Molecular Modeling—CAChe Instructions
Molecular Modeling—Instructions
C
hemists have for years been using their hands, pieces of paper, or bits of
wood and plastic to make models of molecules to see how molecules fill
space and to have some insight into how another molecule might attack to initiate a chemical reaction. Now we have very powerful computer software that
allows us to construct easily and quickly a model of a molecule. In this experiment you will learn how to use computer software for constructing models of
models and will use that software to answer some basic questions about molecular structure.
This experiment uses the popular software from The CAChe Group of
Fujitsu, a program known by the name CAChe, which stands for Computer
Aided Chemistry.
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Student Copies of
CAChe Software
Available —FREE
Oneonta has a license
for the CAChe software
that allows each student
to have a copy. See your
instructor if you want to
install this on your own
computer. You can learn
more about the CAChe
software at
http://www.cachesoftware.com/
The software you will use is called the CAChe Personal Version. It allows
you to do the following:
• Build a molecule by connecting atoms on the screen
• “Minimize” the structure of the molecule. This uses a program called
“Mechanics” to find the basic structure of the molecule. It treats the molecule as though it were a collection of balls (the atoms) connected by
springs (the bonds). This portion of the program also allows you to find
the energy of a molecule as its structure changes and then view the result
as a “movie,” which shows the energy as a function of structure.
• Derive the molecular orbitals for the molecule. This is done by the extended Hückel method.
The CAChe software is available on both Macs and PCs
in PS 122. It is NOT available in other labs on campus. If you wish a copy of
the software to install on
your own computer, see
your instructor.
The instructions for using this software are based on the documentation in
the CAChe folder on the General Chemistry Interactive CD-ROM that
accompanies Chemistry & Chemical Reactivity (5e).
INSTRUCTIONS FOR WINDOWS VERSION
Part 1: Building a Molecule
In the START menu go to PROGRAMS and then CAChe. From the CAChe
menu select “Workspace.” This will open a new window (file) on the screen.
A portion of the CAChe software is on the General
Chemistry Interactive CD-ROM
along with a library of hundreds of models already constructed. Also note that all
of the models on the CD-ROM
are to be found on the textbook website.
A Workspace opened in the Windows version of CAChe.
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Molecular Modeling—CAChe Instructions
Select an atom or
group of atoms
On the left side of the screen is a strip that shows the functions that are
performed by the mouse. Select the icon that looks like a pencil drawing a
string of atoms. When the drawing tool is selected go to the menu at the top
of the Workspace and select “O-oxygen” from the atom menu. Click on the
screen, and a red sphere representing an O atom appears on the screen.
Drawing tool
Rotate a molecule
Move a molecule
Resize a molecule
Now go to the “Beautify” menu at the top of the screen. Select
“Comprehensive” from this menu, and the O atom on the screen is converted
to the water molecule.
Atom selection menu in
Windows version of
CAChe. Note the “periodic
table” item that allows
the selection of any other
atom.
The function of “Beautify” is to adjust the valence of the atoms in the molecule, fix their hybridization (see Chapter 10 of Chemistry & Chemical
Reactivity), and then calculate a reasonable geometry based on a set of rules
contained within the software.
The molecule may be viewed as a “wireframe,”
“ball-and-stick,” or “space-filling” model by clicking on the small icons at the far left of the icon bar.
The screen below shows a ball & stick model of
water after clicking on “Beautify” and selecting
“ball & stick.”
Wireframe Space filling
model
model
Ball & stick
IMPORTANT: In the “View”
menu, select “Show
Hydrogens” and “Show
Electrons.” Then go to
“Atom Attributes.” Click on
this item, then on “Label.”
In this dialog box, click
“Atomic Symbol.”
model
In many cases,
Model selection icons
an atom is surrounded by
in Windows version of
not only other atoms but
CAChe software.
also by electron pairs,
often referred to as “lone
pairs” or “nonbonding pairs.” To see these, go to
the “View” menu and select “Show electrons.”
Water molecule showing
2 H atoms and 2 lone
electron pairs around
the O atom.
Your water molecule should now appear
as shown here. Notice that the O atom is surrounded by two H atoms bonded to the central O
atom and two lone pairs of electrons.
