1. Work Space
Upon launching WinmostarTM , following window will be shown, with the default molecule, C-H, in the graphic editing area.
- ① Graphic editing area
- Display editing molecule. Construct molecule using button ⑥～⑫ to add and delete parts.
- ② Zoom slider
- Enlarge or reduce the size of the molecule.
- ③ Keyword editor area
- Edit keywords for submitting order for culculation program and assign title of the job.
- ④ Z-Matrix text area
- Z-matrix of the editing molecule is shown. Direct editing is possible.
- ⑤ Auxiliary text area
- Aditional parameters will be set in this area.
- ⑥ Add button
- Add a new atom on the target atom. Target atom can be selected by pointing and clicking left button of your mouse. The target atom is indicated with red bold circle. The parts tobe added is chosen from the list-box ⑪.
- ⑦ Del (delete) button
- Delete target atom (indicated by bold red circle), or substitute by hydrogen if the target is not a terminal atom, i.e., the whole -CH3 group will be substituted by hydrogen, since the target carbon atom in -CH3 has terminal hydrogen atoms and one bond with other atom.
- ⑧ -CH3,-C2H3,-C6H5 button
- set parts for substitution. Same as the list-box ⑨.
- ⑨ Parts list-box
- Select the parts to substitute. Frequently used parts (-CH3,-C2H3,-C6H5) can be selected by the buttons described above.
- ⑩ Rep (replace) button
- Substitute the target with the parts selected by ⑧ or ⑨. If you right click the target atom with your mouse, the target will be replaced in single action.
- ⑪ Atom selection list-box
- Select the atom for substitution.
- ⑫ Chng（change）button
- Change atom with those selected in list-box ⑪.
2. How to use your mouse
|key board||left button||left button +drag||right button||right button +
|none||select||rotate||select & replace||zoom||zoom|
|Shift||select & delete|
|Ctrl||multi select /
multi select cancel
|multi rectangle select|
3. Tips for modeling molecule
In the initial window, or refreshed window after selecting [New] in file menu, the default atoms will be shown in molecule editing area. Starting with this, click -CH3 button followed by clicking [Rep] once, then you will have methane molecule. You will have ethane, propane, n-butane as you keep clicking [Rep] and adding -CH3 to the molecule.
You can rotate the molecule in either directionby dragging with your mouse left-button down.
Any kind of molecule can be constructed using such menu items or buttons like change parts, change atoms, replace bond position etc.
As shown right, you can set two target atoms at a time by consecutive click with left button of the mouse, and by using [Rotate Group] or [Move Group] in [Edit] menu, you can rotate or move the group of atoms along the axis set by the two atoms.
4. Saving your molecule
Choose [Save As]in the [File] menu, and select an appropriate folder and assign the name (file extention is automatically added).
5. Modeling styrene molecule and MOPAC calculation
Simple basic work-flow is explained taking styrene molecule as an example.
Default carbon atom with hydrogen will appear in the molecule editing area when winmostar is launched.
Click default carbon atom to set it as a target atom. Then click [-C6H5] in the parts list shown above the window.
By clicking [Rep] (replace) button, benzene structure will be constructed.
the group [-C2H3] can be added by; first set target hydrogen atom by mouse click, then click [-C2H3] in the parts list and replace the target by clicking [Rep]. Now you get styrene molecule in your molecule editor.
When you move to [Calculation 1] menu and click [(1)MOP6W70 Start], you are asked to save your molecule. Responding with Yes, dos window will pop up and calculation will be initiated.
After the calculation is successfully finished, output of the result will be automatically shown in text editor and optimized structure of the molecule will be shown in molecule editing window. In case GRAPHF keyword is specified, the molecular orbitals can be displayed by importing mgf file by clicking [Calculation 1]-[Import]-[MO(mgf)]
.........End of Quick Manual. ©X-Ability Co.,Ltd. 2012-2015 All rights reserved.