Experiment 4 – Molecular Polarity and Computational Chemistry Chem 128 – Fall 2019

Introduction:

Let's introduce a concept, molecular polarity, which chemists frequently use. Polar
molecules are attracted to an electric field. On the other hand, nonpolar molecules are unaffected
by an electric field. This experiment is based upon the actions of polar and nonpolar molecules in
electric fields. Interestingly, molecular polarity also has another easily measurable effect. To a
large degree, molecular polarity determines whether or not chemical compounds are soluble in one
another as we shall examine in the second half of the experiment.
Being good scientists, chemists want to understand what makes a molecule be polar or
nonpolar at the molecular and electronic level. Molecular polarity is a function of two components
of molecules, electron distribution and molecular symmetry. Let’s look at these two components.
Electrons on molecules are not always evenly distributed across the molecule. If the molecule
contains highly electronegative elements (ex. halogen, nitrogen, or oxygen), electrons can be
concentrated in that area of the molecule. Concentration of electrons in one area of a molecule
increases the electron density (number of electrons per volume) in that area. The overall effect of
high electron density is to generate a region of localized negative charge on the molecule near the
electronegative atoms. Electrons that are concentrated in one portion of the molecule have been
removed from other regions, which decreases the electron density in that part of the molecule. This
generates a region of localized positive charge. Chemists designate the localized positive and
negative areas on molecules using the symbols δ+ and δ-, indicating the existence of partially
positive and partially negative charges, respectively, on those parts of the molecule. As shown
below, carbon monoxide and carbon dioxide are two simple molecules having electropositive and
electronegative regions indicated with the δ+ and δ- symbols. In both molecules the highly
electronegative O atoms are draining electron density away from the C atom.

Molecules containing atoms that have small or zero differences in electronegativity, like
H2 or O2, have equivalent electron distributions across the molecule, making them nonpolar.
Returning to carbon dioxide, which is a molecule consisting of two atoms, the dipole moment of
the molecule overall depends on both the polarities of the individual bonds and the geometry of
the molecule. For each bond, we consider the bond dipole, which is the dipole moment due only
to the two atoms in that bond. These bond dipoles and dipole moments are vector quantities and
have both a magnitude and direction. The dipole moment of a polyatomic molecule is the vector
sum of its bond dipoles. As shown in the CO2 figure below, the two bond dipoles in this molecule
are equal in magnitude, but opposite in direction. Adding them together, they “cancel,” and we can
say that CO2 has an overall dipole moment of zero, making it a nonpolar molecule.

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Experiment 4 – Molecular Polarity and Computational Chemistry Chem 128 – Fall 2019

Now if we consider water (H2O) below, which has two polar bonds that are identical and
equal in magnitude, we could say that these cancel. However, we have to take into consideration
the shape of the molecule, which is bent. Knowing this, the vectors cannot cancel and we observe
an overall nonzero dipole moment therefore making it a polar molecule. Here are some examples
of other molecules to help understand this concept better.

Returning to carbon monoxide and carbon dioxide, we can examine the other necessary
component of molecular polarity, symmetry, in more detail. Symmetry refers to whether or not
one side of an object corresponds in shape to the other side of the object. For example, humans are
bilaterally symmetric. If we pass a plane from head to foot through a human, as indicated below,
the left side of the body has the same shape and placement of body parts as the right side.

However, if we pass a plane across the center of our bodies, like below, we see that the top of
our bodies is not symmetric with the bottom. Humans are symmetric with respect to the first
plane and asymmetric with respect to the other.

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Experiment 4 – Molecular Polarity and Computational Chemistry Chem 128 – Fall 2019

Likewise, molecules can be symmetric with respect to one plane and asymmetric to other
planes. Carbon dioxide is symmetric with respect to two planes as shown below.