Molecular Modeling—CAChe Instructions
Use the following procedure to rotate a model. With the molecule on the
screen, click on the rotate button in the toolbar on the left side of the
screen. A “rotate circle” will appear on the screen. While holding down
the left mouse button, drag the mouse to rotate the molecule.
To scale a model (make it bigger or smaller), click on the scale button on
the toolbar on the left side of the screen, click and hold the left mouse button, and drag the mouse. (The cursor will change from an arrow to a magnifying glass.) Dragging to the left decreases the size, and dragging to the right
increases the size.
To move (translate) a model, click on the move button on the toolbar on
the left side of the screen, click and hold the left mouse button, and move the
mouse. (The cursor will change from an arrow to a hand.)
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Rotate model
Scale model
Move model
2. Determining Bond Lengths and Bond Angles
To determine the distance
between two atoms, you must
first select the two atoms. Using
the selection tool (the arrow icon
at the left) select the first atom by
placing the tip of the arrow cursor on the center of the atom and
clicking the left mouse button. To
select the second atom, hold
down the shift key while you
point and click on the center of
the second atom. Only the two
atoms of interest should appear
solid, and all of the other atoms
and bonds should appear “grayed out.” (If you make a mistake, simply click
anywhere on the screen away from the molecule to deselect the entire molecule and begin again.) With the two atoms selected, click on the Adjust menu
and select Atom Distance. A dialog box will appear, showing the distance
between the two atoms. Click the OK button to exit the dialog box.
To determine a
bond angle, you
must select three
atoms. Select the
first atom by clicking on it, then
select the other
two atoms by
holding down the
shift key and clicking on each one
(making sure to
click in the atom’s
center).
It
is
important to click
To measure bond
distance or bond
angle you can also
use the small icon (7th
from the right) in the tool
bar at the top of the
screen.
NOTE: bond lengths are
given in Ångstrom units,
where 1 Å = 10-10 m =
100 pm.
Atom distance dialog box.
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The H–O–H angle in
water. To measure a bond
angle you MUST click on
the three atoms in succession. Here you click
on an H, then, holding
the left mouse button
down, click on the O
atom and then the other
H atom.
Molecular Modeling—CAChe Instructions
on the atoms in the correct order. For example, to determine the H—O—H
bond angle in water, first click on an H atom, then shift-click on the O atom,
and finally shift-click on the other H atom. Once the three atoms are selected,
choose Bond Angle from the Adjust menu. A dialog box will appear, showing
the value of the bond angle. Click the OK button to exit the dialog box.
4. Modifying a Model to Build Another Molecule
It is often convenient to convert a simpler molecule into a more complex
one. Start with your water molecule to build methanol, CH3OH.
• Click on one of the H atoms of a model of water. This will cause the other
atoms (the O and other H) to be “grayed out.”
• Delete the highlighted H atom by using the “delete” key or by going to the
“edit” menu item and selecting “delete.”
• Using the atom drawing tool, go to the atom selection menu and select carbon, C. Place a C atom on the screen by clicking on the screen in some
location near the O atom.
• Still using the atom drawing tool, hold the left mouse key down and draw
a line from the center of the C atom to the center of the O atom. Your
screen should now look like this.
H atom
C atom
Before you “beautify” a
molecule you must make
sure it is “active.” That is,
no atoms should be “grayed
out.” To do this use the
“select” tool and click anywhere on the screen.
O atom with
two lone
pairs of
electrons
• Click on the “select tool” (the arrow at the top of the tool bar at the left)
and then click anywhere in the screen (except on the molecule itself). All of
the atoms will be “active.” That is, they will not appear “grayed out.”
• Go to the beautify menu and select “comprehensive.” This will give the
result shown here.
Measure the H–O–C and
H–C–H bond angles in
methanol and record them
on your report form (page
3) of the Experiment.
5. Molecules with Multiple Bonds
Now let us create a model of carbon dioxide, O=C=O, by modifying the
methanol structure.
Molecular Modeling—CAChe Instructions
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The CO2 molecule is linear with two
C–O double bonds.
• Delete the H atoms on the methanol molecule (or use the drawing tool and
start over by placing the atoms O, C, and O on the screen).
You could build CO2 directly
by placing a C atom on the
screen, then two O atoms,
one on each side. When you
draw a bond between the
atoms, select “Double” in
the “bond type” menu.
Beautify the structure. This
same general approach can
be used to build any molecule.
