D Chemical drawing software (ChemSketch)

Although this exercise refers to ACD/ChemSketch (free software from

www.acdlabs.com), drawing molecules using other chemical drawing
packages (eg CambridgeSoft ChemDraw or !D "S"S Draw) is broadl#
similar.
!oad ChemSketch b# choosing it from the $rogram menu or double clicking
its icon (#ou will be told where this is). Click %&'( to an# windows that appear
until #ou see the opening screen.
ChemSketch is a powerful program with man# features. )he focus here is
on basics that allow #ou to draw and use images for teaching. *efore #ou
start to draw an#thing, familiarise #ourself with the few features labelled in the
+iew of the Structure screen below and described o+er the page. ,o+er the
mouse cursor o+er a particular button to +iew a note describing what the
button does.
Undo - a most useful feature!
-etting used to this kind of software is necessaril# an explorator# process
which in+ol+es unexpected and unwanted things happening. 'nowing how to
step back if this happens is +ital to a+oid frustration.
)o re+erse a change select the .dit menu and click /ndo. 0epeat this to step
back through a se1uence of e+ents. Alternati+el# use the ke#board shortcut of
holding down both the Alt and backspace ke#s at once.
"f #ou step back too far through a se1uence and want to mo+e forward again,
select the .dit menu and click 0edo. )he ke#board shortcut for this is holding
down three ke#s2 Shift, Alt and backspace all at once.
click an element to
make it available in
a structure,
note bonds to
hydrogen are
assumed unless
other connections
are made
clean structure and 3-D optimisation buttons
select / move
and rotate / resize
buttons
templates button
Drawing 2-D formulae
Skeletal and partially displayed formulae
Spend a few minutes pla#ing remembering that the undo! feature allows
you to re"erse changes2
ake sure the C (Carbon) button is clicked. Click once on the screen and C,
3
will appear. Click elsewhere and a second C,
3
appears. Click and drag the
mouse from one methane to the other to form a C4C bond and therefore
ethane. Click and drag elsewhere to attach another meth#l group. 5ith the C
button selected, right clicking an# C4C bond once con+erts it to a double bond,
clicking again con+erts makes a double bond triple.
)r# drawing a h#drocarbon structure containing branches and unsaturated
bonds. 6ote that the default structure is a skeletal formula with onl# the
terminal atoms identified. )o tid# up a rough drawing click the %clean structure(
button.
)o displa# all the atoms along the chain follow these steps2
7. /se the Select / Move button or Select All (Ctrl8A) from the Edit menu to
select the molecular structure.
9. &pen the $roperties window b# selecting the Tools menu and clicking
Structure Properties (or hold down the Ctrl8Shift8S ke#s all at once). )hen
select Common and tick All for Show Carbons. )he $roperties window
also allows the colour of indi+idual atoms and bonds to be customised.
:. Click Apply, note this only applies changes to a selected structure.
0emember the %clean structure( button will tid# up an# changes.
3. Click the Select / Rotate / Resize button. Click outside a structure and drag
the mouse across it to select all of it and then change its orientation and,
most usefully, its si;e.
Clicking a different element button at an# time allows the +arious functional
groups to be added.
Changing symbol order in a formula
)he default ChemSketch structure ma# ha+e formulae units written
differentl# from what is preferred eg C,
:
might be preferred as ,
:
C.
Click the Change Position button, point the mouse at the indi+idual
formula unit that is to be changed (eg ,
9
C ) and left click repeatedl# until the
formula is satisfactor#.
eg might be
preferred as
$ractice creating, tid#ing, customising and deleting a few skeletal and semi4
displa#ed structural formulae until #ou are familiar with these steps.
#ully displayed formulae
<or example, (C,
:
)
9
C,C,
9
&,
might be drawn as2
7. <irst ensure all the carbon atoms within a structure will be displa#ed.
