This preview shows page 1. Sign up to view the full content.
Unformatted text preview: a template file rather than simply a user file. It can be opened and read with any text editor, although you will likely never need to do so. The Template window accesses TEMPLATE.CFG to let it know what files to display as templates. If an .SK2 file is not shown in the Template window, it will be added to TEMPLATE.CFG when you open .SK2 as a regular ACD/ChemSketch file and select the command to save as a user template. If TEMPLATE.CFG is moved or lost, the Template window will not display any templates. If the TEMPLATE.CFG file is found (by Windows Explorer, for example, or the system “Find File” utility) it can be restored to the default directory or the user’s private folder. If it cannot be found, it can be retrieved by reinstalling ACD/ChemSketch or by adding each template as described above. ACD/ChemSketch Tutorial 63 6. Calculating Macroscopic Properties 6.1 Overview
In addition to the drawing capabilities, ACD/ ChemSketch offers predictions of numerous properties for your compounds. In this chapter, the simple means to calculate these properties is described. 6.2 Calculating Macroscopic Properties
6.2.1 Menu Command
To determine some or all of the available molecular properties, follow the steps: 1. When in Structure mode, draw a structure, for example, benzoic acid:
O OH 2. On the Tools menu, point to Calculate, and then choose All Properties or one of the available properties. 3. Once chosen, the calculated property is displayed in the Calculation Results dialog box. For example, choosing All Properties for benzoic acid will show the following dialog box: ACD/ChemSketch Tutorial 64 Calculating Macroscopic Properties 4. The result can be immediately pasted on the workspace if desired by clicking Copy to Editor. As the text is inserted, you are switched to the Draw mode that allows you to edit the text if necessary. On the Tools menu, point to Calculate, and then choose Select Properties to Calculate to define a set of properties to be calculated. In the dialog box that appears, mark the properties and click OK. If you now choose Selected Properties only the selected properties will be calculated. 5. Switch back to the Structure mode and save the document to CALC_PROP.SK2.
Note 6.2.2 Automatic Display on Status Bar
It is also possible to view the macroscopic property for the structure selected in the workspace directly on the status bar. Note that if no structure is selected in the workspace, the property is calculated for all the structures displayed; if there are no structures drawn, the field on the status bar is not available. Click the field to the right on the status bar and choose the property desired. By default, this is set to formula weight. In the example shown, the dielectric constant, ε20, has been specified. ACD/ChemSketch Tutorial 65 Calculating Macroscopic Properties 6.3 Calculating Monoisotopic Mass for a Fragment (MassSpec Scissors)
In this section, we’ll calculate monoisotopic mass for a structural fragment: 1. On the General toolbar, click New Page
CH3 NH N O CH3 OH O to open a new empty page.
O OH 2. Draw a structure, for example, the following one: 3. Select a bond to cut (it should be a non-cyclic one). 4. From the Tools menu, choose MassSpec Scissors, or, on the Structure toolbar, click the corresponding button the workspace: . It will display monoisotopic mass underneath BOTH fragments in
CH3 NH N O CH3 OH O O OH C10H13 133.1017 Da
Note C6H9N2O5 189.0511 Da You can change the style of the separating line in the Draw mode: select the line, double click it, and, on the Objects Panel, change the style. You can also see the nominal and average mass, using the Calculate Macroscopic Properties option (refer to Section 6.2). ACD/ChemSketch Tutorial 66 7. Special Function Keys 7.1 Objectives
The ACD/ChemSketch is an extremely versatile molecular structure editor. For this reason, several ACD/Labs modules are now accessible as buttons from the ACD/ChemSketch interface. This chapter describes three special modules which can also be accessed from the ACD/ChemSketch interface. ACD/Tautomers and ACD/ Name Freeware are now included with both commercial and freeware versions of ACD/ChemSketch; ACD/Dictionary is also available but only with the commercial software. 7.2 Tautomers
For certain compounds, there is a mixture of two or more structurally distinct forms which exist in rapid equilibrium in solution. In most cases, tautomers result from a form of proton transfer. ACD/Tautomers is designed to generate the most reasonable tautomeric forms of drawn organic structures. It is available as the Check Tautomeric Form command through the Tools menu or as a button on the Structure toolbar. The possibility of the alternative tautomeric forms should always be carefully considered, if the drawn organic structure contains two or more double or triple bonds conjugated with or attached to oxygen, nitrogen, sulfur, or other heteroatoms. The current ACD/Tautomers algorithm provides only the suggested tautomeric forms, but no...
View Full Document
- Spring '10