data and determination of the molecular formula from both the empirical formula and
experimental data.
Topic 2.1-the nuclear atom
Topic 5.3-bond enthalpies
Aims
Aim 7: Spectral databases could be used here.
Aim 8: The effects of the various greenhouse gases depend on their abundance and their ability to
absorb heat radiation.

21.1 Spectroscopic identification of organic compounds

Nature of science: Improvements in modern instrumentation-advances in spectroscopic techniques

(IR, 1H NMR and MS) have resulted in detailed knowledge of the structure of compounds. (1.8)

Understandings

Essential idea: Although spectroscopic characterization techniques form the backbone of structural
identification of compounds, typically no one technique results in a full structural identification of a
molecule.

Structural identification of compounds involves several different analytical techniques including

IR, 1H NMR and MS.

In a high resolution 1H NMR spectrum, single peaks present in low resolution can split into further
clusters of peaks.
The structural technique of single crystal X-ray crystallography can be used to identify the bond
lengths and bond angles of crystalline compounds.

Applications and skills

Explanation of the use of tetramethylsilane (TMS) as the reference standard.

Deduction of the structure of a compound given information from a range of analytical

characterization techniques (X-ray crystallography, IR, 1H NMR and MS).

Guidance

Students should be able to interpret the following from 1H NMR spectra: number of peaks, area
under each peak, chemical shift and splitting patterns. Treatment of spin-spin coupling constants will
not be assessed but students should be familiar with singlets, doublets, triplets and quartets.

High resolution 1H NMR should be covered.

International-mindedness
The chemical community often shares chemical structural information on the international stage.
The Cambridge Crystallographic Database, ChemSpider developed by the Royal Society of Chemistry
and the Protein Data Bank (RCSB PDB) (at Brookhaven National Laboratory, USA) are examples which
highlight the international nature of the scientific community.
Theory of knowledge
The intensity ratio of the lines in the high resolution NMR spectrum is given by the numbers in
Pascal's triangle, a mathematical pattern known independently over a thousand years ago by a
number of different cultures.
Why is mathematics such an effective tool in science?
Is mathematics the science of patterns?
Utilization:
Protons in water molecules within human cells can be detected by magnetic resonance imaging
(MRI), giving a three-dimensional view of organs in the human body. Why is MRI replacing
computerized tomography (CT) scans for some applications but is used as a complementary
technique for others?
MS (and other techniques such as TLC, GC, GC-MS and HPLC) can be used in forensic investigations
at crime scenes.
Analytical techniques can be used to test for drug abuse by high-performance athletes
Syllabus and cross-curricular links
Topic 11.3-spectroscopic identification of compounds
Option B.2-chromatography and protein separation
Option B.9-chromatography and pigments
Option D.7-chiral auxiliaries
Aims
Aim 7: Spectral databases can be used here
11.1 Uncertainties and errors in measurement and results
There is a basic difference between counting and measuring. A class has exactly 16 students in it, not
15.5 or 15.4. That's counting. But a given student is never exactly 6 feet tall, nor is she 6.000 feet tall.
There is always some limit to the accuracy and precision in our knowledge of any measured property
- the student's height, the time of the event, the mass of a body. Measurements always contain a
degree of uncertainty. Appreciating the uncertainty in laboratory work will help demonstrate the
reliability and the reproducibility of the investigation, and these qualities are hallmarks of any good
science.

Why do measurements always contain uncertainties? Physical quantities are never perfectly defined
and so no measurements can be expressed with an infinite number of significant figures; the so
called 'true' value is never reached. There are also hidden uncertainties which are part of the
measurement technique itself, such as systematic or random variations. The resolution of an
instrument is never infinitely fine, analogue scales need to be interpreted, and instruments
themselves need calibration. All this adds to the uncertainty of measurement. We can reduce
uncertainty but we cannot escape it. In order to do good science, we need to acknowledge these
limits.

