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Unformatted text preview: rom the group of buttons shown in step 3 above and click the NH2 group to draw a free radical: H3C N CH3 and click to draw the positive radical ion: 7. Right-click in an empty part of the workspace to quickly switch to the Positive Radical Ion tool or choose the corresponding button H3C NH + CH3 tool 8. Right-click in an empty area of the workspace to switch to the Negative Radical Ion and click to draw the negative radical ion: H3C NH 9. On the top General toolbar, click Delete CH3 and click the right CH3 group to delete it. ACD/ChemSketch Tutorial 23 Drawing More Complex Structures 10.From the group of buttons in step 3, click Radical until the following singlet biradical is obtained: H3C and click the NH group several times N 11.Click again with the radical tool until the triplet biradical is displayed: H3C N 12.On the General toolbar, click Save File , then click New Page . 3.8 Markush Bonds To denote structures with an undefined attachment point, use one of the Markush bond tools: 1. In the Table of Radicals workspace. , click Benzene , and then click an empty area of the 2. On the Atoms toolbar, click Carbon automatically activated. . Note that the Draw Normal tool is 3. Click the topmost atom of benzene to sprout CH3: 4. On the Atoms toolbar, click Bromine 5. Using the Select/Move structure: . tools select five lower atoms of the or Select/Rotate/Resize 6. On the Structure toolbar, click either Markush Bond or Markush Bond with Shadow tool. The selected element connected by the Markush bond appears: CH3 CH3 Br OR Br ACD/ChemSketch Tutorial 24 Drawing More Complex Structures On this structure, Br might be connected to any of the five carbon atoms of toluene. ACD/ChemSketch allows you to highlight this phenomenon by pointing to the variable attachment point of the Markush bond. 3.8.1 Markush Bond with Added or Removed Fragment Starting with version 9.0, you can draw structures with the attached mass or formula difference values, instead of the added or removed structural fragments itself. This special type of Markush structures is useful for designation of metabolic or mass-spectral transformations of chemical structures. 1. To apply this option, draw toluene as described above and select five lower atoms of the structure. 2. On the Structure toolbar, click Markush Bond with Added or Removed Fragment button: either or . 3. In the Define Markush Mass Difference dialog box that appears, select the Addition and Mass options, and then, in the adjacent box, type 79.9: 4. Click OK. You can see one of the following structures: CH3 CH3 [+79.9] OR 5. On the General toolbar, click Save File [+79.9] , then click New Page . 3.9 Generating Stereo Descriptors ACD/ChemSketch allows you to generate stereo descriptors for chiral and pseudo chiral centers, and for a double-bond configuration. 1. Draw the following set of structures using the tools described above: CH3 CH3 Cl H3C Cl CH3 H3C CH3 ACD/ChemSketch Tutorial 25 Drawing More Complex Structures Tip To draw a stereo bond, on the Structure toolbar, click Up Stereo Bonds or Down Stereo Bonds . Then change a bond to a stereo bond by clicking the desired bond on the chemical structure, or drag from the atom to an empty space, or simply click an existing atom (if the existing atom is of the same type as that currently active on the Atoms toolbar). To change the direction of the stereo bond, click this bond as many times as you need. 2. Select all of the structures. 3. On the Tools menu, point to Generate, and click Stereo Descriptors (you can do this both in Structure and Draw modes). Stereodescriptors appear on the selected structure(s) near the corresponding chiral center or double bond: 4. The following stereodescriptors are available: • S and R describe a chiral center configuration. • E and Z describe a double-bound configuration. • Small r and s describe configurations of pseudo chiral centers. 5. To change the color of stereo descriptors, from the Options menu, choose Preferences. 6. In the Preferences dialog box that appears, switch to the Structure tab, and then select the appropriate color in the Auto/Manual Numbering Color box. The next time you generate stereodescriptors, the defined color will be used. Note If no structure(s) is(are) selected in the workspace, stereodescriptors are automatically generated for all structures on the current page which have stereo centers or double bonds for which Z/E or R/S isomerism is possible. , then click New Page . 7. On the General toolbar, click Save File 3.10 Drawing Coordination Bonds There are numerous ways to draw coordinating bonds. ACD/ChemSketch allows you to draw four different types. We are going to draw the following structure: O O Li O CH3 CH3 1. Using the Table of Radicals or the buttons on the Reference toolbar, paste the benzene ring to the workspace: ACD/ChemSketch Tutorial 26 Drawing More Complex Structures 2. On the Structure toolbar, click Set Bond Horizontally below to rotate the ring: and then click the bond as shown 3. Activate the Draw Normal tool and, i...
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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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