Basic Molecular Mechanics Modelling

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# 2. User's Manual

# 2.1 Molecular Mechanics Modelling

# 2.1.1 Quick Start : modelling Ethanol

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

### Step 1

After starting ghemical you must open a new project. To do this, click on the File menu and select "New"

### 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 missing oxygen atom, and after this step we have all the heavy (non-Hydrogen) atoms ready. To do this, we must first change the atom type from carbon to oxygen. 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, oxygen is selected.

### Step 5

In this step the additional oxygen atoms is added to the molecule in same way the second carbon atom was added.

### Step 6

Finally, the hydrogen atoms are added. This can be done (for simple organic compounds) using an automated tool that will add hydrogen atoms (find popup-menu item Build/Hydrogens/Add).

Alternatively, the hydrogen atoms can be added manually, as carbon and oxygen atoms were added earlier. Now all atoms of an ethanol molecule are added.

### Step 7

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 (find popup-menu item Compute/Geometry Optimization).

After running Geometry Optimization, the bond lengths, bond angles and other structural features of the ethanol molecule are set in their ideal values (according to the molecular mechanics force field used for geometry optimization).

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, double, triple and conjugated. 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.

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