• To create a double bond between the C and O atoms, use the “select tool”
to click on the C–O bond to select it. (The atoms will be “grayed out.”)
Next, go to the “bond type” menu and select “Double.” The bond will
now be a C=O double
bond.
• Place another O atom on
the screen somewhere near
the C atom.
"Double" is selected in
the "bond type" menu.
• Leaving the bond type
selected as “Double,”
draw a bond between the
C atom and the new O
atom.
Note that
the bond is
selected.
Atoms are
grayed out.
• Beautify the molecule.
Creating a double bond in a model. After
selecting a bond, use the “bond type” menu to
select the type of bond required.
5. Using Mechanics
We can ensure that the geometry the beautify procedure gives us represents a
minimum in energy for the molecule by using the Mechanics calculation
engine.
• First, save the methanol molecule you have drawn.
• Go to the Experiment menu (or click on the icon that has a small flask and
beaker on it).
• Select “optimized geometry.” (This is the default selection in the menu.)
Click “Start.” (The screen should appear as shown here.)
NOTE: This is an optional
part of the laboratory
experiment.
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Molecular Modeling—CAChe Instructions
After some seconds, the calculation will be complete. Click the “close” box
in the upper right corner of open windows until you have returned to the
structure of methanol on the screen.
6. Fragment Library
The General Chemistry
Interactive CD-ROM contains
a library of hundreds of
models of molecules that
can be viewed using the
CAChe software on the CD.
(Note that this software
allows you to build molecules as well, but offers no
other functionality.)
The CAChe system includes a very large library of molecular structures
already prepared. All reflect the structure of the molecule in its most stable
form. To find a molecule, use the “File” menu to open a new file. Go to the
“Fragment Library” folder. Double clicking on this folder (or clicking “open”)
will open the Library and reveal many subfolders, each containing a number
of models. For example, opening the folder marked DRUGS-ALL reveals files
of approximately 100 common drugs. Double clicking on any one of these
files will open the model in a new window.
The DRUGS-ALL file in the Fragment Library.
Molecular Modeling—CAChe Instructions
7. Other CAChe Functions
The CAChe software can do many other types of calculations and view molecules and their properties in other ways.
• Perform calculations to view the electron density “envelope” of the molecule, view the molecular orbitals of the molecule, and calculate the energy
of the molecule in a variety of conformations.
• View hundreds of molecules already made and for which calculations have
been done. These are found in the Fragment Library and on the PC or in
the Models folder on the General Chemistry Interactive CD-ROM. See the
documentation in the CAChe folder on the CD-ROM
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FINDING MOLECULES
IN THE CD-ROM MODELS FOLDER
There are hundreds of
models in the CAChe
Models folder on the CDROM. To locate a molecule, you can find the
name used by the CAChe
system in the various
databases FOLDER.PDF
or NAME.PDF.
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Molecular Modeling—CAChe Instructions
INSTRUCTIONS FOR MACINTOSH VERSION
CAChe Scientific originally built the molecular software to run on a
Macintosh, and it was only recently adapted to Windows PCs. As a consequence, there are basic similarities, but some of the Macintosh functionality is
still not incorporated in the Windows version.
1. Building a Model
• Open the CAChe folder on the hard disk and then open the program called
the Editor by double clicking the icon for the program. A blank window
will open in which you can build a molecule. (If the Editor is already open,
select “New” from the “File” menu.)
• Enter the drawing mode by selecting “Atom Tool” from the “Tool” menu.
When you do this, the cursor will change from an arrow () to a cross with
a dot in the middle.
CAChe menu on the Apple Macintosh.
CAChe menu after selecting the “atom tool” in the “Tool” menu.
• Next, select an atom of the element you wish to place on the screen. The
“Atom” menu lists commonly used elements and a “Periodic Table” option
allows you to select an atom of any element. Select an O atom.
• Click on the screen with the atom tool, and an O atom will appear as a red
sphere on the screen.
• Go back to the “Tool” menu and choose the “Select Tool.”
The function of
“Beautify” is to adjust
the valence of the atoms
in the molecule, fix their
hybridization (see Chapter
10 of Chemistry &
Chemical Reactivity), and
then calculate a reasonable geometry based on a
set of rules contained
within the software.
