revised 11/3/04 mtm
Visualizing Molecular Shape and Polarity
Using SPARTAN
I. Introduction
After completing this exercise you should be able to:
i) Use VSEPR to predict the electron pair geometry and molecular geometry for a given
molecule based on its Lewis Structure, and sketch its 3D shape
ii) Use computer modeling software to calculate the optimal 3D shape of a molecule
iii) Classify a molecule as either “polar” or “non-polar” according to its shape and the
polarity of its individual bonds
iv) Use MacSpartan computer modeling to help you visualize charge distribution in a
molecule
We will investigate these issues using a powerful piece of molecular modeling software
(SPARTAN). The field of molecular modeling, or more broadly, computational chemistry, refers
to investigating molecules strictly through calculations. It has grown rapidly in the past two
decades, primarily because advances in computing speed have enabled the use of very
sophisticated (quantum mechanical) models to simulate the electron distributions of molecules.
The field has had such a broad impact on chemistry that the 1998 Nobel Prize in Chemistry was
awarded to a pair of individuals who were instrumental in developing efficient numerical
procedures to execute such calculations. Today, a substantial fraction of chemists are exploiting
computational methods for their research, and such methods are even making their way into
biochemistry courses…
The plan for this lab exercise is to learn the basics of the program by “building” and simulating a
few simple molecules that you are quite familiar with. At the same time, you will be drawing
Lewis Structures and predicting the geometries of these molecules using VSEPR (Valence Shell
Electron Pair Repulsion) Theory. The basis of VSEPR theory is that the electron pairs about a
given atom move away from each other as far as possible to minimize the repulsive forces
between them (all are negatively charged). As a result, for a given number of electron pairs about
a given atom (either bonds or lone pairs), there is a standard arrangement called the electron pair
geometry. This dictates the overall shape. The actual shape of the molecule is called the
molecular geometry. At the end of this document there are some appendices that describe
electron pair geometry, molecular geometry, and guidelines for drawing Lewis Structures. Our
investigation of shapes will conclude with an examination of molecules with more than 8
electrons about the central atom.
After investigating shape, we will then exploit the graphical capabilities of SPARTAN to
illustrate “polar” bonds. Then, we will combine this insight with that that we have gained
regarding shape and learn to predict whether or not a given molecule (as a whole) is polar - that
is, has a dipole moment.
You will need some scratch paper for sketching some Lewis structures and VSEPR geometries.
Questions to be answered are in bold, and are separated from the body of the text. Others
embedded in the text (and usually in italics) are to provoke thought.
II. Outline of the process for running SPARTAN
The process for modeling molecules in SPARTAN follows the same general outline:
a. Build a molecule - the program makes a “best guess” as to how the atoms are arranged,
but the shape at this point is just the initial guess.
b. Calculate and minimize molecule energy - SPARTAN next adjusts atom positions and
the electron distribution in the molecule to find the lowest energy shape and electron
distribution. This is the real power of this program - sophisticated models for atom
bonding determine a refined view of what the molecule “looks like”.
c. Calculate surfaces - electron density surfaces (to better envision shape) and charge
distribution in the molecule (to better envision molecular polarity).
SPARTAN allows for a wide range of molecule shapes and bonding, but just because the
program will let you build it doesn’t mean that your molecule is stable. Step “b.” is therefore
crucial to the process. During step “b.”, three different things could happen i. The program returns a structure with the same general shape (the bond lengths and angles
may have changed a bit). But it is not necessarily the best structure. You will need to
examine the energy values for all stable structures to determine which is “best”. (More on
this below)
ii. The program returns a structure with a completely different shape, which means that your
starting structure was something of a poor guess.
iii. The calculation takes a long time, and the structure it returns is not bonded at all – the
distances are very long, and there is no definite shape (i.e. the molecule “exploded”),
which means that your initial guess was extraordinarily bad.
Controls for moving and rotating molecules on canvas “Free-form” rotate
Click and drag the mouse on the
canvas
Rotate molecule in canvas’ plane Apple+drag
Drag one molecule across canvas Option+drag
Drag all molecules across canvas Control+drag
Zoom in
Option+Apple+drag
Upon starting the program an unlabelled window appears - the “shortcut” menu:
III. Molecular Geometry
A. 3-D Shapes from Lewis Structures
Consider the shapes of three molecules, H2O, NH3, and CH4 based on VSEPR.
