ACD/Structure Drawing Applet (SDA)

Introduction Docking and Floating modes; Exporting/importing the drawn structure into/from MDL Molfile format; Loading a structure into the applet from the server; Loading a structure into the applet by a JavaScript function call; Composing substructure queries based on a drawn structure; Removable toolbars for maximum structure visualization area; 2D molecule optimization (Clean) function for normalizing your molecular drawing even forstructures including several Markush bonds (server support required); and Copying/pasting image as mol text and image to/from Windows Clipboard.1.2 Related SoftwareACD/Web Librarian gives your chemists and analysts the resources and tools necessary toperform these tasks in an efficient manner. Web Librarian is an enterprise solution that offersyour organization a fully customizable, browser-based service for viewing ACD/Labs databases.With ACD/Web Librarian, your chemists and analysts can optimize their valuable time by gainingunified access to structure and spectra data collected throughout the enterprise. Data isdisplayed in a virtual, centralized repository that is accessible to authorized members of theorganization. Furthermore, Web Librarian provides a collaborative framework for sharinganalytical record data to ensure that accurate information is available to all members of a projectteam. This not only speeds up their research and analysis, but also eases information retrievaland creates an efficient work environment in order to make effective mission-critical decisions.ACD/Labs Online (I-Lab), the Interactive Laboratory, is an Internet-based service for instantaccess to chemical databases and property predictions programs. Since 1996 it has gained areputation as one of the most innovative online services for prediction. With over three thousandusers worldwide, I-Lab is being successfully used for teaching chemistry in several leadingAmerican universities as well.With I-Lab online access, you can: Search databases by structure and substructure; Obtain NMR spectra; Generate systematic chemical names for your molecules; and Predict properties such as pKa, logP, or solubility for the chemical structures.You can get these facilities from both your Internet browser and from inside ACD/ChemSketch(with ACD/I-Lab Add-on for ChemSketch 5.0 installed), a powerful structure drawing tool that canbe downloaded from our Web site FOR FREE.We do offer a two week demonstration period for new I-Lab users. The demonstration periodenables you to use all I-Lab services free of charge for two weeks. To make use of this offer, visitus now at:http://www2.acdlabs.com/ilab.ACD/Structure Drawing AppletTutorial2

2. Drawing Simple Structures2.1 ObjectivesThe objective of this chapter is to give you an overview of the chemical drawing features of SDA.You will learn how to: Draw atoms, bonds (single, double, triple, wedge, undefined, and Markush), and polymers; Select and resize drawn structures; Generate stereo descriptors; and Clear the screen.2.2 Drawing Atoms and Bonds2.2.1 Using the Draw Normal ToolThe Draw Normal tool is the default tool when the applet is started. In this mode you can easilydraw normal or branched chains and replace the drawn atoms with other atoms from the PeriodicTable of Elements.1. Make sure that the Draw Normal toolCarbon atomis enabled on the Structure toolbar and that theis selected on the Atoms toolbar.2. Click in an empty space to draw CH4.3. Click the CH4 carbon to add a —CH3 group, creating CH3—CH3 with a standard bond length.Click the same carbon twice more to draw:4. In the Templates pop-up window, open Chains (saturated) and select the C6 chain byclicking the leftmost carbon atom of the C6 fragment, and then click the rightmost carbon ofour structure to drawACD/Structure Drawing AppletTutorial3

Drawing Simple Structures2.2.2 Double and Triple Bonds1. On the last structure drawn, hover over the terminal bond until it is highlighted and then clickonce to convert it to a double bond:2. Click again to convert it to a triple bond:3. Click again to convert it back to single bond.2.2.3 Deleting Atoms IndividuallyIf you have added too many atoms, you can remove them.1. Click Delete.2. Click the atom highlighted in the picture:ACD/Structure Drawing AppletTutorial4

Drawing Simple StructuresThe molecule now looks like this:2.2.4 The Undo CommandAnother important operation is the Undo command. Click Undo, and the SDA screen willrevert to exactly what it was before your last change.Note As soon as the Undo button is clicked, the Redo button becomes active.Click the Undo button several more times until you return to the following structure:NoteThe Undo command can be repeated up to 7 times. When you begin to draw morecomplex molecules or graphical objects, we recommend that you develop a habit ofsaving your work to a file after making several changes.2.2.5 Polymers1. Left-click and drag to include all of the specified atoms in the closed Lasso line to select them:ACD/Structure Drawing AppletTutorial5

Drawing Simple Structures2. Release the mouse button. The fragment inside the Lasso line becomes selected:on the Structure toolbar to display the Polymer options panel, and then3. Click Polymerschange the settings as shown:The polymer structure appears in the workspace:ACD/Structure Drawing AppletTutorial6

