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Dr. Buckley
e-mail: gbuckley@cameron.edu
Experiment #14 – Molecular Modeling
Laboratory Overview
CHEM 1361
November 2012
Gary S. Buckley, Ph.D.
Department of Physical Sciences
Cameron University
Table of Contents
(you may click on any of the topics below to go directly to that topic)
•Accessing the Scigress Software
•Drawing Lewis Structures
•Determining Formal Charges From the Lewis Structure
•General Software Use
•Notes on Scigress Workspace
Software Access to Scigress
You may install Scigress on your computer through the following process:
Go to the link: http://192.240.12.35/cameron/ScigressCD.zip
Enter the username:
cameron
Enter the password:
goaggies
You can choose to either open the file or save it – that choice is yours. If you choose to save it, be sure
to remember where you saved it.
An additional file called the license key is required for installation. It may be found here. Click on Save
As, choose a file type of .txt., and save this file under the name license on your desktop so you can find
it later.
Double-click on the zipped Scigress folder. Then double-click on Scigress. Early on it will ask for the
license key. Browse using the icon to the right of the blank space to where you have the license key
stored and click on it. Then continue the installation. When it asks about Gaussian, tell it you don’t
have it (unless you are a closet molecular modeling expert).
If you have any problems please don’t hesitate to contact me at gbuckley@cameron.edu or 580-5812885.
This information may also be found as an announcement in your Blackboard Laboratory Section.
Drawing Lewis Structures
The computer program you will use in this experiment – though powerful and
sophisticated – is actually pretty stupid. It relies entirely on you providing
input in a format it recognizes that makes chemical sense. Our means of
getting to that stage is through the drawing of the Lewis structure, a topic you
have probably visited in class by now.
A short lab PowerPoint is not the best venue to become acquainted with
drawing Lewis structures. Section 8.5 of your textbook
(Brown/LeMay/Bursten/Murphy, 11th ed.) is a good starting point if you are
not familiar with this process. More information may also be found by going
to the Molecular Modeling experiment in your lab book.
A Lewis structure provides a means of showing the distribution of valence
electrons in a molecule or ion. It also provides information about the type of
bonding involved – single, double, or triple and formal charges on atoms. It is
important to recognize that the Lewis structure is just an approximation, but a
good starting point for using the software in this experiment.
Determining Formal Charges From the Lewis Structure
Proper entry of starting information to the Scigress program
requires the input of the formal charge (see Section 8.5 and/or the
lab book) of each atom in the species. Briefly, the formal charge on
an atom may be found from:
Formal charge = # valence electrons - #nonbonded electrons on the
atom – ½ • # bonded electrons
Consider the molecule to the right:
For the left oxygen: FC = 6 – 4 – ½ •4 = 0
For the sulfur:
FC = 6 – 2 – ½ •6 = +1
For the right oxygen: FC = 6 – 6 – ½ •2 = -1
The valence electrons come from the group number. In every case,
the sum of the formal charges equals the total charge on the
molecule or ion.
General Software Use
There are two key parts of Scigress you will use to complete this laboratory:
• The Workspace to draw your structures, label bond lengths and angles,
and save for later calculation.
• ProjectLeader to process the calculations from your saved molecules and
ions.
Step-by-step instructions for using this software are provided in the lab
manual. To see a step-by-step set of instructions using Scigress, go to this
link:
https://cameron.blackboard.com/webapps/bb-collaboratebb_bb60/guest.recording.launch.event?uid=8f04cdbe-6a99-49cd-9d5dff7f81d36a20
The information at the link will also provide some tips on being efficient
during your lab time while you are working with Scigress.
Notes on Scigress Workspace
A few trouble spots you may run into:
Problem
Potential Solution
You can’t find your element in
the drop-down list of
elements
Click on the Periodic Table choice in the dropdown, then click on your element
When you Beautify, other
things show up
Three potential solutions:
1. You did not start out with the hybridization
unconfigured.
2. You either did not have your formal charges
correct in your Lewis structure or entered
them incorrectly in the molecule.
3. You either did not have the bond types
correct in your Lewis structure or did not
enter them correctly.
Labeled bond angle looks
weird
Be sure in labeling the angle that you click FIRST
on an OUTSIDE atom of the angle, then the
CENTER atom, then the other OUTSIDE atom.
End of Slide Show