Ghemical : a kickstart tutorial
This tutorial tries to complement another tutorial [1] for the real newbie who does not even know how to draw in the Ghemical canvas.
Install the latest version of Ghemical if necessary. Launch the application and it should start right in the "molecular dynamics mode" with a new black canvas.
Maximize the window, so that the complete toolbar can be reached easily. Otherwise later you would have to click on the downward arrow at the right edge of the window in order to access other menu items such as "element" and "bond type".
Click on the leftmost widget (the pencil) which looks selected but in fact not truly selected at the beginning (it might be a little bug).
Then just click and drag some distance "in the air" in the black canvas, and a pair of linked carbon atoms should appear when you release the mouse.
Repeat the click and drag operations (starting from existing carbon atoms), you can make some irregular closed hexagon.
Then right-click on the background and chose the following from the contextual menu: Build->Hydrogens->Add; 10 hydrogen atoms should appear immediately.
Right-click and choose the following: Compute->Geometry Optimization and a "Geometry Optimization" dialog appears. Just validate (press OK) to proceed the computation. The molecule will be optimized by using a simple interatomic potential.
Select the Orbit XY from the toolbar and rotate the molecule to make the hydrogen atoms easily distinguishable by mouse clicks.
Select the Pencil (Draw) tool again and click on a hydrogen atom, which should be changed into a carbon atom. Then Build-Hydrogen->Add again and Compute->Geometry Optimization … [Validate] again; You will probably get a methyl cyclohexane in equatorial form.
Its energy can be computed more precisely if you export this molecule and use a more completely validated modelling tool to do this job (for example, GAMESS). You can also use the Quantum mechanics tools which come with Ghemical to do this job, but I cannot help you to do this, and I ignore the possible gotchas.
If you want to prepare the axial conformere of methylcyclohexane it may be a little more tricky: you must start from the exactly optimized equatorial conformer, then use the Eraser tool and rub out the 4 atoms of the methyl group. Then back to the Draw tool and change the axial hydrogen which was near the methyl group into a carbon atom. Then again Build-Hydrogen->Add and Compute->Geometry Optimization … [Validate].
It is not guaranteed, but chances are that the molecule will be trapped in the higher energy minimum which is the axial conformere.
[1] http://ghemical.ki.ku.dk/wiki/Ghemical_Tutorial|Ghemical Tutorial
