Molecular Orbital & Properties: YNU-Simulator : Optimize Structure with MM method
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 support 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.
Please make this structure explained at 3D structure builder.
Then push Panel+ and find Clean Panel.
Then push Clean button.
You will get cleaned structure very easily.
Bond energy and Torsion energy become 0. This means Bond lengths and Torsion angles are optimized to standard value. This molecule is 3 member ring compound, so bond angle energy is very large. You can get cleaned structure very easily.
With this calculation, charge is not input. i will explain it at QEQ method.
You can choose several atoms that are not include this Clean Operation.
For example, you already have transition state structure that Acrylic Acid Radical attack to monomer. If you want to change radical structure and want to get other Transition structure like below
If you use Builder, you can get this structure easily. But epoxy ring structure is very dirty. In that case, if you select several atoms around radical and monomer tail, then push Clean Button, program will clean other parts. And you can get very good initial structure to perform real Molecular orbital calculation.
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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Optimize Structure with Molecular Mechanics |
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