1a) Sketch Lewis structures for H2O, NH3, and CH4. Also specify the electron pair
geometry and molecular geometry for each one.
1b) Specify the values of bond angles you’d expect according to the VSEPR model.
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B. 3-D Shapes from SPARTAN
Now use SPARTAN to answer these questions. We’ll build the molecules and calculate their
minimum-energy structure.
1. Building molecules
To build molecules, select ‘New’ from the File menu.
the “Model Kit” popup window, use the ‘Entry’ mode.
In
Water
In the ‘Entry’ palette, click on the
, then click on
the green canvas. Click and drag on the canvas to rotate
the molecule for a better view. Then, select the “-H”
from the model kit, and click on an “empty bond” to add
the H’s. Then choose ‘View’ from the Build menu (or
click on
in the shortcut menu). Select ‘Save’ from
the File menu, and save your file in a new folder on your H: drive there is a ‘New Folder’ button in the save dialog box.
There are several “models” for viewing the molecule in the Model menu experiment with them, and pick the representation you like the best. Be
sure to look at the molecule as a ‘Space Filling’. You can switch to a
different model at any time; the model does not influence the
calculations.
Methane
Drag the water molecule out of the center of the canvas, choose
File/’New’ (or click
from the shortcut menu) and build CH4, (use
from the ‘Entry’ pallet); note that if you don’t put H atoms on the C,
the program will do it for you automatically when you select
. Save
the molecule. You can switch from molecule to molecule by clicking on
any part of the molecule that you want; the title of the main window
tells you which is selected. The atom that you click turns brown; if
you next click on the canvas, you can deselect that atom but not the
molecule.
Ammonia
Again, move the methane away from canvas center, start a new molecule
and build NH3 (use
from the ‘Entry’ pallet). Save the molecule as
before.
2. Calculating molecule structure and energy
Next, we will have SPARTAN calculate the optimum (i.e. minimum energy) structure for these
molecules. Select a molecule by clicking on it and then set up the calculations by:
Select ‘Calculations…’ from the Setup menu. In the dialog box, choose
the following:
‘Calculate:’ Equilibrium Geometry,
‘with:’ Hartree-Fock / 6-31+G*.
Then click “OK”. We will use these settings for the most of the
exercise.1 To start the calculation, select ‘Submit’ from the Setup
The first line was tell the program to adjust the bond lengths and angles until the potential energy of the molecule reaches a
minimum value. The “Hartree-Fock/6-31+G*” describes the method the program is using to model the electron distribution –
which ultimately dictates the structure. The only tidbit you need to take from this is the following fact: The program calculates
the molecular structure with the lowest energy.
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menu. The calculation should finish in less than a minute.
first molecule is done, move on to the others.
When the
Now, we’ll examine the calculated bond angles, and see how the structures of H2O, NH3, and
CH4 compare with what you expect based on VSEPR theory.
To measure the bond angle in water, select “Measure Angle” from the
Geometry menu (or click on
in the shortcut menu) and click on “H”,
then “O”, then the other H. The atoms will be shaded in brown as they
are selected, and the value will appear in the lower right corner of the
SPARTAN window when you have three atoms selected. It is critical that
the central atom (“O” in this case) is selected second – otherwise the
value you get will not be for the H-O-H bond angle. SPARTAN tells you
the order that you selected the atoms at the bottom of the window to the
right of the word ‘Angle’. Record the H-O-H bond angle. Select
View( ) to get the other molecules back to the screen.
bond angles in CH4 and NH3 and record the results.
Measure the
Note the trend in bond angles, and try to explain its origin. Here are some considerations to guide
you: For which molecule does the bond angle deviate the most from the ideal VSEPR value?
Which deviates least? Is the bond angle larger or smaller than in the ideal VSEPR value? Can
you explain the trends in bond angle deviation?
1c) Are any of the calculated angles different from the ideal VSEPR values? If so, can you
explain why? If not, see the next section.
C. Effect of Lone Pairs on VSEPR Bond Angles: Electron Density Surfaces
“Electron density surfaces” are maps of where the electrons are located in the molecule SPARTAN produces a shape that literally corresponds to the electron density that you specify.
