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5.02.1 Chemical Sketcher Widget

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Quick Links:

How to Import a .Mol File

How to Export a .MOL file from LabArchives

 

INTRODUCTION

This is the Chemical Sketcher widget. You can use it to draw bond-line representations of molecules and molecular reactions.

Drawing a Structure

You can draw a structure atom by atom using the Point-Drawing tool. Any atom of any element can be placed on the canvas with this tool.

 

To change the element selected, open the drop down by clicking the arrow on the right. You can select from any element on the periodic table, as shown below.

 

You can also draw bonds between atoms with this tool.

The bonds themselves can be modified with the bond line tool, shown here.

 

To modify the charge on any atom, use the Charge tool, as shown here. You can modify the charge as positive or negative by opening the drop down menu to the right of the charge icon. You can also add radicals and lone pairs using this tool.

 

You can quickly build more complex structures by using additional tools available in the canvas. These are the Carbon Chain tool, the Cyclic Builder, and the Molecular Templates.

Using the Carbon Chain tool, you can quickly construct a hydrocarbon chain with as many carbons as you can fit in the canvas.

 

 

Using the Cyclic Builder, you can quickly add cyclopentane, cyclohexane, and benzene rings right onto the canvas. You can then add more fused rings if you wish, or use other structure editing tools to modify the rings as needed.

 

Using the Templates Database, you can add entire named structures quickly to the canvas. A number of structures are already available to you and are organized into separate chemical categories.

 

In addition to the above tools, you can save entire molecular structures to your local hard drive and re-load them to the Chemical Sketcher Widget canvas later using the Save MOL file and Load MOL file tools. See information on how to import and export MOL files below.

 

Drawing a Reaction

 

Once you have drawn your structures, there are a variety of other tools you can use to help annotate your structures and construct a cohesive representation of a chemical reaction. These tools include the Text Annotator, the arrow tool, the Flip Structure tools, and the Copy/Paste Structure tools.

 

Using the Text annotator, you can label structures, describe reaction conditions, and do any other number of things that can be shown in linear text.

You can also write some chemical formula (eg ‘C6H12O6’). When you do this, the text will automatically format itself with the proper subscripts (in this case ‘C6H12O6’ becomes ‘C6H12O6’).

 

Using the Arrow Tool, you can draw arrows of several different types to help represent the different steps of your reaction. Many types of arrows, including curved arrows, straight arrows, equilibrium arrows, single electron, and electron pair arrows are available.



Using the Flip Structure tools, you can flip any selected molecule vertically or horizontally. This can help you position molecules for some reaction more easily.

Using the Cut/Copy/Paste structure tools, you can more easily move and replicate structures. You can quickly add many copies of the same structure if needed.

 

Adding a Stoichiometry Table

Stoichiometry allows you to understand the relative quantities of each substance that takes part in a reaction or a compound that is formed – as making these calculations by hand can be time consuming and can be error prone. After drawing a chemical reaction, you can create a stoichiometry table to quickly calculate multiple parameters of the reaction drawn. To create your stoichiometry table, click the ‘Create Stoichiometry Table’ button.

Two tables will appear. One for Reactants and one for Products. These tables serve as forms that help you calculate different values for a reaction. They are self-calculating, chemically aware and will maintain proper balancing while editing.

Hover over and click on a cell to see a pop up where you can enter a value and unit. By default, the Formula and Molecular Mass will automatically be filled for you. Note: Some fields may be unitless.

After defining a value and unit, press the enter key on your keyboard or click anywhere else in the widget. The form will self-calculate and update. Note: You cannot edit the values for the Formula or Molecular Mass cells. These are defined by the reaction.

In some cases, you may encounter flagged results that will appear as red in the table. These are caused by uncertain/incorrect user input.

Clicking ‘Create Stoichiometry Table’ after a table has already been generated will produce a window with an option to overwrite the current table. Overwriting the table will reset the table and clear all values from the cells.

You can remove the tables by clicking the ‘Remove Stoichiometry Table’ button under the chemical sketcher canvas. Doing this will clear all the values from the cells.

Searching Chemical Structures

See this article to learn more about how to Search Chemical Structures contained in Widgets or attachment entries.

Import a .MOL file

It is possible to import a .MOL file into the Chemical Sketcher Widget or export them to another application.

.MOL files are a fairly standard way to represent molecules. Although there are other common file types, most chemical programs can handle .MOL files.

In LabArchives, you can follow these steps to import a MOL file:  

1. Copy the .mol file to the clipboard. Here is an example of a MOL file:

Guanine.txt

2. In the “Add Entry,” toolbar click Widget. It can also be under the “More” option & select the Chemical Sketcher widget.

3. Click the folder icon to open the Load Molecule dialog window. See below for elaboration

4. Paste the MOL file into the dialog screen. 

5. Click the “Load”  button.

6. The Chemical Sketcher will convert the .MOL file into a figure that will appear on your canvas. In the example .MOL file we used, the resulting structure appears as shown below


7. In order to add this as a permanent entry into your notebook, be sure to click “save to page”.

Export a .MOL file from LabArchives

If you create a molecule in LabArchives using the Chemical Sketcher widget and want to use it in another program,

  1. Click the Save icon to open the Save Molecule dialog (just to the right of the Open Icon, shown above).
  2. Copy the .MOL file to the clipboard and paste into another application (Notepad works well). Save your file.

Embed an image into your notebook

If you want to embed a molecule image into the Rich Text Editor (RTE), one of the most reliable ways to do this is to take a screenshot, then use local image editing software (Microsoft Paint or equivalent) to crop out the molecule from the screen capture, then copy/paste into your Rich Text entry.

Chemdoodle chemical sketch chemdoodle chem doodle ChemDoodle

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