My thought process for this learning module...

I just had a nice chat with Chimera Cosmos in SL and we became friends.  Afterwords, I realize that I never explained why I'm spending so much time on the backside of making molecules using Hiro Sheridan's Rezzer and not having the students build them or work directly with the programs.  Teaching first year chem is a challenge and although I've been giving review sessions in SL, only a few students show.  Part of the reason is the steep learning curve for building in SL.  So I'm working to develop these VSEPR learning modules so that the emphasis is on learning VSEPR theory and not on learning more than the fundamentals of SL.  That's my ultimate goal.  I'll be trying it out in Spring 2011 since I teach off-sequence - Chem 101 in the spring.  Here's how I will incorporate this activity into the gradebook.

In my class - I give optional 3 writing assignments using Calibrated Peer Review as part of the syllabus (I'm the university administrator for this on-line program).  I plan on adding an SL assignment on VSEPR theory so that I have 4 assignments.  So their final score is based on 3 exams, 1 final, and a virtual 4th exam where I average the best 3 scores of their writing assignments (+ now their SL assignment) and their 3 exams.  The students like the ability to have some control in how their grades are determined.  As a note, I also have their on-line homework count as 100% or 20% of an exam.  I calculate their final grade both ways and give each one their better score.  I love how I can use an Excel spreadsheet to individualize student grades.

I'm looking forward to seeing how this will work.  I'll have to have an alternative for my students under the age of 18 since they won't be able to get into SL.

Making a Specific Molecular Rezzer - Part 2 - Finishing up your rezzer

(1) Once you have the hin code for your molecule or ion, the easiest way is to use a molecular rezzer that has already been built and edit it.  So enter Second Life, go to my VSEPR area.  Here is the SLURL: http://slurl.com/secondlife/12th%20Man/231/225/26 .  Right click on one of the boxes on the TOWER of VSEPR and take a copy.  

(2) Find a public sandbox where you can build, or use TAMU's sandbox.  Go to the entrance of my area and click on "Sandbox" on the 12th Man Map.  You'll get a landmark to the sandbox that will allow you to teleport to the sandbox that is about 750 meters above the ground.  You can build here for a couple of hours before your objects will be returned to your inventory. 

(3) Drag the Hiro Sheridan Molecular Rezzer box from your inventory to the sandbox.  Now we will edit it.  Right click on the box and pick edit.  In the General tab, change the name and make sure all the desired boxes are clicked. In the Texture tab, choose the texture you want.  (I use CorelDraw to produce appropriate jpg files.  I then upload the textures at L$10/texture to use in SL.  I'll be providing all the molecules and rezzers I use to anyone who wants them.).  Finally, under the content tab, we will only be editing the MoleculeNotecard, so right click on the notecard and choose Open.  Now, simply edit.  Change the title to the molecule of your choice - I'll use CO2.  Then copy and paste the hin data for atom 1, 2, etc.  The notecard now looks like:

mol 1 "CO2" (the quotes aren't necessary)

atom 1 - O ** - -0.18608 0.99436 0.00000 0.00000 1 2 d
atom 2 - C ** - 0.37217 2.19152 0.00000 0.00000 2 1 d 3 d
atom 3 - O ** - -0.18608 3.38867 0.00000 0.00000 1 2 d

Now hit the Save button and get out of edit mode.

(4)  To check your work,  left click on the box, and CO2 will appear before your eyes!  You can link the parts together by right clicking on an atom, choosing edit, holding down the shift key, then clicking on each individual atom and bond, then hitting control l (the letter L).  Try to click on the center atom last.  You'll see all the objects in blue with the last object you linked in yellow.  (Note: to unlink, hit Control Shift l (letter L).  Now the molecule is a single unit.  To name it, go into edit mode, and change the name.  To get the molecule to rotate, open your inventory and search for rotation script.  You'll find one in your library.  Drag the script into the contents tab of your molecule and exit edit mode.  You'll find it rotates very fast around the center carbon atom - the last one that was linked.  To edit the script so that the molecule spins more slowly, go back into edit mode, under the contents tab and click on the rotation script.  You'll see:

default

{

state_entry()

{

llTargetOmega(<0,0,1>,PI,1.0);

}

}

The coordinates in the angle brackets set the spin (x,y,z) and the number sets the speed of the spin.  Change the 1 (I have it bolded and in red) to 0.2, then hit save.  The spin speed will be much nicer.  Now, exit edit and right click on your rezzer box again to pick "Take" which will add it to your inventory. 

