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Chemistry
ChemSketch
A Guide for Learners
Calum Worsley
Acknowledgement
Crown copyright 2012. You may re-use this information (excluding logos) free of charge in
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Contents
Introduction
Drawing structures
Cleaning structures
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Naming molecules
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16
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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 its 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.
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.
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 well 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 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 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 without having to redraw all the bonds.
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 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
Cleaning structures
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.
CLEANING STRUCTURES
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. OH groups can be
shortened to OH. To do this with propan-2-ol, simply click on the OH bond
and select Tools > Remove Explicit Hydrogens [Ctrl+Shift+R] to make the
structure look like this:
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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)
(4)
(3)
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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
benzenes delocalised electron ring (3).
(1)
(2)
(3)
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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 cant 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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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 radicals 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 righthand carbon atom.
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NAMING MOLECULES
Naming molecules
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:
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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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To optimise it (make all the bond lengths and angles exactly as they should
be), click the 3D Optimization button:
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Whats going on here isnt 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
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. Dont
worry, you wont close the whole program you will go back to the white
drawing page.
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