3D Molecular Modeling with MarvinSketch
To start click here
(Allow a few moments for the program to load. If the Sun Java plug-in is not already installed on your computer, you will be asked if you want to download and install it.)
For a run-through, follow these steps to create this 3D model the methyl amine (CH3NH2) molecule:
1. First open the MarvinSketch workspace:
For a quick overview, once you open MarvinSketch, you can either click on the Quick Help option in the menu, or you can look over the brief tutorial that follws to cover some of the basics.
2. Next, click on the methane picture and drag to create an ethane molecule:
3. Click on one of the carbons
and create bonds to the CH3 groups to create
the (CH3)3CH molecule.
4. Click on the nitrogen (N) on the menu; and then click on the central carbon to create the (CH3)3N molecule.
5. Now click on the hydrogen (H) and replace the carbon atoms in two of the CH3 groups with hydrogen atoms to create the CH3NH2 molecule.
6. You have now created the molecule and can now view the molecule in 2 dimensions or 3 dimensions. Go to the View menu choice and and open the 2D viewer.
You will see a 2D view of the molecule.
Let's include the lone pair electrons in this molecule, and display the molecule as a ball and stick model. Two menu selections are required to do this.
Note that the CH3 group is shown as a large sphere; the two smaller spheres are hydrogen atoms. Since this is a 2D display, you will not see the proper geometry. Exit this view (Select File-exit from the menu, or click on the X on the upper right-hand corner of the window) and select the the Open 3D View. Add the lone pairs as before. You will get something that looks like this:
(The lone pairs of electrons are still there even if you don't display them.) You can now rotate the molecule or create an animation. Try it. You can change the background color.
Try some of the other options. For example, calculate the molar mass or some other property. After you have created a molecule you want, click on the File Save.in
There are a variety of image file types. Select one, and after saying OK to whatever you accept in the Image Export Options window (I usually accept the default), name and save your image in a folder on your computer.
Piece of cake!