(5)  Now the trick is to get out of the sand-box.  Ours is so high, most folks cannot fly out.  You can teleport home or to another site.  However, the "funnest" way is to parachute out.  Find the ramp and on your way out of the sandbox, click to buy an E-Chute.  At the top of the ramp, open your inventory, and search for the chute.  Either drag it to your back, or right click and choose wear.  Either way, the unopen chute will appear on your backside.  Now the hard part:  walk off the end of the platform and fall.  The chute will automatically open at about 100 meters.  You can use your arrow buttons to direct your descent.  It's fun!  Here I am parachuting onto our "Aggie Beach."  Unfortunately, I landed in the water. (LOL!)

Making a Specific Molecular Rezzer - Part 1 - Getting the right code for your molecule

The backbone of the VSEPR learning modules is preparing Hiro's Sheridan Molecular Rezzer boxes to create the molecules and ions you want the students to study.  Here's the way to do this for molecules/ions with 2, 3, or 4 regions of high electron density around the atom of interest.  Lone pairs of electrons are not shown and the species created are the ones that minimize formal charge.  So the sulfate ion shows 2 oxygens bonded to S with single bonds and 2 oxygens bonded to S with double bonds.

(1) Download and open the free OpenBabelGuI program from http://www.openbabel.org/.  OpenBabel is an open source chemistry toolbox.  We will use it to translate the SMILES chemical file format for our molecules into hin (HyperChem HIN) format; this is the formate that the Hiro Sheridan's Molecular Rezzer uses to create molecules.

(2) Go to  http://www.chemspider.com/ and type the name or formula of the molecule you want the rezzer to create into the search box.  ChemSpider.com is an on-line chemistry community that provides free access to millions of chemical structures.  Type in CO2.  You can now find that the SMILES formate for CO2 is
C(=O)=O after you click on Machine readable identifiers.  Hit the COPY button.

(3) In the open program, OpenBableGUI, select smi (SMILES) as your input format and click on "Input below" box.  Paste the SMILES data (e.g. C(=O)=O) into the input box.  In the center section, make sure that "Add hydrogen" and "Generate 3-D Coordinates' boxes are checked.  In the right section, select hin-HyperChem HIN as your format, and put a check in the box "Output below only." Now, click on "CONVERT" button in top middle.  In the right hand box, you'll see:

mol 1 ""
atom 1 - O ** - -0.18608 0.99436 0.00000 0.00000 1 2 d
atom 2 - C ** - 0.37217 2.19152 0.00000 0.00000 2 1 d 3 d
atom 3 - O ** - -0.18608 3.38867 0.00000 0.00000 1 2 d
endmol 1

You'll only be using the bolded part.  Here's what the OpenBabelGUI page should look like.

VSEPR Species Giver

Hi, all - I've now got the prototype for my VSEPR learning module - see June 28th blog.  You can try it out as a student and get a copy of it for yourself to see how it works from an instructor perspective.  The instructions are given in the contents list.  It is set to give the student 2 molecules that are simple octet violators - the molecules aren't rezzed yet.  They will build themselves before the students' eyes using Hiro Sheridan's Molecular Rezzer.  I plan then on giving the students an assignment sheet to:

(1) rez the molecules/ions and take a picture of yourself with the molecule/ion.

(2) draw an appropriate dot stucture for the molecule.

(3) give the electronic and molecular geometry

(4) give the bond anges and the hybridization of the center atom.