Lab 6: Determination of Molecular Structure
Laboratory Goals
In this lab, you will:
• Determine the infrared spectrum of a polymer sample
• Learn how to use a Fourier Transform Infrared Spectrometer to obtain information about
molecular structure
• Use GaussView and a molecular model kit to visualize the specific bonds stretching
associated with the major peaks for a simple molecule observed
• Pull a thread of freshly made nylon
Introduction
In the previous laboratories, you have used spectroscopy to investigate the electronic
structure of atoms and to make quantitative determinations of solution concentrations. In this
laboratory we return once again to the relationship between spectroscopy and structure, the new
feature being that today you will use infrared (IR) radiation–light with wavelengths longer than
the red portion of the visible spectrum–to help you determine molecular structures. Appendix I
explains the basics of how an infrared spectrometer works.
IR spectroscopy is an
extremely powerful tool that is
commonly used by chemists. It can
be used quantitatively since Beer’s
law holds for any type of radiation,
but its most prevalent use is in the
determination of how molecules are
put together, so it is usually thought
of as a qualitative technique. IR
spectroscopy works exactly the
same way as visible light absorption
spectroscopy in that both involve a
transition from a lower energy level
to a higher energy level upon the
absorption of a photon.
The
difference lies in which energy
levels are involved. In visible
absorption spectroscopy, it is excitation of
electrons from one orbital to another. Infrared
light, being of longer wavelengths and hence
smaller energies than red light, does not have
the energy to cause this electronic excitation
(see Figure 1).
2p
2p
2s
2s
ΔE=hc/λ; λ=600nm, ΔE=2.1 eV
a)
2p
2p
2s
2s
ΔE=hc/λ; λ=5000nm, ΔE=0.25 eV
b)
Figure 1. The shorter-wavelength photon in a) has
enough energy to excite an electron from the 2s
orbital to the 2p, whereas the longer-wavelength
photon in b) has insufficient energy to cause this
excitation.
6-1
So what kind of energy levels can be excited by infrared radiation? As you know, molecules are
not stationary, but are dynamic–they are constantly moving. This motion really breaks down
into three different types (called degrees of freedom): translation, vibration, and rotation, and it
is the vibrations that are excited when IR radiation is absorbed. It turns out that, like electronic
energy levels, the translational, vibrational, and rotational motions are all quantized as well–
hence we can talk about vibrational energy levels. Consider what this means for a typical bond,
say a C-H bond in methane, CH4. If we think of the C-H bond as a spring connecting two
masses (here the masses are the C and H atoms while the spring represents the bonding electrons;
this model is called the harmonic oscillator, which you will see again in physics):
Figure 2. Two masses on a
spring are a model for a
chemical bond.
We know that there must be some frequency (ν) of vibration corresponding to the stretching
motion of the spring. In classical physics (also called Newtonian physics, in comparison to
relativistic or quantum physics) ν can take on any value, and the masses can vibrate as fast or as
slow as the energy allows. In quantum physics, ν is quantized which means that only certain
frequencies are allowed–this directly results from the Planck equation ΔE = hv and the fact that
energy levels are quantized.
Aside from the existence of vibrational energy levels, bond vibrations are very similar to
“normal” vibrations. Consider the system in Figure 2 again: How would the vibration be
affected if the two masses on the spring were very heavy? You would probably expect the
vibration to be very slow because of the large mass. The same is true for atoms of greater mass–
the heavier the atoms, the slower the bond vibration and hence the smaller the vibrational
frequency. Now, again thinking of the system in Figure 2, how do you think the vibration would
be affected if the spring were very tight? You would now probably expect the vibration to be
very fast–if you have ever had a Slinky and tried to make it vibrate you know that it doesn’t
vibrate very fast because it is a very loose spring. The same is true of molecular bonds–stronger
bonds, like double or triple bonds, vibrate faster than weaker bonds, like single bonds. So the
stronger the bond, the faster the vibration and the higher the frequency; the heavier the atoms, the
slower the vibration and the smaller the frequency. Mathematically,
2
⎛
⎜
f
1 ⎜
ν=
⎜
2πc ⎜ M x M y
⎜ M +M
y
⎝ x
1
⎞2
⎟
⎟
⎟
⎟
⎟
⎠
where f is called the force constant and essentially accounts for the strength of the bond. Mx and
My are the masses of the two bonded atoms.