Select the Tools menu, Structure Properties, Common tab. )hen tick All
within the Show Carbons section. <inall# click Set e!ault.
9. 5ith the carbon button selected, and whilst pressing the shift key, draw
a propane chain. ,olding the Shi!t ke# forces the
bonds hori;ontal and onl# allows fixed lengths to be
drawn.
:. Still pressing the shi!t ke#, draw a meth#l side group
down from the central carbon atom but drag it two bond
lengths clear of the chain.
)his additional length is essential to pre+ent side chain
h#drogen atoms o+erlapping with main chain ones.
3. Select the ox#gen button and, whilst pressing the shi!t
ke#, add an &, group to the end of the chain.
C ,
:
C ,
C ,
9
C,
:
C,
:
C,
:
C,
C,
9
C,
:
C,
:
C C C $
$
$
C
$
%
$
$
$
$ $
$
C ,
:
C,
9
C,
:
C ,
:
C, C,
:
C,
:
C ,
:
C, C,
9
C,
:
&,
=. Select the h#drogen button and, whilst pressing the shi!t ke#, drag 4,
bonds from the carbon atoms . 6ote that whilst
the shi!t ke# is pressed, onl# fixed bond lengths
ma# be drawn which maintains a consistent
structure.
)o full# displa# the &, bond, select the , button
and drag a bond. $ressing the shi!t ke# whilst
doing this keeps the bond hori;ontal or +ertical.
Alternati+el#, the bond can be set at an angle.
>. Control the length, thickness and colour of the
bonds and the font, si;e and colour of the atoms
b# selecting the whole structure and opening Structure Properties in the
Tools menu.
?. )o illustrate the shape around a double bond, first draw an ethene
structure, click the " #ptimization button and then the Clean button
.
)o extend the h#drocarbon chain, con+ert one of the ,
atoms to a C b# pointing the mouse at it and clicking. )hen
use the techni1ues described pre+iousl# (7 to 3 abo+e) to
draw and displa# the rest of the structure.
Structural formulae
<ormulae such as C,
:
C,ClC,
:
can be written using ChemSketch2
7. Switch to the raw +iew screen (button towards the top left of the screen).
9. Select the Te$t button towards the bottom left of the screen (remember2
ho+ering the mouse o+er a button identifies it). Click and drag a text box
on to the screen.
:. )#pe a formula, making use of the Subscript (S4) and Superscript (S8)
buttons immediatel# abo+e the screen.
)he completed structural formula is a ChemSketch picture which can be
copied and pasted into another application b# using Paste Special, unless a
link to load ChemSketch is re1uired.
Charges and free radicals
)o add charge to a structure or indicate a free radical select the atom to be
gi+en charge and then click the %ncrement &'( Charge or ecrement &)(
Charge button2
Clicking the bottom right triangle of this allows
negati+e charge, unpaired electrons,
or combinations of these to be displa#ed2
C ,
:
C
8
&
C ,
:
C C C
C
&
,
,
,
, ,
,
, ,
,
,
C C
,
, ,
,
&romaticity
<or example, draw a ben;ene %'ekule( structure2
)o change this to a representation of the delocalised
ring, first select the structure then select Tools menu, Show Aromaticity to
gi+e2
which can be con+erted to
ChemSketch includes se+eral templates, and one of these is for a range of
pre4drawn aromatic molecules. Select the Templates *indow from the
Template menu (or press the +, ke# o the #pen Templates *indow button).
Select the Aromatics template from the drop4down menu.
<unctional groups and h#drocarbon chains
ma# now be added as re1uired2
Drawing enantiomers
)o create an enantiomer from a structure drawn using the :D @stereo@ wedge
bonds2
7. Draw an enantiomer illustrating the chiral centre using the up and down
@stereo@ representations as well as the normal line representations.
9. Cop# and paste a structure drawn using the wedge bonds
:. Switch off the A'eep Stereo configuration on <lipsA in the #ptions menu,
Pre!erences, Structure tab.