Uncertainties and errors

Some textbooks treat errors as equivalent to uncertainties. Errors, of course, are mistakes, and you
can often find your mistake and correct it. Human errors arise from carelessness.
In contrast to errors, an uncertainty is a limit to the precision of a measurement or calculation. In
this booklet the terms 'error' and uncertainty' will be kept distinct.

Uncertainty and Error in Measurement

Accuracy of a result is a measure of how close the result is to some accepted value.
Accuracy is measured as a percentage deviation from the accepted value.

Experimental value – Accepted value

Percentage deviation = x 100
Accepted value

The precision of the result is a measure of the certainty of the value (usually quoted as a ± value.
For example : The ideal gas constant has an accepted value of 8.314 J mol -1 K -1.
Experimental determination of this value resulted in 8.34 ± 0.03 J mol -1 K -1 for group 1 and 8.513 ±
0.006 J mol -1 K -1 for group 2.
Group 1 = more accurate (closer to accepted value)
Group 2 = more precise (smaller uncertainty)

Suppose 10 thermometers gave readings of a room in degrees celsius as

19.9, 22.3 , 20.2 , 20.0 , 20.0, 20.1 , 19.9 , 20.3 , 19.9 and 20.2.
If we ignore the anomolous result of 22.3 and average the other 9
results we get an average of 20.06 oC.
We can assume from these results that the temp of the room is 20.1 ±
0.2 oC. (the 9 results are between 19.9 and 20.3)
Significant figures
There are some general rules for determining significant figures. (1) The left most non-zero digit is
the most significant figure. (2) If there is no decimal point, the rightmost non-zero digit is the least
significant figure. (3) If there is a decimal point, the rightmost digit is the least significant digit, even
if it is zero. (4) All digits between the most significant digit and the least significant digit are
significant figures. For instance, the number "12.245" has five significant figures, and "0.00321" has
three significant figures. The number "100" has only one significant figure, whereas "100." has three.
Scientific notation helps clarify significant figures, so that 1.00 x 103 has three significant figures as
does 1.00 x 10 -3, but 0.001 or 1 x 10-3 have only one significant figure.

Significant figures reflect precision. The result of any calculation cannot improve upon the number of
significant figures. A rule can be stated here. the quantity with the least number of significant
figures tells you the number of significant figures you may give in your final answer. The product of
22 x 0.10145 = 2.2319 must be rounded off to two significant figures, so we can only say that 22 x
0.10145  2.2.

When adding experimental uncertainty to measured or calculated values, uncertainties should be

rounded to one significant figure. We might say  6 or  0.02 but we should not say  63.5 or 
0.015. Also, we cannot expect our uncertainty to be more precise that the quantity itself because
then our claim of uncertainty would be insignificant. Therefore there is another guideline. The last
significant figure in any stated answer should be of the same order of magnitude (in the same
decimal position) as the uncertainty. We might say 432  3 or 3.06  0.01 but not
432  0.5 or 0.6  0.02.

Random Uncertainties (errors) arise mostly from inadequacies or limitations of 43

equipment.
Level read as 43.60 ± 0.05. (43.55< and < 43.65)
Read the uncertainty as half of the last digit
(ie if reading is 28.2360
then uncertainty is ± 0.0005)

44
23.0

In cases where the scale is not in single units, the uncertainty

24.0 is still half of the preceding unit for the last digit.
ie 23.2 ± 0.1

25.0

Quantitative apparatus usually has stated uncertainty reflecting the tolerance used in the
manufacture of the apparatus.
Volumetric pipette may be 25.0 cm3 ± 0.03 cm3 (good quality)
or 25.0 cm 3 ± 0.06 cm3 (poor quality)
There are different conventions for recording uncertainties in raw data.
The simplest is the least count which simply reflects the smallest division of the scale. For example
±0.01 g on a balance.
The instrument limit of error. This is usually no greater than the least count and often half of the
least count. For example a burette.
The estimated uncertainty takes into account the concepts of least count and instrument limit but
also, where relevant, higher levels of uncertainty as indicated by the manufacturer, or qualitative
considerations such as parallax problems or reaction times when timing or difficulties in reading
colour changes. In these cases the experimenter should do their best to quantify these observations
into the estimated uncertainty.

