Molecular Orbital & Properties: YNU-Simulator : Read and display molecule
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.)
The most popular Molecular Orbital Calculation is MOPAC. So, I implement the function to read MOPAC File. There are two type of input file. One is Cartesian Coordinate(XYZ coordinate), and the other is Inter Coordinate(Z matrix).
The first example is Ethanol Inter Coordinate structure.
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. If your browser support HTML5, link will appear.
Start Up window
You need to enter PassCode that I give my first Class. Then you can use all function. Otherwise, you can use only C, H, N, O as web user. The web user can not get structure, can not get calculation summary. After you enter Code, please push Panel+ button.
On this Panel, you can read MOPAC input data. (Get Structure button will work for only authorize user) Please Paste Ethanol stucture here. This structure is Inter coodinate, so you need not check XYZ checkbox.
If you push Read button. YNU-Simulator read the input file and display molecule.
Please push Panel- and go back to the top Panel.
You can change molecular size with Shift+Drag. Push shift Key and mouse push. And keep pushing mouse button and move left or right. The molecule become larger or smaller. If you are accessing with iPad, 2 fingers movement equivalent to Shift+Drag. Fix one finger and move the other one. You can translate windows position with Alt + Drag. 3 fingers movement equivalent to Alt+Drag. Without key (or one finger) drag make molecule rotate.
You can select Ball & Stick model with radio Button.
Then Let's see the bond ditance, bond angle, torsional angle.
Push Pannel+ several times and search above panel.
Push the mouse above atom. Then that atom is selected.
If you select 2 atoms then Distance will apear. If you select 3 atoms, Bond Angle, 4 atoms Torsional Angle will appear. If you click same atom twice, seselction will clear. Torsional angle range is set to 0-180 with negative value. You need not select connected atoms.
I will explaine Part Move option at molecular builder page.
For this molecular reader, Program estimate bond from standard bond length. And do not consider double or triple bonds. You need assign manually.
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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