3. Select the cop# and press the @<lip !eft to 0ight@ button to create its
enantiomer.
)he resulting structure is the enantiomer of the initial structure.
eg can be
con+erted to
C,
:
*r
6 ,
9
&,
C ,
:
*r
6,
9
&,
C
&
C,
:
C ,
C ,
C,
C,
C,
C,
C ,
C ,
C,
C,
C,
C,
using Tools menu, Structure
Properties, Common tab and
choosing not to %show carbons(
'aming structures
ChemSketch includes a feature that automaticall# generates a name for a
selected structure.
Select an# structure and click the -enerate .ame button2
"f there is onl# one structure on the page there is no need to select it , simpl#
click the button.
Using templates( including laboratory apparatus
)o the extreme right of screen is the Table o! Radicals button. Click this (or
press the <> ke#) to displa# its window. )his pro+ides a wide range of pre4
drawn structures or useful fragments to build from.
)here are a large number of other templates a+ailable from the Template
*indow. &pen this in the Templates menu (or b# clicking its button or
pressing +,) and selecting a choice from the Template /ist drop4down menu.
)wo useful examples are2
the se+en pages of apparatus diagrams in the %/ab 0it( template
examples2
lone pair electrons in the %/ewis Structures( template, simpl# select one of
this and then click where these should appear in the structure.
eg added to a structural formula to create2
Sa"ing ChemSketch screens
)o sa+e a ChemSketch screen, choose the +ile menu and then Save As.
6a+igate to the folder where #ou want this to be stored b# double clicking on
the +isible folders until the one re1uired appears in the Save %n box.
"f #ou want to create a new folder, na+igate so that the folder to contain the
new folder appears in the Save %n box, click the Create .ew +older button
and name this. &pen the new folder and sa+e the ChemSketch file as
abo+e.
)he screen is sa+ed as a ChemSketch file with %sk9( as the file extension.
=B
3B
:B
9B
7B
B
CH
3
6,

)asting drawings into other applications

&nce a drawing is completed it can be sa+ed or simpl# pasted into the
application where it is to be used eg a 5ord document or $ower$oint
slide.
)here are two wa#s of pasting into another application2
!" As a ChemSketch obCect. $ointing the mouse at a ChemSketch
obCect and double clicking launches ChemSketch, if it is a+ailable, so
that the drawing can be changed. )o do this simpl# cop# (select the
drawing in ChemSketch and press the Ctrl8C ke#s together) and
paste (open the application then press the Ctrl8D ke#s together). "f this
option is used there is no need to sa+e the drawing as a ChemSketch
file.
9. As a picture. Cop# as abo+e (Ctrl8C) then switch to the application
where the drawing is re1uired, open the Edit menu, select Paste
Special and choose Picture. )his then appears as a simple image.
:. )o position the picture on the page, point at it with the mouse and left
click to displa# a menu. Select +ormat Picture, /ayout and eg %n !ront
o! te$t.
*e"iew e+ercises
7. Draw a structure for 74amino494meth#lpropane. Displa# all of its atoms,
tid# the structure and add a lone pair of electrons to the nitrogen atom.
Select the whole structure and make it larger. Cop# it and paste to another
application.
9. Assemble the apparatus for a reflux experiment, cop# this and paste into
another application.
Con"erting to ,-D interacti"e molecular structures
ACD/ChemSketch includes a :4D Diewer that produces a range of images
of structures drawn in the 94D mode. "t does not represent non4bonding
electrons.
7. Draw a molecule on the Structure screen.
9. Select the AC//abs menu and click " 1iewer. )his loads the +iewer and
displa#s the structure as (balls and stick( with hidden , atoms. Click the
" #ptimisation button to re+eal the , atoms.
0emember that ho+ering the mouse o+er a button displa#s a text
description.
