Drawing Structures Using JSME

This page provides instructions on drawing chemical structures in JSME.  More detailed help can be obtained by clicking here, but the information provided here is adequate for use in this site.  

How To Use This Page

Read the notes below on how to draw and edit structures in JSME.   Then try the exercises at the bottom of the page to check if you have mastered the use of JSME.

Learning Objective:

  • Draw complex organic structures in the JSME molecular editor.

Drawing structures in JSME is a straightforward two-step process:

  1. Choose the bond drawing and ring drawing tools from the menu and click in the drawing window to draw the bonds; C-C bonds will be drawn by default.
  2. Choose the element and functional group tools from the menu and click on the ends of bonds in the drawing window to convert C atoms into other elements, or into some common functional groups.

The procedure is described in detail below.

The bond & ring drawing tools are outlined in blue in the figure.

  • To draw a bond click on the single, double or triple bond tool and then click anywhere in the drawing area.   To add another bond click on one end of an existing bond.
  • Bonds will be drawn at conventional angles by default, but if you click on an atom and drag, you can draw the new bond at any angle.
  • Stereochemistry can be shown by using the "wedged" tool. Click again on a "wedged" bond to convert it into a "dashed" bond.
  • Convert any type of bond (single, double, wedged, etc.) into any other by selecting the desired tool and clicking on an existing bond.
  • The chain drawing tool easily creates a chain by clicking in the drawing area, or on an existing atom, and dragging the mouse to draw a chain of the desired length.
  • Test yourself by trying Exercise 1 below.
  • Ring systems can be drawn in a similar way by selecting the relevant tool and then clicking in the drawing area, or on one end of an existing bond.
  • Selecting a ring tool and then clicking an existing bond will create a "fused" ring system.
  • Test yourself by trying Exercise 2 below.

The element and functional group addition tools are outlined in green in the screenshot.

  • Carbon-carbon bonds are created by default.   To add other elements, click on the relevant tool and then click on one or more existing atoms.   the keyboard shortcuts listed on the right provide an easier way to add elements other than carbon.
  • A number of common functional groups can be added using the functional groups tool.   Experiment with this tool to see how it works (an issue with JSME means that it only works properly if Firefox is used).
  • Test yourself by trying Exercises 3 and 4 below.

The editing tools are outlined in red in the screenshot below.   They are self-explanatory.

JSME tools

Keyboard shortcuts are very convenient alternatives to selecting the corresponding tools with the mouse.

  • Atoms: Position the cursor over an atom and type C, N, O, P, S, F, L (for Cl), B (for Br), I, H, or R.
  • Rings: Type 3…8 for 3 to 8 membered rings, or 1 for phenyl, and draw the ring in the usual way.

Choose an Exercise.

Exercise 1
Exercise 2
Exercise 3
Exercise 4

Draw this molecule in the JSME editor.
Draw it as shown, do not draw any C-H bonds.


When you are finished:

ChemInteractive

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