In your classroom text, review the following topics thoroughly:
If you are having difficulty mastering Lewis diagrams and resonance, try this handout: Drawing Lewis Diagrams
Download and print the Report Form for this experiment.
To get more experience drawing Lewis diagrams of molecules and predicting their geometry, and to learn how to build and study molecular models with computers.
During the lab period, you will get extensive practice in writing Lewis diagrams, predicting the three-dimensional structure of molecules, and constructing simple models of molecules. You will also receive an introduction to Spartan, a computer program for molecular modeling. During the following week, you will use Spartan to build some molecular models and measure such parameters as bond lengths and angles.
The program Spartan is easy to use for building, viewing, and analyzing simple molecular models. In learning its basics, you will merely scratch the surface of what this powerful program can do. You will use the program in future chemistry courses to carry out much more powerful and sophisticated analyses that can give insight into the relationship between molecular structure and the properties of substances.
How does the structure of water molecules produce the shape of a snowflake?
You are about to enter the heart of chemistry.
The following problems require skills similar to those called for in the report on this experiment. Similar questions may appear on your pre-laboratory quiz. For guidance, look at the Assignment/Report Form for this experiment. Answers are provided in the tutorial that follows.
|
Lewis Diagram |
Resonance? |
Number of Central Atoms |
Electronic Geometry |
Molecular Geometry |
|
|
EXAMPLE |
|
no |
1 |
1. tetrahedral 2. (only one central atom) |
1. trigonal pyrimidal 2. |
|
methylamine |
. |
. |
. |
1. 2. |
1. 2. |
|
tetrachloroiodate ion |
. |
. |
. |
1. 2. |
1. 2. |
|
nitrite ion |
. |
. |
. |
1. 2. |
1. 2. |
Spartan Student Version 2.0.0 is currently available only in the USM and Gorham computer laboratories, on Windows computers. This means that you must carry out the tutorial and the computer portions of the experiment in one of the USM computer labs. The number of students who can use the program at one time is limited, so do not wait until the last minute to do this experiment. Unavailability of the program will not be accepted as an excuse for a late project.
The following exercises introduce you to Spartan, a molecular graphics program. This tutorial will show you how to build molecular models using the Entry and Expert tool kits, how to minimize the energy of the model to make its bond lengths and angles realistic, and how to measure bond lengths and angles. Later, in carrying out the exercises on the Report Form, you will need to decide whether you need to use the Entry or Expert kit to build the model you need.
Follow the instructions of this section to learn how to load models, manipulate structures, change model type, and make measurements.
Before you start Spartan, you need to download and save a model file to use in your first exercises. Click HERE to download a Spartan model of the narcotic pain reliever morphine. Your computer will instruct you to save the file. Save it to the desktop of your computer. The file should appear on the desktop with the name morphine1.sxf. (The suffix .sxf stands for Spartan Exchange File.)
Start Spartan from the Windows Start menu, by picking the following submenus in succession: Start:All Programs:Chemistry Applications:Spartan Student V2.0.0.
When the Spartan program window appears, its lower right corner may be hidden by the Windows Task Bar. If so, <left-click drag> the top edge of the Task Bar and push it down, out of the way. Its top edge will still be visible. Next, <left click-drag> the lower right corner of the Spartan window to adjust its size so that the Task Bar will not hide it, and so that it covers only about two thirds of the width of the screen. Then <left-click drag> the top edge of the (hidden) Task Bar to put it back in place.
Now adjust the width of this browser window to about one-third the width of the computer screen. Move it to the right side of the screen. This will allow you to read the tutorial while you use Spartan.
On your left, you will now see the Spartan window with its menu bar along the top, and the buttons of the Spartan tool bar below the menu bar. For all of the following commands, make sure that you use the menus of the Spartan program window, not the menus of this browser window.
On the Spartan program window,
File:Open
On the dialog box that appears, click Desktop to see a
list of files on your desktop. You will not see the file
morphine1.sxf at first. To reveal it, use the bottom menu of
the dialog box to set Files of Type: to All Files. Then
<left click> morphine1.sxf in the file list, and
click Open.