Drawing Simple Structures2.2.6 Markush BondsTo denote structures with an undefined attachment point, use the Markush bond tool.1. In the Radicals Table dialog box, select benzene, and then click in the workspace.2. Make sure that the Draw Normal toolCarbonis enabled on the Structure toolbar and that theatom is selected on the Atoms toolbar.3. Click the topmost atom of benzene to sprout the methyl group:4. On the Atom toolbar, select Bromineto attach it with a Markush bond.5. Select the five CH atoms of the structure using the Select/Move tool6. On the Structure toolbar, click Markush BondMarkush bond appears:Note. The selected element connected by theIn this structure, bromine atom might be connected to any one of the five carbonatoms of toluene. All five carbon atoms are highlighted by moving the mousepointer over to the variable attachment point of the Markush bond.ACD/Structure Drawing AppletTutorial7

Drawing Simple Structures2.2.7 Changing the Atom1. On the Atoms toolbar, click Periodic Table2. In the Periodic Table of Elements, click Fluorinethe Atoms toolbar.to open the Periodic Table of Elements:. The Fluorine button now appears on3. Click the left-most carbon atom to replace it with a fluorine one:ACD/Structure Drawing AppletTutorial8

Drawing Simple Structures2.2.8 Using Mouse DragWith the Draw Normaltool, dragging from one atom to another draws a single bondbetween them. If you drag to or from an empty space, a new atom is inserted at the start or endof the drawn bond.With the Draw Normal tool active, point the mouse arrow to one of the terminal carbons and dragto another terminal carbon to draw the following structure:2.2.9 Cleaning the StructureImportant The Clean tool works with the help of external “cleaning” software presentwhen ACD/SDA is launched from ACD/Web Librarian or ACD/I-Lab.On the Structure toolbar, click Cleanto standardize all the bond lengths and angles in thedrawn structure to obtain the following image:NoteThe Clean command not only standardizes all bond lengths and angles to makethe structure look nice—it makes the drawn structures closer to being chemicallycorrect. For acyclic fragments, for example, it places the bonds near the sp2carbons at 120o angles, and the bonds near the sp carbon at 180o (linear). If youdraw geometrical and stereoisomers, the Clean command standardizes their bondlengths and angles while retaining all of their structural significance.ACD/Structure Drawing AppletTutorial9

Drawing Simple Structures2.2.10 Using the Stereo and Undefined Bond ToolsClick the bottom-right triangle of the Draw Normal buttonexpand it to the following group:on the Structure toolbar toDraw NormalDraw Up StereoDraw Down StereoYou can draw a wide variety of chemical bonds:Select any of these tools and click any bond in the drawn structure. Click repeatedly on a stereoor coordination bond to change its direction. Click once more to change the bond to theundefined type (without definite direction).2.3 Selecting Structure FragmentsYou can select atoms, bonds, and other fragments of your molecular structure or reactionscheme: On the Structure toolbar, click Select/Move. In the Drawing area, click and drag toinclude all of the specified atoms of your structure in the closed Lasso line to select them:Release the mouse button. Once the fragment(s) has been selected, you can move it as theSelect/Movetool is active:Additionally, you can perform other operations with the selection as well using the correspondingtools: Delete. For more information, refer to Section 2.2.3. 2D Optimization (or Clean)ACD/Structure Drawing Applet. For more information, refer to Section 2.2.9.Tutorial10

Drawing Simple Structures2.4 Zooming In/Out on a StructureYou can zoom in/out on the structure by clicking Zoom In/Out. If the structure is largerthan the Drawing area you may scroll it with the help of scroll bars.To zoom a structure to fit completely in the window, click Fit to Page.2.5 Input/Output2.5.1 Embedding the Structure in a DocumentSometimes you need to insert the structure into a report written in different applications (e.g.,Microsoft Word document, Excel spreadsheet, etc.).1. Select the required structure(s).2. Click Copy as Imageto copy the selection to the Clipboard.3. Switch to the application where you want the structure(s) to be inserted, and paste using thePaste function of that application.2.5.2 Copying/Pasting the Structure as Mol TextTo copy the contents of the Drawing area as mol text, click Copy as Mol Text.To paste a structure stored as mol text from the clipboard to the Drawing area, click Paste fromMol Text.2.6 Clearing the ScreenTo clear the screen, you can do one of the following: From the Structure toolbar, click Clear On the Structure toolbar, click Delete. Click in an empty space away from the drawnstructure to select all of the structures, and then click any structure to delete the entirescreen.ACD/Structure Drawing AppletTutorial11

3. Drawing More Complex Structures andReactions3.1 ObjectivesNow that you have studied the basics of structure drawing described in Chapter 2, you may wantto draw more complex structures using the advanced tools of ACD/Structure Drawing Applet.In this chapter you will learn how to: Use the Radicals Table to draw typical chemical fragments; Use Templates to move a step closer to advanced drawing expertise; Delete and replace atoms; Set double and triple bonds; Set an atom’s charge, and draw cations and anions; and Draw single-step chemical reactions.3.2 Using the Radicals TableACD/Structure Drawing Applet includes the following two structure template tools: Radicals Table dialog box Templates windowThe Radicals Table is a set of chemical radicals for structure drawing. It includes structures ofamino acids, their protecting groups, as well as nucleotides and other frequently used radicals.Their names and, in some cases, abbreviations are listed to help you quickly translate “chemistryshorthand” into a meaningful molecule.1. Clear the screen using the directions given in previous section.ACD/Structure Drawing AppletTutorial12

