Molecular Orbital & Properties: YNU-Simulator : 3D Structure Builder
2011.5.29
(YNU-simulator: Yokohama national University(YNU Japan) simulator is design for YNU Chemical Engineering Course students. Only YNU students can use full version.)
YNU-Simulator was made with HTML5+CSS+JavaScript. So you need Web Browser that can run HTML5. For PC/Mac Chrome, Safari or FireFox4.0 is recommended. iPad with Mobile Safari is also one choice. IE9 may not work because HTML5 implementation is very poor. IE below 9 are not supported HTML5. If your browser support HTML5, link will appear.
If you click this link, YNU-Simulaor will run on child window. At first, you need enter pass code. Otherwise you can use only C, H, N, O atoms.
Push Panel+ button and search above Panel. At first, no molecule will display. Select functinal group and click main panel. Then molecule will appear. SP3 is Carbon with 4 hydrogens, SP2 is C with 3 H, SP is C with 2 H. C3R-C6R are ring structure. Pheny is benzen.
Select SP3 and click main panel, then you will see Methan molecule. Please Drag on main Panel, molecule will rotate. And test Shift+Drag or Alt+Drag operation.
Please click on one Atom. And click on the other Atom.
Red circle will appear. The first atom is Fixed to operation. The second atom is Operated atom. The second atom need not to be terminal atom. All the atoms conected to second atoms become operated atoms. Then select Functional Group with radio button and push Substitute button. If you select SP2 and do this operation, you will see the next molecule.
If you choose 2 atoms that are part of ring, nothing happen. Because the first atom also become operation atom.
Then select SP3 and change one hydrogen to CH3.
Then push Atom Type button.
And select Atom type radio button. And click all the atoms that you want to change to. Then push Change button.
Then all selected atoms are change to Radio Button Atom Type. Program calculate standard bond length and determine atom position. If chenged atom is part of ring, then standard bond length calculation will ignore.
If you are authorize user, you can use H to Cl. Web user can use C,H, N, O only.
Then go back to Builder panel.
Select 2 atoms and push Make Bond button.
You will get acetone structure.
Back to main panel and erase molecule. Then try next example.
Please make this structure.
And Select 2 hydrogen atoms.
Push Delete Selected Atoms.
Select 2 carbon atoms.
Push Make Bottun.
You will get cyclo-propane. But trianle shape is wrong. Erase Bond and push Part Move button.
If you select 3 carbon atoms, then you will see this bond angle is 109.69.
Then check Part Move, and select BA（Bond Angle). If you shift drag mouse, the bond angle will move. please set it around 60.0.
Then back to Builder panel and make bond. You will get much better structure.
But these operation is hard for Chemical Engineering Students, in that case, please use Optimize Structure function.
YNU-Simulator was made with HTML5+CSS+JavaScript. So you need Web Browser that can run HTML5. For PC/Mac Chrome, Safari or FireFox4.0 is recommended. iPad with Mobile Safari is also one choice. IE9 may not work because HTML5 implementation is very poor. IE below 9 are not support HTML5.
At the first time of my lecture, I will give you pass code that enable run full version of program.
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