Carbon monoxide, however, is symmetric with respect to one plane and asymmetric with respect
to a second plane.

symmetric asymmetric
If we then recognize that the asymmetric plane also divides the molecule with respect to fts
partially positive and negative ends it is obvious that carbon monoxide has a property that carbon
dioxide does not. Carbon monoxide is asymmetric with respect to both atom position and charge
distribution. Molecules that have both these properties are polar. Carbon dioxide is nonpolar.
Carbon monoxide is polar. Electrons in carbon monoxide reside more frequently near the O atom
than near the C atom, generating a measurable electric and magnetic field on the molecule.

Let's look at two other simple possibilities, BF3 and NH3. BF3 is a planar molecule while NH3 is
trigonal pyramidal. This makes a significant difference in their symmetry. Because it is planar,
BF3 is symmetric. However, because NH3 is trigonal pyramidal, it is asymmetric to both atom
position and charge distribution. BF3 is nonpolar and NH3 is polar.
-
- δ
δ

+ +
+ δ δ
δ
- - +
δ δ δ
symmetric asymmetric

Deciding whether a small molecule is polar or not, can often be done on paper as described above
and explored through experiments like you will be doing in Parts A and B. In order to quantify,
however, how polar a molecule is (i.e. its dipole moment) or other molecular properties (such as
bond lengths or bond angles) more sophisticated techniques are required. In Part C of the lab, you
will be will be using the program WebMO to calculate the structural properties of the same small
molecules you used for the experiments in Parts A and B. What this means is the computer will
take the initial coordinates that you supply, and work to solve a set of mathematical equations in
order to determine the physical and chemical properties of the molecule.

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Experiment 4 – Molecular Polarity and Computational Chemistry Chem 128 – Fall 2019

Part A
When polar molecules are put in the presence of an electric field, they can align themselves as
shown below.

In the experiments in Part A you will observe how streams of liquid composed of polar vs.
nonpolar molecules react when a “charged” balloon is brought into close proximity. Before it’s
introduction, you will produce static electric field will be formed on the surface of the balloon
with a piece of felt. One possible explanation for the expected observations you will record is
that aligned molecules, such as those pictured above, result in an overall charged region which
will then react to the charge on the balloon surface.

Part B
Liquid solubility is also affected by molecular polarity. Liquids composed of polar molecules are
soluble in other liquids made of polar molecules. Nonpolar molecular liquids are soluble in other
nonpolar molecular liquids. Otherwise known as, “like dissolves like.” However, polar liquids and
nonpolar liquids are insoluble in one another. The basic cause of these solubility differences is that
the forces between molecules, intermolecular forces, are similar when polar molecules are mixed
with other polar molecules or when nonpolar molecules are mixed with nonpolar molecules. In
contrast, when nonpolar molecules are mixed with polar molecules the intermolecular forces are
so dissimilar that the molecules do not attract one another and do not dissolve. Water is a polar
molecule. Cooking oil is a mixture of nonpolar molecules. Cooking oil does not dissolve in water
because of the two liquids' intermolecular force differences.

Part C
Computational chemistry is a branch of chemistry that has been steadily growing in importance
over the last few decades. Where scientists could once only use computers to obtain information
about simple molecules without visualization, the increase in computing power over the last fifty
years has enabled an explosive growth in the versatility of computer modeling. Programs can now
be used to design new pharmaceutical drugs, test organic synthesis reactions without wasting
valuable chemicals in the laboratory, or even predict how the atmospheres of other planets behaved
in times long past. A much more common application of computational chemistry is to determine

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Experiment 4 – Molecular Polarity and Computational Chemistry Chem 128 – Fall 2019

some basic structural properties of a molecule such as the bond lengths and angles, ground-state
energy, and dipole moment.

