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A Guide for Learners

Calum Worsley


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Introduction 4
Setting display properties 5
Drawing structures 7
Cleaning structures 9
Rings and radicals 11
Naming molecules 15
Transformations: rotating and flipping 16
Viewing in three dimensions 18

This guide will show you the basics of ChemSketch, a powerful molecular modelling program that will help you in your study of Advanced Higher Chemistry. It is available to download free from (Google ‘Chemsketch’) – it might take a while, but it’s worth it!
There is a small part of the Advanced Higher course that requires you to have used a program like this, but there are many other reasons to use it. It can help you find out more about molecules you learn about in class, it makes visualising the three-dimensional shapes of molecules very simple, and it will certainly make your investigation report look a lot neater!
Another free download that allows you to display any molecule, large or small, in three dimensions is JMol. You will find more information about JMol at
This guide will give you the skills to explore the limitless uses of ChemSketch.
Setting display properties
The first thing to decide when using ChemSketch is how you would like the structures you draw to be displayed to you. By default, the structures will be skeletal, showing carbon and hydrogen atoms only at the end of chains, eg hexanoic acid and benzene appear like this:

However, is often better to be able to see all atoms, like this:

To apply this setting, click Tools > Structure Properties and in the box that appears select All, as shown below:
group 5

Give the new style a name and click Save, then Apply. This will make drawn structures appear in the new way and will allow you to select this style easily the next time you use ChemSketch. Clicking Set Default makes this the standard way of displaying structures in any new sheet.

Drawing structures
Now you need to know how to draw your structures on the sheet in front of you. By default, clicking anywhere on the page will produce a methane group, so we’ll start with that:

Structures are built using a click-and-drag process. Click the CH4 and drag it to any white space to create ethane, and again to form propane. Side branches are added in the same way; click and drag from the middle carbon in propane to create 2-methylpropane, as shown below.

You will notice that at all stages the program fills any valency gaps with hydrogens, so all available bonds will be used unless you designate a charge for that atom. This only happens with non-metals; metals will always initially be displayed as single ions.

You will notice, on the left of your screen, this column of chemical symbols, with carbon highlighted at the top. This is where to choose the building blocks for your structures. Everything builds up in exactly the same way as the organic structures above, so you click and drag things to build up structures. Click on O in the menu on the left and click and drag from the middle carbon in 2-methylpropane to create 2-methylpropan-2-ol.

With oxygen still selected, click on any of the other CH3 groups to turn it into a hydroxyl group. This swapping principle is the easiest way to change an atom or group in a particular position without having to re-draw all the bonds.

Highlighting structures
You will notice that the default option for highlighting structures is the standard drag a selection box method. However, clicking the icon above changes the selection tool to a lasso, which is much more useful for selecting a particular part of a molecule. Experiment with this method to get used to using it. It becomes incredibly useful when you are drawing more complicated structures.
Cleaning structures

When drawing structures at first, there is no requirement for your drawings themselves to be as neat as can be. ChemSketch’s Clean function will do this for you. Oxalic acid and propan-2-ol can be drawn in loosely the right shape like this:

The Clean function, shown above, standardises the shape of the molecule drawn, adjusting bond lengths to be all the same and bond angles to be the correct predicted shape, so oxalic acid and propan-2-ol look much neater:

However, even when neat and standardised, it can often be much better to see organic molecules with straight carbon backbones and all the bonds shown.

Continuing with propan-2-ol, clicking Tools > Add Explicit Hydrogens [Ctrl+Shift+Y] turns the above structure into this:

Clicking Clean once again produces:

This sequence (Add Explicit Hydrogens  Clean) can be used on any organic molecule to make it easier to name and to show condensation/dehydration reactions etc.
It is not necessary to have the whole molecule expanded. O–H groups can be shortened to OH. To do this with propan-2-ol, simply click on the O–H bond and select Tools > Remove Explicit Hydrogens [Ctrl+Shift+R] to make the structure look like this:

Rings and radicals
When drawing common, but complex, structures in ChemSketch, you can use some of the handy shortcuts found in the toolbar on the right of the window. These fall into two categories: rings and chains.

Adding a ring to another molecule can happen in one of two ways.
Consider adding a phenyl group to the second carbon of a propane molecule. With propane drawn (1), click the Benzene button in the right toolbar (2), hold your mouse over the CH2 group of the propane molecule (the shadow should appear bonding to the propane) (3) and click to place the group (4).

  1. (2) (3) (4)

Now consider adding another ring to the structure above, so that the two rings share a bond. Keep the Benzene button highlighted and hold your mouse over the bond you wish to add the ring to. The shadow will appear again (1), then click to place the ring (2). Clicking Tools > Show Aromaticity will show benzene’s delocalised electron ring (3).

