Molecular Modeling
Minneapolis Community and Technical College
v.9.15
Before you come to lab:

Complete the Lewis dot structures for all 15 molecules (see listings and worksheets in this
handout). Your Lewis structures will be checked for completion at the beginning of lab.

You should also bring your textbook or a copy of the table on pg. 370 (2nd edition) for reference.
Introduction
Over the years, chemists have used many clever and innovative ways to display molecules, atoms and chemical
bonds. These days plastic molecular modeling kits are often used by students in general and organic chemistry
courses. By building three dimensional models you can develop an appreciation for the molecular shapes as they are
seen, touched and rotated.
Obtaining a molecule’s structure follows a series of steps:
 Determine the Lewis Dot Structure
 Determine the number of regions of high electron density around the centermost atom and use it to decide
electronic and molecular geometries.
o Electronic geometries are names given to the shapes of molecules determined using Valence Shell
Electron Pair Repulsion (VSEPR) theory.
o Molecular geometries are names given to the shapes of molecules with invisible lone pair electrons.
 Use valence bond theory to determine how atomic orbitals can be mixed together to reproduce the electronic
geometries previously determined.
ChemBio 3D Ultra
After you have constructed physical models of several molecules, you will use ChemBio 3D Ultra to explore other
molecular properties and more complex molecules. ChemBio 3D Ultra is a computer program that permits the
construction, optimization and manipulation of both simple and complex molecules.
After opening a molecular file you must first perform an MM2 energy minimization before attempting anything else.
As you will observe, ChemBio 3D Ultra systematically moves atoms around in ways to reduce the molecule’s energy.
When the lowest energy arrangement is found, the program stops and presents its results; an optimized molecule
with atoms in all the correct positions. If a reasonable arrangement of atoms cannot be found, it may be necessary
to manually move them to new starting positions and the try MM2 again.
After MM2 is completed successfully we can perform a GAMESS calculation which determines bond angles, bond
lengths, molecular energies and dipole moments for the molecule of interest. Instructions for these determinations
can be found in the “Recipes” section of this packet.
Dipole moments
ChemBio 3D Ultra can calculate dipole moments for various molecules. Dipole moments for several families of
molecules are determined to see if the results are consistent with our predictions.
As discussed in class, the dipole moment of a molecule is the result of differences in electronegativities resulting in
polar bonds. If the polar bonds shift electrons in a common direction, the entire molecule will be polar which means
it will have positive and negative ends. In some cases the polar bonds point in opposite directions thus cancelling
themselves out. In these cases the bonds are polar but the molecule is non-polar.
It is true that the dipole moment depends on the differences in electronegativities, but the dipole moment also
depends on the distances that separate the positive and negative poles or ends of the molecule. The mathematical
definition for dipole moment is:
=qd
where  is the dipole moment, q is the charge at one end of the molecule and d is the separation between the
positive and negative poles. Thus, the dipole moment for a molecule can be large if the electronegativity differences
OR the charge separation distances are large. Both q and d cannot be zero if there is to be a dipole moment. In any
case, the effects of charge AND distance must be considered in any prediction of molecular dipole moment.
The dipole moment is recorded in units of “Debye” where 1 D = 3.33564×10−30 C·m
“C” is for Coulombs (charge) and m is for meters (distance).
Important Note: In most chemistry textbooks, the dipole moment vector points in the direction of the negative
end of the molecule. ChemBioUltra 3D follows the physics convention where the dipole moment vector points in the
direction of the positive end of the molecule. When recording dipole moment vectors, you should follow our text
book’s convention and aim the dipole moment vector at the negative end of the molecule.
Experimental procedure
I. Before coming to lab, determine the Lewis dot structures for the following 15 molecules and record them on their
respective worksheets. You will be graded on your Lewis structures before lab begins and you will not be allowed to
participate if you fail to bring the 15 worksheets with completed Lewis structures with you to lab.
BeCl2
PF5
* BrF5
BH3
* SF4
* XeF4
SO2Cl2
BrF3
C2H6
* CH3* I3* C2H4
* ClF2+
PF6C2H2
II. For EACH species with an * above, construct a physical model using the plastic molecular modeling kits.
For each molecule you build, fill out the
worksheet with the following information:


Formal Charges for the centermost atom
# electron regions around centermost
atom. Remember that double and triple
bonds only count once.

# bonding regions

# lone pair regions

Electronic picture and name (based upon
the number of electron regions)

Molecular picture and name (considers
the lone pair invisible)

Show your molecule to the instructor who will then initial your worksheet. Completing more than one
molecule will save time.
You must have the instructor’s signature for all * molecules in the listings above
before proceeding to the computer exercises.
III. Bond length/angle measurements.