“In chemistry internal assessment it is not specified which protocol is preferred and a moderator will
support a teacher when it is clear that recording uncertainties has been required and the
uncertainties recorded are of a sensible and consistent magnitude.”
(IBO website)

Rejecting data
Sometimes one measurement in a series of repeated measurements of the same quantity appears
to disagree with the pattern of the others. When this happens, you must decide whether the suspect
measurement resulted from some mistake and should be rejected, or was a bona fide measurement
and should be used with all the other data.

Random errors can be reduced by repeating (if the same student or group does the experiment a
number of times) or reproducing (if several students or groups do the experiment). The random
errors statistically cancel out.

Systematic errors always affect the result in a particular direction. They arise from flaws (not
limitations) in the instrument or from errors in the way the measurement was taken. (not reading
the meniscus properly, not emptying the pipette properly etc.)

Read pp 529 – 533

Do qu 1 - 12

Calculations:
The uncertainties of calculated results are of two types.
Absolute uncertainty 28.50 ± 0.05.

0.05
Percentage uncertainty x 100 = ± 0.18 %
28.5

When adding or subtracting numbers add absolute uncertainties.

When multiplying or dividing numbers add percentage uncertainties.
When you multiply or divide by pure numbers (constants) you multiply or divide the absolute
uncertainty by the pure number.
Examples:

A = 123 ± 0.5 B = 12.7 ± 0.2 C = 4.3 ± 0.1

B – C = 12.7 – 4.3 = 8.4 uncertainty = 0.2 + 0.1 = ±0.3

B-C = 8.4 ± 0.3

0 .5
A ( B-C) = 123 x 8.4 % uncertainty in A = x 100 = 0.407%
123

0 .3
% uncertainty in (B-C) = x 100 = 3.571%
8 .4

% uncertainty in A(B-C) = 3.571 + 0.407 = 3.978%

A (B-C) = 123 x 8.4 with 3.978% uncertainty

=1030 with 4% uncertainty

Or
3.978
= 1033.2 ± ( x 1033.2)
100

= 1033.2 ± 41.1

= 1030 ± 40 [ uncertainty given to 1 sf  round off value similarly]

When using literature values assume the precision is limited to the number of digits
Given ie 35.45 should be taken as ± 0.005
In some cases the uncertainty of one quantity is much greater than that of all of the others so the
uncertainty of the final value can be considered to be due to only that factor. (You must state that
you are ignoring other minor uncertainties)

Consider the following calorimeter experiment

Initial temp 21.6 ± 0.1 oC

∆T = 2.6 ± 0.2 oC % uncertainty = 7.7%
o
Final temp 24.2 ± 0.1 C

Mass of water 200.0 ± 0.5g % uncertainty = 0.25%

Amount of reagent 0.05000 ± 0.00005 mol % uncertainty = 0.1%

Specific heat water 4.1830 ± 0.0005 J g -1 K -1 % uncertainty = 0.12%

As the uncertainty of the temperature change is so much higher than the other quantities, the
percentage uncertainty for the final result will be taken as 7.7%
Q = m c ∆T

= 200.0 x 4.18 x 2.6

= 2173.6 J

Q
∆H = -
n

2173.6
=-
0.05000

7 .7
= - 43472 J mol -1 uncertainty = x 43472 = 3347 J mol-1
100

∆H = - 43000 ± 3000 J mol -1

= -43 ± 3 kJ mol -1

Percentage error is different to percentage uncertainty.