Theoretical Models (Of Atoms and Molecules)

In order to calculate the structural properties of a molecule, the computer applies a computational
theory to a set of mathematical functions that describe the molecule; these functions are
collectively known as a basis set. While there are many different levels and types of computational
theory that can be performed, during this lab you will be using a fundamental theory known as
Hartree-Fock (the Self-Consistent Field method). It uses a set of approximations to solve the
Schrödinger equation (HΨ= EΨ) and obtain Ψ (the wavefunctions) which can be used to describe
the most probable locations of each electron (|Ψ|2). More intensive levels of theory, known as Post-
Hartree-Fock methods, provide more accurate descriptions of the system, but are more
computationally expensive in terms of resources and time.
We can use these computational theories to perform many types of calculations: ‘Molecular
Energy’, which calculates the energy of the molecule for a given set of coordinates; ‘Geometry
Optimization’, which performs multiple single-point energy calculations and moves the atoms of
the molecule until it finds the lowest energy geometry; or ‘Molecular Orbitals’, which obtains and
visualizes the electron densities of the molecule.

Finding Stable Structures of Molecules

You will be performing geometry optimizations to find the most stable structure of the molecule.
During this calculation, the program incrementally moves an atom and solves for the energy of the
molecule; if it is lower than the previous energy, the program keeps the new coordinates and
repeats the process until no lower energy is found.

The figure on the left below shows a magnified view of the energies of a molecule at various
geometries during the optimization process. The coordinates of molecule at the energy denoted by
the red circle is the most stable geometry. The figure on the right below is an example of the overall
path that the optimization process takes to find the lowest total energy of the molecule.

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Experiment 4 – Molecular Polarity and Computational Chemistry Chem 128 – Fall 2019

Procedure:

Supplies:
 Buret
 Balloons
 Felt
 6 beakers
 9 test tubes

Chemicals and hazards:

 CH2Cl2 – dichloromethane, is a skin and eye irritant
 C2H5OH – ethanol, highly flammable, and a skin and eye irritant
 CH3COCH3 – acetone, highly flammable, and a skin and eye irritant
 C6H14 – hexane, highly flammable, and a skin and eye irritant
 C6H4Cl2 – 1,2-dichlorobenzene, skin and eye irritant

Waste disposal:
Aqueous

Part A – Examining Polarity with an Electric Field

1. Your TA will assign six groups who will each

setup one of the buret stations. You will then go
around the lab and visit each station to collect your
data.
2. Label the buret station with the chemical that it
will be filled with.
3. Fill the buret completely (to the zero mark!) with
the assigned liquid. You will then use this setup
as your first station for lab today.
4. Take one of your beakers and place it under the
buret that you are at.
5. Blow up a balloon and tie it closed. Rub the
balloon several times with the provided piece of
felt until it has a significant static electric charge.
6. Open the buret stopcock until a slow and steady
stream of liquid is flowing into the beaker.
7. Hold the charged balloon near, but not in the
stream of liquid, as shown below.
*Important!* The balloon should not touch any
of the liquids. If the balloon does come in
contact with a liquid, you must discard that
balloon and start with a new one.

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Experiment 4 – Molecular Polarity and Computational Chemistry Chem 128 – Fall 2019

8. Observe what happens to the stream of liquid and record this in your lab notebook. Reserve
the liquid in your beaker for Part B.

9. Repeat the procedure with the rest of the liquids listed in the lab, using a new beaker each
time, until you’ve completed all stations.

Part B – Effect of Polarity on Solubility

1. Collect 9 test tubes from the equipment area and order them 1-9.

2. Fill the test tube 1/3 of the way with the listed solvent, and then the other 1/3 of the way
with the liquid we are observing from what you reserved in Part A according to the chart
below:

Test Tube # Solvent Liquid to observe

1 H2O Acetone
2 H2O Ethanol
3 H2O Dichloromethane
4 H2O 1,2-dichlorobenzene
5 H2O Hexane
6 Hexane Acetone
7 Hexane Ethanol
8 Hexane Dichloromethane
9 Hexane 1,2-dichlorobenzene

3. Record all observations in your lab notebook.

a. Are the two liquids soluble or insoluble in each other?
b. Do the liquids separate into two layers or is there just one layer?
c. Does this observation confirm what you learned in the balloon experiment?

Part C – Computational Chemistry

All students will work in pairs in this lab. Those students who do not have laptop computers or
tablets will have to pair up with someone who does.