There are two electron density surfaces we will look at:

“bonds” of a molecule, which represents the region where there is enough electron density
to constitute a bond, or a lone pair of electrons.

“size” of a molecule, or the “outermost edge” of the molecule’s electron cloud
To calculate these surfaces, select a molecule and choose ‘Surfaces’
from the Setup menu. In the popup window click on the ‘Add’ button while
holding down the Option key. Accept density in the Surface pull-down
menu, click the Static Isovalue checkbox, select bond (in the mini
scroll down menu), and choose High for Resolution. Then click “OK”.
To calculate the “size” surface, Option-click on ‘Add’ again, accept
density in the Surface pull-down menu, click the Static Isovalue
checkbox, accept size and choose High for Resolution. Then click “OK”.
NOTE: This is the underlying basis of the VSEPR model. Since the electron pairs (either bonded or lone) are negatively charged,
molecules adopt geometries that render them as far apart as possible, minimizing the repulsion of the negative charges, which in
turn gives the lowest potential energy.
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Note that the bond surface and size surface are the same operation to SPARTAN - only the
electron density value changes: 0.08 for the bond surface, 0.002 for the size surface.
‘Submit’ these from the Setup menu. To view the surfaces, click the
checkbox next to the left of the surface you wish to view
(Isovalue=0.002 is “size”; Isovalue=0.08 is “bond”) in the ‘Surfaces’
dialog box. You will not be able to see the “bond” surface and the
“size” surface at the same time since the bond surface is inside the
size surface.
Make the surfaces transparent so that you can see the skeleton of atoms inside:
Select ‘Properties’ from the Display menu. The dialog box should be
labeled ‘Surface Properties’ - set the Style to Transparent. Note:
this function is a bit “buggy” - if you have problems, leave the window
open and click on the molecule that you want to see. In the ‘Surfaces’
window toggle the surface off and on by clicking on the checkbox.
Calculate and examine the bond surfaces for each molecule and answer the following:
Comparing the “bond” surfaces of water and ammonia to that for methane,
2a) Why is there such a large electron density on the central atom away from the H’s.
2b) Why do you suppose that the electron density described in 2a is more diffuse than that
between the central atom and H atoms?
2c) Generalize: Are the spatial requirements for a “lone pair” and a “bonded pair” the
same? Which requires more space - a bonded pair, or a lone pair? Why?
While viewing the “size” surfaces for each molecule, consider the following. Recall that this
view is meant to represent the molecule at its nearest contact distance.
3a) How does the molecule’s electron density compare to the “Ball and Wire” or “Ball and
Spoke” molecular models? Are these models accurate descriptions of the molecule?
Explain.
3b) Which molecular model best describes the molecule’s “size” surface?
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3c) What are the advantages and disadvantages of a “Ball and Spoke” model vs. a “Space
Filling” model in describing a molecule?
3d) Which simple shape best describes the molecules: tetrahedron, cube, or sphere ?
Save and close all three molecule files before continuing.
D. Molecules with “Expanded Octets”-OPTIONAL
Molecules with 5 electron pairs about the central atom assume a trigonal bipyramidal electron
pair geometry, and those with 6 electron pairs assume an octahedral electron pair geometry.2
When no lone pairs are present, the molecular geometry and electron pair geometry are the
same, as is the case with PF5 and SF6, viz.
F
90°
F
120°
F
P
F
F
F
S
90°
F
F
F
90°
F
F
Trigonal Bipyramidal (PF5) and Octahedral (SF6) Geometries.
When lone pairs are present, however, it is difficult to determine the best
orientation of lone and bonded pairs of electrons. Consider the trigonal
bipyramidal case (as depicted by PF5 above): the key issue is that the five
locations around the central atom are not equivalent. Those directly above
and below the P are called axial sites, and the other three are called
equatorial. That is, there are three positions around the central atom in the
same plane (the equitorial plane) and two positions above and below that
plane (the axial positions). To better visualize this, do the following:
Create a new project, and select the ‘Expert’ tab in the
“Model Kit” window. Click and hold on the “C” icon next to
“Element” and a periodic table appears. Drag over to Cl.
To make a Cl atom with five electron groups around it,
choose
from the list below the element icon. Click on the canvas and
then rotate the molecule around until you understand its shape.
