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# 2. User's Manual

# 2.1 Molecular Mechanics Modelling

# 2.1.1 Quick Start : modelling Ethane

This section covers the features required to build a simple molecule (Ethane) using ghemical.

### Step 1

After starting ghemical you must open a new project. To do this, click on the file menu and select "mm1pg - molecular mechanics"

### Step 2

Select Draw from the toolbar on the left hand side. The Draw tool is the method that all bonds and atoms are added with.

### Step 3

Now begin to add atoms and bonds to your molecule. The default atom type is carbon. To add a single atom to the molecule, single click on the location you would like to put the atom.

To draw a bond between two atoms, single left click on the first atom in the bond, drag the mouse over to the second atom and then release the mouse button. You may also create atoms and bonds at the same time by left clicking on an existing atom, dragging the mouse to where you want to place the second atom and then releasing the mouse button.

### Step 4

Now that the carbon backbone is created, we can now add the hydrogens. To do this, we must first change the atom type from carbon to hydrogen. This is done selecting the periodic table button from the top toolbar.

A dialog box of the periodic table will appear. To select an element, simply click on the button corresponding to it. All further atoms drawn on the molecule will be of this element until it is changed by the same method. In this example, hydrogen is selected. This menu can also be opened by right clicking on the view windows, selecting Settings from the popup menu and then selecting Set Current Element.

### Step 5

In this step additional hydrogens are added to the molecule in same way the second carbon atom was added. This process can be simplified using the Add Hydrogens tool.

Although the all the correct atoms and bonds are present, the molecule is not in the most stable conformation. Ghemical can attempt to do this for you using the Geometry Optimization tool.

You can also change the bond type by clicking on the "Set the current bond type" button on the top tool bar.

This button will launch a dialog box that lets you select the bond type from a list of single, conjugated double and triple. All further bonds that you create will be on the type that you select until you change the bond type again. Conjugated bonds are drawn as a single solid tube with a second dashed tube parallel to it. Double bonds and triple bonds are drawn as two and three parallel tubes respectively. This menu can also be opened by right clicking on the view windows, selecting Settings from the popup menu and then selecting Set Current Bond.

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