Percentage error is a measure of how close the experimental result is to the literature or accepted
value.
Suppose the literature value was given as -45.6 kJ mol -1
The percentage error would be
45.6  43
= 6%
45.6
In this case the percentage error is less than the uncertainty (7.7%)  the result is in agreement with
the literature value.
The major errors in the experiment would  be related to precision, in particular the thermometer
so improvements should focus on a more precise thermometer.
If the percentage error was much higher than the uncertainty then this could be accounted for by
some major systematic errors (ie heat loss to the surroundings.)

When calculating averages of repeated experiments, the final answer should be given to the same
error as the component values (ie do not add the errors for each value)

Read pp 535 – 540

Read NOS pg 538
Go through worked examples
Do qu 13 - 21
11.2 Graphical techniques
In order to plot an effective graph the following criteria should be used
 The graph must have a explicit heading or title.
 The dependent variables are usually plotted vertically (y-axis) whilst the independent
variables are usually plotted horizontally (x-axis).
 Scales must be chosen which make it easy to interpret the graph and highlight any pattern or
correlation. The axes do not have to start from zero.
 Axes must be clearly labeled to include units.
 The line of best fit should be either a smooth curve or a straight line. Extrapolated points
should be marked differently (ie with a dotted line)

Obvious correlations should be stated. For example direct proportionality (lin\ear relationship) or
indirect proportionality (inverse linear relationship).
Care must be taken to have enough data points to ensure the correlation (ie that the graph really is
linear).

Slopes of lines in some cases may give other information and, in these cases, may be useful to
calculate or observe (either the slope of a straight line or perhaps the tangent to a curve).

For example

CO2 cm3
3
O2 cm

Time (sec) Time (sec)

Gas is being given off at a slower rate As the reaction proceeds the gas is being given
represented by the dotted line off at a slower rate

Read pp 540 – 546

Read NOS pg 546
Do qu 22 - 26
11.3 Spectroscopic identification of organic compounds
Modern methods of chemical analysis involve the use of instruments that routinely analyse samples
rapidly and to high levels of accuracy. This is in contrast to experimental techniques using
procedures such as titrations or precipitations. The instruments are sophisticated and complex but
they all use principles of spectroscopy and chromatography.

Chemists use analytical techniques to:

 identify a substance (qualitative analysis)
 analyse its composition and determine its purity (quantitative analysis).
 confirm the structure of a substance (structural analysis)

Often, all of the above analyses can be performed simultaneously. Spectra and chromatograms both
show a series of peaks that can be used to determine the components in the sample (from the
position of the peaks) along with the amount of the component (the size of the peak or area under
it).

The degree of unsaturation or index of hydrogen deficiency (IHD) provides useful information to
determine the structure of molecules. It is a measure of how much hydrogen would be needed to
convert the molecule to a saturated one which, in turn can be used to determine the number of
rings or multiple bonds in a molecule

The IHD can be worked out from the

structure (as in the table opposite) or from
the molecular formula.

Using the molecular formula

IHD = ½[2c+2-h-x+n]
where
c= no of C atoms
h= no of H atoms
x= no of halogen atoms
n= no of N atoms

(note that no of oxygen atoms does not affect IHD)

Using this formula

C4H8O2 has IHD = 1
( has either 1 ring or 1 double bond)

C2H5Cl has ISD = 0

(has no ring or double bond)
Of all of the colours of visible light, violet light has the highest energy (and the shortest wavelength).
It has wavelength 4x10-7m and frequency 7x1014Hz. Ultraviolet are higher energy than visible light.
Red light has the lowest energy (and the longest wavelength). It has wavelength 8x10-7m and
frequency 4x1014Hz. Infrared are lower energy than visible light.

Gamma rays (γ-rays) cause changes in the energy of atomic nuclei.