The following list defines terms you will encounter while performing calculations during this lab
by summarizing the concepts discussed above and introducing others:
 Calculation: the procedure that the program performs.
 Theory: the method used to solve the Schrodinger equation.
 Basis set: a set of mathematical functions describing the atomic orbitals of an element.
 Charge: the total charge on the molecule.
 Multiplicity: proportional to the number of unpaired electrons, and is defined as ‘2S+1’.
‘S’ is the sum of the ms values of the electrons. Remember that ms=± ½. A singlet means
that there are no unpaired electrons: the number of ‘spin-up’ (+ ½) and ‘spin-down’ (- ½)

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Experiment 4 – Molecular Polarity and Computational Chemistry Chem 128 – Fall 2019

electrons is equal, which means S = 0. All calculations we perform during this lab will be
singlet. (Singlet means paramagnetic.)

WebMO Tutorial: Building and Optimizing a Molecule

The purpose of this section is to show the student how to build and optimize a molecule in the
WebMO interface, as well as perform post-calculation analysis. The student should follow these
steps and create the NO3- molecule themselves, then measure and record the geometric
parameters.

Logging In To WebMO
1. In your web browser, go to the web address https://webmo.nics.utk.edu/~webmo/cgi-
bin/webmo/login.cgi)
2. Log in using your NetID and password.
3. The first time you log in, you will have to join a group. Select Chem128 from the drop-
down menu and enter the group password, which your TA will provide during lab.

Once you have logged into the WebMO server, select New Job to open the molecule builder.

To begin building the molecule, choose the drop-down menu ‘Tools’, and ensure ‘Build’ is
selected.

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Experiment 4 – Molecular Polarity and Computational Chemistry Chem 128 – Fall 2019

Click on the drop-down menu ‘Build’, then select ‘N’. (Or click the periodic table along the
ribbon on the left side of the screen, and select the element there.) Click in the white box to place
nitrogen.

Repeat the previous step, this time selecting the element ‘O’. Click and drag from the nitrogen
outwards to place oxygen bonded to the nitrogen. Repeat two more times in different directions
so there are 3 oxygens bound to the nitrogen.
If the three bonds are not dual-colored, the molecule is not built correctly. To delete an
incorrectly placed atom, select ‘Adjust’ (as specified in the next step), and then click on the
atom you wish to remove to select it. The ‘backspace’ key or the ‘Delete Selection’ option in the
‘Adjust’ menu will remove the highlighted object(s).

Click on the ‘Adjust’ button in the left bar (or the ‘Tools’ menu, then select ‘Adjust’). Right
click one of the oxygen atoms and set its charge to ‘-1’ to change the total charge of the molecule
to ‘-1’.

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Experiment 4 – Molecular Polarity and Computational Chemistry Chem 128 – Fall 2019

Click the arrow in the bottom-right corner to proceed to the job submission window and ensure
that the job options match the image below.

Submit the job by once again clicking the arrow in the bottom-right corner; once the job has
finished running successfully, click on the name of the job to open the output.

Click the ‘Adjust’ icon on left toolbar (looks like a mouse):

To obtain bond length:

‐ Click on the central nitrogen atom (1) then one of the oxygens (2), and record bond
length.

‐ Repeat steps for the other two N-O bonds with oxygens (3) and (4).

To obtain bond angle:

‐ Click on an oxygen (2), then the central nitrogen atom (1), then a different oxygen (3).

Repeat steps for the two other O-N-O angles (2-1-4, 3-1-4).

Molecular Calculations
You are now ready to begin modeling the molecules you investigated in Parts A and B. The
molecules are split into two groups as listed below. For each molecule, follow the procedure below
for its group and be sure to record the required information in the tables provided. You will use

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Experiment 4 – Molecular Polarity and Computational Chemistry Chem 128 – Fall 2019

these results (and images) to answer post-lab questions about the properties and structures of the
molecules.

 Group 1: water (H2O), ethanol (C2H6O), acetone (C3H6O), hexane (C6H14),

dichloromethane (CH2Cl2)
 Group 2: benzene (C6H6) and 1,2-dichlorobenzene (C6H4Cl2)

Molecules in Group 1:
1. Use the internet to look up the structure for each molecule and draw it in your lab notebook.