• Now go to the “Beautify” menu at the top of the screen. Select
“Comprehensive” from this menu, and the O atom on the screen is converted to the water molecule. In many cases, an atom is surrounded by not
only other atoms but also by electron pairs, often
referred to as “lone pairs” or “nonbonding pairs.”
To see these, go to the “View” menu and select
“Show electrons.” Your water molecule should
now appear as shown here. Notice that the O
atom is surrounded by two H atoms bonded to the
central O atom and two lone pairs of electrons.
2. Rotate, Move, and Scale a Model
Rotate ( and shift)
With the molecule on the screen, hold down the command key (the key with
the  or symbol) and the shift key at the same time. A “rotate circle” will
appear on the screen. While still holding down the two keys, click and hold
the mouse button, and drag the mouse to rotate the molecule. (The cursor will
change from a straight arrow to a curved arrow.)
Molecular Modeling—CAChe Instructions
Scale ( and control)
To scale a molecule (make it bigger or smaller), hold down the command (« )
and control keys at the same time, click and hold the mouse button, and move
the mouse. (The cursor will change from an arrow to a magnifying glass.)
Translate ( and option)
To translate (move) a molecule, hold down the command and option keys at
the same time, click and hold the mouse button, and move the mouse. (The
cursor will change from an arrow to a hand.)
3. Wireframe, Ball & Stick, and Space-Filling Models
The default status of
the CAChe is generally to prepare ball &
stick models (such as
the water molecule
above). Space-filling
models may give a
better idea of molecular shape, however.
To view a space-filling model, you must
first have a molecule
file open. In the View
menu, make sure
Atoms and Bonds are
The Atom shape dialog box in the View menu on a
checked, and then
Macintosh.
choose Atom shape
from the View menu. The dialog box that appears allows you to decide what
the atoms in the molecule will look like. Make sure the circles next to Spheres
and Shaded are on and that the Radius pop-up box says “van der Waals.”
Change the value in the Scale box from “0.20” to a number closer to “1.00.”
Click the OK button. Now your molecule will look something like the picture
shown here of a space-filling model of ethanol.
To change back to a ball-and-stick model, open
the Atom shape dialog box and change the value
back to “0.20.”
A space-filling model of
ethanol, CH3CH2OH.
Note that the Atom shape dialog box
allows you to turn on or off the atom labels and
atom configuration or to display the atoms as
shaded spheres, wireframe spheres, dotted
spheres, or as coordination polyhedra. You
should experiment with the various options.
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Molecular Modeling—CAChe Instructions
4. Determining Bond Angles and Bond Lengths
Bond length (atom distance)
IMPORTANT: When you
select atoms you must click
in the center of the atom’s
sphere. If you make a mistake click anywhere in the
screen to deselect the molecule and start over.
To determine the distance between two
atoms, you must first
select the two atoms.
Select the first atom by
placing the tip of the
cursor on the center of
the atom and clicking
the mouse button. To
select the second atom,
hold down the shift
key while you point
and click on the center
of the second atom.
The C–O bond distance in the carbon dioxide moleOnly the two atoms of
cule, CO2, is 1.317 A or 131.7 pm.
interest should appear
“solid,” and all of the
other atoms and bonds should appear “grayed out.” If you make a mistake,
simply click anywhere on the screen away from the molecule to deselect the
entire molecule and begin again. With the two atoms selected, click on the
Adjust menu and select Atom distance. A dialog box will appear, showing the
distance between the two atoms. To place the measurement on the model,
click Define Geometry Label, then Apply and Done. If you wish to remove the
geometry labels later, click Geometry labels in the View menu.
Note that distances can be measured in solid state structures as well as in
various inorganic and organic molecules. Also note that distances are measured in Ångstrom units, where 1 Å = 10-10 m or 100 pm.
Bond angle
To determine a bond angle, you must select
three atoms. Select the first atom by clicking on
it, then select the other two atoms by holding
down the shift key and clicking on each one in
succession. It is important to click on the atoms
in the correct order. For example, to determine
the H—O—H bond angle in water, first click
on an H atom. Then, holding down the shift key, click the O atom, and finally on the other H atom.
Once the three atoms are selected, choose Bond angle from the Adjust
menu. A dialog box will appear, showing the value of the bond angle. To place
the measurement on the model, click Define Geometry Label, then Apply and
Done. If you wish to remove the geometry labels later, click Geometry labels
in the View menu.
