April 2020: Update and sneak peek

Hi All – sorry for the hiatus, a lot has happened in personal life since starting this blog and my challenges of printing all the space groups/zeolite topologies have been delayed slightly!

I am delighted to say however that there is now progress! I have started a new(ish – been there since October) job at UCL and will be getting a SLA printer as soon as I can to carry on with the space group challenge. I will also be carrying on with the zeolite challenge (biweekly) and will be starting a new ‘Curiosity corner’ (weekly) where I share the stories and images of some of the weird and wonderful materials I’ve collected over the years.. Watch this space!

Stay safe in these strange and uncertain times, B.

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Faujasite (FAU)

Tl:dr: Here is the printable STL: https://www.thingiverse.com/thing:3676897

Part two of our zeolitic exploration and it is on to one of the most important ones. If you drive, fly or do anything relying on petrol or other short-chain hydrocarbons, then you have faujasite to thank.

Faujasite is a naturally occurring zeolite with sodium (Na, the most dominant), calcium (Ca) and magnesium (Mg) forms. It was first discovered in the early 1840s in Germany and forms exquisite tiny crystals (see: https://www.mindat.org/min-35126.html ). It is one of the key components of a hugely important process called ‘Fluid Catalytic Cracking’ (FCC) which is used to convert crude oil into petrol and other short-chain hydrocarbons we currently use for energy storage and fuelling our cars.

It also has a gorgeous structure, formed of sodalite β cages (like zeolite A: https://crystalprint.home.blog/2019/05/11/zeolite-a-lta/ ) connected by double six rings (d6r):

Gif of FAU framework, sodalite β cages in purple, double 6 rings in blue. The sodium or other extra-framework cation would sit in the pores/holes.

Rare in nature, this structure is commonly used as it’s synthetic versions zeolite X or Y both commonly used as absorbents or as previously mentioned, catalysts.

Right you are now probably thinking – what is the difference between X and Y?

Well these are both synthetic versions of faujasite, discovered by our old friends Robert M. Milton and Donald W. Breck of the Linde Division, Union Carbide Corporation back in the 1950s (along with zeolite A). Zeolite X has a very low silicon to aluminium ratio, the less aluminium, the higher the charge on the framework, the higher the charge on the framework, the more extra-framework cations like sodium or calcium are needed to balance the charge (remember, basic rule of chemistry – everything wants to be stable). So zeolite X is great for cation exchange and can effectively be tailored for different reactions by swapping in and out cations.

Zeolite Y has a much higher silicon to aluminium ratio so it is more stable at higher temperatures and used in FCC.

The print:

I won’t go through the structure modification process here – if you are interested about how I make the models check out my zeolite A post: https://crystalprint.home.blog/2019/05/11/zeolite-a-lta/

After getting rid of some rogue double 6 rings we get something like this:

FAU framework viewed down 111 axis, purple polyhedra are the sodalite β cages, light blue polyhedra are the double 6 rings

Looks gorgeous doesn’t it? Like a strange fractal flower. Imagine trying to make this without a 3D printer, I’m always in awe of the craftsmanship in jewellery or other intricate designs. When I was younger I wanted to be a jeweller – maybe I should look into it again!

Put through our slicing software, rotated and scaled up 130 % we get the following:

Which I’ve uploaded to thingaverse as: https://www.thingiverse.com/thing:3676897

It prints beautifully, after 10 hours a very little post production work we get this:

Success! The printed FAU framework.

I’ve been talking a lot about sodalite in this and the LTA post, so I think with the next post I might take a break from zeolites and try my luck with some unusual filaments and the sodalite structure.. Stay tuned!

Snapmaker down!

Tl/dr: If you are using a Snapmaker – I recommend re-tightening the screws frequently otherwise it will shake itself apart!

Picture the scene: It’s morning, I’m sat downstairs sipping a warm cup of yorkshire gold tea. The soft hum of my Snapmaker 3D printer is in the background as it works its way through the next print (Faujasite). It’s mechanical rhythm oddly soothing against the backdrop of bird song and the distant roar of an A road. Suddenly the song changes. The soothing mechanical purr is no more. Instead a deep, thumping, screech comes from up the stairs. I spring into action. Taking the steep, carpeted steps two at a time, yanking myself up using the wobbly banister I make it upstairs. I dash into what we call the ‘Student room’ and find the Snapmaker doing it’s best impression of a CNC machine with it’s hot end.

The print is ruined.

The beautiful print plate is scraped (brass is harder than aluminium). The heating block is dangling out of the bottom of the FDM (Fused Deposition Modelling) head.

My tea is cold.

This could happen to you!

So what happened?

I’ve noticed in the nearly a year I’ve been working with the Snapmaker that it slowly shakes itself apart, so am always tightening external screws. I didn’t think the internal ones would be as susceptible. I was wrong.

One of the grub screws holding the print head in place to the heat sink had come loose, dropping the heating block, causing a homing error which caused mass destruction.