2. Draw each one of the molecules from Group 1 on your computer or tablet screen in WebMO
using the instructions provided in the WebMO Tutorial previously. Don’t worry about
drawing a perfect structure, just make sure the atoms are bound together correctly.
Note: When drawing the molecules from Group 1, it is more time-efficient to draw the
period 2 & 3 elements (C, Cl, O) and then ‘Add Hydrogens’ using the ‘Cleanup’ menu.

3. Once a molecule is drawn on your screen, before submitting the job, clean up your
structure by selecting the ‘Cleanup’ menu, then ‘Comprehensive – Idealized’. This will
greatly reduce the amount of time required to optimize the geometry of the molecule.

Does the idealized geometry look similar to what you would predict using VSEPR theory?

4. The only box you need to change before submitting your job is the ‘Calculation’ to
‘Geometry Optimization’. Submit the job and wait for the geometry optimization to
finish; this should take no more than five minutes. Once it has done so, open the job and
record the bond lengths and bond angles of the molecule in the tables provided. The dipole
moment of the molecule can be found just below the ‘View Job’ window, in a table titled
‘Calculated Quantities’. Be sure to record the information requested in Table 1 below
into your lab notebook.

What does the dipole moment tell you about the molecule?

5. Take a screenshot of each molecule before you leave the lab. Windows users can use the
‘PrtSc’ button and paste the resulting image into the Paint program. Mac users may use the
sequence ‘Command + Control + Shift + 4’ to click and drag a selection over the area they
wish to capture; the resultant image will be copied to the clipboard and can be easily pasted
into Microsoft Word or PowerPoint.

6. WebMO can also detect the types of symmetry elements discussed in the introduction.
Click the Display Symmetry Elements icon ( ) in the 3-D Editor or Visualizer toolbar to
view these and make notes about what you observe.

Molecules in Group 2:
Unlike the molecules of Group 1, the molecules of Group 2 have a benzene core, as a result it is
more efficient to use the benzene fragment available in the fragment option in the build menu.

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Experiment 4 – Molecular Polarity and Computational Chemistry Chem 128 – Fall 2019

1. Click on the Build button. From the "Build" pull-down menu, select the "fragment" option.
A new dialogue box will appear. Select “Ring” and then “Benzene.” When these options
are selected, select "OK." In the "builder" window, click anywhere and a benzene ring
should appear.

2. Build the rest of the molecule using individual atoms as was done for Group 1.

3. As done in Group 1, optimize the geometry of your molecule. Once the geometry
optimization of the molecule has finished, record the bond lengths, bond angles, and dipole
moment just as you did for the molecules in Group 1. But now we also have a 4th column:
bond order. These are in a table labeled ‘Bond Order’ at the bottom of the output.

4. Record screenshots of each molecule as you did for Group 1.

5. Molecular orbitals (MOs) are combinations of atomic orbitals that describe the most
probable locations of the electrons of the molecule. To view an individual MO them for
your molecule, navigate to the Molecular Orbitals section of Calculated Quantities and
click on the View icon ( ) for the molecular orbital of interest. For both of the Group 2
molecules, take screen shots of the 11th molecular orbital.

Table 1: Group 1 molecular properties

Molecule Bond Length(s) (Å) Bond Angle(s) Dipole Moment (D)
C-H:
C3H6O C-O: O-C-C:
C-C:
C-H:
C-O:
C2H6O C-O-H:
O-H:
C-C:
H2O O-H: H-O-H:
C-C:
C6H14 H-C-H:
C-H:
C-H:
CH2Cl2 Cl-C-H:
C-Cl:

Table 2: Group 2 molecular properties

Bond Length(s) Dipole Moment
Molecule Bond Angle(s) Bond Order
(Å) (D)
C-C: C-C:
C6H6 H-C-C:
C-H:
C-C: C-C:
Cl-C-C:
C6H4Cl2 C-H:
H-C-C:
C-Cl:

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