Straighten Up: Lose those Electrons!
A Molecular Geometry exercise to better understand the role of the Electron
in determining the molecular shape and chemical properties of compounds.
Materials: Worksheet(s), Pen/Pencil and Chemistry textbook
Computer with Internet Access and Printer
WebMO Computational Chemistry Tool
WebMO Structure Tutorial (optional)
WebMO is a web-based interface for computational chemistry programs.
From any computer using only a web browser one can set up, run, and
visualize calculations that form the basis of the field of computational
chemistry.
The directions for this activity assume no prior knowledge of the WebMO
interface and provide detailed click by click instructions on building
molecules and setting up calculations. There is an online tutorial under the
Help command in the WebMO structure editor. Alternatively, a user’s guide
can be found at http://webmo.net/download/WebMO_Users_Guide.pdf
Preferred browser: Internet Explorer (IE)
We will be using the NCSA server located at
http://neo.beckman.uiuc.edu/~webmo/cgi-bin/webmo/login.cgi
Login to WebMO using the userid and password provided by your
instructor. Click ‘Login’. You will enter the ‘Job Manager’ page where you
will begin this lesson.
Please read the next page before beginning this activity.
©2011 University of Illinois Board of Trustees • http://islcs.ncsa.illinois.edu/copyright
VSEPR Key: All of the compounds in this activity represent molecules
with a particular shape that can be described using VSEPR terminology.
VSEPR: Valence shell electron-pair repulsion theory contends that the
3-dimensional shape of a molecule is determined by a particular
arrangement of groups of valence electrons around the central atom
which minimizes repulsions between them.
Valence electron groups: can be defined as any number of electrons that
occupy a localized area around the central atom. This could be electrons
that make up a single, double, or even triple bond which involves the
central atom in a molecule. It can also represent a lone pair of electrons
or even a single electron around the central atom.
The molecules in this activity can be described by using this general
VSEPR terminology: ABmXn
Where:
A = central atom
B = surrounding atom
X = nonbonding valence-electron group which is usually a lone pair of
electrons
M,N = Integers (positive whole numbers and zero)
For example: AB2X represents a molecule with 2 atoms separately
bonded to the central atom and one additional nonbonding electron group
around the central atom.
Look for these designations next to the name and molecular formula of
the compounds used in this activity.
©2011 University of Illinois Board of Trustees • http://islcs.ncsa.illinois.edu/copyright
Part I: Building the Molecules and Optimizing Their Geometries
A) Structure of a Bent Compound NO2- (Nitrite ion)
VSEPR: AB2X
1. In the WebMO ‘Job Manager’ click ‘New Job’ which sends you to
the ‘Build Molecule’ window where you will then click on ‘Open
Editor’. A small window opens up where you build molecules.
2. Click on the Periodic table icon ,
, located 5th down the left side of
the window. Choose “N” by clicking on it.
3. Click once in the center of the workspace. A blue Nitrogen atom
appears.
4. Click again on the Periodic table Icon. Choose “O” by clicking on it.
5. Click once near the N atom. A red Oxygen atom appears. Click again
on the other side of the N atom. A second red Oxygen atom appears.
6. Click and hold on the blue N atom. Drag the cursor over to an O atom.
A N-O bond has formed as a result. Continue to hold as you drag the
cursor from the oxygen atom back to the N atom. A N=O bond has
formed.
7. Release the cursor briefly, before clicking and holding again. Drag the
cursor from the N atom to the other oxygen atom and release. You have
now created a single N-O bond. The structure should look like O=N-O.
8. Click on the O atom which is single bonded to the N atom. A drop
down menu appears. Scroll down to click on and select ‘Charge’.
9. A new screen appears in the upper left corner. Type in -1. Click on
‘Apply’. The -1 charge should now appear on that O atom. Click on
‘OK’ and the screen will disappear. You have now created the nitrite ion.
10. Choose “Clean-Up > Comprehensive”. This produces a bent
molecule in the ‘WebMO editor’ window
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11. Experiment with the ‘Rotate, Translate, and Zoom’ tools which are
the top 3 icons on the left side and represented by the following icons:
.
12. Click ‘Close Editor’ in the ‘Build Molecule’ window. The nitrite ion
now appears in the ‘Build Molecule’ window.
This structure now contains idealized bond lengths and angles. At this
point you can create a more accurate structure by carrying out geometry
optimization calculations using one of several computational chemistry
calculation packages. Specifically, you will use the semi-empirical
method PM3 to obtain reasonable results in a short amount of time.
