O R G A N I C L I G U I D S , I R & G C

Experiment

7
Organic liquids: Infrared spectroscopy and
separation by gas chromatography.
Skeletal structures.

INTRODUCTION
In the first part of this experiment you will use infrared spectroscopy to confirm identity of your
“unknown” organic liquid.
The infrared (IR) is the segment of the electromagnetic spectrum lying between the visible and the
microwave regions (wavelengths of 2.5×10-6m to 25×10-6m). Since 10-6m is a micrometer, μm, the range is
from 2.5 to 25 μm. Any compound containing covalent bonds absorbs electromagnetic radiation in the
infrared region of the spectrum.
In the absorption process, those VIS
frequencies of infrared radiation X-Rays Microwave
that match the natural Gamma UV IR
vibrational frequencies of a Rays Radio
molecule are absorbed, and the
energy absorbed increases the
amplitude of the vibrational
motions of the bonds in the
molecule. The vibrations are of two types, bond stretches and bond angle bends.
The stretching frequency of a bond increases with the strength of the bond but decreases with the
masses of the atoms joined by the bond. In the unknown liquids, there are five types of bonds. Recall that
the higher the energy and frequency of radiation, the shorter the wavelength,
E = hν = hc/λ
where h is Planck's constant and equals 6.63x10-34 Joules-second, c is the speed of light in a vacuum and
equals 3.00x108 m/s, ν represents frequency and λ represents wavelength. To avoid the inverse relationship
between wavelength and energy, the reciprocal of the wavelength (called wavenumber) is cited in units of
reciprocal centimeters, cm-1. 1 μm (micron) = 10-4 cm and 1 μm-1 = 104 cm-1.

In another part of this experiment, the compounds in a mixture will be separated by gas
chromatography. In a gas chromatograph (GC), a sample of gases is blown by an inert carrier gas
across the surface of an adsorbent on the walls of a chromatographic column. Typically, the
component with the highest vapor pressure is held back least by the adsorbent and travels the fastest
over the surface of the adsorbent. The time it takes for a particular compound to pass through the
system (from the column inlet to the detector) is called the retention time. At the exit end of the
column, the components generally leave in order of declining vapor pressure at room temperature (or
increasing normal boiling point). The temperature of the column can be programmed so that it starts
at a low value with only very volatile compounds getting through it, and then the temperature of the
column is increased to get components of relatively low vapor pressure off the column.
In the last part of this experiment you will use the chemical drawing software package ChemDraw
available in the lab to draw skeletal structures of all 11 organic liquids from the Table of Liquids.

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IR SPECTRA
-1
Name Symbol Absorbances at wavenumbers (cm )
3600-3100 3100-2700 1800-1600 1600-1300 1300-1000
methyl alcohol A-1 3347 2939 1458 1033
ethyl alcohol A-2 3362 2975 1381 1051
propyl alcohol A-3 3350 2964 1458 1056
isopropyl alcohol A-4 3334 2972 1380 1130
methyl acetate E-1 2956 1760 1439 &1372 1275&1049
ethyl acetate E-2 2985 1743 1375 1243&1049
normal propyl acetate E-3 2972 1747 1366 1230&1065
isopropyl acetate E-4 2983 1741 1375 1250&1112
dimethyl ketone K-1 3005 1711 1364 1223
methyl ethyl ketone K-2 2958 1718 1363 1173
diethyl ketone K-3 2944 1711 1461&1415 1122

Bond Energy Bond Stretch

Bond type
(kJ/mol) Wavelength (μm) Wavenumber (cm-1)
O-H 464 2.8 - 3.2 3600 - 3100
C-H 414 3.3 - 3.5 3300 - 2800
C=O 736 5.7 - 5.8 1800 - 1600
C-O 360 8.0 - 10.0 1300 - 1000
C-C 347 longer than 12 less than 850

Angle Bend
Group Wavelength (μm) Wavenumber (cm-1)
CH2 6.8 - 6.9 1500 - 1450
CH3 6.9 - 7.3 1450 - 1350
C-C(=O)-C in ketones 9.1 - 8.1 1230 - 1100

PROCEDURE
Part 1. Infrared spectrum of organic liquid
Step 1. Obtain two 25 × 4 mm KCl crystal windows and put them on a paper towel. Moisten a
Kimwipe with a dichloromethane (also called methylene chloride), CH2Cl2, and wipe the two
KCl windows with it. Wear rubber gloves!
Step 2. Place one Teflon spacer into a hex metal holder and insert one of the KCl windows
on the spacer. Put few drops of your liquid on this window. Tilt it slightly to spread the
drop over the window. Cover the sample with the second KCl window before the liquid has
evaporated and screw a plastic retainer with another Teflon spacer until the assembly is
sealed. The seal must be firm but not too tight, because a tight turn may damage the potassium chloride
windows. Use more drops for more volatile liquids.
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Starting Nicolet FT-IR instrument

1) Open OMNIC program
2) Check that in the Experiment pull-down menu Default IR200 Chem18_19 is selected
3) Click on Col Bkg to run background scan
4) When asked “Add to window ?” click No
Instrument is now ready for the measurement
Step 3. Recording a spectrum.
Place the prepared cell in the cell compartment, metal end of the
hex holder next to the metal inset. Cover the sample. Click Col
Sample.
When asked for title Enter your liquid label and your name, e.g. MB03
John DOE. Then click OK.
When asked “Add to window?”, click Yes.
Click Find Peaks to annotate the spectrum. Click Replace.
Adjust the view of your plot using arrows or tools in display setup.
Save the plot and Print two copies of your IR spectrum.
Step 4. Remove the cell from the spectrometer, disassemble it and use a Kimwipe to wipe out your liquid
from the windows and the holder. WARNING: Do not use water to clean the KCl windows!
Step 5. Compare the shape and major peaks in the IR spectrum of you liquid with the spectra of 11
organic liquids and confirm identity of your liquid. Use the sorted list of compounds that have the highest
probability to be your liquid from previous lab. Then verify with your TA and enter the correct identity
of your liquid on both printouts and exchange one printout with your partner.
The annotated IR spectra of your’s and your partner’s liquid are required as part of this lab report.