Let’s reiterate this relationship with some specific examples. The mass dependence of ν
means that an O-H bond will have a higher frequency than either a C=O or a C-O bond because
hydrogen is less massive than carbon. We would also expect the C=O bond to absorb IR light at
a higher frequency than the C-O bond because double bonds are stronger than single bonds. The
experimental values for these bonds are:
Bond Stretch
Vibrational Frequency, cm-1
O-H
3200 – 3650
C=O
1700 – 1850
C-O
1070 – 1150
You may be wondering about the strange frequency units of cm-1. These are called
wavenumbers. A wavenumber, ν⎯, is equal to 1/λ, where λ is the wavelength of excitation. It is
related to the frequency in Hertz (1/s) through the speed of light:
ν⎯ = ν/c
Considering units, this definition makes sense because frequency in Hertz has units of 1/s and the
speed of light has units of m/s. Dividing frequency by the speed of light then gives units of 1/m.
Traditionally, wavenumbers have units of 1/cm, so we need to divide by 100 to get 1/cm.
The truly powerful aspect of this is that these frequency values change only slightly for
different molecules with the same pair of atoms bonded. For example, consider pentane, C5H12,
and butanol (actually 2-butanol since the OH is on the second carbon), C4H10O:
H
H
H
H
H
H
C
C
C
C
C
H
H
H
H
H
H
Figure 3. Pentane
6-3
Figure 4.
2-Butanol.
Both are quite different molecules, but both show absorptions at a frequency of 3000 cm-1 due to
excitation of the C-H bonds (see Figures 5 and 6). Note that in Figure 5 you can also see an
absorption at approximately 1500 cm-1 which is due to an excitation of a C-C bond; in Figure 6
there are absorptions at 1000, 1500, 2950, and 3500 cm-1 corresponding to stretches of C-O, C-C,
C-H, and O-H bonds. The process of identifying certain bonding groups by their placement in an
IR absorption spectrum
is called fingerprinting,
and is one method of
determining molecular
structure, particularly
certain reactive groups
in organic (carboncontaining) molecules
which are termed
functional groups.
Figure 5: Infrared Spectrum of Pentane3
Figure 6: Infrared Spectrum of 2-butanol3
4
In this laboratory you will look at a small organic molecule from the list below, as well a
polymer:
$
$
$
$
$
acetone, C3H6O
acetaldehyde, C2H4O
diethyl ether, C4H10O
ethanol, C2H6O
methanol, CH4O
Organic compounds such as these are often classified by the functional groups that they contain.
A functional group is a certain arrangement of atoms that is frequently seen in organic
molecules, provides many of the molecules properties (both physical and chemical) and is often
used as a means of classification. A partial list of functional groups is provided toward the end
of these instructions. All of these molecules above obviously have an oxygen in their structures,
which is what defines the functional group in each case. Acetone is classified as a ketone,
acetaldehyde as an aldehyde, diethyl ether (not surprisingly) is an ether, and both ethanol and
methanol are alcohols.
You should also bring in a sample of some polymer for which you will find the infrared
spectrum (and possibly the formula as well.) From the IR spectrum you will identify many of
the bond types present in the polymer as well as potential the actual chemical composition.
Prelab Exercise
Answer the following and be prepared to turn them in:
1) What changes in the molecule does IR spectroscopy allow us to observe?
2) Energetically, how do these changes compare to the excitation states observed previously
in the atomic emission/absorption lab?
