This section deals with how we can use VRML to represent chemical data, especially molecules, electon system etc. Although the language is less than ideal for use in drawing molecules, we can still create educationally valuable models. Below are some examples of how the basic shapes available to us can be combined to create these. All of the examples include the VRML files for you to view. To keep file sizes to a minimum, the VRML are not commented, but several have a seperate page explaining the nodes used ion the scene.
Atoms are very easy, and can be represented by a sphere as in the ball-and- stick model often used. You could represent the nucleus by a small solid sphere, and if necisary, use a second semi-transparent sphere to represent the electron cloud around it.
Example 1: A single sphere to represent an atomElectron orbitals are also relatively simple. "s" orbitals can be represented by a single sphere. "p" orbitals can be constructed by using a cone and ball combination to create a teardrop shape, and using two of these to construct the orbital. 4 of the "d" orbitals (d(x2-y 2), d(xy), d(yz), d(zx)) can be constructed by combinations of teardrop shapes, as used in the "p" orbitals. The d(z2) orbital is a little more complex due to the "rubber tyre". This can be approximated by the use of a very squashed sphere.
Example 3: An s orbitalHybridisation of atoms is no more complicated than atomic orbitals, and you can use the same teardrop shape as you use for p orbitals. The only slight complication is that angles of 109 degrees for example have to be used, instead of just 90 and 45 degrees.
Example 7: An sp2 hybridised atomSigma bonds are easily represented by a simple ball-and-stick method, where the ball is drawn by a sphere, and the stick by a cylinder which has the center of each cap in the center point of the sphere.
Example 9: A simple diatomic moleculePi bonds are harder to represent than signma bonds for obvious reasons. One way to show a pi bond is to show the two p orbitals, and then to build a semi-transparent cylinder between them. The p orbitals can be constructed in exactly the same way as they are in exaples 4 and 5.
Example 11: An N2 (nitrogen) molecule (which has one sigma and two pi bonds)Larger molecules present many problems, the main one being their complexity. Creating a VRML file manually for something like Asparin would take a huge amount of time and patience, and even this is a relatively small and simple molecule. In order to create VRML files for large molecules, you would really need to use a software tool which did most of the work for you. Such tools are few and far between at the moment. As far as the representation of such molecules, the ball-and-stick method can become unsuitable for large molecules, and instead the use of nothing more than cylinders for the carbon skeleton, and ball-and-stick models for the functional groups could be one alternative. Other methods posible inlcude using nothing more than spheres for each atom, the radius being propotional to the covalent/ionic radius of the the atom.
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