X-rays have enough energy to remove electrons from inner filled shells of atoms.
Ultraviolet and visible light can produce electron transitions and give information about electron
energy levels within an atom.
Infrared radiation is absorbed by certain bonds causing them to stretch or bend and stimulating
vibration in molecules thereby giving information about bonding.
Microwaves affect the rotational state of molecules giving information about bond lengths.
Radio waves can be absorbed by certain nuclei causing them to reverse their spin and are used in
NMR spectroscopy.

Mass Spectrometry

In a mass spectrometer, the gaseous sample

is bombarded with a high energy electron
beam to produce positive ions by knocking
electrons off the sample atoms or molecules.
These ions are then accelerated through an
electric field and deflected by a magnetic
field onto a detector screen.
The degree of deflection depends on the
mass to charge (m/z) ratio of the ion.
Assuming that only one electron is knocked off the atom or molecule, the lower the mass, the
greater the deflection. By varying the strength of the magnetic field, the beam can be focussed onto
the detector. Thus, ions are separated by mass and collected, and the mass of the ion is determined.
The intensity of the beam provides a measure of the relative abundance of the ion. Results are
usually plotted as a mass spectrum- a plot of relative mass versus abundance.
Mass spectrometry is used largely as an analytical tool for molecules rather than isotopes. The
bombarding high energy electrons will form molecular ions but the excess energy often breaks the
molecule apart giving rise to a fragmentation pattern with the pattern of peaks in the spectrum
representing the different fragments that have been formed.
A chemist pieces together the fragments to form a picture of the complete molecule.

Consider the mass spectrum on the right

The molecular ion corresponds to the peak at
46.
The ion that appears at 45 corresponds to
the loss of a hydrogen atom.

The figure below shows a fragmentation path which explains the spectrum.

Note that-

The loss of H forms the C2H5O+ ion (not H+) there

is a peak at 45 not 1

Cleavage of the C-O bond forms the C2H5+ ion in

preference to the OH+ ion  there is a peak at 29
not 17.

Worked example

A molecule with the molecular formula C2H4O2 has the

simplified mass spectrum shown. Deduce the probable
structure of the compound.

Solution

Mr = 15 represents presence of CH3+ and loss of COOH

Mr = 43 represents presence of C2H3O+ and loss of OH
Mr = 15 represents presence of COOH+ and loss of CH3

H
H O
Read pp 549 – 552
Probable structure is H C C Go through all worked examples
H Do qu 27 - 30
O
The principles of spectroscopy

The basis if spectroscopy is the effect that electromagnetic radiation has on matter.
The study of the radiation absorbed or emitted by matter is called spectroscopy.
Electromagnetic radiation ranges from very high energy γ- rays through to low energy radiation such
as radio waves.

The wavelength (λ) of a wave is the distance between

its peaks.

The frequency (f) of the wave is the number of peaks

that pass a point every second.

All electromagnetic waves travel at the same speed

(the speed of light) 3 x 108 m s -1.

The velocity of light = frequency x wavelength (c = f λ)

(includes all electromagnetic waves)

Electromagnetic radiation has a particle nature and each photon (particle of light) carries a quantum
of energy.

The wavelength and energy of light are related by the equation

E = energy (J)
hc h = planck’s constant (6.626 x 10 -34Js)
E = hf =
 f = frequency (Hz)
λ = wavelength (m)
c = speed of light (3 x 108 m s -1)

High frequency radiation carries high energy.

1
Wavenumber is another wave property, and is equal to the inverse of wavelength ( ).

Wavenumber corresponds to the number of cycles the wave produces in a centimetre and has the
units cm-1. The greater the wavenumber, the lower the wavelength and the greater the energy.
It has been traditionally the most common method of specifying IR absorption.