3) You should also have drawn the structures for the following compounds: acetaldehyde,
acetone, diethyl ether, ethanol, methanol, chloroform
Experiment Logistics
Your LA will arrange your class into five or six groups, assign each group a specific
simple molecule that they will investigate on the computer and also build a model. You will also
determine the IR spectrum of this compound as well as the IR for each of your polymer samples.
After each group is assigned a molecule, one LA will help rotate the groups through the usage of
the IR spectrometer. The three portions of the lab are outlined below. Since one of your LAs
will be mainly working with the IR, you are expected to handle the computer aspect mostly on
your own.
6-5
Procedure
Using the IR spectrometer
Liquid Samples
For the small organic molecules that you are sampling, you will need to prepare the
computer to take a scan (click on the scan button, then enter the name of the compound along
with any additional compounds.) You will need to put one or two drops on the center of the
metal disk and begin the scan. If you have a particularly volatile sample, you may need to add
another drop or two as the sample scans. If you get a warning that the bands are too weak,
accept it anyway and look for yourself to see if there are obvious peaks. If the peaks are indeed
really weak, then you may need to rescan the sample (be sure that the is liquid on the spot in the
center of the disc during the scan.
Plastic Sample
Again, prepare the computer for a scan by clicking on the scan button then entering the
pertinent information about your sample. Then click on the monitor button (within the scan
setup window). This should take you to a window that shows the “Force Gauge.” Place your
sample on the center of the disc and then move the pin directly over the sample. Tighten the pin
down on your sample and increase the pressure until the force gauge reaches about 75. This
pressure should be good for most samples. You can then click on the “stop” button followed by
the “scan” button to begin the scan.
Examining the spectrum
The most important information that you will get from your spectrum is the location of
the peaks. If you click on the “Peaks” button, this will automatically label your peaks. If you
happen to find that a major peak remains unlabeled, then you will need to click on the “VCusr”
button to bring up a cursor. Move the cursor to the desired local and double click on the green
cursor line to label a peak. You can then print out a spectrum of your sample.
Assigning Absorptions
Once you have your IR spectrum you will want to try to identify what types of bonds are
present in your compound (based on the peaks.) Use Table 1 as a reference for matching spectral
peaks with bond types. Be careful as you may observe many more peaks than you will be able to
assign; focus on the most intense peaks, particularly ones above 1500 cm-1. If a specific recycle
symbol is present on your plastic, you should determine what material it is (the internet is good
for this) as well as the structural formula. If your polymer does not have a recycle symbol on it,
then compare your spectrum to other groups’ and see if you can find someone else who had the
same polymer.
Computer Calculations and model building
The second portion of the lab will be to use the computer to help you visualize exactly
how a molecule reacts to the IR light, specifically trying to identify the atomic movement that
results from excitation at the different wavelengths of light. In the lab we will be using the
6
program GaussView 2.1 to help us visualize the molecular movements. All the students in the
group should take turns using the program.
Molecule Loading/Building
You will need to start GaussView 2.1 if it is not already running on the computer. Upon
starting, an error “Cannot find wordpad.exe” will come up. Hit okay and the program will start.
Three windows will appear. You can then either open an existing molecule file or build a
molecule from scratch.
You should begin by building your assigned molecule. To build a new molecule, use the builder
window to select the atom (and geometry) you wish to add and click in the “View” window to
add the atom. Clicking on a hydrogen (white sphere) will add the atom to an existing atom
forming a single bond. You can change atom type by clicking on the periodic table button and
selecting a new atom type. You can the change the bonding type by clicking on the bonding
button (2 below the periodic table.) [Yes, this is more obvious if you actually have the computer
running in front of you.] All single bonds are assumed to be connected to hydrogen (so you do
not have to specifically add them.) At any time the molecule that you are building (or viewing)
can be rotated by left clicking inside the view box and holding the button down while moving the
mouse. This will better allow you to view the molecule in 3D.
