NATIONAL QUALIFICATIONS CURRICULUM SUPPORT
Chemistry
ChemSketch
A Guide for Learners
Calum Worsley
[ADVANCED HIGHER]
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Contents
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
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INTRODUCTION
Introduction
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
http://www.acdlabs.com/download (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 http://jmol.sourceforge.net/.
This guide will give you the skills to explore the limitless uses of
ChemSketch.
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SETTING DISPLAY PROPERTIES
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:
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SETTING DISPLAY PROPERTIES
To apply this setting, click Tools > Structure Properties and in the box that
appears select All, as shown below:
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.
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DRAWING STRUCTURES
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 CH 4 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 yo u 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 2methylpropan-2-ol.
With oxygen still selected, click on any of the other CH 3 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 with out having to redraw all the bonds.
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DRAWING STRUCTURES
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 i s 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.
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CLEANING 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.
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CLEANING STRUCTURES
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:
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RINGS AND RADICALS
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.
Rings
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 CH 2 group of the propane molecule (the shadow
should appear bonding to the propane) (3) and click to place the group (4) .
(1)
(2)
(3)
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(4)
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RINGS AND RADICALS
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:
This
would be more
conventionally displayed
without the carbon atoms
shown in the rings,
like this
To get this style, highlight the rings in the structure and click Tools > Structure
Properties, then uncheck the boxes below Show Carbons, circled below:
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RINGS AND RADICALS
Chains
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.
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RINGS AND RADICALS
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.
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NAMING MOLECULES
Naming molecules
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.
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TRANSFORMATIONS: ROTATING AND FLIPPING
Transformations: rotating and flipping
In the SQA AH Chemistry course arrangements, suggested possibl e 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.
Rotating
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)
Flipping
The 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.
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TRANSFORMATIONS: ROTATING AND FLIPPING
Aligning horizontally or vertically
Just 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.
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VIEWING IN THREE DIMENSIONS
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:
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VIEWING IN THREE DIMENSIONS
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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