When lone pairs are present, a natural question is: “Do they go into the axial sites or the
equatorial sites, or is there really any difference?” We’ll answer this question by examining the
ClF3 molecule.
2 It may seem unusual that the central atom has more than four electron pairs - atoms in most molecules have eight electrons –
a.k.a. the “octet” rule. But, atoms from the third row (e.g. S, P, Cl) and below are larger, and can accommodate 10 or even 12
electrons in some instances.
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Question: What is the “best” structure for the ClF3 molecule?
4a) Using the appendices, sketch the Lewis structure of ClF3.
4b) With three bonded pairs and two lone pairs about the central atom, there are three
possible structures. Sketch them.
Now, build the three possible structures in SPARTAN that you sketched, saving each one:
Select a single-bonded F atom ( ) from the ‘Expert” palette and add a F
atom in three locations on the central Cl. Then delete the last two
bonds by selecting “Delete” from the Build menu (or
from the shortcut
menu) and clicking on the gold parts of the empty bonds. You must
delete the bonds or they will become H’s in the calculation.
Make sure that each structure is unique (and that you didn’t somehow make two of the same) in
the molecule view. Then calculate the structure for each molecule in turn using the same
calculation settings you used for water, ammonia, and methane. When you are done, you should
have two structures that are the same, despite your care in building three unique structures. What
happened?
For SPARTAN, recall that the ‘best’ structure is the one with the lowest energy.3 Recall the
three possible outcomes for a calculation (described in section II above). The program will
return:
 a molecule with the same general shape  reasonable initial guess
 a molecule with a different shape  poor initial guess
 an “exploded” molecule  extremely poor initial guess
To determine which structure is best, compare the energy for each structure:
Select each molecule in turn (click on an atom for the structure that
you want, then click on the canvas). The energy will be displayed at
the bottom of the View window.
Two points: You’ll notice that the energy is 1) negative, and 2) expressed in units called
“Hartrees”. The value is negative by convention (the “zero of energy is taken to be a set of bare
nuclei with no electrons present, and adding the negatively-charged electrons to the arrangement
of positively charged nuclei lowers the energy.) A Hartree is large amount of energy by chemical
standards (1 Hartree = 2625.5 kJ/mol). So a structure that is a 0.1 Hartree lower in energy
more stable by about 262 kJ/mol.
3
A stable structure is not necessarily the best, minimum energy structure. Rather it could be a “meta-stable” or “quasi-stable”
structure. This situation is illustrated in the picture below, a graph of energy vs. bond angle for a hypothetical molecule XY2,
which has a bent minimum energy structure and a linear structure that is quasi-stable.
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X
Y—X—Y
Y
Y
E
110°
*
155°
180°
Y-X-Y Bond Angle (°)
The 180° (linear) structure corresponds to a stable shape, but it is not as low (stable) as the 110° (bent) structure. When
SPARTAN calculates the best structure for XY2, the “starting guess” for the Y-X-Y angle will affect the result: if we guess an
angle between ~90 and 150, the calculated shape will be bent; if we guess an angle between ~160 and 200, the calculated
shape will be linear; if we guess 155 (right at the top of the peak), either shape could result. The program adjusts the geometry
to lower the energy (that is, it will try to march “downhill” in energy), even if there’s a more stable structure the other way.
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So, examine the energy values for the stable structure you obtained, and determine which is the
minimum energy structure.
4c) Based on SPARTAN, specify the electron-pair geometry and molecular geometry for the
most stable (i.e. lowest energy) structure of ClF3.
4d) Based on SPARTAN’s results, which structure for ClF3 is the least stable. Explain.
4e) What are the values of the bond angles of ClF3 based strictly on VSEPR theory?
4f) Sketch SPARTAN’s lowest energy geometry, label it with the calculated the bond
angles, and briefly explain why they differ from the ideal VSEPR values?
4g) Generalize: Which sites in a trigonal bipyramidal geometry have more space for lone
pairs – axial or equatorial?
When you are done, close all three ClF3 molecules and reopen water, methane, and ammonia.
IV. Polarity: Dipole Moments
In this part, we will combine our understanding of 3D shape with some new insight into bond
polarity, and determine whether a given molecule is “polar” or “non-polar”. In order for a
molecule to be considered polar, it must:
i) have polar bonds
ii) have an asymmetrical orientation, such that the bond polarity is unbalanced.