A model of the morphine molecule appears in the Spartan program window.
Carbon atoms in Spartan models are colored black, hydrogen is white, oxygen is red, and nitrogen is blue. The model you are viewing might seem quite complex compared to the first models you will build, but do not be daunted by it. It contains many central atoms, but each is just like central atoms in small molecules. This model will serve you well for the following exercises.
Model:Wire
This action displays the model as the simplest type, a wire
model. Use other commands under the Model menu to see other
model types. Each type shows different aspects of model structure.
Wire models and Ball and Wire models show bond angles
clearly, and they show double and triple bonds as double or triple
lines. In Tube (sometimes called Stick) models and
Ball and Spoke (or Ball and Stick), atoms in front hide atoms
behind, making it easy see the model as a three-dimensional object.
Double bonds appear as two flattened sticks, and they may not be
apparent until you rotate the model (described below). Space
Filling models show the surface of molecular contact and depict
the relative sizes of atoms realistically, but they obscure bond
angles. Each model has strengths and weaknesses for exhibiting
different aspects of structure.
For the exercises that follow, display the model as Ball and Spoke.
Rotate (spin the model)
With the mouse pointer anywhere on the graphics window, hold down the
left mouse button and, without releasing the button, move the mouse
(<left click-drag>). The model rotates about an axis
perpendicular to the direction of mouse motion. Dragging vertically
on the screen rotates the model about its x-axis; dragging
horizontally rotates about y, and dragging diagonally rotates
about a diagonal axis. Rotating helps you to see that the model is
three-dimensional, and allows you to bring any part of the model to
the front, where you can see it clearly for measuring or for adding
atoms. Next, <shift/left click-drag> vertically. This
action rotates the model around its z-axis, which is
perpendicular to the screen.
Translate(move the model around the
screen)
<right click-drag> to move the model across the screen.
Translating is handy when you display more than one molecule and want
to move them to different parts of the screen or superimpose
them.
Zoom (move the model farther away or
closer)
<shift/right click-drag> Drag the mouse pointer up the
screen to zoom in on the model, or make it larger. Drag down the
screen to zoom out, or make the model smaller. Zooming allows you to
adjust model size in order to see details, such as bond types, more
clearly.
Bond Lengths and Other Distances
<left click> any bond to measure its length. Notice that Spartan highlights the two atoms joined by the bond. The bond length, in angstroms, appears in the lower right corner of the Spartan window, beside the words Length (bond #) =.
In the vertical tool bar next to the graphics
window, click the distance measurement tool, which looks like this:
.
Now <left click> any two atoms, whether they are
adjacent or not. Spartan highlights each atom as you click it, and
reports the distance between them.
About how long is the morphine molecule? (Answer: between 8 and 9 angstroms across its longest part.)
To turn off the distance tool, click the button with the large V (for "view"). Use the V button when you want to turn off any tool.
Bond Lengths and Bond Orders
The morphine model contains single bonds, as well as double bonds (represented as double lines in ball-and-wire models) and aromatic bonds (repesented as a single line plus a dotted line). Compare the lengths of double and aromatic bonds with those of single bonds between the same elements (that is, compare carbon-carbon single bonds with other carbon-carbon bonds). In general, aromatic bonds are shorter than single bonds, and double bonds are shorter still. Do you find this correlation in your measurements? Do you know why it is true?
Bond Order
The number of bonds between two atoms, or the number of shared electron pairs, is called the bond order. The bond order of a single bond (one pair of shared electrons) is 1.0. The bond order of a double bond (two pairs of shared electrons) is 2.0. A bond represented as a solid line plus a dotted line has a bond order between 1.0 and 2.0. The dotted line represents a partial bond.What is a partial bond? It represents two atoms sharing fewer than two electrons. As you learn from your chemistry text, molecules that are stabilized by resonance, which are called resonance hybrids, must be represented by more than one Lewis diagram, each called a resonance contributor. The bond order for a specific bond in a resonance hybrid is computed by averaging the orders for that specific bond in the various diagrams. Thus the bonds that differ within a set of resonance contributors have non-integral bond orders. If the bond order is 1.5, then we say that there is a single bond plus a partial bond (in this case, a "0.5 bond"). For example, the two C-O bonds in acetate ion (below) have bond order of 1.5. The are neither single nor double bonds; they are "one-and-one-half" bonds.