Open the formaldehyde (CH2O) and ammonia (H2O) molecular files found in the Chemistry -> C1151 ->
Molecules folder.

For each of these two molecules determine the bond angles and bond lengths for the central atoms (recipe 5)

Record your results in the table.
IV. Dipole Moments of Several Molecules

Important: ChemBio3D ultra displays the dipole moment vector pointing at the positive end of the
molecule. This is the opposite of the convention used by your textbook. You should draw all dipole moments
according to our text book’s convention.

Open the following molecular files found in the Chemistry -> C1151 -> Molecules folder.
a. Cl2C2CF2
d. Cl2C2CFCl
g. H2O


V.
b. FClC2FCl (trans)
e. BF3
h. H2S
c. FClC2FCl (cis)
f. BCl2F
i. NH3
Determine the dipole moment (recipe 4), for each molecule and record its value in the table.
Sketch each molecule in the data table and accurately draw its dipole moment vector .
Use longer arrows for larger dipole moments and shorter arrows for smaller dipole moments.
Molecular Atom Hunt.
In this exercise you will determine the electronic geometry, molecular
geometry and hybridization for atoms in three large molecules:
a. Aspirin:
O (11)
C (10)
C (17)
C(5)
b. Nicotine:
N(23)
N(1)
C(8)
C(10)
c. Cocaine:
O(13)
N(23)
C(10)
C(4)
# Electron
regions
Electronic Geometry
2
Linear
3
Trigonal
4
Tetrahedral
5
Trigonal Bi-pyramidal
6
Octahedral

First load the molecule and perform an MM2 minimization. Locate the atom of interest and count the
number of electron regions around it. Remember that double bonds, triple bonds only once.

Use this result to determine the electronic
geometry according to the table above. Record the
result in the table.

Count lone pair regions around the atom and use
this information to determine the name of the
molecular geometry. Record the result in the table.

Lastly, determine the hybridization for the atom.
This is easily determined again from the number of
electron regions previously determined. See
diagram at right.
Molecular Modeling (Front Page)
Name___________________
Section: ________
Minneapolis Community and Technical College
v.9.15
Staple this page, the next page and all 15 worksheets together before handing in.
Instructor Initials: __________
BeCl2
PF5
BrF5*
BH3
SF4*
XeF4*
SO2Cl2
BrF3
C2H6
CH3-*
I3-*
C2H4*
ClF2+*
PF6C2H2
ChemBio 3D Ultra Results
Part III
j. Formaldehyde (CH2O)
g. Water H2O
H-C-H Bond Angle ______
O-C-H Bond Angle ______
C-H Bond Length ______
C=O Bond Length ______
H-O-H Bond Angle_______
O-H
Part IV
Sketch the
molecule
along with
its dipole
moment
vector in
the space
provided
Bond length ______
a. Cl2C2H2
 = _______ Debye
b. FClC2FCl (trans)
 = _______ Debye
c. FClC2FCl (cis)
 = _______ Debye
d. ClHC2H2
 = _______ Debye
e. BF3
 = _______ Debye
f. BCl2F
 = _______ Debye
g. H2O
 = _______ Debye
h. H2S
 = _______ Debye
i. NH3
 = _______ Debye
Part V
Molecule:
Aspirin
O(11)
C(10)
C(17)
C(5)
Electronic Geo.
Molecular Geo.
Hybridization
Molecule:
Nicotine
N(23)
N(1)
C(8)
C(10)
Molecule:
Cocaine
O(13)
N(23)
C(10)
C(4)
Questions: Answer each question in the space provided.
1.
H2O Why are the measured H-O-H bond angles smaller than what is predicted by VSEPR?
________________________________________________________________________________________
________________________________________________________________________________________
________________________________________________________________________________________
CH2O: Why is the measured H-C-O bond angle larger than what is predicted by VSEPR?
________________________________________________________________________________________
________________________________________________________________________________________
________________________________________________________________________________________
2. Why is a B-F bond shorter than a B-Cl bond?
________________________________________________________________________________________
________________________________________________________________________________________
Why is a C-O bond longer than a C=O bond?
________________________________________________________________________________________
________________________________________________________________________________________
3. Look up “Hydrogen Bonding” and explain why H2O can hydrogen bond but H2S does not. Refer to the dipole
moments you determined from ChemBioUltra3D for each molecule in your answer.
________________________________________________________________________________________
________________________________________________________________________________________
________________________________________________________________________________________
________________________________________________________________________________________
4. Draw a picture of the planar BClF2 molecule and include its dipole moment vector.
ChemBio 3D Ultra Recipes:
The following recipes are used when using the ChemBio3D ultra software.
0. Useful information

All molecular files used throughout the experiment are found via the “Chemistry” shortcut on the computer’s
desktop. Navigate to the “C1151” folder and then to the “Molecules” folder.