13. Click on the blue ‘continue’ arrow in the lower right side of the
‘Build Molecule’ window.
14. Choose ‘Mopac’ as the computational engine and click on blue
‘continue’ arrow in the lower right side.
15. Type In/Choose the following:
Job Name: O2N(-1)PM3XY where XY are the initials of your first-last
name
Calculation: Geometry Optimization
Theory: PM3
Charge: -1
Multiplicity: Singlet
16. Click on the blue ‘continue’ arrow in the lower right side.
17. This brings you to the ‘Job Manager’ window where you will find
your job listed.
18. Click on the refresh button every ten seconds until you see that the
job is complete under the status section. During this time, if you need to
kill the job all you would need to do is to click on the red ‘X’ under
Actions on the right side of the window.
©2011 University of Illinois Board of Trustees • http://islcs.ncsa.illinois.edu/copyright
19. Click on the hyperlinked name (O2N(-1)PM3XY) to open the ‘View
Job’ window. Scroll Down to view the results of the Geometry
Optimization of the NO2- job.
20. You will use the results of this job later to answer questions on the
nature of the NO2- molecule and/or to submit this data for additional
calculations.
B) Structure of a Bent compound NO2 (Nitrogen Dioxide)
VSEPR: AB2X
1. In the WebMO ‘Job Manager’ click ‘New Job’ which sends you to
the ‘Build Molecule’ window where you will then click on ‘Open
Editor’. A small window opens up where you build molecules.
2. Click on the Periodic table icon ,
, located 5th down the left side of
the window. Choose “N” by clicking on it.
3. Click once in the center of the workspace. A blue Nitrogen atom
appears.
4. Click again on the Periodic table Icon. Choose “O” by clicking on it.
5. Click once near the N atom. A red Oxygen atom appears. Click again
on the other side of the N atom. A second red Oxygen atom appears.
6. Click and hold on the blue N atom. Drag the cursor over to an O atom.
A N-O bond has formed as a result. Continue to hold as you drag the
cursor from the oxygen atom back to the N atom. A N=O bond has
formed.
7. Repeat step 6 for the other O atom. This produces a second N=O bond.
The molecule should look like O=N=O. You have now created nitrogen
dioxide.
8. Choose “Clean-Up > Geometry”. This produces a bent molecule in
the ‘WebMO editor’ window.
©2011 University of Illinois Board of Trustees • http://islcs.ncsa.illinois.edu/copyright
9. Experiment with the ‘Rotate, Translate, and Zoom’ tools which are
the top 3 icons on the left side and represented by the following icons:
.
10. Click ‘Close Editor’ in the ‘Build Molecule’ window. The nitrogen
dioxide molecule now appears in the ‘Build Molecule’ window.
This structure now contains idealized bond lengths and angles. At this
point you can create a more accurate structure by carrying out geometry
optimization calculations using one of several computational chemistry
calculation packages. Specifically, you will use the semi-empirical
method PM3 to obtain reasonable results in a short amount of time.
11. Click on the blue ‘continue’ arrow in the lower right side of the
‘Build Molecule’ window.
12. Choose ‘Mopac’ as the computational engine and click on blue
‘continue’ arrow in the lower right side.
13. Type In/Choose the following:
Job Name: O2NPM3XY where XY are the initials of your first-last
name
Calculation: Geometry Optimization
Theory: PM3
Charge: 0
Multiplicity: Doublet
14. Click on the blue ‘continue’ arrow in the lower right side.
15. This brings you to the ‘Job Manager’ window where you will find
your job listed.
16. Click on the refresh button every ten seconds until you see that the
job is complete under the status section. During this time, if you need to
kill the job all you would need to do is to click on the red ‘X’ under
Actions on the right side of the window.
©2011 University of Illinois Board of Trustees • http://islcs.ncsa.illinois.edu/copyright
17. Click on the hyperlinked name (O2NPM3XY) to open the ‘View
Job’ window. Scroll Down to view the results of the Geometry
Optimization of the NO2 job.
18. You will use the results of this job later to answer questions on the
nature of the NO2 molecule and/or to submit this data for additional
calculations
C) Structure of a Linear Compound NO2+ (Nitronium ion)
VSEPR: AB2
1. In the WebMO ‘Job Manager’ click ‘New Job’ which sends you to
the ‘Build Molecule’ window where you will then click on ‘Open
Editor’. A small window opens up where you build molecules.