Acetate ion, represented as two resonance contributors (unshared electrons not shown).
The vertical C-O bond is double (bond order = 2.0) in the left contributor,and single
(bond order = 1.0) in the right contributor. So in the hybrid (the real acetate ion) the
order of this bond is the average of 2.0 and 1.0, which is (2.0+1.0)/2 = 1.5. The same
is true for the other C-O bond.Spartan represents partial bonds as dotted wires or striped spokes.
Bond lengths decrease as bond orders increase. As atoms share more electrons in covalent bonds, they are pulled closer together.
Polar Bonds
Measure the lengths of C-N and C-O single bonds, and compare them with that of C-C single bonds. A C-O bond is shorter than a C-N bond, which is shorter than a C-C bond. Do you find this correlation in your measurements? Do you know why more-polar bonds are shorter?
Bond Polarity and Bond Length
The greater the difference between the electronegativies of two bonded atoms, the more polar the bond between them. More-polar bonds are shorter than less-polar bonds. So bonds between atoms of unlike electronegativity are shorter than bonds (of the same bond order) between like atoms.Of carbon, nitrogen, and oxygen, which is the most electronegative? Do this trend fit with your measurements of bond length?
Bond Angles
A bond angle is the angle formed by two bonds to the same atom, or the angle formed by a chain of three successive bonded atoms.
Click the angle-measurement tool --
.
Now you can measure bond angles by clicking two adjacent bonds, or three successive atoms.
Find a tetrahedral carbon central atom (surrounded by four single bonds) in the model of morphine. Measure several bond angles around the central atom (by the way, how many are there?). According to VSEPR theory, they should all be about 109 degrees. Find a trigonal carbon central atom (surround by one double and two single bonds). Measure bond angles around the central atom. They should all be about 120 degrees. Do you find significant deviations (more than 5 degrees) from these values? Can you explain them? Rings of atoms sometimes force atoms to adopt unexpected bond angles.
Find the only nitrogen in morphine. What is its molecular geometry? According to VSEPR theory, bond angles around such an atom should be about 109 degrees. What bond angles do you find? Can you explain why? What type of electron group takes up more space around a central atoms: unshared electrons or bonded electrons? Does this explain your observations?
You can also measure other angles in your model, by clicking any three successive atoms, whether they are connected to each other or not.
Click the V button to turn off the angle-measurement tool.
Take time now to drag the mouse curser slowly accross all the tools on the Spartan tool bar. As you pause over each button, Spartan displays a brief description of what the tool does. Many of these functions are duplicated in the menus.
File:Close to remove this model from the display. If a Save dialog appears, click Don't Save this model.
Now you know how to open a model file; change model type; rotate, translate, and zoom the model; measure bond lengths and angles; and recognize the order of bonds. Use these tools to help you study your models as you carry out the remaining parts of the tutorial.
Spartan has for tool kits for building models: Entry, Expert, Peptide (for proteins), and Nucleotide (for DNA and RNA). Each tool kit provides tools for controlling the geometry of central atoms and the types of bonds (partial, single, double, and so forth). Each tool kit also provides tools for adjusting models (making and breaking bonds, deleting atoms). Finally, some of the tool kits provide prebuilt groups of atoms for building more complex models.
Follow the instructions in this section to learn how to build models with the Entry tool, minimize their energies to make bond lengths and angles realistic, and save your models.
File:Close to remove any model currently on display.
File:New
or click the New Model button, the first button at the
left of the Spartan tool bar (displays a piece of paper with the
corner folded over).
This command opens the tool kits at the right side of the Spartan
window.
At the top right of the window, click the Entry tab to activate the simplest of the tool kits.
