Molecular model set

by betawolf, published

Molecular model set by betawolf May 18, 2014


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This is a set of model atoms that can be connected together with flexible tubing to create molecular models. I've created them to assist me in my tutoring of high school students in chemistry. True, these can be bought in scientific book shops, but then they are incredibly expensive. In addition, you never get S+, O+, O-, and N+ to build ozone, sulfur oxides, nitrogen oxides and derived substances.

With this set of drawings, you can print your own, you can freely extend your set if you need more, and with the added SCAD files you can even customize them.

Print Settings

Printer Brand:



Ultimaker Original




.1 mm layer size




190 °C print temp, bed 55 °C with PLA


Print the atoms in different colours. In commercial sets, usually the following colours are used for the atoms:

  • C atoms --> black
  • H atoms --> white
  • O atoms --> red
  • Halogens --> green
  • N atoms --> blue
  • P atoms --> purple (but I used orange)
  • S atoms --> yellow

The difference with a commercial set is that this one also includes an aromatic C6-ring for your phenyl groups, some positive ions (sulfonium, oxonium, nitronium) and a negative ion (oxide). This enables you to also create O3, SO2, NO2, NH4+, etc.

I used an Ultimaker (v1), and a print speed of 20 mm/s, wall thickness 1 mm, temp 190°C, bed temperature 55°C, but still, on the bottom side of the spheres, I have problems with curling edges. Maybe try lower bed temperature and lower print speed. Results may vary for different PLA qualities. I advise to use some support for the overhanging parts. The 'PlusMinus.stl' file contains very small pluses and minuses to print in either black or white. I used these to insert into the plus and minus signs on the ions, makes them stick out a bit more. Simple two-component epoxy resin can be used to permanently fix them in their places. It's a little fiddly and it will test your patience, but it looks great in the end.

To complete the molecular modeling set, I used flexible hoses that can be purchased at a pet store or fish tank specialist. It's 3mm internally, which fits perfectly snug around the 3.2 mm pins. If you have hoses with a different diameter, it is easily adapted in the SCAD file (at the end, a 'pin' module is defined, change the pinradius to half the hose diameter + 0.1 mm). Create

  • short bonds, about 40 pieces of 2 cm
  • medium bonds, about 20 pieces of 3.5 cm (for double bonds)

Enjoy your molecule set.

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Hi, I like very much your work about the molecules and am interested to know what kind of software you used to design them.
And also the angles of separation, how do they come about.
I'm a teacher in a school in Argentina and it would be of great help for a project to do with my students.

Hey, thanks, glad you like the design. I made it in OpenSCAD, an open source 3D design tool. You can build your structures out of simple spheres, cubes, cylinders, and some other custom shapes. It can be downloaded for free and is available in the main platforms (windows, mac, linux) from http://www.openscad.org/.

The angles I took from sources on internet. It takes a little 3D thinking and some knowledge of maths to figure out how the bond angles should be implemented.

I think this is a perfect project for students. I use the molecule set for my own tutoring session of high school students and it is great. When you can visualize molecules, it is easier to imagine how reactions take place, what hydrogen bridges are, what chirality is, etc. Good luck with your project!

Hello! Thanks immensely for the model. I'm fairly new to 3d printing so please excuse my lack of knowledge.

I having an issue where the bottom half of the spheres is coming out really rigid. The top half is perfectly smooth, but the bottom is almost steppe like.

I'm using a Lulzbot mini, HIPS filament, nozzle at 230, bed at 100 (Wanted to go the suggested ones you use, but afraid since it's HIPS not PLA, would have issues).

Any input or suggestions would be greatly appreciated.

It was a pleasure creating the model, hope it serves its purpose well.

Yes, the bottom half of the spheres will give problems, not only on your printer, I also experienced it. Printing overhangs, like the bottom half of spheres or slanted sides, is always a challenge. There are people that have tuned their printing speed, fan speed, type of plastic and nozzle temperature to print these overhangs well, but this is a time consuming and tedious process. You could check user communities for your type of printer, I am sure there are people who can help you tune your printer.

Overhangs can sometimes be minimized by placing the object with a different side on the printer bed, but with balls, that is not possible. Most printer software provides the possibility of putting support material under your object, and you would have to play around with the minimum angle at which the overhangs are supported. I work with Cura in which this is fairly simple. Downside of this method is that you have to remove the support material after printing and your object will have a bit of a rough surface where the support material used to be.

You could also consider cutting the design in two and printing the two separate halves. I've included the OpenScad files, so you can freely change the design, cut pieces off, splitting objects etc. OpenScad has a bit of a learning curve, but if you can program a bit and you are somewhat familiar with object programming, you'll get the hang of it pretty fast.

Regarding HIPS, I can't say I have the experience of using it. The type of plastic you use is definitely a factor influencing overhang printing. You may be lucky and find that PLA gives you less problems.

Hope this helps.

Thank you immensely for all of the information! I've been playing around with the fan and print speed and have managed to get it a little better. I'll take your suggestion and check out the community for the printer I have.

Thanks again!

How about an addition (please!) for dual extruders where the bottom of the letter cutout is a separate object to be printed in a different colour?

That sounds like a great idea, however I have no means to test it since I have no double extruder printer. Also, I wouldn't know how to get it designed in OpenSCAD. The OpenSCAD files are all included in the download, so feel free to use and adapt them and publish (as long as you include a reference to my original design ;-).

I have been playing with them, and added a few atoms like Cl and F. I was thinking of aligning all the sizes to scale with the actual covalent radii.

To use a multi extruder, all you need is for there to be separate objects for each colour. I don't know SCAD well, so am not sure how to approach that. Using Fusion 360, I have done a successful test using a font to cut into a surface, and then extrude back up from the face at the bottom of the cut a part of the way creating a New Body. That needs to be fed into MeshMixer to split the surfaces, then exported as an STL.

Can you share your CL and F file?

Hi there! Sure I can. The way I did it is that a script repeatedly calls the SCAD script and generates all the atoms. I will upload them now....

do you need PeeB's files? I am not sure whether he got your message this way. Maybe you need to contact him directly.

Please see, comment, make and improve! http://www.thingiverse.com/thing:1692457

Molecuar Modelling set
by PeeB
Jun 18, 2016 - Modified Jun 19, 2016
PeeB - in reply to PeeB

Just wrote in SCad for the first time, and managed to get the recess/coloured letter thing to work, albeit perhaps crudely:
rotate([15,20,0]) translate([0,0,atomradius-0.2]) scaledletter("N");
rotate([15,20,0]) translate([0,0,atomradius-1.5]) cube([3.5,5,0.61],center=true);
rotate([15,20,0]) translate([0,0,atomradius-1.5]) cube([3.5,5,0.6],center=true);
I comment out the one to create the pieces with a hole, then the other to create the block that fits in that hole, and export them as separate STLs

I have started to redo this whole idea, using parameterised data drive atomic models, with recessed second colour labels.

I would like to add a tweak to the pins to visually indicate the type of bond, so that for e.g. H2O can been seen to be a lower energy than H2 and O2. Any ideas? A collar around the pin maybe?

wow, you're going further than I did. I like your ideas. To indicate bond energy you could also use differently coloured tubing.

Thanks. For some reasons no photos can be uploaded to this thread, so I stared a 'I made (hypothetical) one' and put some screen grabs from the SCad session. Please see there for more ideas and questions re bond energy... http://www.thingiverse.com/make:230494

Molecular model set
by PeeB

Great! Can you say how you chose the radii?

those were partly based on a commercial set I saw, partly based on convenience (ie. fitting the number of pins)