Infrared Spectroscopy

A double beam infrared spectrometer

(or spectrophotometer) allows the
radiation passing through the sample
to be continually compared with
identical radiation that has not passed
through the sample.
Radiation from the source is passed
through a monochromators, which
only allows radiation of a particular
wavelength to pass through.
This then strikes a beam splitter and is split into two beams that pass along parallel paths. One
through the cell containing the sample and the other through an identical reference cell.
The two beams then pass through a detector where they are compared electronically to determine
the amount of absorbance due to the sample.
As the spectrum is scanned, the frequency (or wavenumber) of the radiation is graphed against
absorption. Comparison with a data bank enables the identification of the unknown.

When molecules absorb infrared radiation, changes occur to their bonds. Just as electrons can only
occupy discrete energy levels, molecules are only able to occupy discrete vibrational energy levels.
Absorption of infrared radiation will give a molecule enough energy to move from one vibrational
energy level to a higher one.

The bond lengths may become longer or shorter (stretching motions) or the angle between the
bonds may alter (bending motions).
Stretching motions generally require more energy and therefore occur at greater wavenumber than
bending motions.

When a molecule absorbs infrared radiation, the bending or stretching motions change the polarity
of the bond and hence the overall dipole moment (the strength and direction of the charge
separation) of the molecule.

As the hydrogen atoms in a water molecule bend away from each other, the geometry and hence
the dipole moment of the molecule,
changes.

All of the vibrations of water lead to

a change in dipole moment and
hence absorption of IR radiation.

The symmetrical stretch in CO2 will be IR inactive, whereas the asymmetric stretch and the bending
are both IR active because they result in a dipole change.

Diatomic molecules with only one element, such as H2 and N2, do not
absorb IR radiation because neither the covalent bond, nor the molecule
has a dipole moment.

Generally, the range of energies absorbed depends on the strength of

the bonds and the mass of the atoms attached by the bonds.
IR spectroscopy is particularly useful in analysing organic compounds, because the various bonds in
the functional groups absorb at different frequencies.
Computers store the spectra of all known compounds.
There are several key absorptions that can be used to identify particular bonds and a list can be
found in the IB Data Booklet.
The spectra tend to be complex due to the large numbers of vibrations possible. Most compounds
can be identified from their ‘fingerprint region’ which is a complex region between about 500cm-1
and 1500cm-1.

This is an infrared spectrum which identifies

propanoic acid
C2H5COOH.
If the fingerprint region is the same as that of a
known compound then an identification can be
made.

This is an infrared spectrum of 2-methylpropanoic

acid.
Note the similarities.
Note that the horizontal scale is a non-linear axis.
This is common for many instruments. (Take care
when reading spectra wavenumbers off such a scale.)

These two spectra have quite different

fingerprint regions, even though they both
show absorption peaks that correspond to the
stretching of C-H and C=O bonds.
They represent butanal and butanone

Read pp 554 - 559

Read NOS pg 559
Do qu 32 - 41
 Proton Nuclear Magnetic Resonance (1H NMR) Spectroscopy

NMR Spectroscopy is based on the fact that the nuclei of some atoms, when placed in a strong
magnetic field, absorb radiation in the radio wave region of the electromagnetic spectrum. It is a
powerful tool for investigating the structure and shape of molecules and has important medical
applications.
Nucleons (protons and neutrons) have a property called spin which has a magnetic moment
associated with it. If there is an even number of nucleons, they pair up and their spins cancel each
other out (as with electrons) and the nucleus does not have an overall magnetic moment. Where
there is an odd number of nucleons, ie 1H, 13C, 19N and 31P, the nucleus has a net spin and magnetic
moment. These nuclei create a magnetic field and behave like tiny bar magnets. These have the
same energy unless an external magnetic field is present in which case some of these nuclei will
absorb radiation of radio frequency. The nuclei will then line up in the same direction as the applied
magnetic field or, if they have absorbed enough energy, some will line up against it. [If radiation of
the correct wavelength is absorbed, the spinning nuclear magnet flips and becomes aligned at the
higher energy state] These nuclei are said to be in resonance with the applied radiation (hence the
name nuclear magnetic resonance).

