FAQ: IR, MS and NMR Spectroscopy

The questions are grouped into the following themes. Click the title to explore questions of the
corresponding theme.

Spectroscopy

1. How can we know the type of vibrational motions that the molecules exhibit?

There are different types of vibrational motions possible that the molecules can exhibit as
shown in
http://en.wikipedia.org/wiki/IR_spectroscopy#Number_of_vibrational_modes (Links to an
external site.). The vibrational modes of the molecule essentially depend on the symmetry of
the molecule.

2. In IR Spectroscopy, why would IR be absorbed by the molecules? Is there something to do

with resonance? (The IR matches the natural frequencies of the oscillating systems - i.e. the
molecules) What is the source of the energy required for vibration of molecules? Is it from
the IR transmitted through the molecules?

In order for a molecule to absorb the IR radiation, the natural vibrational frequency of its
bonds must match the frequency of the electromagnetic radiation (infrared in this case). An
IR beam is used to excite the molecule, so the source of the energy comes from the IR beam.
For further details, please see Figure 3 in the supplementary note on IR and NMR
spectroscopy.

3. How can the action of the atoms affect the measurement of the NMR spectroscopy, like
spinning and vibrating?

Spinning and vibration are two different types of electronic transition resulting from two
different types of electromagnetic radiation. With reference to the supplementary note on IR
spectroscopy and NMR spectroscopy, each type of electromagnetic radiation corresponds to
only one type of the electronic transition. Vibration is the electronic transition in IR
spectroscopy while nuclear spinning is the electronic transition in NMR spectroscopy.

For the measurements of IR spectroscopy, please see the supplementary note on IR

spectroscopy and NMR spectroscopy and supplementary note on IR spectroscopy.

For the measurements of NMR spectroscopy, please read the article "How is NMR spectrum
produced".

4. What molecules spin and vibrate when they are subject to EM wave? What has happened
during the wave absorption process?

If the molecule is excited by wave of frequency in the Infrared region, the bonds in the
molecule vibrate. If the molecule is excited by wave of frequency in the radio wave region,
the nuclear spins will align with the external magnetic field either in parallel or anti-parallel
 directions. For further details, please see the explanatory note on IR spectroscopy and NMR
spectroscopy.

For the absorption process, please see Figure 3 in the explanatory note on IR spectroscopy
and NMR spectroscopy.

Infrared Spectroscopy

1. What is the relationship between the vibrational frequency and masses of the nuclei that form
the bond in a compound in IR spectroscopy?

There is a relationship between the masses of the two atoms in a bond, bond strength and the
vibrational frequency (wavenumber) as explained by Hooke's Law. In Hooke's law, a bond
between two atoms is thought as a spring that connects the two atoms. For the equation of
Hooke's Law and further information, please see
http://www.chem.ualberta.ca/~inorglab/spectut/IRpg7.html.

2. How a carbon-carbon single bond stretches differently from that of a carbon-carbon double
bond? Do they just have the same degree of stretching (i.e. maximum percentage change in
reduction of bond length)?

With reference to Hooke's law as mentioned in Question 1, bond strength is also a

deterministic factor of vibrational frequency. Since carbon-carbon double bond is a stronger
bond than carbon-carbon single bond, the bond strength of carbon-carbon double bond is
greater than that of carbon-carbon single bond and consequently carbon-carbon double bond
vibrates more energetically than carbon-carbon single bond. As a result, the wavenumber of
carbon-carbon single bond is greater than that of carbon-carbon single bond.

3. Why do linear molecules have more vibrational modes than non-linear molecules for the
same number of atoms in IR spectroscopy? (Reference from Wikipedia: For molecules with
N atoms in them, linear molecules have (3N - 5) degrees of vibrational modes, whereas
nonlinear molecules have (3N - 6) degrees of vibrational modes.)

Some of the modes of non-linear molecules are rotational modes but not vibrational modes,
so linear molecules have more vibrational modes than non-linear molecules for the same
number of atoms.

Mentioned article in Wikipedia: Molecular Vibration (Links to an external site.)

4. How would you show that propene consists of a carbon-carbon double bond?

The IR spectrum of propene is available at

http://webbook.nist.gov/cgi/cbook.cgi?Spec=C115071&Index=1&Type=IR&Large=on (Link
s to an external site.). You can see that there are medium peaks at around 1620 cm-1.
According to the supplementary note on IR, the range of C=C absorption is 1610 cm-1 - 1680
cm-1 and 1620 cm-1 falls in that range, so C=C is present in propene.
NMR Spectroscopy

1. What is the difference between spin and rotation?

Spin is a new quantity in quantum mechanics that has no counterparts in classical world. It is
like a characteristic property of an atom. Rotation refers to the actual rotation in daily
English.

2. What is another application of NMR spectroscopy besides structural determination of

chemicals?

NMR spectroscopy is widely applied in medical field for scanning human body and tissue. It
is called MRI (magnetic resonance imaging). Please see the special topic in MRI for further
information.

3. In the presence of external magnetic field, why will isotopes of some elements have different
splitting of energy levels?

Since different isotopes of the same element have different spin values, they have different
splitting of energy levels.

4. Are macromolecules allowed in NMR analysis, such as plastics, and DNA?

Yes they are allowed in NMR analysis. NMR is widely applied in analyzing DNA and
proteins in research. For your further information, please see http://www.innovations-
report.com/html/reports/life_sciences/report-31346.html. (Links to an external site.)

Mass Spectrometry and Other Spectroscopies

1. What is fragmentation? How does it take place in MS? How do we determine the
fragmentation patterns of different molecules in MS?

In MS, the sample molecule is hit by an electron beam to be ionized to form radicals and
cations and this process is called the fragmentation process. The fragmentation pattern
depends on the stability of the molecular ion. For further information, please see
http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/Spectrpy/MassSpec/masspec1.ht
m. (Links to an external site.)

2. How are radical ions generated by MS?

A high energy electron beam is used to bombard the sample and this fragments the compound
of interest. Consequently, there are radicals (no charge) and ions (charged) formed after the
fragmentation. Only molecular ions are sent to the detector while the radicals are not detected
by MS.

3. How are IR spectroscopy, MS, and NMR spectroscopy applied to determine the structure of
medicines, inorganic, and organic compounds?

Medicines can be inorganic or organic compounds so it is discussed in here. The procedures

of determination of chemicals, regardless they are organic or inorganic, are essential the
 same. These three techniques work together to give different types of information of the
compound of interest. We can do an IR analysis to determine what functional groups are
present in the compound by correlating the wavenumbers to the reference value that can be
looked up in reference materials. We get the information of the bonds of the chemical and
then we can determine the mass of it by MS. Finally, we can run a NMR analysis on the
chemical to get the structural information by interpreting the NMR spectrum.

4. Other than IR spectroscopy, visible light or UV light is also known to be used for
spectroscopy. What is it used for?

UV/Vis spectroscopy is used to determine the electronic transition in the compounds. It is

usually used in analysis of transition metal complexes.