How to Use Your Molecular Model Kit
Molecular model kits: every instructor recommends them, many students buy them, but fewer end up actually using them. In this tutorial I want to talk about a few different styles of molecular model kits, their benefits and drawbacks, and how to use them properly.
Spike and Tube Set
The first style I want to discuss is what I like to call the spike-and-tube set. I love and hate this set at the same time. The first thing that jumps out right away is the unconventional colors for the atoms: hydrogen is orange, and oxygen is blue, which is very uncommon. The connecting pieces, the tubes, are also a little flimsy. When I was working with them, they stretch slightly to accommodate the spikes on the atoms, and because of how flimsy they are, they can be fairly easily broken if you bend them too aggressively. On the other hand, a huge advantage of this set is how compact it is. It is barely over six inches in length, which makes it extremely portable. It also comes in a handy little box so that once you are done with it, you can slip it right back in and toss it in your backpack. If you are willing to work with the unconventional atom colors, this set is actually pretty nice.
Polyhedral Set
My second set is a rather interesting-looking polyhedral set. One thing I noticed immediately when I started working with it is that the structures are very snappy and hold their shape remarkably well. With other sets you can relatively easily force a structure out of position, but these are quite rigid and resist being deformed. That rigidity is a real advantage when you are changing conformations, for example doing a chair flip. The flip is smooth and snappy, and you do not have to readjust and fidget with the structure afterward. The biggest issue with this set is its storage: it comes in a little envelope-style pocket, which is essentially a collection of bags inside of bags. The individual connecting pieces are quite small, and when I was building molecules I had already managed to lose a few of them. If you plan to carry this set to class or an exam, that can be a real hassle. But the definite advantage is that it enforces correct geometry, because it will not yield if you try to force it into the wrong shape.
Ball and Stick Set
The last set, and my personal favorite, is the classic ball-and-stick molecular model set. Being my favorite does not mean it is perfect. The way you build molecules with this set is by fitting sticks into holes in the balls, and the fit is not always consistent: some combinations are too tight, others are loose and wobbly, so you occasionally have to experiment with different pieces to get a good fit. Another limitation is that because the set is plastic, conformation changes, like flipping a cyclohexane ring, are not as snappy as with the polyhedral set. You have to work the structure a bit to get it into the right shape, and if you do not already know what the conformation should look like, that can be misleading. From a purely aesthetic standpoint, though, I really like how this set looks and the structures it produces. If you want something that looks good and works well for stereochemical purposes, this is a solid choice. It typically comes in a nice box that may even include instructions for building common molecules, which is handy if you are just getting started with molecular modeling. While it is a little larger than the spike-and-tube set (around seven inches), it is still very portable and fits easily in a backpack.
What’s Inside Your Molecular Model Kit
Now that you have a sense of the different sets, let’s look at the building blocks. For atoms, the standard colors are: black for carbon, red for oxygen, blue for nitrogen, yellow for sulfur, and white for hydrogen. Depending on the set you get, you may also have pieces in green, silver, orange, or other colors to represent additional atoms.
One very important point about carbon atoms: depending on your set, you may have several different styles. The most common is the sp3-hybridized carbon, which has four holes so you can attach four bonds. But some sets also include sp2-hybridized carbons with three holes, or even sp-hybridized atoms. Some sets include a carbon with five holes, which represents an sp2-hybridized atom where you can also attach p orbital pieces. If your set has those less common atom types, I strongly suggest pulling them out and setting them aside right away so you do not accidentally use one in your model, because grabbing the wrong atom will throw your geometry completely off.
When it comes to bonds, there are also several styles. The short bonds are typically used for hydrogens or for space-filling models, where you want the hydrogens to stay close and not take up too much space. The medium-length bonds are your main workhorses for building the molecular framework. The long bonds are specifically designed to be flexible, so you can use them for double or triple bonds, representing π bonds. Those long bonds do not hold their shape well at all, so if you try to use them for single bonds your structure will be extremely wobbly. Always use medium bonds for single bonds and save the long flexible ones for π bonds. Depending on the size of your set, you may also have pieces representing orbitals, though those tend to come only with larger sets. If yours does not include them, that is perfectly fine.
A Few Tips to Make the Most Out of Your Molecular Model Kit
Here is one more tip for getting the most out of your kit. While the whole point is that you can build and rebuild different structures, I recommend pre-building a few key models and keeping them on your desk for easy reference. The three I suggest are: a tetrahedral carbon with four different substituents, a two-carbon fragment (useful for visualizing Newman projections), and a six-membered ring in the chair conformation.
The tetrahedral model is especially useful when you are assigning R and S configuration descriptors, because you can physically rotate it and watch how the priorities follow each other around the center. You will likely outgrow the need for it with practice, but at the beginning it is a real help. The two-carbon fragment is something I find students return to again and again, because you can flip it around and directly visualize what a Newman projection would look like, and rotating substituents becomes much more intuitive. The chair conformation model is invaluable for identifying axial and equatorial positions, visualizing antiperiplanar relationships (for example, seeing that two atoms are antiperiplanar to each other, or that a substituent is antiperiplanar to a particular carbon), and predicting reactivity in six-membered ring systems. All three of these models sit on my desk permanently and I reach for them constantly when working with students.
Whether or not you choose to use a molecular model kit is entirely up to you, but like any instructor I do recommend it. We are not born with three-dimensional spatial intuition; it is a skill you have to build. In organic chemistry, thinking in 3D is absolutely essential, and having a physical model in your hands is one of the best ways to develop that skill.
