Tips for Users
Create a reaction database with Molecular Modeling Pro version 6
- 1. Draw in a reaction. You can draw in the reaction of your choice or follow these instructions for a simple acid-base reaction.
With the screen free of molecules (Hit Clear in upper right if not clear) click on the "Cl" button then click near the middle of the screen. Hit the "New Mol" button. Click on the Other button on the left and choose sodium off the periodic table [note that right clicking on the periodic table causing lists of elemental properties to appear]. Click on the screen (but not on the chlorine atom). Click on the "O" button on the left. Click on the sodium (Na) on the screen. Click on the Labels menu item on the Display menu if it is not checked. Click on the Other button and choose sodium again. Click on the New Mol button. Click on the screen. Click on the Cl button. Click on the new Na on the screen. Click on New Mol. Click on "O". Click on the screen away from the other atoms. Click twice on the "H" button on the left and say yes to adding hydrogens to all atoms.
- 2. Check out the reaction and have MMP draw it. Go to the Tools menu and choose Reactor. Type in the names of the molecules. Select the cell which reads molecule 1. Hit the delete key. Type in the name of the molecule (hydrogen chloride). Repeat with the other three molecules (sodium hydroxide, sodium chloride and water). Double click on the column next to water that says "Start". "Intermediate" will appear. Double click again and this will change to "Product". Do the same for sodium chloride. In the center right where it says "Reaction balanced:" the answer should now read Yes if everything was done correctly. Type "water" in the "Text below arrow 1" box. Click on the "Draw" button on the lower right.
- 3. Inspect the Drawing. Is everything as you expect? If not go back to the Reactor and change things to your liking.
- 4. Go to "Database save" on the File menu and choose "Save this molecule to database".
- 5. We'll save the database as an ACCESS mdb file with external connection tables. This is the recommended way of saving data for larger databases. Do not call the database Reactions as there is already a database with this name and we want to create a new one. Call the database "test1".
- 6. The program will ask you if you want to store the molecules as a reaction or mixture. Click on Yes.
- 7. The Reaction editor will reappear. All the information should be correct in the top form and the reaction should be balanced (this is another chance to edit it). You can also fill in the information in the lower table (Trade name, Manufacturer and CAS number) as this information will be stored too. Hit Done or Draw.
- 8. Give the reaction a name. AcidBase will do (or use your own name).
- 9. Next we need to tell MMP to store the reactions as MDL Molfiles in external connection tables. Click OK on the informational panel. When the File saving dialog screen appears, select MDL Molfile from the list at the bottom. Make sure that the correct directory is selected. Type in hydrogen_chloride as the filename (or give your own appropriate name to the first molecule you drew). Do the same for the other molecules (I called them sodium_hydroxide, sodium_chloride and water).
- 10. Next the list of properties to calculate appears. Click on the "Check all fast fields" box near the lower right. If you used the examples above (simple acid-base reaction) or have a reaction with only smaller molecules, click on the CNDO fields at the bottom as well (CNDO on small polymers can take a long time to calculate). Hit the Done button. MMP will now automatically calculate well over 100 chemical properties of the molecules from structure and place them in our database.
- 11. Next the program asks if you would like to create some additional fields for experimental or literature values. Let's say Yes and look at this option. Type in "MyTextField" and hit the OK button. Type in "MySingleField" then click on "Single precision real numbers" then hit OK. Hit Done. We have created two blank fields, one for text and one for numbers.
- 12. The database will now be created in ACCESS 97 format, with 4 separate MDL Molfiles containing the structural information.
- 13. The program will ask you if you want to view the database. Let's say No and add another reaction.
- 14. Repeat steps 1-4 (to save time make a simple change such as changing the chlorines to bromines). Choose "Test1.mdb" (or the name you gave to the database) when the program asks for a database name. Call the reaction AcidBase2. Give the connection table files names. Make sure that if the structure has changed, you give the connection tables new names.
- 15. The program will know which properties to add and not ask you again. When the program asks if you want to open the database, this time click on Yes.
- 16. Click once on the spreadsheet, then double-click on a molecule. Say Yes when the program asks if you want to clear. The molecule you clicked on appears.
- 17. Go back to the spreadsheet. Select "Views structures as reaction or mixture" from the Options menu. Now double-click on a molecule on the spreadsheet. Instead of the molecule, the entire reaction now appears.
- 18. Go back to the spreadsheet. Select "View Reaction Table" from the View menu. Double clicking on this table will cause the reaction to appear.
- 19. Click on "View Reaction Table" again. The Data Table reappears. Go to the View menu and select "Structure in Drawing Window". Click on the gray margin to the left of the molecule name on the spreadsheet and the molecular structure will appear in the drawing window. Click on the molecule name and the spreadsheet data will be displayed instead.
- 20. Click on the View menu item called "File Card". This is another way that MMP displays the data. Click on the page 2 tab at the top of the file card to see the next several fields.
- 21. All the fields in the file card and the spreadsheet can be edited. You must save the data for the changes to become permanent.
- 22. Off the view menu choose "Edit Reaction Description." Give the rtf file we are about to create a descriptive name like "acidbase". The text editor that appears allows you to save formatted text that is attached to your reaction. You can drag drawings from other programs into this text editor. You can highlight text, then use the editor's format menu to change font appearance and alignment. When done click on the close button and the rtf file will be created and saved.
That's the brief tour. The Help button on the database window connects to a special html file containing further descriptions of the database functions of Molecular Modeling Pro. We have also placed this help file on-line, if you are interested in looking into the database capabilities of MMP.