Look over the buttons provide for the Entry
kit. Each button provides an element with specified bonding pattern.
The 
button,
for example, is for a tetrahedral carbon with four single bonds.
Below it is trigonal carbon with two single bonds and one double
bond, and so forth. You should realize by now that, in order to build
a model, you must tell Spartan what element to add, along with its
geometry. In other words, you have to know what you are
building. This means starting from correct Lewis diagrams, and
correct predictions of electronic geometry and molecular geometry.
You must rely on the accuracy of your work in Part I in order
to succeed with Spartan (or any molecular graphics
program).
We will use the examples in Preparing for Lab. Here is the completed entry for CH3NH2, which is called methylamine:
|
Formula |
Lewis Diagram |
Resonance? |
Number of Central Atoms |
Electronic Geometry |
Molecular Geometry |
|
CH3-NH2 |
|
no |
2 (C and N) |
1. C: tetrahedral 2. N: tetrahedral |
1. C: tetrahedral (AX4) 2. N: trigonal pyramidal (AX3E) |
Here's how to build a model of methylamine:
Click the tetrahedral-carbon button, and then click anywhere on the blank graphics window. A carbon atom model appears, with four bonds called unfilled valences (colored yellow) arranged tetrahedrally around it. Unfilled valences will become hydrogen atoms at the end of building, unless you replace or delete them. Rotate the model (<left click-drag>) so that you can see all four unfilled valences. You may also need to zoom in on your model, (<shift/right click-drag>, moving the mouse pointer vertically).
Click the trigonal pyramidal nitrogen button -- 
--
and then click on one of the unfilled valences of the carbon atom in
the graphics window. Spartan adds a trigonal-pyramidal nitrogen to
the carbon at the unfilled valence.
You have now built a model of methylamine. Spartan will treat the unfilled valences as hydrogen atoms. Rotate the model to see its overall shape. After assembly of a model, its bond lengths and angles may not be exactly right. In the tool bar, click the button displaying an arrow pointing down at the letter E. Spartan adjusts the structure to minimize its energy, giving it bond lengths and angles that correspond to greatest stability. After minimization, Spartan displays the energy of the model at the lower right, next to the words Energy =. Note the energy and click again to repeat the minimization. If the energy goes down, keep clicking the minimizer button until the reported energy no longer changes.
In the tool bar, click the V (view) button to put away the tool kit.
Measure the angles of the following bonds: H-C-H, H-C-N, H-N-H. VSEPR theory predicts angles of approximately 109.5 degrees, the tetrahedral angle, for bond angles on both the carbon and the nitrogen. Which angles deviate most from this value? Why?
Look at the model with all types of representations: ball and spoke, space filling, and so forth.
File:Close to remove the model of methyamine from the display. Spartan asks if you wish to save the model. Save it to the desktop with the name methylamine.
For reliability of future use of files, name all files with lower-case letters only,
and do not include spaces, periods, or slashes in your file names.
If Spartan adds an ending to the name, do not change it.
Failure to follow this advice may make it impossible for your instructor to read your files.
The Entry tool allows you to build models in which the atoms have the most common valences and bond types. But many molecules contain atoms with less common valences, as well as partial bonds, such as those that require resonance structures to represent them. For these models, you need the Expert tool kit.
Follow these instructions in this section to learn how to build models with the Expert tool, minimize their energies to make bond lengths and angles realistic, and save your models.
Here is the completed Preparing for Lab entry for tetrachloroiodate ion ICl4- ion.