Performing Calculations
Once you have built a molecule you will need to use the program to calculate the IR
vibrations. First click on the “Clean” button on the builder and this should pretty up your
structure. You can then start the calculation by opening the “Calculate” menu and selecting
“Gaussian.” This will bring up a new window called “Gaussian Calculation Setup.” Here we
must instruct the program what to calculate. For Job type select “Frequency” from the button
menu and in the box labeled Method, change the button saying “Hartee-Fock” to “MP2”. Click
on Submit and let the computer begin its calculations. It will ask you if you want to save the file,
click on yes and give the computer a name for the molecule. A Gaussian 98 window will appear
and it will begin the calculation (this may take some time. The calculation time for this method
increases approximately by the square of the number of atoms.) Meanwhile you may wish to
look at some of the other pre-calculated molecules. You will only need to calculate your own
molecule.
Examining Molecules
First you will have to open up a molecule file. Open a (molecule name).log file under the
File/Open menu. Upon doing this, the selected molecule should appear in a new View window.
This molecule can be rotated as before by using the left mouse button and moving the mouse at
the same time. To view the vibrational movements, select “Vibrations” under the Results menu.
This will bring up a new window. You can select any of the calculated vibrations in the pull
down menu which shows the frequency and the relative intensity. Click the “start” button to
have the computer put the molecule in motion. You can scroll through the different frequencies
6-7
to see the different ways that the molecule can stretch, bend and twist (and yes, molecule are
constantly doing all these.) If you decrease the Frames/Cycle (using the slide bar) the movement
will appear to go faster or slower. If you click on “spectrum” it will show you what the predicted
spectrum will look like (though it has no width to the peaks.) You should compare this to your
obtained spectrum to see how well they compare. You are highly encouraged to look at other
molecules to see a range of different atomic motions. You may also calculate other molecules if
you wish. See the section below and keep in mind that molecules with fewer atoms calculate
much quicker!
General Comments about Calculations
It is important to recognize the strength and weakness of calculations. First, the
calculations that you are doing are being done on a single molecule (there are no intermolecular
interactions present here.) Thus the calculation is most like examining a single molecule in the
gas phase. The IR that you are taking on the instrument in lab though, is taken of molecules in
the liquid state. Secondly, the MP2 calculations that you are doing (and are done for you) are all
based originally on experimental data. This data mostly comes from simple molecules and then
is extrapolated to whatever molecules you submit. In this case we would expect fairly accurate
calculations since we are using simple molecules. Other more complex calculations can rely less
on experimental data, but the computational requirement increase at a power of 3, 4 or more
based on the number of atoms. Thus the computer in lab would take days, weeks or months to
do some only moderately more complicated molecules.
Building the model using the kit
Each group will be provided with a molecular model kit. These have balls which represent
various atoms (eg yellow-H; black-C; red-O etc) and coils which are used for bonds. You are to
build a model of your assigned molecule using the appropriate color balls. Notice how each
bond can bend and vibrate. Draw a diagram of the molecule showing the 3-Demensional
structure. Give the basis shape of all interior atoms and the hybridization of the orbitals on these
atoms (pg 417 of text). Indicate the major vibrational frequency of each bond.
Making Nylon
Nylon, a common polymer, is formed by a condensation reaction but its structure can vary.
Analyzing a piece of nylon fiber using an IR can display the bond structures for that particular
sample. Nylon is prepared by combining the two monomer units, sebacoyl chloride in hexane
and 1,6 hexanediamine in water. Since the hexane and water are immiscible, an interface is
created the polymer is formed.
8
Æ
+
+
You will be provided with solutions of 0.05 M 1,6 hexanediamine and 0.02 M sebacoyl chloride
in hexane.
Place 25 ml of the 1,6 hexanediamine in a 100 ml beaker. Place a stirring rod in the center of the
beaker and carefully pour 25 ml of the sebacoyl chloride solution down the glass rod taking care
not to disrupt the interface. Carefully remove the glass rod and use a forceps to pull a string of
the nylon. How long can you make a single strand? To do this, follow the example that will be
done by the LA in lab. Rinse the nylon in an ethanol/water bath. Examine the FTIR spectrum of
the nylon. After you are done observing and stretching the sample, dispose of the nylon in the
solid waste container.
