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Unformatted text preview: blue color in the Auto/Manual Numbering Color box. 4. Click OK. Now, we can get down to mapping as it is. ACD/ChemSketch Tutorial 49 Advanced Structures, SMILES and InChI Notations, Reaction Schemes 5. On the Structure toolbar, click Atom-Atom Map enable the mapping mode: to display the Map Tools panel and Note that the Manual Mapping mode is automatically enabled (the corresponding button is active). 6. Point to the atom in the reactant and drag to the corresponding atom in the product. Note As you release the mouse button, 1 appears on the reaction scheme denoting manually mapped atoms. 7. Point to the next atom and drag again to its counterpart in the product: As you release the mouse button, 2 appears near the reactant atom and near its counterpart on the product. 8. Now, on the Map Tools panel, click Auto Mapping assigned to each other: . All other atoms are automatically Note The mapped atoms are only visible when the Map Tools panel is displayed. , then click New Page . 9. On the General toolbar, click Save File ACD/ChemSketch Tutorial 50 Advanced Structures, SMILES and InChI Notations, Reaction Schemes 4.6.4 Calculating Reaction Data—Commercial version only!
1. Using the acquirements (see Section 4.6.1), draw the following reaction:
O H3C Cl O N H3C O +
OH + Reactant Formula C2H3ClO 1 2 3 Product 1 C6H6O C5H5N C8H8O2 FW 78.4976 94.1112 79.0999 K 1 1 n - C - m - V - d - Yield - 1 1.1 mol - 86.3 g 78.5 mL 1.1 g/mL 136.1479 1 2. On the Structure toolbar, click Reaction Calculator The Reaction Calculator dialog box appears: , and then click the reaction arrow. 3. On the row that corresponds to acetyl chloride (C2H3ClO), double-click the Quantity cell (n) to select it. 4. Type 0.11 mol, and then press ENTER. 5. To calculate the volume, you need to enter the density of the compound. Double-click the corresponding Density cell (d), and then type 1.1 g/mL. After you press ENTER, the calculated value appears in the Volume cell (V). 6. Similarly, insert the following values into the corresponding Components table cells: for phenol—0.1 mol for quantity (n), for pyridine—0.11 mol for quantity (n) and 0.983 g/mL for density (d). All of the dependent data is automatically calculated. ACD/ChemSketch Tutorial 51 Advanced Structures, SMILES and InChI Notations, Reaction Schemes 7. Double-click the Mass cell (m) corresponding to the product and type 12.9 g. 8. Press ENTER. You will see that the yield is calculated and the Based on notation appears under Yield in the row corresponding to phenol: 9. Click OK to close the Reaction Calculator dialog box and paste the filled in Components table in the ChemSketch page. ACD/ChemSketch Tutorial 52 5. Advanced Drawing: Templates 5.1 Objectives
This chapter brings you yet another step closer to advanced drawing expertise once you have mastered the powerful Template feature. You will learn:
• Some ways of template usage; • How to apply the Instant Template tool to drawing the structures containing repetitive fragments; • More ways of using the Table of Radicals; • How to use the Template window for drawing DNA structures and complex biomolecular structures; and • How to create your own templates. 5.2 Overview
ACD/ChemSketch includes the following three template tools for drawing structures:
• Table of Radicals • Instant Template • Template Window While the binding point of any template in the Table of Radicals is fixed (invariable), the Template window and the Instant Template tool allow you to specify any atom or bond to be the binding point simply by clicking it directly. However, no matter what the source of template is, the principles of joining 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 to the bond so that the corresponding bonds of the structure and the template shadow are fused and then click. • By attaching the template to the structure: point to the corresponding atom on the structure so that the connecting bond appears, and then click. • By drawing a spiro connection between the template and the structure: point to the atom you want to be the binding point while holding down SHIFT, and then click.
Note You can flip the template shadow before fixing it by pressing TAB. ACD/ChemSketch Tutorial 53 Advanced Drawing: Templates 5.3 Table of Radicals
The Table of Radicals is a set of chemical radicals for structure drawing. Their names and, in some cases, abbreviations will help you to quickly translate “chemistry shorthand” into a meaningful structure. 5.3.1 Creating the Structure of Fluorescamine
This section is based on the movie fluor.exe which can be downloaded from our Web site or found in the \\MOVIES folder. We will draw the following structure using the templates taken from the Table of Radicals. O O O O Make sure you are in the Structure mode. 1. On the General toolbar, click New Page to open a new empty page. , choose Cyclopentane . 2. On the Reference toolbar or from the Table of Radicals 3. Click in...
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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.
- Spring '10