COMPUTER EXERCISES: General Information

The computer-based component for CH 210C is an important adjunct to the “wet chemistry” part of the course. A set of
exercises is available that will acquaint you with various ways in which computer software can enrich your laboratory
experience. The exercises require that you work with the following two different softwares: the “Spectra” program located
on the web, which allows detailed analysis of 1H NMR spectra and IR Spectra; and the “ChemSketch” program for drawing
chemical structures and predicting 13C NMR chemical shifts.

Some of the exercises will require that you use the machines housed in the departmental computer laboratory, WEL 2.306.
Because there are a large number of students enrolled in the course this semester, the limit in the number of machines
running ChemSketch requires that you perform assignments in the computer facility in a timely manner. In other words, if
you wait until the last minute to do an assignment, you may not get the needed access to a machine to meet the specified
deadline. So plan your time accordingly!!

The departmental computer laboratory will be open M–Th from 9 AM to 10:45 PM, Friday from 9 AM to 7:45 PM and
Sunday from 2–10:45 PM. It is closed on Saturday. Students enrolled in chemistry and biochemistry courses are given
priority access to the computers between 9 AM and 5 PM.

Note: Some of the assignments require that you print the results of your work. If you are using the computers in the
departmental laboratory, there may be significant delays in receiving your printouts. We suggest that you enter your output
in the printing queue and return to the laboratory at a later time to pick it up.

Finally, when working with the various software, do not hesitate to seek assistance if you experience difficulties in executing
the required commands. Your laboratory TA is knowledgeable about the software and can assist you in their use. The
proctor in the departmental computer laboratory may also be able to help, but bear in mind that such assistance is not part of
her/his “job description.”

COMPUTER EXERCISES: Directions For Chemsketch

1. Open the software by clicking Start/Programs/ACDLabs/CNMR Spectrum Generator.

2. Once a new file has appeared on the screen, make sure that you are in the “Structure” mode by ensuring that the

button, located in the top left corner of the screen, is selected. The tools you will need to use are as follows:

Allows highlighting and moving of structures.

Allows addition of bonds (single, double or triple) to a structure.

Allows the generation of “zigzag” molecular skeletons.

The carbon atom selection button. Select this button when you wish to draw carbon bonds. Select other atom
buttons when those atoms are required.

Allows the generation of a 6-membered ring. Comparable tools are available for creating other sizes of rings,
including benzene rings.

Allows you to undo any mistakes that you may have made.

Puts a charge on the atom.

Draws stereobonds directed outwards. There is also one for inwards.

3. “Highlight” the structure you’ve created by using the “pointer” tool on the upper left of the Palette menu to click on an
atom or bond of your structure; the structure should now appear surrounded by small boxes. Note that by highlighting a
 structure in this way and then putting the pointer inside the boxed area, you may move the structure wherever you wish
on the screen.

4. Note: When structures that you are generating are similar to one another, sometimes it is useful to “Copy and Paste” one
structure and then modify the copy to produce the analogous one. To do this, highlight the original structure with the
pointer, press the Command-C and then Command-V. The copy will appear and can be dragged to wherever you wish
on the page. You may then use the elemental symbol tool described above to modify the copy.

5. To calculate the 13C-NMR spectrum of your structure press the button located in the bottom left of the
screen. Once a spectrum has been generated, you will want to obtain the predicted chemical shifts of each carbon. By
moving the mouse cursor over each carbon, the corresponding peak lights up. Record the value for each carbon.

6. Be aware that the generalized algorithm used for the calculation of 13C NMR shifts is not perfect, so do not expect an
exact match between the calculated and observed 13C chemical shifts!

7. You can have each carbon numbered, where the number corresponds to a peak. To do this, pull down the “Show” menu
and make sure that the “Carbon Numbering” option is checked. You will then see that all the carbons will have numbers
that correspond to the numbers in parenthases at each peak.

8. You may print your result. To print the 13C-NMR spectrum, select print in the “Spectrum” menu. To return to
ChemSketch to draw other structures, press the “ChemSK” button located in the bottom left corner of the screen.

9. There are instructional movies and manuals available for the Chemsketch Software that you may choose to watch and
read for further instructions and help. These are located under Start/Programs/ACDLabs.

COMPUTER EXERCISES: Computer Problem Set 1, Learning Chemsketch

This problem set requires that you work on the computers located in WEL 2.306. You are reminded that only 50 computers
are loaded with the two types of software to be used, so don’t wait until the last minute to undertake this assignment!