Bonds are considered polar when the electronegativity values for the atoms involved differ by
more than ~0.5. In the absence of a table of electronegativity values, the following rough
guidelines may help you identify bonds that are considered polar:



F bonded to any non-metal = polar, with excess negative charge on F.
N,O,Cl bonded to anything (except F) is polar, with negative charge on N, O, or Cl.
Bonds between other non-metals (H,S,C,P…) are most often non-polar
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Clarification: It should be noted that any bond between two different atoms has some degree of
charge separation (or “polarity”). In spite of this, chemists refer to bonds with minimal charge
separation as “non-polar”.
To visualize how polar bonds add up to render a given molecule polar or non-polar, chemists use
“bond dipoles”, arrows that point along the polar bonds, the components for which reinforce
each other (that is, are added) or cancel out (are subtracted) to give the overall polarity of the
molecule. The molecule’s polarity is represented by a quantity called the dipole moment, which
is real and measurable. “Bond dipoles”, however, are strictly hypothetical. Note below how the
horizontal contribution of the bond dipoles cancels out in water, while the vertical part
reinforces.
O
H
O
H
H
O-H bond Dipoles
H
The Dipole Moment in H2O
Before we begin the calculations, answer these questions:
5a) Are C-H bonds polar? ______
Are N-H bonds polar? ______
Are O-H bonds polar? ______
Rank them in order of increasing polarity and rationalize the trend.
Look at the shapes of water, methane, and ammonia and try to decide if the bond dipoles cancel
out or not in each case.
5b)
Is CH4 polar?
Is NH3 polar?
Is H2O polar?
In each case, sketch how the dipole moment is oriented for the molecule. If a molecule is
not polar, briefly explain why. (There may be more than one reason – if so, state both).
SPARTAN can display the dipole moments for each molecule:
Select a molecule and choose ‘Properties’ from the Display menu. In the
“Molecule Properties” popup window the calculated dipole moment appears
in the lower left. Clicking on the checkbox will display the dipole
moment vector on the molecule. This will also show its actual
orientation. The arrow points toward the negative charge.
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5c) Record SPARTAN’s results (polar or nonpolar, and direction of dipole moment) for
each molecule.
Do your answers in 5b agree with the SPARTAN results?
Try three more molecules: BF3, PF3, and CH2F2. Provide answers based either on what you
know and have learned, or use SPARTAN.
5c) Are BF3, PF3, and CH2F2 polar molecules (Lewis structure for CH2F2 is below)? Make a
3-D sketch with an arrow that shows the orientation of the dipole moment, or write “no net
dipole” as appropriate. If the molecule is not polar, explain why.
H
F
C
F
H
V. Polarity: Visualizing Charge Distribution
In this last part, we will use SPARTAN to illustrate molecular polarity. Returning to H2O, NH3
and CH4, we will calculate ‘surfaces’ on which the net electric charge in the molecule is mapped
onto an electron density surface using variations in color.
The “Potential” or electric charge is mapped by coloring the positively charged part of the
surface blue, and the negatively charged part red. Neutral regions are greenish or yellowish in
color. Recall that charge within the molecule arises because electrons spend, on average, more
time around electronegative elements; these elements don’t have the nuclear charge to offset the
excess electron density they attract, so they appear negatively charge. The reverse is true for
electropositive elements.
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To map surface potential onto the “size” electron density for water,
open the ‘Surfaces’ window from the Setup menu, Option-click on ‘Add’,
choose density for Surface, potential for Property, click the Static
Isovalue checkbox and accept size, and High for Resolution. Then
‘Submit’ the jobs from the Setup menu. Note that you can map charge
onto “bond” surfaces in a similar manner.
Repeat this mapping for NH3, and CH4. As before, make the surface transparent so you can see
the molecule model inside.
The program employs the widest range of possible colors for each molecule so that all bonds
may appear to be polar until we set a common scale for all.
This scale can be set in the “Surface Properties” window (accessed via
‘Properties’ in the Display menu). Note the From/To values for all
three molecules (e.g. for H2O, the default values are (about): From: 48.6…, To: 58.3); find a From/To range that will work for all three
molecules and set this range for all three (preferably with round
numbers like -50 to +50).
