Exe which can be downloaded from our web site or

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Unformatted text preview: the ChemSketch workspace to paste the ring. 4. Click the indicated atom while holding down SHIFT to obtain the spiro-connection with the second cyclopentane ring: SHIFT+Click 5. On the Reference toolbar or from the Table of Radicals , choose Benzene . First click the indicated bond to fuse the benzene ring and then click the indicated atom to connect the phenyl radical: ACD/ChemSketch Tutorial 54 Advanced Drawing: Templates 6. On the Atoms toolbar, click Oxygen (note that the Draw Normal tool enabled). Click the indicated atoms to replace them with oxygen atoms: is automatically 7. Right-click to quickly switch to the Draw Continuous atoms to attach the OH groups to them: tool. Double-click the indicated 8. Click the indicated single bonds to replace them with double bonds: 9. On the General toolbar, click Save File , then click New Page . ACD/ChemSketch Tutorial 55 Advanced Drawing: Templates 5.4 Instant Template Tool You might want to copy a molecular fragment that is not in the Table of Radicals. You can think of the Instant Template tool as a “Paste” command. It is better than simple paste, however, because you can specify the point of attachment. 5.4.1 Creating the Structure of a Cyclic Oligomer This section is based on the movie oligomer.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 ( ), choose Benzene Point to the upper middle part of the workspace and click to place a benzene ring. 2. From the Table of Radicals, choose Ethynyl to attach it to the ring: . and click the atom indicated by the arrow 3. On the Structure toolbar, click Instant Template instant template: and click the indicated atom to create an ACD/ChemSketch Tutorial 56 Advanced Drawing: Templates 4. Click the atom indicated by the arrow to attach the template: 5. Click Instant Template fragment: again and click the atom to create the template of the whole 6. Click the atoms to attach the template as shown. To hide the template shadow, right-click in the workspace after you finish drawing: 7. On the Structure toolbar, click Draw Normal ring: and click the indicated atom to complete the 8. On the General toolbar, click Save File , then click New Page . ACD/ChemSketch Tutorial 57 Advanced Drawing: Templates 5.5 Template Window The Template window feature is the most sophisticated of the three template features in ACD/ChemSketch because it allows you to organize and store structures or drawings that you might want to copy later. A brief tour of available ACD/ChemSketch Templates is given in the movie templ_st.exe which can be downloaded from our Web site or found in the \\MOVIES folder. 5.5.1 Creating the Fragment of a DNA This section is based on the movie dna_st.exe which can be downloaded from our Web site or found in the \\MOVIES folder. 5.5.1.1 Drawing the Chain of Deoxyriboso-5-phosphate Fragments 1. On the General toolbar, click Template Window choose 2-Deoxyriboso-5-phosphate (chain form): O HO P OH O OH O . On the tab, OH 2. Click in the workspace to paste the chosen template. 3. Point to the indicated atom and holding down SHIFT click to attach the next 2-Deoxyriboso-5phosphate fragment: SHIFT+Click O HO P OH O O OH O O OH P OH OH HO O O O P OH O OH O OH ACD/ChemSketch Tutorial 58 Advanced Drawing: Templates 4. Click Select/Rotate/Resize . 5. Select the indicated part of structure by dragging the selection rectangle around it. Drag the onto the oxygen atom indicated by arrow. Then, holding down SHIFT, action center drag the selected part of structure clockwise to rotate it by 90o: O HO P O OH HO O O O P OH OH O OPO OH OH O OH HO O O O P OH OH O OPO OH OH OH O OH O HO P O O OH O OH O 5.5.1.2 Adding the Bases 1. Open the Template Window . On the tab, choose the base you need by clicking the atom that will be the attachment point. For example, choose uracil, clicking the N atom shown so that this will be used as the attachment point: 2. Point to the atom indicated below and click while holding down SHIFT: Tip You can flip the template shadow before fixing it by pressing TAB. ACD/ChemSketch Tutorial 59 Advanced Drawing: Templates 3. Repeat steps 1 and 2 to add bases to other nucleotides such as adenine: Now try to draw your own DNA or RNA fragment of any other length. 4. On the General toolbar, click Save File , then click Close Document . 5.6 Drawing Complex Structures of Biomolecules Here are some examples for creating complex structures of biomolecules using different ACD/ChemSketch tools. 5.6.1 Creating the Structure of Beta-Maltose This section is based on the movie maltose.exe which can be downloaded from our Web site or found in the \\MOVIES folder. 1. In the Template Window , switch to the tab, and confirm that . If not, select it in you are viewing the Haworth formulae page: the corresponding box. 2. Click α-D-Glucopyranose to select it and click in the workspace to copy it. 3. Repeat steps 1–2, but this time select th...
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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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