The problems are designed to acquaint you with the ChemSketch software. Problems 1 and 2 are examples that show you
how to use the ChemSketch software available on the PCs in the computer laboratory.

1. Use the drawing software to generate the structure of benzoic acid and then use the NMR software to provide the
predicted 13C NMR Chemical shifts of the five magnetically distinct carbon atoms. Use the “numbered carbons” in the
“Show” menu.to indicate which carbon corresponds to which peak. Print out the result.

ANSWER:

a. Start ChemSketch and make sure that you are in “Structure” mode.

b. Click on one of the button that corresponds to the benzene ring. If this button is not located on the right side of the

screen, press the Table of Radicals button “ ” with the left mouse button. Then select the benzene ring.

c. Now, press the button and the button to draw the carbon atom for the carboxylic acid group. Move the cursor
over one of the carbon atoms in the benzene ring and press the left mouse button. While still holding the mouse button
down, drag it away from the benzene ring. You should now see the appearance of a CH 3 group bound to the benzene
ring.

d. Now, we need to add the oxygens. Press the oxygen atom button. Move the cursor over the newly formed CH 3 and
press the left mouse button. While still holding the mouse button down, drag it away from the CH 3. You should see the
formation of an OH group attached to the selected carbon atom. Repeat this one more time so that there are two OH
groups.

e. Now we need to make one of the oxygen-carbon bonds a double bond. Move the cursor over one of the oxygen-carbon
single bonds and press the left mouse button. You should now have a carbon-oxygen double bond.
f. Now you need to clean up the structure so that it looks presentable. You can do this by either selecting the “Clean
Structure” option in the “Tools” menu, or you can press F9. You should then have a structure that looks like the
following:

13
g. Follow step 5 in the general directions, located above, for using the ChemSketch software to predict the C NMR
spectrum. The result is shown in the figure. Ignore the fact that the oxygen atoms get numbered too.
 2. Use the software to generate a structure of 1-bromohexane and provide the predicted 13C-NMR chemical shifts of the six
magnetically distinct carbon atoms.

ANSWER:
a. Open a new file.

b. Select the and the buttons.

c. Put the cursor where you want the structure to appear and click and drag to create the acyclic bond skeleton so that six
carbon atoms are created.

d. Now select the “Bromine” atom button and the button.

e. Return to the bond skeleton, place the cursor at the end of one of the terminal carbon atoms, press the left mouse button
down and drag it away from the skeleton. This should result in the formation of a carbon-bromine bond.

f. Now clean up the structure as you did in the first problem.

g. Follow step 5 in the directions for using the ChemSketch software to calculate the 13C NMR spectrum as you did in the
first problem. You should obtain a spectra like the one below.
COMPUTER EXERCISES: Computer Problem Set 1, Learning “Spectra”

The main purpose of this problem set is to introduce you to the “Spectra” software for analyzing 1H NMR spectra. Note that
Tables 8.3 and 8.4 of the laboratory textbook provide representative data on 1H NMR chemical shifts to assist you in making
the required assignments of resonances. Tables 8.5 and 8.8 do the same for 13C NMR chemical shifts. Comparable tables are
found in your lecture textbook.

Note: may use any modern PCs or Macs you wish for working with this software as it is web based.

Note: The web address is:

http://thomsonedu.com/chemistry/book_content/049501334X_gilbert/prelabs

What you need to turn in for this assignment: (1) Answers to the questions on a separate sheet of paper; (2) the required
print-outs of the 1H NMR spectra on which you have entered the information specified in the questions; and (3) a print-out
showing the structures and associated values of predicted 13C NMR shifts as derived from using the ChemSketch software;
these structures should have the shifts located so as to be clearly visible, as shown in the “Modified” structures on the
instruction sheet for using this drawing software.

The following questions refer to file 1-bromopropane, Figure 15.7

 Note: Bold-faced words or letters in the following discussion are for purposes of emphasis only.
  Go to the web address shown above
 Click on the chapter 15 tab and select figure 15.7

1. Determine the areas of the three groups of resonances in the spectrum.

 Answer: Press the button that says Integrate. Now, using the mouse, left-click on the left side of the peak you
want to integrate and keep the button pressed. Drag the cursor over the peak until it is on the right side of the peak
and record the area. The area of the peak near  is 1.0 as is that of the peak near  2.0. The peak near  1.0 has
an area of 1.5. Ignore the peaks near 7.3 and 1.5 as they are impurities.

