Last edited 5dec16 by arehma5@illinois.edu
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DOCUMENTATION

OVERVIEW

Goal

The goal of my project was to animate the interconversion of cyclohexane from one chair conformer to the other in VPython in order to better visualize the interaction between atoms and bonds.

Summary

The project was essentially divided into three phases: drawing the main cyclohexane structure, determining the frames of the atoms and bonds relative to each other, and animating the interconversion.

ABSTRACT

The beauty of chemistry is its simplicity. Even the seemingly uncomplicated movement of atoms and bonds often has its own poetry. The fantastic shapes different molecular species conform to often depend on the smallest factors, such as ring strain, electron repulsion, and bond rotation.

Ring strain

Ringed structures are a common occurence in chemistry. An important example is cyclohexane, a humble hexagon of six carbon atoms and twelve hydrogen atoms (figure 1). Cyclohexane is interesting in that its ringed structure is actually as stable as its linear counterpart, which is not true of most other ringed structures.
Figure 1. Cyclohexane
Atoms and bonds twisting cause strain on the molecule, so the molecule will adjust to a conformation that minimizes that strain. The ideal bond angle is 109.5°, as illustrated by the methane molecule (figure 2). This angle minimizes strain.
Figure 2. Methane
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The table below describes several ringed structures in chemistry, as well as their bond angles. Molecules like cyclopropane and cyclobutane have bond angles that deviate so greatly from the ideal that they are highly unstable in nature. These molecules are incredibly reactive. Cyclopentane is closer to the ideal bond angle of 109.5°, which is why it is stable. Cyclohexane, however, is incredibly unique in that it exactly matches the ideal bond angle. This ideal bond angle gives cyclohexane many unique properties.
Table 1. Bond angles of various ringed structures
Structure Name Bond angle
Cyclopropane
60°
Cyclobutane
90°
Cyclopentane
108°
Cyclohexane
109.5°

Electron repulsion

Another factor in determining conformation is electron repulsion between atoms. It is known that molecules will conform to certain shapes in order to minimize the electron repulsion between atoms. By minimizing these repulsions, the molecule also minimizes its potential energy.
Figure 3. Ammonia
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Ammonia also has four groups around the central atom, but one of these groups is a lone pair. This lone pair repels the electrons in the hydrogen atoms, leading to bond angles of approximately 107°. Although this deviates from the desired 109.5°, ammonia is still stable because electron repulsion was minimized. Thus, electron repulsion can cause a deviation in bond angle that still allows for stability.

Bond rotation and chair interconversion

Single bonds between atoms are relatively flexible, which allows the bonds to rotate and move. The most visible example of this movement is the chair interconversion, which is a special term to describe the concerted movements of carbon bonds in the cyclohexane conformation.
Figure 4. Chair interconversion
This interconversion is interesting, as the movement of atoms can actually become quite complicated, especially if there are more molecules attached to the carbons on the main structure, as in the figure above. I chose to focus my project on this interconversion, in order to animate the complex movements.

WEEKLY PROGRESS

Week Progress
1-7
 Introduction to DPGraph, LaTex, and basic programming ettiquete. As a complete novice, this is very interesting to learn, but it also feels like I am studying three different languages at once. Slightly intimdated.
8
 Assigned to VPython and debating between working with sound waves or some sort of chemical structure. Picked cyclohexane and chair interconversion because we are learning about it in organic chemistry and it interests me.
9
 Getting a feel of VPython. Language is actually very straightforward to work with, and I feel like I'm getting a deeper understanding of the program.
10
 I made a cyclohexane molecule! It only took me 4 hours!
11
 Trying to figure out frames between bonds and atoms. A bit tricky, but just need to stay organized with respect to the frame and the other atoms.
12
 Figuring out frames and preliminary animations. A bit stressful. I feel behind.
13-14
 Finalized frames! Stress is almost over.
15
 Animation done! Not as hard as I thought, probably because having the frames made it a lot easier and faster.