  1. (2) (3)

Again it is possible to show different parts of the molecule in different ways. Taking structure (3) above as an example:

autoshape 8

would be more conventionally displayed without the carbon atoms shown in the rings,

autoshape 9
To get this style, highlight the rings in the structure and click Tools > Structure Properties, then uncheck the boxes below Show Carbons, circled below:

This section deals with things like carboxyl and acetyl groups.
Consider again a propane molecule (1). We are going to add a carboxyl group to it to form butanoic acid. In the right-hand toolbar, click the carboxyl button (COOH) (2a). (If you can’t find it, click the Table of Radicals (2b) and look for it there). Once again, place the mouse over the carbon it is to be added to (3) and click to place it (4).

(1) (2a) (2b) (3) (4)

To display butanoic acid with the carbon atoms in a straight line follow the same procedure as used before. Highlight the molecule, click Tools > Add Explicit Hydrogens [Ctrl+Shift+Y] and press Clean to make the atoms move into a straight line. Occasionally the hydrogen bonded to the oxygen ends up at a funny angle. If this happens, click Clean again until it rights itself (which it will eventually). Use the Set Bond Horizontally/Vertically buttons to make things clearer still.

Table of radicals
The table of radicals contains all sorts of groups you may wish to add to a molecule. Hold your mouse over any of the abbreviations and its structure will be displayed in the white box. The rest of your molecule will go where ‘R’ is in the radical’s structure. Shown below is the display obtained when methoxy (OMe) is highlighted.

Click onto this structure of the radical and click any atom in a structure you have drawn to add this radical in the same way as the carboxyl group was added in the last section.

Below, ethane has been made into methoxyethane by clicking on the right-hand carbon atom.

Naming molecules
rectangle 3
As well as orientating molecules to make it easier to name them yourself, ChemSketch also has a feature that calculates the IUPAC name of small compounds you have drawn. While it doesn’t give common names for molecules (eg it will show ethanedioic acid instead of oxalic acid), it is useful for simple small organic compounds.
Click on the structure you wish to name, then click the button highlighted in the picture above and the name will be added below the structure:

To obtain the common name of a molecule (perhaps a drug), the four search functions indicated above in the red box can be used. Each enters the structure into a different online chemical database and then lists the common names of structurally similar molecules. Consider propofol, the anaesthetic:

2,6-di(propan-2-yl)phenol isn’t the most helpful name, but clicking the PubChem link will take you to chemistry articles on propofol, where other information, such as its physical and chemical properties, can also be found.

Transformations: rotating and flipping
In the SQA AH Chemistry course arrangements, suggested possible activities include using a molecular drawing package such as ChemSketch to draw molecules and then to rotate these molecules or flip and align any chosen bond either horizontally or vertically. Let’s look at doing this, using phenylalanine as an example.

Click the Select/Rotate/Resize button, and click and drag to highlight the molecule (1). The red cross in the circle is the centre of rotation; you can move it by clicking and dragging. To rotate, click on any bond and drag it to rotate. The red lines that appear will give you an idea of how far it has been rotated (2).

  1. (2)

Trectangle 8he three icons in the red rectangle allow you to (from left to right) flip on bond, flip top to bottom and flip left to right. Click flip on bond then click a bond to flip the molecule around that bond; clicking flip left to right or top to bottom flips the molecule in that axis.

Aligning horizontally or vertically
Jrectangle 9ust to the left of the flipping buttons are the set bond horizontally and set bond vertically buttons, which do exactly what they say. Click a button then click on a bond to rotate the molecule so that the bond is in the desired direction.
Viewing in three dimensions
One of the more impressive features of ChemSketch is its ability to display and manipulate in three dimensions any molecules you draw. To demonstrate, we will use propan-2-ol. If you have more than one molecule drawn on the sheet you need to highlight the one you wish to view in three dimensions.

To move to the 3D viewer, click the 3D Viewer button in the toolbar:

The following molecule will then appear on your screen:

To optimise it (make all the bond lengths and angles exactly as they should be), click the 3D Optimization button:

This will turn it into something like this:

What’s going on here isn’t entirely clear, so make use of these buttons on the left of the toolbar:

Balls and Sticks (highlighted in the picture) is perhaps the most helpful in terms of seeing the molecule, although Spacefill and Dots only (to the right of it) show the relative sizes of the molecules clearly. The pictures below show what propan-2-ol looks like in the more useful display modes:

Sticks Balls and Sticks Spacefill
Click and drag in the black space to rotate the molecule in three dimensions to have a proper look.
To exit the 3D viewer click the red ‘X’ in the top right-hand corner. Don’t worry, you won’t close the whole program – you will go back to the white drawing page.

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