Molecular Orbital & Properties: YNU-Simulator for Chemical Engineering Students
(This lecture notes are made for Yokohama national University Japan chemical engineering students. )
When you want to handle newer chemicals, you can get no data even you search largest DataBase. In that case, we need to estimate properties. With this lecture (Yokohama National University Japan chemical engineering course), they ask me to teach Computational Chemistry. So, I will lecture from Molecular orbital calculation to chemo-informatics propertise estimation with this YNU-Simulator. This course is for Chemical Engineering Students, so Specialist for Molecular orbital calculation need not access further articles.
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.
YNU-Simulator |
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| YNU-Simulator:O | |
At first, I explain the information that come from 3 dimesional molecular structure. Charge of atoms, Dipole moment of molecule, HOMO(Highest Ocupied Molecular Orbital, LUMO(Lowest Unocupied Molecular Orbital), molecular volume and surface and Heat of formation.
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.
The very old chemist might have experience of building molecule with ball and stick model kit. Seeing is Believing. Seeing 3D molecular structure is very important. But with real model kit, it is very difficult to get bond distance, bond angle nor torsional angle. So these day, we are using model by software. Let's try read molecular structure and see the structure.
For most chemical engineering students, the first barrier of Computational Chemistry is obtaining 3D structure. The Carbon atom have 4 hands, hydrogen have one hand. Such fundamental knowledge is very needed. The concept of double bond, triple bond are also important.
If you understand SP3, SP2 and SP sturtures, it is enough.
Let's try YNU-Simulator.
Optimize Structure with Molecular Mechanics
Students can build rough structure with Molecular Builder, but still difficult for building ring structure. So I implement Simple Molecular Mechanics (MM) calculation routine into YNU-Simulator. With MM calculation, every Bond length, Bond Angle, Torsional Angle are thought as Spring. And the value is small compair to standard value, then Spring Expand. If lager, Spring shrink. With this procedure, 3D Structure will optimize.
Calculate Charge with QEQ method
The organic chemist know which atom have δ-, which atom have δ+ just seeing molecule. But for chemical engineering students may not assume it. You need not worry about it. Just build molecule, YNU-Simulator do that. We can get dipole moment value, and utilize it to predict Viscosity or other properties that are imprtant for chemical engineering. QEQ method is very fast and can apply every atoms in periodic table.
CNDO/2 Molecular Orbital Calculation
HOMO and LUMO values are very important value for predicting logP, toxicity, color so on. And orbital shape is also very important. There are many Molecular Orbital calculation software, but for Chemical Engineering Students, CNDO/2 is enough. CNDO/2 is very fast and can calculate H to Cl atom.