In practice, the sample is placed in an electromagnet. The field strength is varied until the radio
waves have the exact frequency to make the nuclei flip over and spin in the opposite direction. This
resonance is detected electronically and recorded in the form of a spectrum.
Most commonly this is applied to hydrogen atoms present in all organic molecules.
H
The signals are measured against the standard signal produced by the 12 hydrogens in H C H
H H
tetramethylsilane (TMS) (shown on the right). The position of the NMR signal
relative to this standard is called the chemical shift (δ). H C Si C H
H H
H C H
Hydrogen nuclei in different environments have characteristics called chemical shifts.
H
Some of these values (given in ppm) are listed in the data booklet or on pg 562 of the text

The spectrum of ethanal is shown on

the right. It has a peak at 9.7 which
corresponds to the CHO proton and a
peak at 2.1 which corresponds to the
three protons in the CH3 group.

The area under the CH3 peak is three

times as large as that under the CHO
peak as it indicates the relative number
of protons in the different environment. The integrated trace gives this information more directly, as
it goes up in steps which are proportional to the number of protons. This is easier than calculating
the relative areas.

H
H C H
H H
H C Si C H
H H
H C H
H
Worked example 1

The NMR spectra and structural formulae of (a) propanone and (b) dimethoxymethane are shown
below.

(a) In propanone, there is only one environment for the hydrogen atoms. They are all in CH3
groups bonded to a carbonyl atom. As a result, there is only one peak in the NMR spectrum

(b) The ether has hydrogen atoms in two different environments. There are two CH3 groups
bonded to the ether functional group (-O-). The other two H atoms are in the CH2 group in
the middle of the molecule. The NMR spectrum has two peaks with intensities in the ratio
3:1 resulting from the 6:2 ratio of H atoms in each environment.

Worked example 2

The NMR spectrum of a compound which has the formula C3H8O is shown on the right.
(a) Draw the full structural formulae and give the
names of three possible isomers of C3H8O.
(a) Identify the substance responsible for the peak at
0 ppm and state its purpose.
(b) Identify the unknown compound from the
number of peaks in the spectrum.
(c) Identify the group responsible for the signal at
0.9ppm.

Solution

(a) The structures are

H H H H H H H H H
H C C C O H H C C C H H C O C C H
H H H H H
O H H H

Propan-1-ol Propan-2-ol methoxyethane

 (b) TMS is used as a reference sample

(c) For each structure

I – IV identifies the different environments of the H atoms whilst the numbers 1 – 3

represent the number of H atoms in each environment. There are four different peaks in the
spectrum. Propan-1-ol has four peaks in the correct areas.

(d) Peaks at 0.9 ppm correspond to the CH3 group.

NMR is the basis of Magnetic Resonance Imaging (MRI) used in body scanning. The main
constituents of the body that contain H atoms and hence produce signals are water and lipids.

It is a non invasive technique (unlike the use of X-Rays) and is used to study blood flow, tissues,
muscles and other soft parts of the body. Different parts of the body have different water/lipid
ratios which absorb radio frequency radiation in different ways.

The non-invasive procedure of MRI has replaced many invasive, exploratory surgical procedures. It is
used to diagnose and monitor conditions such as cancer and cardio-vascular disease.

The structural identification of compounds typically involves a combination of several different types
of analytical techniques including IR, 1H NMR, and MS

Read pp 560 – 566

Go through all worked examples
Read NOS pg 564
Do qu 42 - 45
21.1 Spectroscopic identification of organic compounds
Magnets used in different NMR spectrophotometers are not identical so resonance frequencies of
identical protons may vary from one instrument to another. An NMR spectrophotometer is
calibrated using an internal standard which is added to the sample.
As mentioned earlier, NMR signals are measured against a standard produced by the 12 hydrogen
nuclei in tetra-methyl-silane (TMS) which has the formula (CH3)4Si.