Report
This report will be written with the other members of your group. Your report will
consist of the following:
1.
2.
3.
4.
The spectrum of your small organic molecule with labeled peaks (indicating bond type
they correspond to) as well as the molecular structure. For one peak you will also need to
indicate the molecular motion that gives rise to that peak.
The drawing of the 3-Demensional structure of your molecule, showing the angles and
shape of all internal atoms and the hybridization of the orbitals.
The spectrum of the nylon you made. This should have the type of bond indicated by
each peak above 1400 cm-1 labeled.
The spectrum of your plastics. This should have on it labeled the type of bond indicated
by each peak above 1400 cm-1. Additionally you should include small description of
what the plastic was as well as the structural formula (if determined.)
Also, answer the following questions:
1. How does the molecular structure of the nylon account for its resistance to tearing?
2. Where does the formation of nylon occur?
3. You know that an interface is formed between the immiscible liquids hexane and water.
Why is it necessary that the liquids be immiscible and what would happen if they were
miscible?
4. What are the bond types for the nylon? What intermolecular forces are present?
6-9
Lastly, draw out the step by step mechanism to show how two monomers combine to form a
dimer of the polymer.
Although this “lab report” will not be due until the following week, you may wish to treat
yourself and sit down with your partners and try to finish it before then end of the lab session.
Once the LA has helped everyone collect their data and pull the nylon, they will then be
available for any questions you might have.
Chemicals
acetaldehyde, acetone, diethyl ether, ethanol, methanol, chloroform.
Chemical Disposal
Dispose of chemicals in the appropriate waste container.
Equipment
50 mL volumetric for organic solutions, pipets, salt windows, cell holder, o-ring, pens for plotter.
References
1.
A. Streitwieser, Jr., and C. H. Heathcock, Introduction to Organic Chemistry; Macmillan:
New York, 1985.
2.
J. E. Swartz and K. Schladetzky, J. Chem. Ed., 73 188 (1996).
3.
SDBS Spectral Data Base for Organic Molecules, http://riodb01.ibase.aist.go.jp/sdbs/cgibin/cre_index.cgi?lang=eng accessed on October 21, 2000.
10
Table 1: Some common bond types and IR stretching frequencies
Bond
C-H
C=C
Type of bond
Specific type of
bond
Absorption range and intensity
Alkyl (saturated) methyl
1380 cm-1 (weak), 1460 cm-1 (strong) and
2900-3000 cm-1 (strong to medium)
Alkyl
(unsaturated)
3000-3050 cm-1 (weak to medium)
benzene/sub.
benzene
alkynes
3300 cm-1 (medium)
aldehydes
2720, 2820 cm-1 (medium)
acyclic C=C
1650 cm-1 (medium)
alkenes
aromatic C=C
1450, 1500, 1580, 1600 cm-1 (strong to
weak) - always ALL 4!
C≡C
alkyne
2050 cm-1 (weak)
C=O
saturated
aldehyde/ketone aliph./cyclic 6membered
1650-1775 cm-1
O-H
alcohols
3500-3700 cm-1 (concentrating samples
broadens the band and moves it to 32003400 cm-1)
N-H
primary amines
doublet between 3400-3500 cm-1 and
1560-1640 cm-1 (strong)
secondary
amines
above 3000 cm-1 (medium to weak)
C-O
alcohols
ethers
C-N
primary
1050±10 cm-1
secondary
around 1100 cm-1
tertiary
1150-1200 cm-1
aliphatic
1120 cm-1
aromatic
1220-1260 cm-1
carboxylic acids
1250-1300 cm-1
esters
1100-1300 cm-1 (two bands - distinction to
ketones, which do not posess C-O!)
