An Introduction To ChemOffice, IT workshop

Objectives
At the end of this workshop you should be able to:

1. draw chemical structures using ChemOffice software,

2. manipulate chemical structures using ChemOffice,
3. add chemical structures to written documents.

Introduction

It is very important for written reports, theses and other scientific

documents to have chemical structures represented in a clear and
professional way. The simplest way of achieving this is by using
computer software that enables the production of chemical structures
and the subsequent copying of these into a word-processed document.

There are several chemical drawing software packages available

commercially and, in this School, the CambridgeSoft ChemDraw
Professional 17.0 product is available which is the most widely accepted
for publishing.

Throughout the MPharm course there will be occasions where you will
be required to draw chemical structures for inclusion in written reports
and this exercise is designed to show you how to do this.

The software is easily accessed from the University’s computer network

and is very user-friendly and even fun!

Procedure

A demonstration of the use of ChemDraw Professional will be followed by

asking you to experiment with it, in order to learn the best way of
mastering the software.

Make sure you can draw various types of structures from the tools
available, experiment with the templates provided and edit the structures
that you have produced. Make sure you look at the 3D software and be
sure that you can export your structures to word-processed documents.
This will be particularly useful when writing your laboratory report!
Remember to save after each paste operation. Try to make your drawings
(and text) match those in these pages as best as you can so that you get
used to editing.

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First, we will learn to draw the structural representations of
1,3-butadiene 1 and 2 shown below to see how the various tools work.

1 2

To get started:
 Log in to the computer network: MyApps (Citrix Workspace)
 Click on Start (bottom left of screen), then scroll down until you see
ChemOffice 17. Select ChemDraw Professional 17.0
 Once the program has loaded, you will see a palette of tools arranged
vertically on the left, a series of pull-down menus along the top and a
clear drawing area.

To start drawing structure 1:

 From the palette of tools, select the single bond by clicking on it.
Move to the drawing area on the screen place the cursor where you
want it and then click and drag the mouse to draw the bond.

 With the bond tool still selected, move the cursor to the right end of
the bond – a pale blue square will appear and if you click and drag
from here, a second bond will appear:

 Add two further bonds on the left hand C atom to give the structure
below:

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  To create the double bond between C1 and C2, with the bond tool
selected, click and drag the cursor along the length of the bond:

 To insert the H atoms, select the text tool A and place the cursor
at the end of a bond - you should get a blue square. Click and insert
H atom. The size and font can be changed at the top of the screen:

 Complete the structure by repeating the above stages.

To draw structure 2, select the text tool and place the cursor on a C atom
and you will see the blue square – insert a C atom:

The lasso tool at the top left of the tools palette lets you manipulate, copy,
rotate structures. Click on the lasso tool and practise the following on
structure 2

 Hold down the mouse and circle around the structure – it will be
highlighted in a box. Then try each of the following:
o Moving the cursor into the middle of the highlighted box will
give you a hand symbol; click and drag to move the molecule
o Look at the corners of the highlight box and move the cursor to
each - the straight double headed arrow allows you to shrink or
enlarge the structure. The rotation tool attached to the middle
of the box lets you rotate the structure.
o With the cursor in the middle of the highlight box press the
“control” (Ctrl) key on the key pad while still holding down the
mouse – the hand shows a + symbol and if you drag the
mouse, this will copy the structure.

The lasso tool also lets you copy and paste structures into a Word or other
Office document.

 Lasso structure 2 to highlight it. From the menu at the top of the
screen, choose Edit and select Copy. The structure can then be
inserted into your Word document by opening it, selecting where you
want the structure placed and then selecting Paste in the Edit menu.

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You can also lasso parts of a molecule and modify that part. Try this with
structure 2. Lasso part of it and select the Color option from the menu at
the top.

Explore the rest of the tools in the palette, including the very useful eraser!
You can draw more specific bond types called wedge bonds that are useful
with 3-D structures, orbitals and curves. There are many pre-drawn
templates of ring structures and much more complex molecules, as well.

NOW TRY THESE:

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Other useful tools:

 Click on View, then Show Crosshair – lets you align structures

 Highlight a structure (lasso tool), click on View and work your way
down the list of tasks.
 Click on Structure and see what you can do here, especially Check
Structure, Clean Up Structure, Convert Structure to Name etc.
For more advanced users, 1H and 13C NMR spectra can be predicted
with high levels of accuracy.

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3-D structures

You can view any structures that you have drawn in 3-D.

Lasso a structure that you have drawn and then click on View, then click on
Show ChemBio3D HotLink Window. You will see a miniature 3-D
structure. Click on the bottom left of this window to Launch Chem3D. Your
structure will be displayed in large 3-D form and you can manipulate this
structure in many ways – try it! Try rotating the structure and changing its
view by selecting View, then Model Display then Display Mode then
Choice. Look at the options available for viewing the structure.

The structure shown is that of benzoic acid.

Make sure you look at the various options available in View