Space-filling molecular models: Transition Metal expansion pack by Harfigger

Last crawled date: 3 years, 3 months ago

This expansion set is at the request of wramsay, and a shout out for the request; it shows someone is interested. The transition metals are most of the metals that we think about as "metal;" that is, hard, shiney, and present in pure form (the period I and II metals are much too reactive to exist in pure form normally). The transition metals can form more bonds than you might expect because of their distinctive electron configuration; they can also form these in different configurations. I have included models for octahedral iron, tetrahedral copper and square planar platinum, but the truth is that most of the transition metals are about the same size, so you can use these models for pretty much any transition metal you like with the same configuraton. "OK, those don't look anything like your other atoms; they look more like plumbing fittings" I hear you exclaim. Yes, that's because they're not actually atoms; they're ions. My models are based on two measurements; the bond radius, which describes the electrons involved in the bond, and the Van der Waals radius, which describes where you will find the rest of the electrons. Practically all transition metals form compounds as positively charged ions, therefore the electrons are attracted closer to the nucleus and the Van der Waals radius is smaller than the bond radius (in fact it just fits in the enlarged hub at the center of the model). "I'll pretend I understood that, but do they really look like that?" Well, probably not. The electrons from the adjacent atoms probably fill in the extra space, so the model of copper chloride on the right is probably more accurate than the one on the left. That chlorine model doesn't play well with the other atoms though (it's also harder to print), so you're probably better off using your imagination. Nitroprusside is a medication sometimes used for high blood presssure. Cisplatin is a medication used to treat cancer. Heme B is the business end of hemoglobin and most other enzymes where you have a change in oxidation state. Other enzymes that change oxidation state often use iron-sulfur centers. These come in different flavors; I made the one with four irons and four sulfurs because it looked cool. The bond angles for the tetrahedrally bonded iron aren't all the same; the three off the build platform are different from the last one. See Moriarty and Adams, Acta Crystallographica D75:16-20 (2019) for more information. I should mention that I don't usually work with transition metals, so I may have gotten this slightly to spectacularly wrong. If so I would appreciate being corrected; references would be helpful. In addition to the metal models I have included the tri-valent sulfur for the iron-sulfur center, the spherical chlorine atom, and the aromatic linker that joins the four pyrole groups for heme B.
if you decide you want to print more molecules, check out the starter set (http://www.thingiverse.com/thing:1720048
), the carbon expansion set (http://www.thingiverse.com/thing:1730299
), the aromatic expansion set (http://www.thingiverse.com/thing:1754393
), halogen expansion set (http://www.thingiverse.com/thing:1730099
), nitrogen expansion set (http://www.thingiverse.com/thing:1753583
), and sulfur/phosphorous expansion set (http://www.thingiverse.com/thing:2350618