2. Click on the Periodic table icon ,
, located 5th down the left side of
the window. Choose “N” by clicking on it.
3. Click once in the center of the workspace. A blue Nitrogen atom
appears.
4. Click again on the Periodic table Icon. Choose “O” by clicking on it.
5. Click once near the N atom. A red Oxygen atom appears. Click again
on the other side of the N atom. A second red Oxygen atom appears.
6. Click and hold on the blue N atom. Drag the cursor over to an O atom.
A N-O bond has formed as a result. Continue to hold as you drag the
cursor from the oxygen atom back to the N atom. A N=O bond has
formed.
7. Repeat step 6 for the other O atom. This produces a second N=O bond.
The molecule should look like O=N=O.
8. Click on the N atom. A drop down menu appears. Scroll down to click
on and select ‘Charge’.
©2011 University of Illinois Board of Trustees • http://islcs.ncsa.illinois.edu/copyright
9. A new screen appears in the upper left corner. Type in +1. Click on
‘Apply’. The +1 charge should now appear on that O atom. Click on
‘OK’ and the screen will disappear. You have now created the nitronium
ion.
10. Choose “Clean-Up > Comprehensive”. This produces a bent
molecule in the ‘WebMO editor’ window.
11. Experiment with the ‘Rotate, Translate, and Zoom’ tools which are
the top 3 icons on the left side and represented by the following icons:
.
12. Click ‘Close Editor’ in the ‘Build Molecule’ window. The nitronium
ion now appears in the ‘Build Molecule’ window.
This structure now contains idealized bond lengths and angles. At this
point you can create a more accurate structure by carrying out geometry
optimization calculations using one of several computational chemistry
calculation packages. Specifically, you will use the semi-empirical
method PM3 to obtain reasonable results in a short amount of time.
13. Click on the blue ‘continue’ arrow in the lower right side of the
‘Build Molecule’ window.
14. Choose ‘Mopac’ as the computational engine and click on blue
‘continue’ arrow in the lower right side.
15. Type In/Choose the following:
Job Name: O2N(+1)PM3XY where XY are the initials of your first-last
name
Calculation: Geometry Optimization
Theory: PM3
Charge: 1
Multiplicity: Singlet
16. Click on the blue ‘continue’ arrow in the lower right side.
©2011 University of Illinois Board of Trustees • http://islcs.ncsa.illinois.edu/copyright
17. This brings you to the ‘Job Manager’ window where you will find
your job listed.
18. Click on the refresh button every ten seconds until you see that the
job is complete under the status section. During this time, if you need to
kill the job all you would need to do is to click on the red ‘X’ under
Actions on the right side of the window.
19. Click on the hyperlinked name (O2N(+1)PM3XY) to open the ‘View
Job’ window. Scroll Down to view the results of the Geometry
Optimization of the NO2+ job.
20. You will use the results of this job later to answer questions on the
nature of the NO2+ molecule and/or to submit this data for additional
calculations.
YOU HAVE FINISHED PART I.
GO TO NEXT PAGE TO BEGIN PART II.
©2011 University of Illinois Board of Trustees • http://islcs.ncsa.illinois.edu/copyright
Part II: Analysis of the Molecular Shapes and Chemical Properties
of these Compounds
A) Study of N-O Bond Distances and O-N-O Bond Angles
1. In the WebMO ‘Job Manager’ window Click on the
hyperlinked name (O2N(-1)PM3XY) to open the ‘View Job’
window. Scroll Down to view the results of the Geometry
Optimization of the NO2- job.
2. In the ‘View Job’ window look to find the ‘Select’ icon which
can be found as the fourth icon on the left side and looks like
this:
.
3. Click on this button. On the bottom left corner of the display
you will see this:
This indicates that the tool is
activated to help you find bond distances and bond angles in
this molecule.
4. Click on the blue N atom. The other atoms grey out at this time.
To find the N-O single bond distance press the shift key on
your keyboard while simultaneously clicking on the oxygen
(‘shift-click’).
5. The bond distance will be recorded on the bottom left corner of
the display and looks like this :
6. Record this distance in the designated space in the data table.
7. Repeat steps 4-6 for the N=O bond.
8. Click on a red O atom. ‘Shift-Click’ on the N followed
immediately with another ‘shift-click’ on the other oxygen.
