Chemical drawing software (ChemSketch(r)) is broadl# similar. The focus here is on basics that allow #ou to draw and use images for teaching. 'Nowing how to step back if this happens is +ital to a+oid frustration'
Chemical drawing software (ChemSketch(r)) is broadl# similar. The focus here is on basics that allow #ou to draw and use images for teaching. 'Nowing how to step back if this happens is +ital to a+oid frustration'
Chemical drawing software (ChemSketch(r)) is broadl# similar. The focus here is on basics that allow #ou to draw and use images for teaching. 'Nowing how to step back if this happens is +ital to a+oid frustration'
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 &'.