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Chemistry@Pirika: Molecular Orbital & Properties

Japanese Page

I bought my first PC at 1982, and at that time there is no software for 8-bit PC if one did not enter code by oneself. I enter molecule 3D view code, it take more than 5hrs to show all the molecule and save the code with tape. So writing GUI for Molecular orbital (MO) calculation is one of my hobby from the begining. I had the chance to learn computational chemistry at CALTECH (California Institute of Technology) MSC (Material and Process Simulation Center) prof. Goddard group (1990-1991). At that time I bought Mac IISi and I still use Mac as my main machine. The program language are changing BASIC, C, C++, JAVA, C#, but everytime when I learn new language, I start with molecular viewing software. Molecular orbital calculation is so popular for computational chemistry. It is so powerful and can available for almost all compounds. But to calculate MO, I need very fast machine and expensive software and so much time! I developed neural network properties estimation method. This method is very fast calculation and has high accuracy. I always use hybrid of Neural Network with Theoretical calculation to solve problems.

2011, I start to learn new language JavaScript and translate old program. (For me, writing with program language is much much easier than writing English.)

MOL(SDF) file viewer (HTML5 version 2012.6.15)

Paste MDL MOL format or SDF file, this program show you the structure. For the web user, charge calculation is done for only H, C, N, O.


YNU-Simulator: (HTML5 version 2011.5)

All in one software to calculate CNDO/2, charge equilibration (QEQ) written with HTML5+CSS+JavaScript.

Calculate atomic charge with charge equilibration (QEQ)

HTML5 version (Calculate from 3D structure) 2011.5
HTML5 version
(calculate from 2D structure) 2011.5
JAVA version

Rappe and Goddard have proposed the Charge Equilibration (QEq) approach for predicting charge distribution to the each atom that compose molecule. With only, Atom type(H to Lr), bond type (Sigle bond to triple bond), IP(Ionization Potential) and EA(Electron Affinity), I can easily calculate atomic charge. I made QEQ program for PC or much powerless machine.


CNDO/2 molecular orbital calculation. 2000.2.14

HTML5 version 2011.5
JAVA version

Transition State Libraries for Radical Polymerization

I am re-writing these pages. please wait.


Frequency Analysis at Transition State

To calculate monomers sequence in polymer, simulator need reactivity ratios. With my simulator need Alfrey-Price Q-e parameter. But some of the monomer are lack of this information. In that case, I need to calculate transition state with molecular orbital theory. I need to check vibration direction if the result is correct or not. I summarize the result in TSDB.
HTML5 version 2011.5
JAVA version 2005.1.14 


Heat of formation, HOMO,LUMO Estimation 2001.1.14
(MOPAC PM3 level simulation)

I calculate all compounds listed in my database with MOPAC PM3. Heat of formation, HOMO energy, LUMO energy, surface area, volume and dipole moment is obtained from MOPAC calculation. I built neural network reproduce MOPAC PM3 calculation. Heat of formation, HOMO energy and LUMO energy can be obtained only drawing molecular structure.

JAVA version 2001.1.14


Activation energy estimation by neural network 2005.1.14

If I calculate transition state (TS) of Radical and monomer reaction, I can get activation energy and Frequency factors. Then I know the reactivity coefficient of that system. But semi-empirical method such as MOPAC, result is not accurate enough. Ab inito calculation (B3LYP/6-31G**) result is good, but it is time consuming. I calculated 100 TS with B3LYP/6-31G** and I build the neural network (NN) estimation scheme to predict activation energy and Frequency factor.

JAVA version 2005.1.14