9. The O-N-O bond angle will be recorded on the bottom left
corner of the display and looks like this:
10.Record this angle in the designated space in the data table.
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11. Scroll down until you reach the “Calculated Quantities”
section.
12.Record the dipole moment and heat of formation data in the
designated spaces in the data table.
13.Note the magnifying glass icon next to the value for the dipole
moment. Click on it. A modified window appears to illustrate
the dipole moment (if present) in the molecule in the form of an
arrow which indicates both the magnitude and direction of the
molecular dipole.
14. Scroll down to the “Calculated Quantities” section again and
note the magnifying glass icon in the partial charges box.
Click on it. A modified window appears to illustrate the dipole
moment (if present) in the molecule in the form of partial
charges assigned to each atom as a result of the geometry
optimization calculations on the molecule.
15.Return to Step 13 by clicking on the magnifying glass icon
next to the dipole moment data. In your IE browser click ‘FilePrint’ and proceed to print out the file displayed currently on
your screen. This will ensure that the complete file will be
recorded if the job is mistakenly deleted from the Job Manager.
16. Return to the Job Manager. Repeat steps 1-15 for both of the
NO2 and NO2+ molecules.
17. Proceed to the data table where you will finish completing it
and answer additional questions.
©2011 University of Illinois Board of Trustees • http://islcs.ncsa.illinois.edu/copyright
Straighten Up! Data Table
NO2+
MOLECULAR
FORMULA
CHEMICAL
NAME
TOTAL #
VALENCE
ELECTRONS
LEWIS
STRUCTURE
NO2-
NO2
ELECTRON
GEOMETRY
MOLECULAR
SHAPE/VSEPR
DESIGNATION
N-O BOND
DISTANCES
(A)
O-N-O BOND
ANGLES(◦)
DIPOLE
MOMENT (D)
ΔHf
HEAT OF
FORMATION
Kcal/mol
CHEMICAL
FORMULA
N-O BOND
DISTANCES
(LIT.) (A)
O-N-O BOND
ANGLES
(LIT.)(◦)
NO2
+
REFERENCE TABLE
NO2
NO2-
2 N=O
Each 1.15
2 N=O
Each 1.197
1 N-O ; 1 N=O
Each 1.3
180
134.3
115.7
©2011 University of Illinois Board of Trustees • http://islcs.ncsa.illinois.edu/copyright
Application and Analysis
1. Using the information found elsewhere in this activity, add the
chemical name, molecular shape and VSEPR designation for
each molecule to the data table.
2. Using your chemistry textbook as a reference, calculate the # of
valence electrons for each molecule and add them to the data
table. Show your work below.
3. Review your data table to make sure that N-O bond distances,
O-N-O bond angles, dipole moments, and heats of formation
have been added for each molecule per directions in Part II.
4. Using the WebMO job output for each molecule, sketch the
molecule together with its dipole moment (vector arrow) below.
Add the partial charges assigned next to each atom in the
sketch. You now have an image illustrating how molecular
shape and bond polarity determine whether the molecule
is polar. Show your work below.
©2011 University of Illinois Board of Trustees • http://islcs.ncsa.illinois.edu/copyright
5. Using your chemistry textbook and the results in #4:
a) how would you classify the N-O and N=O bonds in these
molecules? Are they nonpolar covalent, mostly covalent, polar
covalent, mostly ionic, or ionic in nature? Explain.
b) based on your previous answer, how does the shape of each
molecule influence the overall molecular polarity of the
compounds? Explain.
6. Using your chemistry textbook as a reference, the # of valence
electrons present in each molecule, and use the space below as a
practice area to write out Lewis Structures for each molecule.
©2011 University of Illinois Board of Trustees • http://islcs.ncsa.illinois.edu/copyright
7. Place the Lewis Structure for NO2+ in the designated area of
the data table. How many nonbonding valence electron groups
are there around the N atom?
8. Place the Lewis Structure of NO2 in the designated area of the
data table. How many nonbonding valence electron groups are
there around the N atom?
9. How many valence electrons does NO2 have? Is it an odd or
even number? Were you able to completely satisfy the octet
rule for this molecule? If not, why not? Be able to derive a rule
for fulfilling the octet rule for compounds of this type.
10. If, in NO2, you were not able to completely satisfy the octet
rule then be able to explain how you chose which atom(s)
fulfilled the octet rule and why some atom(s) did not.