Drawing More Complex Structures and Reactions2. On the References toolbar, click Radicals Tablebox:3. In the Radicals Table dialog box, click Benzenereturn to the ACD/SDA windowto open the Radicals Table dialogto select the structural element and4. A Benzene button is now located and currently selected on the References toolbar on the rightside of the screen.5. Repeat these steps for SulfoNote.When you select new radicals from the Table of Radicals, the correspondingbuttons are automatically added to the References toolbar.3.2.1 Creating the Structure of Benzenesulfonic Acid1. Delete all structures.2. Click BenzeneRadicals Table.on the References toolbar on the right side or select it from the3. Click in the Drawing area to copy the structure.4. On the same toolbar, click SulfoACD/Structure Drawing Applet.Tutorial13

Drawing More Complex Structures and Reactions5. Click any atom to place the radical:3.3 Using the Templates WindowWhile the binding point of any template in the Radicals Table dialog box is fixed (invariable), theTemplate window allows you to specify any atom or bond to be the binding point simply byclicking directly on it. However, no matter what the source of the template is, the principles ofjoining are the same.There are several ways of joining the template to a drawn structure: By fusing the bonds of the structure and template: point the mouse cursor over thebond so that the corresponding bonds of the structure and template shadow are fused andthen click. By attaching the template to the structure: point to the corresponding atom on thestructure so that the connecting bond appears, and then click.3.3.1 Creating Ring Structures1. Click Templates. In the following Templates window, click Rings, and then click anyatom or bond of the Cyclohexane structure.2. Click in the Drawing area workspace to copy the template.3. In the Templates window, click Rings. Point to any bond of the Cyclopentane structure, and then click it.4. Now sequentially point to the indicated bondscreate the following structure:to highlight, and then click them to.5. In the Templates window, click Rings. Point to any bond of the Cyclohexane structure,and then click it.ACD/Structure Drawing AppletTutorial14

Drawing More Complex Structures and Reactions6. Point to the indicated bondto highlight, and then click it to create the following.structure:7. Click Radicals Tableon the References toolbar.8. In the Radicals Table dialog box, select the carboxyl group OOHby clicking Carboxyl.9. Click the atoms indicated in the structureto sprout carboxyl groups outof them:OOHOHOOHOHOOHOOHOO3.4 Deleting Atoms and FragmentsOOHOHODelete the atoms indicated by arrows inCH3CH3OHOHOOOHOHOto drawOCH3H3COCH3You can do this in two ways: delete each atom individually (for more information, refer to Section2.2.3) or delete several atoms simultaneously.3.4.1 Deleting Several Atoms Simultaneously1. On the Structure toolbar, click Move.2. Drag to include all of the specified atoms in the closed Lasso line to select them:3. On the Structure toolbar, click Delete.4. Click any one of the highlighted atoms to delete all of them simultaneously.NoteTo deselect all fragment(s), click anywhere in an empty space.ACD/Structure Drawing AppletTutorial15

Drawing More Complex Structures and Reactions3.5 Replacing AtomsNH2CH3NHReplace the atoms indicated with arrows inCH3H3CNH2NCH3OHNto drawNOHONHNOHOHCH3, and then click all the carbons denoted by an open-1. On the Atoms toolbar, click Nitrogenhead arrow on the above structure., and then click the three Carbons denoted by a2. On the Atoms toolbar, click Oxygensolid-head arrow.3.6 Setting Double and Triple BondsNH2NHHNNH2NWith the Draw Normaltool active, click the bonds indicated inNOHONNHOHto setOHNH2NHNNH2Ndouble bonds O.NHON OHNOH3.7 Setting Charges and Defining Anions and CationsIn this section we will draw the following set of structures:H3CH3C -NH2 CH3NcationCH3anion1. Click Carbonon the Atoms toolbar and make sure that the Draw Normal toolon. Click three times in one place to draw the following structure:isH3CCH32. Click Nitrogenand click the middle carbon in the fragment to replace it with a nitrogen:ACD/Structure Drawing AppletTutorial16

Drawing More Complex Structures and Reactions3. Click Charge Minusand then click the NH group to make an anion:H3C-N4. Click Charge PlusCH3, and then click twice to make a cation:H3C NH2 CH3NoteWhen you use the Charge buttons,or, to change the charge of anonmetal, the corresponding number of hydrogen atoms is automatically added toit, or removed from it, to preserve proper chemical valency. If you change thecharge of a metal, the charge is changed in increments or decrements inaccordance with the next chemically valid charge of the corresponding ion. (Youcan view common valences used in the Periodic Table of the Elements.)3.8 One More Example: Creating the Structure of Testosterone1. Delete all structures.2. Click Templates.3. In the following Templates window, click Steroid(1), and then click the androstane structure.4. Click in the Drawing area workspace to copy the template.ACD/S

applications ranging from electronic conferences to online database searches. ACD/SDA is featured in ACD/Web Librarian and ACD/I-Lab. ACD/Structure Drawing Applet is fully compatible with JDK 1.3.0 specifications, but may also run in a browsers’ built-in Java Virtual Machine. ACD/