It has been chosen as the standard because:

 The hydrogen nuclei are all in the same environment, one strong signal is recorded,
 Si has a lower electro-negativity than C, therefore TMS absorbs radio waves in a different
region from that absorbed by H atoms attached to only C. This ensures that the standard
signal does not interfere with other absorption signals.
 It is chemically un-reactive
 It is easily removed from the sample after the measurements have been taken

An NMR spectrophotometer is calibrated by reporting other signals in terms of how far they have
shifted relative to the reference signal.

The chemical shift (represented by δ) of a proton in a molecule is defined as:

( f  fo) Where f = freq absorbed by sample

δ = x 106 ppm
fo fo = freq absorbed by TMS

Although the absolute frequency of the signal depends on the magnetic field, the chemical shift
(relative to the standard) remains the same.

High Resolution 1H NMR spectroscopy

Absorptions of hydrogen atoms on neighbouring carbon atoms interfere with each other and in a
high resolution spectrum this leads to splitting of some absorptions into a group of smaller parts.
The splitting of the peaks occurs as the effective magnetic field, experienced by particular nuclei, is
modified by the magnetic field produced by neighbouring
protons.

In the high resolution 1H NMR spectrum of ethanal on the

right, the magnetic field experienced by the protons in the
methyl group depends on the spin of the proton attached
to the C in the carbonyl group. The magnetic field will be
increase when the external field from the proton in the
carbonyl group is aligned and decrease when aligned
against it. This results in two possible values for the signal
of the protons in the CH3 group.

The peak corresponding to the CHO proton is split due

to the 3 neighbouring protons in the neighbouring CH3
group. As there are two possible orientations for each
proton, a total of 23 combinations are possible,
resulting in 4 different local magnetic fields. This
produces four signals with relative intensities 1,3,3,1
as shown in the table.
A useful rule is that the number of peaks that a proton has is given by the number of hydrogens on
the neighbouring carbon atom plus one.

In summarising the information that a 1H NMR spectrum provides:

 The number of peaks indicates the number of different environments of 1H atoms in the
molecule.
 The chemical shift of the peaks indicates the nature of the neighbouring atoms
 The integrated ratio of the peak sizes indicates the ratio of the numbers of hydrogen atoms
with the same environments.
 Splitting patterns in high resolution helps locate the hydrogens by identifying how many
hydrogen atoms are bonded to neighbouring atoms.

Extension

The reason for the chemical shift is that when electrons are in a magnetic field they orbit in such a
way as to set up an opposing magnetic field. Hence, the magnetic field experienced by the nucleus
(and hence the frequency at which it absorbs radiation) depends on the electron density near to the
nucleus (the chemical environment).

The differing electro-negativities of the surrounding atoms influence the chemical shift of the 1H
nuclei.

In TMS, silicon is less electro-negative than carbon, so the electron density (and hence the shielding)
around the methyl hydrogens is greater than in the carbon derivative ( 2,2-dimethylpropane).
Elements that are more electro-negative than carbon reduce the electron density around the carbon
atom and de-shield the hydrogen atoms bonded to the carbon.

As the electro-negativity of the

atom bonded to the methyl
group increases, the shielding of
the methyl protons decreases
and their chemical shift
increases.
 This effect can be seen by
comparing the methyl
protons in halogenalkanes

Read pp 566 – 570

Go through worked examples
Do Qu 46 - 48

Single X-Ray crystallography

Bond lengths and bond angles can be identified using a technique called X-ray diffraction (developed
at Adelaide university).
X-rays pass through crystalline solids and get scattered by their interaction with the electrons in the
substance. These scattered waves interact with each other causing a diffraction pattern. Some of the
waves interfere in phase and some interfere out of phase causing different alignments of amplitude.
A map of electron density can be determined from this pattern and this can be used to determione
the identity of the atoms and the structure of the molecule.

Read pp 571-573
Read NOS pg 573
Do Qu 49 - 53

Do Practice questions pg 574