11.Refer to the N-O and N=O bond distances for the NO2molecule. What is interesting about these values?
12. Now, look at the bond orders calculated for this molecule,
which can be found in its WebMO job ouput file. Round the
Bond Order for N to its nearest whole number and record
below. For the O atoms, round it to whatever they are closest to
either 1 or 1.5 and record below.
13.Place the Lewis Structure of NO2- in the designated area of the
data table. Based on your answers to #11-12 can you write an
©2011 University of Illinois Board of Trustees • http://islcs.ncsa.illinois.edu/copyright
additional Lewis Structure that completely satisfies the octet
rule for this compound ? If so, record this structure in the same
designated area where you placed the first Lewis Structure.
14.Using your chemistry book as a reference and looking at the
Lewis Structures for these compounds, determine the electron
geometry around the central atom for each of these molecules.
List these geometries in the designated areas in the data table.
15.Based on your analysis of the NO2- molecule what property
associated with Lewis Structures does this compound possess?
Explain.
16.List below the number and nature of the nonbonding valence
electron groups around the N atom for each molecule. Now, list
the O-N-O bond angles calculated for each molecule. Explain
the data in terms of the influence of these nonbonding electron
groups on the shape of each molecule as illustrated by the
differences in the bond angles. In other words, what happens to
the O-N-O bond angle as the number of electrons around N
increase? Why?
17. The relative stability of these molecules can be determined by
observing their individual heats of formation. The least stable
©2011 University of Illinois Board of Trustees • http://islcs.ncsa.illinois.edu/copyright
species is the one with the most positive heat of formation. Which
one is it?
18.Extra Credit: If 2 NO2 molecules came close enough to each
other to react what would the product be? Write the Lewis
Structure for the product in the space below keeping in mind that
the Lewis Structure of the reactant holds an important clue to the
answer.
©2011 University of Illinois Board of Trustees • http://islcs.ncsa.illinois.edu/copyright
ANSWER KEY
Straighten Up! Data Table
MOLECULAR
FORMULA
CHEMICAL
NAME
TOTAL #
VALENCE
ELECTRONS
LEWIS
STRUCTURE
ELECTRON
GEOMETRY
MOLECULAR
SHAPE/VSEPR
DESIGNATION
N-O BOND
DISTANCES
(A)
O-N-O BOND
ANGLES(◦)
DIPOLE
MOMENT (D)
ΔHf
HEAT OF
FORMATION
Kcal/mol
CHEMICAL
FORMULA
N-O BOND
DISTANCES
(LIT.) (A)
O-N-O BOND
ANGLES
(LIT.)(◦)
NO2+
NO2
NO2-
Nitronium Ion
Nitrogen Dioxide
Nitrite Ion
16
17
18
Written
Out
Instructor
Linear
Trigonal Planar
Trigonal Planar
Linear/AB2
Bent/AB2X
Bent/AB2X
2 N=O
Each 1.137
2 N=O
Each 1.180
N-O
N=O
Each 1.234
180
137.730
115.653
0
1.126
0.840
+208.35338
-1.04140
-42.95941
NO2
+
REFERENCE TABLE
NO2
NO2-
2 N=O
Each 1.15
2 N=O
Each 1.197
1 N-O ; 1 N=O
Each 1.3
180
134.3
115.7
©2011 University of Illinois Board of Trustees • http://islcs.ncsa.illinois.edu/copyright
Answer Key:
Q’s 1-18: Written out at the appropriate time by the instructor. Many of
the answers already provided by referring to the table’s answer key.
Activity Keywords: High School; Curriculum; Internet-Web-Based
Learning; Computational Chemistry; Lewis Structures; Molecular
Mechanics/Dynamics;
Molecular
Properties/Structure; Quantum
Chemistry; VSEPR Theory; WebMO
Literature Cited:
1) Myers, R. T. ; Oldham K.B; Tocci, S. Holt Chemistry:
Visualizing Matter, Technology Ed.; HRW: Austin, 2000; pp
192-231.
2) Polik, W.F. ; Schmidt, J.F. WebMO User’s Guide; WebMO
LLC: Holland, MI,2003.
3) Silberberg, M.S. Chemistry: The Molecular Nature of Matter
and Change, 2nd ed.;McGraw-Hill; Boston, 2000; pp 360-394
©2011 University of Illinois Board of Trustees • http://islcs.ncsa.illinois.edu/copyright