|
Formula |
Lewis Diagram |
Resonance? |
Number of Central Atoms |
Electronic Geometry |
Molecular Geometry |
|
ICl4- |
|
no |
1 (I) |
1. I: octahedral 2. (only one central atom) |
1. I: square planar (AX4E2) 2. |
|
|
|
First, take time to look over the buttons in the Expert Tool Kit. Below its main window is a periodic table, from which you pick the element of the next atom you will add to your model. Below the periodic table is a set of valence/geometry buttons, from which you pick the valence and geometry of the next atom you will add to your model. The first button on the left represents a monovalent atom (which has no geometry), the next one is divalent linear, then trivalent trigonal, divalent bent, trivalent trigonal pyramidal, and so forth. See if you can name the remaining buttons. The third row contains bond-type or bond-order buttons, which allow you to set the change any bond in your model to a specified type, or in other words, to set the bond order of a bond. The bond types available are partial (bond order between 0 and 1), single (bond order of 1.0), single-plus-partial (1 to 2), double (2.0), triple, and quadruple. The last set of tools in this kit are menus that provide complex molecular groups, already built, for adding to a model. When you make selections from any tool kit, its window displays the element (or group) and geometry that Spartan will add when you click in the main graphics window. When you click on a free valence in the model you are building, Spartan adds the atom shown in the tool-kit window to your model, attaching it at the free valence on which you click. Now you will use this tool to build some models that you could not build with the Entry tool kit. |
 |
File:New
In the Model Kit, click Expert.
On the periodic table, find iodine and click its chemical symbol.
Then click the octahedral electronic geometry button :
.
Next, click anywhere in the graphics window. A hexavalent iodine atom
appears. Rotate it so you can see all six unfilled valences.
Next, click chlorine on the periodic table, and click the
univalent atom button: 
.
Then click an unfilled valence on the iodine atom. A univalent
chlorine atom appears attached to the iodine atom. Notice that this
action adds the specified atom, with the specified valence and
geometry, to the unfilled valence. Add three more univalent chlorines
to the iodine, placing them make a square-planar arrangement, with
two unfilled valences perpendicular to the plane of the square-planar
model.
Build: Delete
or click the Delete button in the Spartan tool bar. The
Delete button has a red dot with six red lines around it
(according to Southwestern archaeological research, this is the
Anasazi symbol for deleting an atom). Now click on one of the
remaining unfilled valences to remove it. By the same method, remove
the last unfilled valence. You have assembled the
ICl4- ion. Make sure it is square planar. As
before, minimize the energy of this model until its energy remains
constant.
Click the V button to put away the tool kit. Save the model to the desktop with the name icl4. In the Spartan graphics window, measure the Cl-I-Cl bond angles. VSEPR theory predicts angles of 90 or 180 degrees. If any angles deviate from this value, think about possible reasons for the deviation.
Look at the model with all types of representations: ball and spoke, space filling, and so forth.
Look again at the Expert tool kit. Is there an easier way to build this model? Try it. Minimize your model and compare its bond lengths to your first tetrachloroiodate model. Do both methods give you the same results?
File:Close to remove the model of tetrachloroiodate ion from the display.
Here is the completed Preparing for Lab entry for nitrite ion (NO2- )
|
Formula |
Lewis Diagram |
Resonance? |
Number of Central Atoms |
Electronic Geometry |
Molecular Geometry |
|
NO2- |
|
yes!! |
1 |
1. N: trigonal planar (3 groups of electrons) 2. (only one central atom) |
1. N: bent (AX2E) 2. |
Notice that you must represent this ion as the resonance hybrid of two Lewis diagrams. In the top resonance contributor, the N-O bond on the left is single (having a bond order of 1.0), while in the lower diagram, the same bond is double (bond order = 2.0). So the actual bond order of this N-O bond is the average of what each diagram shows, or 1.5. The same is true for the N-O bond on the right. One way to represent this resonance hybrid ion with a single diagram is to represent partial bonds as dotted lines like this:
A pair of lines, one solid, one dotted, between two atoms implies that the bond order has a value between 1.0 and 2.0.
The position of the negative charge on the ion is not specified. In fact, there is approximately 1/2 of a negative charge on each oxygen atom. In a resonance hybrid, charges on atoms, like bond orders, are the average of what each Lewis diagram shows.
Now, referring to our representation of the resonance hybrid (not the two Lewis diagrams), let's build a model of nitrite ion.
File:New
or click the New Model button. Click the tab for the
Expert took kit.