You should see a clear trend in the charge distribution for this trio of molecules. Recall again
that for the molecule as a whole to be polar, two things must hold true. First, it must have polar
bonds. Second, the symmetry of the molecule must be such that polarity of the individual bonds
(the bond dipoles) does not cancel out. Do these trends agree with your predictions in 5b?
6a) Based on these surface views, which molecule is most polar? Which is least polar?
6b) Looking at the areas of a potential-mapped density surface is positive or negative, is
the charge is distributed the same for each molecule? If not, what kinds of molecular
features concentrate positive charge? Negative charge?
Molecules used in the Boiling Points Lab
In the lab (which you did not do) where you measured the boiling point for hydrocarbons,
ketones, and alcohols, you noted clear trends in the data with increasing molecular weight (or
number of carbons in the chain). There were also clear jumps when changing from hydrocarbon
to ketones to alcohols. We will build representative molecules for each and examine their charge
distribution surfaces.
Below are the Lewis structures for the three molecules (electron lone pairs not included):
pentane, 1-pentanol, and 2-pentanone.
H
H
H
H
H
H
C
C
C
C
C
H
H
H
H
H
H
H
H
H
H
H
H
C
C
C
C
C
H
H
H
H
H
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O
H
H
H
H
H O
H
C
C
C
C
C
H
H
H
H
H
H
Note that these molecules have multiple “centers”, whereas all the prior examples had just one.
7a) Which molecule would you predict to be most polar? Which is least? (Hint: look at
each carbon as a center, examine how the dipole for that center would be oriented - if it has a
dipole at all - and then ask if dipoles from different centers can cancel or not.)
We will use SPARTAN to answer these same questions, but the molecules are large enough that
we will have to change our calculation method or wait a very long time.
Pentane
Choose
from the ‘Entry’ tab in the Model Kit and click on the canvas;
click a second time on a bond and a second C atom appears. Keep adding
C atoms until you get a 5-atom chain (notice already how Lewis structure
is a poor description for this molecule), then select
.
Next ‘Setup’ the calculation:
‘Calculate:’ Equilibrium Geometry
‘with:’ Semi-Empirical / AM1
‘Submit’ this job. When done, ‘Add’ a map of the charge for the “size” surface and ‘Submit’
again.
1-Pentanol
Repeat the process outlined for pentane, except you need to end the carbon
chain with a
.
2-Pentanone
Use
for the second carbon and
for the others in the carbon chain. If
you rotate the chain to an appropriate angle, the ‘Ball and Spoke” model will
show two bonds extending from the second carbon; choose a
O atom and
connect it to the second carbon - you should still be able to see the C=O
double bond when you are done. ‘Setup’ and ‘Submit’ the molecule, and
calculate the charged electron density surface for the “size” surface.
Set the same color scale for all three molecules to allow comparison.
7b) Which molecule’s surface indicates that it is most polar? Which molecule is least
polar? (If you’re not sure, check the dipole moments).
7c) Is each molecule “uniformly” polar? If not, what kinds of molecular structure produce
polar regions and which non-polar? Can you explain these results using a table of
electronegativities?
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Cleanup
When you are finished, you can drag the folder with your files in it to the TRASH.
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Appendices
Guidelines for Drawing Lewis Structures
1) Count total number of valence electrons (including charge).
2) Calculate number of electrons needed to complete octets for all atoms (2 electrons for H).
3) #bonds = [(octet e) - (valence e)]/2
4) Arrange atoms and connect with single bonds. Clues:
a) Formulas reflect order of atoms: HCN
b) ABn molecules: a “central atom” (A), surrounded by a bunch of others (B).
(e.g. CO2, NH3, SF4, …)
c) Element that forms the most bonds is the central atom; this atom is often the least
electronegative atom as well.
d) H &F only bond to 1 atom, are always “terminal” and never “central”. Other halogens
(Cl, Br, & I) are usually “terminal” atoms - rarely central atoms.
5) Add electrons to complete octets of “outer” atoms.
6) Put remaining electrons on central atom.
7) If central atom lacks octet, use multiple bonds.
8) Use formal charge to decide if central atom expands it octet (assuming that it can).
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Electron Pair Geometries
16
Molecular Geometries
17
Electronegativities
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