2. To the nearest 0.01 ppm, provide the chemical shift of each set of protons, writing these values by the corresponding
resonances on your printed spectrum. In the case of multiplets, the value should be that at the center of the multiplet.

 Answer: To do this, click on the zoom button. Move the cursor (it should look like a magnifying glass) over the
peak near 3.4 and press the left mouse button. Repeat this zooming in 2 more times.

 The shifts may then be determined by pressing the measure button. Move the cursor to the tip of the center peak. In
the box below the spectra, you should see a value of 1021 Hz and another value of 3.4 ppm. The spectra were taken
with a 300 MHz NMR and if you divide the 1021 Hz by 300, you obtain the 3.40 ppm. To go back to normal zoom,
press the unzoom button.

 Now repeat the process for the other peaks.

 The shifts for 1-bromopropane are at1.03, 1.89, and 3.4

3. For each of the resonances appearing near the chemical shifts specified below, provide (i) its multiplicity and (ii) to the
nearest 0.3 Hz, the absolute value(s) of the coupling constant(s), J, associated with each multiplet. In this analysis, count
only those peaks in a multiplet that are separated by at least 3 Hz, which serves to eliminate splittings associated with
long-range coupling and other factors. On your printed spectrum, write the multiplicities and J-values beside the
multiplet being analyzed.

i.  1.0 ii.  2.0 iii.  4.3

 Answer: For the multiplicity, zoom in to each peak as above and count the number of peaks. For the peak near 3.4,
it is a triplet.

 Answer: For the coupling constant, click on the zoom button. Move the cursor (it should look like a magnifying
glass) over the peak near 3.4 and press the left mouse button. Repeat this zooming in 6 more times.

 The coupling constants may then be determined by pressing the measure button. Move the cursor to the tip of the
far left peak and press the left mouse button. While holding the mouse button down, drag the cursor to the center of
the peak next to it (the center peak). The value appears above the read line. Note that the shifts are provided in
units of Hertz (Hz) and should be about 6.7 Hz. Now repeat the process, only start at the far right peak and move to
the center of the center peak. Again you should get a value of about 6.7 Hz.

 Repeat this process for each of the other multiplets. Doing so shows that the resonances near2.0 comprise a
sextuplet, J = 7.0 Hz, whereas those near1.0 are a triplet, J = 7.2 Hz.

4. Based on chemical shifts, integrations, and multiplicities, assign the resonances associated with the protons labeled “a–
c,” and write these assignments on your printed spectrum by the peak(s) to which they correspond. On a separate sheet
of paper, provide a justification for each of your assignments.

 Answer: The integration allows assignment of the resonances centered at1.02 as protons “c” of
the methyl group. Referring to Table 8.3 reveals that protons on a carbon atom bearing a bromine group have
chemical shifts in the region of2.5-4, whereas methylene protons on carbon atoms not bearing electron-
 withdrawing groups appear near1.3. Consequently, the resonances at3.40 are due to protons “a” and those
at1.89 are the “b” protons (the chemical shift of the “b” protons is further downfield than normal because of the
electron-withdrawing effect of the bromine group).

 Differentiation of the two methylene groups is also possible by considering their multiplicities,
which are a triplet at4.37 and a sextuplet at2.05. Thus, the “a” protons, having two nearest neighbors, should
appear as a triplet, whereas the “b” protons, with five nearest neighbors, should appear as a quintet.

5. Determine the value of /J for each set of coupled protons in 1-bromopropane and state whether the value fulfills the
criterion for successful use of the “n + 1 rule” for predicting multiplicities (Hint: see Eq. 8.11, p. 269 of your lab
textbook).

 Answer: The value, in Hz, of  for the “a” and “b” protons is 455 (1021 - 566) and J is ~6.7. The ratio /J is
~68. Similarly, /J is ~65 for the “b” and “c” protons [(566-309)/7]~37.. The criterion is fulfilled.

6. What accounts for the fact that the protons responsible for the multiplet near resonate well downfield of the others?

 Answer: One factor defining chemical shifts is the present of electronegative and/or electron-withdrawing
substituents. As a general rule, the nearer protons are to such a functionality, the larger their chemical shift (the
further downfield they appear).

7. The 13C NMR resonances reported for 1bromopropane are, 26.2, and 35.9. Assign these resonances to the carbon
atoms responsible for them and write the answer on your printout of the 1H NMR spectrum.

 Answer: First, use the Chemsketch software to obtain predicted values for this molecule. These values are shown
below.