Part 2. Separation of organic compounds by gas chromatography

A partnership of two students will be assigned to analyze two samples. One sample will contain a mixture of four esters (methyl
acetate, E-1 ethyl acetate, E-2 normal propyl acetate, E-3 and iso-propyl acetate, E-4) and one sample will contain an
“unknown” sample, which may include 1,2,3 or all four of these esters. Your goal is to identify all species in the unknown
sample based on the measured retention times. Your TA will demonstrate how to use the mini GC instrument.
Step 1. Obtain a glass syringe and clean and flush the syringe with acetone. Depress the plunger fully
and submerge the tip of the syringe needle the test tube with acetone. Pull back the plunger to fill the
barrel about 1/3 full of acetone and expel the liquid onto a Kimwipe. Repeat this step two more
times. Important: The glass syringe is fragile. Be careful not to bend
the needle or bend the plunger. Never pull the plunger back more than
50% of its total volume. Be careful not to bend the plunger as you press
it down. If a group of students just cleaned the syringe with acetone, skip
the cleaning and proceed to Step 3.
Turn on the mini-GC instrument and then start Logger Pro from
Desktop.
Step 2 Click Collect in Logger Pro to bring up the
Temperature-Pressure profile and set the values as shown in
the picture. Select Done to initiate the GC warm up.
Step 3 Repeat the process in Step 1 with your “known”
mixture to rinse the syringe three times with your sample.
Then draw up approximately 0.2 μL of liquid. Gently wipe

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the needle from barrel to tip with a Kimwipe. Some mini-GCs require more than 0.2 μL of liquid, higher
pressure or more than 7.0 min of total length. If this is the case, you will find this information on the mini-GC
instrument.
Step 4 When the mini-GC has reached the correct start temperature and pressure, the
message reads, “Inject and select Collect simultaneously ”. One person will operate
the syringe and the other person will operate the computer controls. Insert the needle
of the syringe into the injection port of the GC instrument. Hold the syringe with one hand
and steady the needle with your other hand as shown in Figure to prevent the possible bending of the
needle. Rotate the syringe slightly while inserting. Insert the needle into the injection port until the needle
is completely inserted inside the port.

Step 5 Simultaneously, quickly depress the syringe plunger and click Collect to begin
data collection. After the injection immediately pull the syringe out of the injection port.
While you wait for the run to finish, perform this task:
Clean the syringe as described in Step 1 with acetone and rinse and fill the syringe with the second
sample of your “unknown” mixture as described in step 3.
Step 6 Repeat steps 2-5 with the sample of your unknown mixture. Select “Store latest run and
continue” after you click on Collect.
While you wait for the second run to finish, perform this task:
Use the Examine tool (from the Analyze menu) to determine the retention times (times at which
peak maxima are located in the chromatogram). Use the Annotation tool to enter the retention times
on the plot with the compound name next to each peak.

Step 7 When the data collection with the “unknown” sample stops, determine the retention times of
compounds present in this sample. Compare the sequence of peaks and retention times of your
“unknown” sample with the “known” mixture and identify compounds in your “unknown” mixture.
Enter these retention times and compound names on the plot and also into the Table below. Add the
plot title (include your names and “Mixture of 4 esters and unknown sample” label). Using a Desktop
app “Snipping Tool” scan the plot and save it into a MS Word file. Then save this file on the Desktop. Inform your
TA that you are finished and other students can use the instrument. E-mail the plot to yourself and submit it with
your lab report.

Separation of compounds by GC
Known mixture-compounds:
Retention time (min):
Boiling point (oC)
Unknown mixture label:
Unknown mixture-compounds:
Retention time (min):

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Part 3. Drawing structures of organic compounds

Use the chemical drawing software package available in the lab to draw structures of all 11 organic
liquids from the Table of Liquids.
Tutorial for using the drawing software will be posted on LATTE. In the lab learn how to draw skeletal (carbon
and hydrogen atoms hidden) structures of organic molecules.
Annotate each structure i.e. add a name next to the structure for each molecule. The structures
created with the drawing software can be pasted into a MS Word document or printed directly. Next
to the skeletal formula on a printout draw by hand the full structure for each compound. Scan the
annotated printout and upload it on LATTE.

PLOTS
1. Identify the peaks in the chromatograms obtained in Part 3 using the mini-GC instrument. Write the
retention time and compound’s name next to each peak.

2. Identify the major peaks in the infrared spectrum of your liquid and your partner’s liquid by giving
the molecule vibration for these peaks.
Hint: Check Table with IR spectra on page 55 and find peaks at the wavenumbers listed in this Table for yours and your
partner’s liquid. In each IR spectrum annotate only the peaks at the wavenumbers that are listed in this Table. Your
annotation must include both the bond type and type of vibration. For example, a peak for normal propyl alcohol, A-3 at
3350 cm-1 should be annotated as “O – H bond stretch”.

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