Molecular models (files) must be optimized (low energy) before bond lengths and angles can be measured. Be
sure to run an MM2 and GAMESS energy minimization before measuring anything.
1. MM2 Minimization
Performs calculations on atoms as if they were balls on springs. It is somewhat crude and not good enough for
bond measurements. However, MM2 will often straighten out molecular messes and provides a good starting
point for more accurate simulations. MM2 should always be performed before any other operations.
1. Open the molecular file.
2. Click on the MM2 button (see figure at right) to obtain a low energy
atomic arrangement for the molecule.
3. Also note that lone pair electrons are always shown in PINK after an MM2 procedure has been performed.
2. GAMESS Minimization (AM1)
Performs quantum mechanical calculations on atoms within molecules. Also incorporates experimental data to
improve the results of calculations. A GAMESS minimization will permit relatively accurate bond angles and
lengths, dipole moment and heat of formation predictions.
1. Open the appropriate molecular file.
2. Click on the MM2 button
3. Click on “Calculations” in the upper menu bar.
4. Click on “GAMESS Interface” in the main menu.
5. Click on “Minimize (Energy/Geometry)”
6. Click on “Run” in the dialog box that opens.
When finished, the program will provide you with the “Finish @
Energy” for the molecule in the text window at the bottom of
the screen. It may take several seconds or more for the
calculation to finish depending on the size of the molecule.
3. Finding and Zooming in on an atom
When you want to look at a specific atom within a complicated molecule, you must place the atom of interest in
the center of the screen and then zoom in on it. This will let you see the atom, its bonds and determine the
electronic geometry around the atom.
1. Open the appropriate molecular file.
2. Ctrl – L
.. show atom labels on screen
3. Ctrl - 9
...show the atom serial numbers on screen
4. Ctrl – E
...display the Molecule explorer (table listing of atoms)
Click on the atom of interest in the Molecule Explorer or on screen
1. Ctrl – T
...makes the selected atom the “focus” of the molecule
2. Ctrl – W
...zoom in on selected atom and center in window
4. Calculating a dipole moment.
The dipole moment of the molecule is the result of polar bonds within
the molecule re-distributing charge. Chem 3D Ultra can optimize the
geometry of the molecule and calculate the net dipole moment of the
molecule. We’ll look at several different molecules to determine if the
dipole moment results are in agreement with our expectations.
1.
2.
3.
4.
5.
6.
7.
8.
Open the appropriate molecular file.
Click on the MM2 button
Click on “Calculations”
Click on “GAMESS interface”
Click on “Compute Properties”
In the menu that opens, check the “Dipole” box
Click the “Run” button.
When the “Dipole Computed” box opens click on “Yes” to view the value.
The calculated dipole moment can be found in the lower “Output” box (figure
below).
Record the number labeled Debye (units of dipole moment) Note that this number
represents the strength or magnitude of the dipole moment, NOT it’s direction.
The direction of the dipole moment is shown in the figure as a purple arrow. ChemBio
3D ultra draws the arrow in the direction of positive charge. You should draw a picture
of the molecule and include its dipole moment (as per our book) for future reference.
5. Measuring a bond length
Bond lengths are commonly measured in units of Angstroms. It is
a very small unit of length suitable to be used when describing
distances within molecules.
1 Angstrom =
1Å
=
10-10 meters.
1. Open the appropriate molecular file.
2. Click on the MM2 button
3. Run the GAMESS (see recipe 2 above)
4. Zoom in on the atom of interest (see recipe 3 above)
5. Position the cursor over the bond of interest
6. Record the bond lengths, and orders that appear in the box (see figure at right)
6. Measuring bond angles.
1. Open the appropriate molecular file.
2. Click on the MM2 button
3. Run the GAMESS minimization (see recipe 2 above)
4. Zoom in on the atoms of interest (see recipe 3
above)
5. Switch to the “select” cursor (figure near right)
6. SHIFT click on both bonds (They will now be
highlighted in yellow)
7. Position the cursor over either bond.
8. Record the bond length in degrees. (left figure)