3 smiles notations acdchemsketch can convert smiles

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Unformatted text preview: peptide drawn in Section 4.2.2. 1. On the Tools menu, point to Generate, and then choose SMILES Notation. The generated string appears right below the structure: CH3 O HO HN NH O N H O N H Oc1ccc(cc1)CC2NC(=O)C(C)NC(=O)C(NC2=O)C\C4=C\Nc3ccccc34 2. You can now copy the text string by selecting it and pressing CTRL+C to copy it to the Windows clipboard. Then paste it into any external text editor as text using the menu command or CTRL+V. Note If you have several structures drawn on one page and you want to generate the SMILES string for all of them, you do not have to select them all—just leave them all unselected and repeat step 1. The SMILES notation appears for all the drawn structures as one string where each notation is separated by a point. 4.3.2 Generating Structures from SMILES Notations Now we will try the inverse task—generation of the structure from the SMILES string. At first we will generate the structure from the notation created in the previous section. 1. Select the text string created in the previous section: ACD/ChemSketch Tutorial 38 Advanced Structures, SMILES and InChI Notations, Reaction Schemes 2. On the Tools menu, point to Generate, and then choose Structure from SMILES. The generated structure is placed below the text string. As you can see, it is the same structure from which the SMILES notation was generated in the previous section: Oc1ccc(cc1)CC2NC(=O)C(C)NC(=O)C(NC2=O)C\C4=C\Nc3ccccc34 O H N CH3 O HN O OH NH HN 3. If you do not have the text string inserted into the workspace or it is not selected, selecting the Structure from SMILES command displays the following dialog box where you can type the string manually: 4. Click OK. The generated structure is attached to the cursor as a shadow: 5. Click in the workspace to place the structure. 6. On the General toolbar, click Save File , then click New Page . 4.4 InChI Notations ACD/ChemSketch can convert InChI (IUPAC International Chemical Identifier) notations to structures, and convert structures to InChI strings. InChI procedures were developed under IUPAC project. The technical development was carried out primarily at the US National Institute of Standards and Technology (NIST). More information about InChI is available on the IUPAC website at: www.iupac.org/inchi ACD/ChemSketch Tutorial 39 Advanced Structures, SMILES and InChI Notations, Reaction Schemes 4.4.1 Generating InChI Notations Now we will try to create an InChI string for (1S)-1-(1H-imidazol-4-yl)ethanol. 1. Using the obtained skills, draw the following structure: CH3 HO NH N 2. On the Tools menu, point to Generate, and then choose InChI Options. In the dialog box that appears, specify options as shown and click OK: 3. On the Tools menu, point to Generate, and then choose InChI for Structure. The generated string appears right below the structure: CH3 HO NH N InChI=1/C5H8N2O/c1-4(8)5-2-6-3-7-5/h2-4,8H,1H3,(H,6,7)/t4-/m0/s1 You can now copy the text string by selecting it and pressing CTRL+C to copy it to the Windows clipboard. Then paste it into any external text editor as text using the menu command or CTRL+V. 4. Repeat the generation of the InChI string for the current structure but with the different options; in the InChI Options dialog box, clear the Mobile H Perception option and select Ignore under Stereo Options. The following InChI notation appears in this case: InChI=1/C5H8N2O/c1-4(8)5-2-6-3-7-5/h2-4,8H,1H3,(H,6,7)/f/h6H Note ACD/ChemSketch Tutorial 40 Advanced Structures, SMILES and InChI Notations, Reaction Schemes 4.4.2 Generating Structures from InChI Notations Now we will try the inverse task—generation of the structure from the InChI string. We will generate the structure from the notations created in the previous section. 1. Select the text string that was created first in the previous section: 2. On the Tools menu, point to Generate, and then choose Structure from InChI. The generated structure is placed below the text string. As you can see, it is the same structure from which the InChI notation was generated in the previous section: InChI=1/C5H8N2O/c1-4(8)5-2-6-3-7-5/h2-4,8H,1H3,(H,6,7)/t4-/m0/s1 CH3 HO NH N 3. Now select the second InChI string and choose the Structure from InChI command again. You can see that the stereoisomerism is not reflected: InChI=1/C5H8N2O/c1-4(8)5-2-6-3-7-5/h2-4,8H,1H3,(H,6,7)/f/h6H CH3 HO NH N 4.5 3D-Optimization This section explains how to create structures that have “realistic” angles and bond lengths. There is no need to explain how difficult it is to draw such structures proportionally. The 3DOptimization and 3D Rotation options will help you to quickly cope with this task. These options make it possible to create complex structures in ACD/ChemSketch with ease. 4.5.1 Creating Structure of Bicyclo[2.2.2]octane This section is based on the movie bicyc.exe which can be downloaded from our Web site or found in the \\MOVIES folder. 1. From the Options menu, choose Preferences, and, in the dialog box that appears, switch to the Struct...
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