Acdchemsketch tutorial 44 advanced structures smiles

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Unformatted text preview: ecahedrane ([5]Fullerene-C20) This section is based on the movie fuller.exe which can be downloaded from our Web site or found in the \\MOVIES folder. Make sure you are in the Structure mode. 1. On the Reference toolbar or from the Table of Radicals Click in the workspace to place a cyclopentane ring. , choose Cyclopentane . 2. Sequentially point to each bond of the ring and click to attach five other rings: 3. Right-click to quickly switch to the Select/Move tool. 4. Move by dragging atoms a, c, e, g, i to atoms b, d, f, h, j accordingly as shown in the following scheme to merge them: ACD/ChemSketch Tutorial 45 Advanced Structures, SMILES and InChI Notations, Reaction Schemes 5. On the Atoms toolbar, click Carbon add more atoms and bonds: , and click directly the points indicated by arrows to 6. Connect the adjacent methyl groups with single bonds by dragging from one terminal atom to another to obtain the following structure: 7. On the Structure toolbar, click 3D Optimization structure. to obtain the 3D model of the drawn 8. On the Structure toolbar, click 3D Rotation . Point to any atom or bond on the structure and drag over the workspace to obtain the projection you want. Note From the Options menu, choose Preferences and switch to the Structure tab of the dialog box. You can choose whether the background bond should be broken or not by selecting or clearing the Enable check box in the Bonds Intersections area. You can change the position of the bonds of interest by applying the Bring Bond to Front (CTRL+F) or Send Bond to Back (CTRL+K) commands (Tools menu) to the selected bond. You can also bring the background bond to the front by holding down SHIFT and clicking it with the Change Position tool active. Try to draw the following structures using the technique described above [4,6]Fullerene-C24 [5,6]Fullerene-C24 ACD/ChemSketch Tutorial 46 Advanced Structures, SMILES and InChI Notations, Reaction Schemes Tip If the optimization produces a “Moebius” structure instead of a fullerene-type structure the optimization has converged to an unusual value. Click Undo pre-optimized structure. Then, click Clean Structure to return to your or, using the Select/Move tool, move some of the atoms slightly and optimize again. 9. On the General toolbar, click Save File , then click New Page . 4.6 Drawing, Labeling, and Mapping Reactions This section explains how to draw reactions and complex chemical schemes with manual or automatic mapping. 4.6.1 Drawing a Reaction Scheme This section is based on the movie reaction.exe which can be downloaded from our Web site or found in the \\MOVIES folder. In this section, we will draw the following reaction scheme: + , choose Benzene 1. From the Table of Radicals template, you can find it on the Reference toolbar). (if you have recently used this ACD/ChemSketch Tutorial 47 Advanced Structures, SMILES and InChI Notations, Reaction Schemes 2. Press TAB to flip the template shadow and draw the following structure by clicking in the workspace several times: To draw a fused-ring structure, place the cursor directly over a ring bond and click. 3. Press TAB to flip the shadow again and click beside the drawn structure to place a separate ring. Right-click to hide the template shadow. Note 4. On the Structure toolbar, click Draw Normal it triple: , and then click the bond of the ring to make 5. Draw the structure of Triptycene as described in Section 4.5.2 and place it beside the other drawn structures: 6. On the Structure toolbar, click Reaction Plus second structures by clicking: , and then place it between the first and the + 7. Click Reaction Arrow and click or drag to place it as well: + Note By clicking the bottom right triangle of the Reaction Arrow button you can choose from a variety of arrows. Some arrows are treated as graphical objects, however, and cannot be exported properly. , point to the object, and then drag. 8. To move the plus sign or the arrow, click Select/Move ACD/ChemSketch Tutorial 48 Advanced Structures, SMILES and InChI Notations, Reaction Schemes 4.6.2 Labeling a Reaction In this section, you will study how to add experimental conditions to a reaction scheme: 1. On the Structure toolbar, click Reaction Arrow Labeling . 2. Click the reaction arrow to display the Edit Reaction Conditions dialog box. 3. In the Edit Reaction Conditions dialog box, type "25" in the upper pane, and then click C° on the right side of the dialog box. 4. Type benzene in the lower pane. 5. Click OK to close the dialog box. The reaction now looks like this: 4.6.3 Mapping a Reaction This tool allows you to map a drawn reaction either manually or automatically. To differentiate between the automatically generated and manually inserted numbers, select different colors for automatic and manual mapping. 1. From the Options menu, choose Preferences to display the Preferences dialog box. 2. Switch to the Reaction tab, and then select the red color in the Manual Mapping Color box: 3. Switch to the Structure tab, and then select the...
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This note was uploaded on 06/22/2010 for the course AS 1 taught by Professor Chem during the Spring '10 term at University of Alaska Southeast.

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