Web applications in KemiKS: Quiz and Hückel

This week, we have tried three new visual features in KemiKS.

a) The students were strongly encouraged to use Maple in the solution of one problem, where they are supposed to draw the wavefunction of the hydrogen molekyle ion. This exercise was previously solved by hand, but now was supposed to be solved by using Maple. The students responded positively to it, although they had lots of problems in remembering how to use Maple. But when they finally had plotted the wavefunction, they really liked the fact that they now had created themselves the figures shown in many textbooks.

b) Janus had found a website at http://undergrad-ed.chemistry.ohio-state.edu/H-AOs/index.html, with a good discussion of atomic orbitals up to f-orbitals and a nice quiz. The student were asked to do the quiz in the first exercise class on monday as a repetition of what they had learned in the week on atomic orbitals. We will later in week 7 follow up on this idea and give the students in the beginning of the week a quiz on the key points of the week, which they probably will not be able to answer. At the end of the week, the students will then repeat the quiz and hopefully can see what they have learned in this week. Janus will look for appropriate tools in order to make a quiz with high score and solutions outside of Absalon.

c) as illustration of the discussion of the Hückel method, we have now incorporated two java based Hückel programs (see description in previous blog), which can be run over the net or can be downloaded and run directly on ones computer. This was thought to have the big advantage that we can study much larger systems, which previously were out of question, when one had to diagonlize the Hückel matrices by hand. The students were then asked to use these tools in two of the problems of this week. One problem was newly made and the other was modified so that the students now use these Hückel programs instead of doing it by hand. Talking to the teaching assistants helping the students the response is mixed. On one hand the Hückel programs are nice tools, but the danger exist that the students loose the understanding of how the Hückel matrix should look like, because in these Hückel programs it is generated automatically for them after drawing the molecule in the GUI. Therefore, it might actually didactically more effective to let the students write down the Hückel matrix by hand and then use Maple to diagonalize it, which is without computers typically the limiting factor or to have to exercises: one with the Hückel matrix by hand / Maple approach for a medium size molecule and one with the Hückel programs for a large molecule.

Two Java-based Hückel Theory programs

I here share two examples of online Hückel approximation programs. The first is located here and denoted a) in the following, while the second example, b), may be found here. Please note, that b) may be slightly unstable towards refreshing the site but may still be adequate from a teaching point-of-view, though, as it is readily downloaded as a Java-file. Update: Program a) is available in a newer implementation here (thanks to Rafael R. Pappalardo for pointing this out in the Comments).


a):

The first program is indeed very intuitive in the sense that a molecule is easily sketched on the designated canvas and the calculation carried out by clicking just a single button on the right side of the screen. The individual carbons are marked on the canvas by initially clicking the 'Add' button to the left and subsequently placing the atoms by clicking the mouse at the appropriate locations. The bonds (only one type of bond exists, more on this below) are made by dragging a line between two adjacent atoms, equivalent to GView, Avogadro, Jmol, etc. When the molecule has been build and 'optimized' by clicking the 'Normalize' button in the left column, the calculation is made by clicking the 'Show Data Tbl' tab at the upper right corner. The results of the calculation now appears in a seperate window, divided into:

• MO number
• Orbital energies
• Occupancies of the individual MOs
• Population tables
• Bond tables w/ appropriate Hückel bond orders

This program furthermore enables the option of illustrating the MOs. A MO diagram is build 'on-the-fly' as the user builds the bonds between the individual atoms, and by clicking the 'Show Molecule' tab in the lower right corner, the MOs are shown in accordance with the MO diagram. Note here, that the orbital energies are shown in the lower part of the screen when the user shifts between the individual MOs by clicking the 'Up' and 'Down' tabs next to the 'Show Molecule' tab.
As touched upon in the above, this program only offers sp2-hybridized orbitals in accordance with regular Hückel theory. The bonds may be altered, though, in an indirect manner, as the alpha- and beta-parameters are modifiable.




b):

As this program has shown to be rather unstable towards running directly from the browser, I would recommend downloading it by clicking the download link below the applet. The file is just a regular .jar file but advantages with respect to the browser applet in the fact that it is faster and more reliable. Furthermore, I will not comment on the Lewis part of the program, only the Hückel part.
In this program, the molecule is build following the same guidelines as for program a). Press 'Build' and draw on the canvas. As bonds are generated automatically in this program, the MO diagram to the right is dynamic as is the total energy, shown in the left column. By pressing the 'Results' button to the left, a seperate window appears, including:

• The Hückel Hamiltonian (in contrast to program a)). Note that the form of the matrix is in accordance with the numbering within the molecule and may thus not resemble the expected.
• The orbital energies in terms of the alpha- and beta-parameters.
• The electron density matrix.
• The atomic charges as well as the total charge.

As in program a), the degree of hybridization may be altered but in a fancier manner. By clicking the box 'Parameters' in the left side column, and subsequently clicking on one of the individual carbon atoms, the program lets the user change the atom type and hence the final Hamiltonian, etc.
UPDATE: As pointed out by Markus in the comments, you can also display MOs in HuLiS by clicking on specific MO's on the energy graph. Thanks to Markus for this comment.

Topics:

- Benzene: Use this link (see below) to illustrate the benzene MOs as a supplement to the MOs from program a).
Edit. As Jan mentions in the comments, this section of chemtube3d also serves as a great tool of visualization for the MOs of benzene.


- Naphthalene vs. Azulene. Calculate the differences in the HOMO-LUMO gap. Why does these differences exist and why is azulene dark blue, while naphthalene is colorless?

- Why is it impossible to design and describe 1-methylnaphthalene within the ordinary Hückel approximation? What is the 'Hückel equivalent' to 1-methylnaphthalene?

- Topic of discussion: If we really were to attempt a description of 1-methylnaphthalene, how could the program be manipulated (Hint: Think in terms of alternative ways of describing hybridization).