A Chemist in Second Life: Making a Specific Molecular Rezzer - Part 1

Teaching in SL

Over the years, I have been incorporating more and more technology into my chemistry classes. Now that I retired in 2015, it is fun to look back at what I did. Here's a PP presentation I gave long ago. http://www.chem.tamu.edu/class/fyp/keeney/secondlife/Integrated%20Technology-its.ppt I am editing this in 2017.

Fall 2010 was my 3rd semester at trying to incorporate optional weekly review sessions into SL. Optional for a few reasons. (1) My classes are large; I teach two classes of about 250 students each, so obviously I cannot have everyone in SL at the same time. (2) I do have a few students under 18 - which is problematic. (3) Some students are very uncomfortable in SL. Here I'll be blogging about the trials/tribulations of encouraging students to get involved in SL. Here's the link to a video clip of a tour of my area: http://www.chem.tamu.edu/class/fyp/keeney/secondlife/drwendy-in-SL.mp4

Chemistry World is the island Kurt Winkleman and I developed to see if first year chem students can do labs in SL. This blog is not about that project.

You can visit researchgate.com to keep updated with our papers.

Monday, July 12, 2010

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.