Space-filling molecular models: Sulfur and Phosphorous expansion pack

thingiverse

This expansion pack lets you create compounds that contain sulfur and phosphorous, which, when combined with other packs, will give you almost everything you need to make most biological molecules. Sulfur sits just below oxygen in the periodic table, and like oxygen, it generally forms single bonds with two other atoms at an angle. This angle is typically around 96 degrees, but it can be many others. The sulfur you'll need for most biological compounds (Sulfur96) is what I've shown; the example I provided is ethanethiol, which is the chemical they put in natural gas so you can tell if it's leaking. Sulfur can also have up to two oxygens double bonded to it. The most common example of this is sulfate (Sulfur2), which I've shown as sulfuric acid. Sulfur can also form bonds with just two double-bonded oxygens, resulting in sulfur dioxide (Sulfur120). In this molecule, the oxygens form a 120-degree angle; many other sites will explain why this happens so I won't bother. You can also have one extra oxygen bonded to sulfur. The only example of this that comes to mind is dimethylsulfoxide, or DMSO. "What is DMSO?" you might ask. DMSO is an extremely useful solvent that can dissolve most medications; it works so well that many researchers use it when another solvent (like water) would be better. DMSO readily penetrates the skin and anything dissolved in it, such as a drug. While this sounds like a great way to avoid injections, DMSO tends to give you bad breath, so it's not used much. By the way, since this is the only molecule of its type I can think of, I set the sulfur up to make DMSO exactly (SulfurDMa). So if you really want to make DMSO, you know how to do it. Sulfur also forms aromatic compounds, generally having five-membered rings (the example I show is thiophene). I'm afraid I cheated a bit here; sulfur is actually quite large and distorts the other atoms in the ring. Because I didn't want to remake all the other atoms, I just distorted the sulfur (SulfurPh5b) to give you an idea of how much space it takes up. If someone's thesis depends on this being right, we can talk. As another example of sulfur compounds, I have included sulfathiazole, which has two sulfurs in different chemical environments. Sulfathiazole is an antibacterial agent that isn't used much anymore but has a surprising number of references in popular literature. Phosphorous is almost exactly like sulfur; it sits just below sulfur in the periodic table and generally forms single bonds with two other atoms at an angle. The phosphorous you'll need for most biological compounds (Phosphorus96) is what I've shown; the example I provided is a molecule that has two phosphates bonded together. Phosphorous can also have up to two oxygens double-bonded to it, resulting in phosphate (Phosphorus2). In this molecule, the oxygens form a 120-degree angle. I haven't deemed oxygen worthy of its own expansion pack because most oxygens look pretty much the same; they can bond two other atoms at an angle. For most alcohols and ethers, that angle is about 107 degrees. For water it's 104 (I haven't included it because you can only use it to make water). But I did include one oxygen (Oxygen3S) with a slightly different shape so it would look better bonded with sulfur. I tried to use it to make pyrophosphate, but the phosphates just wouldn't go together. So I looked it up and found that the dihedral angle for oxygen binding two phosphates is between 126 and 129 degrees (OxygenPP2). When I made that, they went together perfectly. This expansion pack includes many other oxygens with different angles, including one with a 117-degree angle (Oxygen117) that's perfect for attaching to the ribose of ATP. The fun thing about 3D printing is that when you need a different oxygen, you can just make it (I've heard some people have a different definition of "fun").