aliphatic amines
1020-1220 cm-1 (often overlapped)
1615-1700 cm-1
C=N
6-11
2210-2260 cm-1
nitriles
C≡N
C-X (X=F,
fluoroalkanes
Cl, Br, I)
1000-1100 cm-1
ordinary
chloroalkanes
540-760 cm-1 (medium to weak)
bromoalkanes
below 600 cm-1
iodoalkanes
below 600 cm-1
Table of some Organic Chemistry Functional Groups
(R, R', R" = any organic group; R', R" can be H if attached to N)
O
R H
Alkane
-ane
H
Aldehyde
-al
R'
Ketone
-one
OH
Carboxylic Acid
-ic acid
OR'
Ester
R’ R-ate
NR'R"
Amide
-amide
R
O
R
Alkene
-ene
R
O
R
Alkyne
-yne
R
O
Aromatic
(Phenyl)
R
R X
R
Alkyl Halide
O
(X = F, Cl, Br, I)
-halide
R OH
R O
R'
R
Alcohol
-ol
R NR'R"
Amine
-amine
Ether
… ether
R C N
Nitrile
-nitrile
12
Appendix 1
INFRARED SPECTROSCOPY: Instrumentation
An IR spectrometer is similar to the Spec 401s you used last week in that it has a light
source, sample holder, and a detector. Like the Spec 401s detector, the IR spectrometer’s
detector also detects the decrease in light intensity by the presence of an absorbing sample. The
only difference between the two detectors is that the IR detector detects light below the visible
range. You will note that you do not need to “zero” the IR spectrometer; this is because the IR
spectrometer has its light from the light source split into two beams and one beam passes through
the sample (this is I–see the Beer’s law lab) while the other beam does not (this is I0). The
“double beam spectrometers” typically give more accurate results since the instrument can adjust
for zero “on the fly”.
The other major difference between this spectrometer and others is the method by which
it scans the IR spectrum. Before the incident light beam is split into two beams, the IR spectrum
sends the initial beam into two directions–in one direction is simply a mirror which sends the
beam back the way it came in, while the other direction has a movable mirror (which also sends
the beam back the way it came). The purpose of the movable mirror is to produce interference
between the light beam sent to the fixed mirror and the beam sent to the movable mirror, which
will produce a (predictable) fluctuation in the power of the radiation ultimately striking the
detector. If the movable mirror is translated in either direction by a distance equal to 1/4 of a
wavelength, this will change the overall path of this light beam by half a wavelength (remember
that the light reflected from the beamsplitter to the movable mirror has to travel this distance
twice–once to the mirror and once back to the beamsplitter). This results in destructive
interference at the detector, and the power of the combined beams will therefore be zero. If the
movable mirror is translated a distance of half a wavelength, then the overall path of the light
beam is changed by one wavelength. The combined beams will then be back in phase, and the
detector will read a maximum value of power due to constructive interference between the two
beams. A plot of the detector power versus time (since the movable mirror moves in time) is
called an interferogram.
The point of all this is that for a polychromatic source, each individual frequency can be
considered to have its own sinusoidal oscillation, and the resulting interferogram is the sum of all
these oscillations. Thus, when the movable mirror is positioned so that the two paths from the
beamsplitter are equal in distance, all the waves are in phase, and constructive interference will
produce a maximum at the detector. As the mirror is translated away from this position, the
waves damp to an average value. Through the mathematical process known as the Fourier
transform, one can obtain the spectrum (a plot of detector power against frequency) from the
interferogram. Such an IR spectrometer utilizing a movable mirror and therefore the Fourier
transform technique is called a Fourier Transform Infrared Spectrometer or FTIR. For those of
you math nerds, this shows that the Fourier Transform is extremely useful here and in other
instrumentation.
6-13
Figure 7. Schematic of the Perkin-Elmer 1605 FTIR.
References
1.
D.A. Skoog, “Principles of Instrumental Analysis”, Saunders College Publishing, New
York: NY, 1985.
2.
J.D. Ingle, Jr., and S.R. Crouch, “Spectrochemical Analysis”, Prentice Hall, Englewood
Cliffs: NJ, 1988.
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