Molecular Modeling—CAChe Instructions
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5. Modifying a Model to Build Another Molecule
It is often convenient to convert a simpler molecule into a more complex
one. Start with your water molecule to build methanol, CH3OH.
• Click on one of the H atoms of a model of water. This will cause the other
atoms (the O and other H) to be “grayed out.”
• Delete the highlighted H atom by using the “delete” key or by going to the
“edit” menu item and selecting “delete.”
• Using the atom tool in the “Tool” menu, go to the atom selection menu and
select carbon, C. Place a C atom on the screen by clicking on the screen in
some location near the O atom.
• Still using the atom drawing tool, hold the mouse key down and draw a
line from the center of the C atom to the center of the O atom. Your screen
should now look like this.
H atom
C atom
O atom with
two lone
pairs of
electrons
If you make a mistake
while drawing a molecule, go to the Edit
menu and “Undo.” This
is one of the most useful menu items in any
software!
• Go to the beautify menu and select “comprehensive.” This will give the
result shown here.
5. Molecules with Multiple Bonds
Now let us create a model of carbon
dioxide, O=C=O, by modifying the
methanol structure.
• Delete the H atoms on the molecule.
• Draw another bond between the
The CO2 molecule is linear with two
C and O atom. Be sure to click on
C–O double bonds.
the center of the C atom and
draw your line to the center of the O atom.
• Place another O atom on the screen somewhere near the C atom.
• Draw two bonds between the central C atom and the new O atom.
• Beautify the molecule.
You could build CO2 directly
by placing a C atom on the
screen, then two O atoms,
one on each side. Finally,
draw a double bond
between the C and each O
atom, and beautify the
structure. This same general
approach can be used to
build any molecule.
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The General Chemistry
Interactive CD-ROM contains a
library of hundreds of models
of molecules that can be
viewed using the CAChe software (the Visualizer) on the
CD
Molecular Modeling—CAChe Instructions
6. Using the Fragment Library
The CAChe system includes are very large library of molecular structures
already prepared. All reflect the structure of the molecule in its most stable
form.
To use this library, first choose “New” from the file menu and then select
“Fragment Tool” from the “Tool” menu. This will bring up a new menu item,
“Fragment.” Choose “Fragment Library” from this menu and a dialog box
such as the one below will appear. Here we have selected the category “DrugsAll” and have selected the model of “Acyclovir from that list.
The Fragment Library dialog box on a Macintosh.
Click “OK” and then click in the new window. A model of acyclovir (or whatever model has been chosen) will appear. The cursor will change shape, and
clicking on the screen will place the model of acyclovir on the screen where it
can be modified. Its bond angles and lengths can be measured.
7. Using Mechanics
We can ensure that the geometry the beautify procedure gives us represents a
minimum in energy for the molecule by using the Mechanics calculation
engine.
• First, save the methanol molecule you have drawn.
• Go to the “Applications” menu and select “Mechanics.”
• The program will ask you to save the molecule. Save it by giving the file a
name such as “methanol” or “CH3OH” or even your name.
• Select “optimize geometry.” (This is the default selection in the menu.)
Click “Run.” (The screen should appear as shown below.) After some seconds, the calculation will be complete.
Molecular Modeling—CAChe Instructions
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• When the Mechanics dialog box says the calculation is done (in the upper
left corner), use the Applications menu to return to the Editor. The file for
methanol will open again. You can measure the bond angles and bond
lengths at this point and save the file again for future reference.
8. Other CAChe Functions
The CAChe software can do many other types of calculations and view molecules and their properties in other ways.
• Perform calculations to view the electron density “envelope” of the molecule, view the molecular orbitals of the molecule, and calculate the energy
of the molecule in a variety of conformations.
• View hundreds of molecules already made and for which calculations have
been done. These are found in the Fragment Library and on the PC or in
the Models folder on the General Chemistry Interactive CD-ROM. To
open one of these files in the CAChe fragment library, go to the “Tool”
menu and select “Fragment Tool.” As explained above, go to the “fragment” library and then select a model to view.
FINDING MOLECULES
IN THE CD-ROM MODELS FOLDER
There are hundreds of
models in the CAChe
Models folder on the CDROM. To locate a molecule, you can find the
name used by the CAChe
system in the various
databases FOLDER.PDF
or NAME.PDF.
Molecular Modeling
Chemistry 112
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