:. .xplore the +arious +iews b# clicking the buttons abo+e the screen or
simpl# right clicking the mouse. 6ote the %*ith ots( option allows the
+arious representations of atoms and bonds with a (+er#) rough
representation of the extent of electrons superimposed.
3. 6ote that the molecule can be rotated b# dragging it with the mouse.
Clicking the Auto Rotate makes this happen automaticall#. Clicking the
Auto Rotate and Change Style button causes the molecule to loop through
the +arious representations whilst rotating, which is a useful screen for an
&pen .+ening.
=. )o change the default colours of the atoms or background click the Set
Colours button. Although the range of colours a+ailable is +er# limited it
can be useful to set the atom colour to match the mol#mod model colours
so that images on the screen look like the models students are handling in
the classroom.
)asting ,D structural images into other applications
:D images can be pasted into other applications as still pictures ie with no
interacti+it#. As abo+e, there are two wa#s of pasting an image into another
application. Cop# and paste (Ctrl8D) produces ChemSketch obCects which,
as long as ChemSketch is a+ailable on the computer, ma# be double clicked
to launch ChemSketch and then edited. Cop# and Paste Special (a+ailable
in the Edit menu) allows the image to be pasted as a Picture, which cannot
then be edited in ChemSketch.
)he 9D ChemSketch structure on the left has been con+erted to
the :D ball and stick with dots image on the right.
6ote that the :D image has been gi+en
a white background in ChemSketch.
*e"iew e+ercise- )r# creating 9D and :D
images of propan494ol and paste both into another application.
*r
C ,
:
C,
9
&dding interacti"e ,D structural images to web pages
)he pre+ious section dealt with pasting :D images into other applications as
still pictures which meant that interacti+it# was lost.
"t is possible to export structural drawings as mol files which can be
incorporated within web pages as interacti+e images as long as suitable
plug-in! software has been loaded. C,". is an example of a plug4in that
is widel# used b# chemists for +iewing and manipulating :D structures. "t is
a+ailable to download free from the C,". site at2
www.mdlchime.com/chime/
An ad+antage of creating chime images o+er the ChemSketch :D Diewer
images is that unlike ChemSketch, chime supports a representation of
multiple bonds.
)o create a %mol( structure image file using ChemSketch2
!" Draw a structure in ChemSketch and click the " #ptimise button whilst
still using the Structure screen.
9. -o to +ile menu, E$port, then select the location where the mol file is to be
sa+ed. "n %Save as Type( choose D! olfiles (E.mol). )#pe in a suitable
filename and click on Save.
:. )he file is now usable in C,"..
)o +iew the structure in a browser, pro"ided the C$./0 plug-in is
installed on your computer2
!" )here are two examples in the 5orkshop <iles / ChemSketch folder,
bromoethane.mol and bromoethene.mol. <ind a mol file on #our computer
and double click its icon. )he browser ma# launch and then the structure
will be seen, possibl# onl# in the 9D +iew. "f instead of the browser
opening, ChemSketch simpl# re4loads, then tr# opening the browser and
make the folder containing the mol file +isible at the same time. /sing the
mouse to drag and drop the mol file on the browser window should open
the file in the browser.
9. 0ight click to displa# a menu which allows the structure to be manipulated2
"f the molecule is displa#ed as 9D click on " Rendering.
isplay obtains different +iews.
Rotate causes the displa#ed structure to rotate.
:. ,olding the shift ke# whilst mouse dragging the structure increases its
si;e.
)o add the C,". structure to a web page use web authoring software.
5ith S <ront $age2
7. &pen an existing web page or create a new one.
9. -o to the %nsert menu and select *eb Components. "n the Component
type window select Advanced Controls (6* with +ersions of <ront $age
before F$ select Advanced from the %nsert menu).
:. "n the Choose a control window select $lug4"n.
3. "n the $lug4"n properties window browse to the mol file to be inserted, set
the height and width to displa# the molecule as re1uired and click &'.