2D Molecular Modeling
To download the molecule builder, click here.
(You can save
the molecule builder program to a folder on your computer so you do not have
to follow this link every time you want to draw some molecules.)
If you do not see the
menu and drawing template after you have downloaded m-builder, you will need
to check that you have downloaded and installed
the proper version of the Java plug-in applet needed to run this program.
to Use m-builder
Here is a brief summary of how to use m-builder to draw
The m-Builder Menu Options
Once you are in the site the first time, you may be asked enter
your name and ID number: Before you get started you may wish to read over these
examples. You may choose 4 types of molecular drawings: Atom Spheres,
Ball & Stick, Lewis (electron dot),
and Ion mode models. Click on each of the choices to see how the water
molecule would be drawn in each of these modes.
Make a selection and click OK. You will be taken to the drawing template
used for that mode. (See the first example below.) I'll give an example of how
the ammonia molecule, NH3, could be drawn in each mode. Let's start
with the atom sphere mode. (At the end of this tutorial are instructions on
how to "Save" the drawings for later viewing.)
Atom Spheres Mode
To create the molecule, simply click on any one of the 9 atoms of and "drag"
it into the workspace by clicking on the atom and holding down the left button.
A sense of "bonding" between 2 atom spheres will be seen in the overlap
of the atom spheres. (It is up to you to decide where to place the atoms with
respect to each other.) To create a picture of a chemical reaction, you can
drag and drop the Plus and Arrow symbols found at the bottom of the template.)
Ball & Stick Mode
To create ball and stick models, drag and drop the atom spheres as described
above. To add a single bond beween any 2 atoms, click on the first atom, and
press the Alt key while clicking on the second atom
of choice. Repete this to create a double bond; the third time, a triple bond.
Use the Delete key to remove a bond.
Electron Dot (Lewis) Structures Mode
To create Electron Dot (Lewis) structures, drag and drop the element symbols,
electron pairs or single electrons located at the bottom of the template menu.
As you click on an element you can see the circular region in which the electron
pairs might reside. As you add non-bonding electron pairs, they may "flip"
to stay within the element's boundry circle. You can also add or subtract electrons
from the Edit menu.
The Ion Mode
The left-hand panel looks a lot like the Lewis Structure mode
above except there are no electron dots at the bottom of the panel.
In this mode you can create ions by placing a charge as a superscript (cations
and anions) and write chemical formula with subscripts. A few representative
elements, as in the Lewis structure mode, are found in the panel. You can access
additional representative elements from the edit menu.
Selecting this option, brings up a periodic table containing
elements through the first 5 periods. (Sorry no transition elements.)
In this veiw we have dragged and dropped the elements bromine and calcium.
The last species placed in the workspace will be surrounded by a circle. It
will disappear when you click anywahre outside of the element symbol.
We will now show you how to place a +2 charge as a subscript
on the calcium; and a 2- charge on an oxygen to make an oxide ion. First close
the periodic table, then click on the number 2 in the number keypad at the bottom
of the panel and drag it until you see a small circle in the place where the
subscript is likely to be placed. (Sometimes difficult to spot this small circle.)
When you click outside of the element symbol, the circle will
To change the sign of the subscript, you must click on the negative
sign (-) at the bottom of the number keypad. You can toggle between positive
and negative charges.
You would then drag and drop the negative number on to the superscript location.
Here we show the generation of the oxide ion - that has a -2 charge.
Subscripts can be introduced in the same way as superscripts;
again you must place the number in the small circle to the lower right of the
A table of the formulas of polyatomic species - without the charge indicated
- can be accessed from the Edit menu.
There is a limit to the number of available formulas. You can move the polyatomic
template around. The polyatomic formulas can be dragged and dropped into the
You may then add superscripts or subscripts. For complex polyatomic formulas,
parentheses will be introduced.
You may have times to write ionic equations in which some of the ions are
considered spectator ions. These are ions that are found on both sides of an
equation. An example might be the sodium and chloride ions that comprise the
species in the reaction of hydrochloric acid with sodium hydroxide. The spectator
ions are identified by placing a green circle of dots around them. You can drag
the circle from the panel.
The File Menu
There are a few other things you can do using the menu at the
top of the page. Let us start with the File Menu.
Once you have created a drawing, you will want to save it to folder in your
computer. I recommend clicking on the last save option, Save for
Submission. (See below for the other options.) This will save
your drawing as a png image file.
The name supplied when you first ran the program will be given as a default
name of your drawing. You will want to change the name to better describe your
molecule. Select a folder in which to save it, and then click the Save
The selection of the Save, or Save As...
will save your drawing as a xml image; be sure this
is a file you can use. However, this image can be opened up later if you want
to modify it.
File New will take you back to the menu so you can
start a new drawing or another type of drawing. File Open
will allow you to retrieve a previously saved drawing.
The Edit Menu
The first 4 selections (plus the keyboard shortcuts) available in the Edit
menu are self-explanatory. (If not, let me know.) Under the Options...
you may now change the size of the build area.
The Help Menu
The Help About pretty much covers
what you are reading now. The Ion Mode help may not be up to date.