Pick nitrogen in the periodic table, and then click the divalent-bent geometry button. Click on the graphics window to produce a model of divalent nitrogen. Rotate the model so you can see both unfilled valences. Put univalent oxygen atoms on both unfilled valences.
Click 
in the row of bond-type buttons. Double click (<left
click-click>) on one of the N-O single bonds. It will appear
as one solid and one dotted or striped bond, a "one and one-half"
bond. Repeat for the other N-O bond, so that both N-O bonds are
single plus partial. Minimize the energy of the model.
Click V to put away the tool kit, and save the model to the desktop with the name nitrite.
In the Spartan graphics window, measure the O-N-O bond angle. The ideal angle is 120 degrees, because this atoms has three groups of electrons: two bonding groups, and one nonbonding pair (see the hybrid or Lewis diagrams above). If the angle deviates from 120 degrees, think about possible reasons for the deviation.
Look at the model with all types of representations: ball and spoke, space filling, and so forth.
File:Close to remove the model of nitrite ion from the display.
Now let's build a biological molecule, the amino acid phenylalanine. Phenylalanine is one of the amino acids that living organisms use to build proteins. A defect in the body's ability to break down excess phenylalanine for excretion is responsible for the inherited condition phenylketonuria, which affects early brain development, and can result in severe mental retardation. Babies born with this condition are kept on low-phenylalanine diets to prevent brain damage until after the susceptible stages of brain development are complete.
As their names suggest, all amino acids have a carboxylic-acid, or carboxyl, group (-COOH) like that of acetic acid, and an amine group (-NH2), which is chemically similar to ammonia. In the class of compounds called alpha-amino acids, from which proteins are synthesized, the carboxyl and amine groups are attached to the same carbon atom.
Here is an unfinished Lewis diagram of phenylalanine, showing all atoms and their connections. Any vertex that has no chemical symbol is a carbon atom.
Phenylalanine is a neutral compound (has a net charge of zero). Complete the diagram to show all multiple bonds, unshared electron pairs, and formal charges. Check the answer at the bottom of this page to be sure you have drawn the Lewis model correctly. Then use it as a guide while using the following instructions to build a model of phenylalanine.
File: New
or click the New Model button.
Click the Entry tab of the tool kit, if it is not already activated.
Click the Rings button, and on the menu next to the button, pick Benzene. A benzene ring appears in the tool kit window. Now click anywhere on the main graphics screen to produce a benzene ring with six unfilled valences, one on each carbon.
Add a tetrahedral carbon to one of the benzene free valences (if you don't remember how, review the molecules you constructed previously). Next, click the Groups button, and on its menu, pick Carboxylic acid. Note the structure of this group in the tool kit window. Click any unfilled valence on the tetrahedral carbon that you just added, to add the carboxylic acid group.
Next, add a trigonal-pyramidal nitrogen to either of the remaining free valences of the same tetrahedral carbon that carries the carboxylic acid group.
Your model of phenyalanine is complete. To build it, you used two of the many complex groups, called functional groups, available in Spartan. These pre-built groups simplify the construction of complex models.
Minimize the energy of this model and save it with the file name phenylalanine.
Complete the Report Form for this experiment.
In preparing your report, you will build, save, and turn in additional models. If you can't remember how to carry out operations requested in the report, refer to this tutorial, which has exposed you to all the tools and operations you should need.
Spartan image of the electron-density surface
of water.
Surface colored by charge (blue = positive, red = negative).
Dipole moment (arrow) points toward negative end of molecule.
Spartan calculates surfaces that display many molecular
properties.
The USM Chemistry Department uses Spartan
in organic, physical, and advanced inorganic chemistry courses,
where you will learn to use its many powerful advanced functions.
Spartan comes with extensive examples and a full set of
tutorials.
You'll learn a lot about structural chemistry by getting to know
Spartan.
Interested? Click HERE.
Correct Lewis Model of Phenylalanine
Note: The benzene ring must be represented by
two resonance structures, so
all six of its C-C bonds actually have bonds orders of 1.5. This is
why
your Spartan model is built to show six equivalent "one-and-one-half"
C-C bonds.