Print head from Snapmaker with casing removed – hot end (blue arrow) with thermocouple (white cable) and heating element (red cable). The offending grub screw is identified by the green arrow recessed in the heat sink

Luckily I’ve discovered that the Snapmaker is pretty good for user repairs (I’d previously junked a old heating block due to filament being forced back inside) and after opening up the case (above) I quickly found the loose grub screw. It’s printed a couple of test prints beautifully now so is now re-printing the P2 space group example as I type.. Wish me luck!

P2 – Thomasclarkite-(Y)

Welcome back! Two down, 227 to go. Gulp.

The first two space groups were pretty simple prints (although my post-print work was a little shocking – if only someone would buy me a duel nozzle printer or an SLA printer… 😉 ) and I am really happy with how they turned out.

However, now things are getting serious.. We’ve moved out of the asymmetric territory of triclinic space groups and are now entering the heady heights of the monoclinic crystal system. Unlike triclinic where none of the sides or angles of the unit cell are equal, in the monoclinic system a, b and c are not the same distance, but the angles α and β are equal to 90 degrees.

P2 is the simplest of the space groups in the monoclinic crystal system and the fantastic people at: https://crystalsymmetry.wordpress.com/230-2/ selected ‘Thomasclarkite’ as their example for it.

Thomasclarkite is a newly (1998) discovered sodium containing rare-earth element carbonate, identified by J. D. Grice and R. A. Gault in Mont Saint-Hilaire, Quebec. Oh how I would love to go mineral hunting there one day! Sadly my one major mineral hunt ended with me falling down a cliff, but that is another story..

The .cif (from: http://rruff.geo.arizona.edu/AMS/minerals/Thomasclarkite-(Y) ) outputs the following in crystalmaker:

Thomasclarkite-(Y) with carbon, sodium, oxygen and yttrium in black, yellow, red and light blue respectively. Water positions are dark blue/grey.

Looks pretty but not printer friendly at all – firstly those floating water positions have to go and we need to increase both the bond sizes and unit cell to be able to print this..

Bumped up the unit cell to crystalmaker’s max (blue line, 10 pixels), changed the hydroxides to pink (wish I had neutron data to play with – then we’d see the hydrogen positions), removed the water and increased the carbon atomic radii to 0.75 angstroms. I’ve also increased the stick bonds to 50% the smallest atomic radii and we get the below:

Thomasclarkite-(Y) with water positions removed.

I think I’m going to take the executive decision not to print water positions (or any other absorbed molecules) unless they are part of the structure. I think it would be too tricky to keep them in for my Snapmaker – although I’m happy to upload .stl files if you want to give it a go – just let me know!

Importing the .stl into the snapmaker3D slicing software we get:

Scaled up to 500 % and rotated in y by 90 degrees

Only 7 hours! Although it is looking flimsy – I’ll give it a go but I’m not sure about this one at all.. Especially considering my record so far with the post-print work..

Check back later to see how it went!

P-1 – Success

After tweaking the deuterium atomic radii the print seemed to work well – although I am starting to discover the limitation of my poor Snapmaker is in the post-print. The scaffold is proving to be very difficult to remove without damaging the print.

A slightly battered print of the P-1 space group

Still – I’m happy with the .stl file so feel free to print out your own version! I’d recommend a soluble scaffold or a breakaway filament.

If you want to have a go yourself – check it out at:

https://www.thingiverse.com/thing:3635053

Let me know how you get on if you give it a go!

P1 – Success (almost!)

We have success! The project begins properly now! After several failed attempts (check out the failures category for more details) we have our first space group print:

As you can see – although the unit cell printed, it was so thin that it snapped easily in post clean-up

Sadly my ham-fisted approach to cleaning up led to a couple of the unit cell axis being snapped. I don’t think you’d have that problem if you scaled it up even more than the 850 % that I used or used a breakaway filament such as PVA for the scaffold. Sadly I only have a single nozzle on my snapmaker so that is just a dream for me!

If you want to have a go yourself – check it out at:

https://www.thingiverse.com/thing:3626954

I would love to see how yours comes out! Good luck and stay tuned for P-1 (it’s printing at home as I type.. Gulp!)

Zeolite A (LTA)

Tl:dr: Here is the printable STL:
https://www.thingiverse.com/thing:3623903

Now I know I said this was about the naturally occurring zeolites (hydrated aluminosilicates) but I couldn’t carry out this project without a nod to zeolite A (Linde Type A). Possibly one of the most famous zeolites as it is one of the earliest synthetic (no natural version) zeolites discovered.

The first synthesis of a zeolite was reported by St. Claire Deville in 1862 with the formation of levynite.[1] It wasn’t until the incredible work of Richard M. Barrer that things really took off however. He classified the zeolites known at the time by molecular sizes [2] and in 1948 presented the first definitive synthesis of zeolites, an analogue of mordenite [3] and an at the time unknown new synthetic zeolite, which was later identified as the KFI framework. [4]

Barrer’s work inspired Robert M. Milton and Donald W. Breck (both of the Linde Division of Union Carbide Corporation) to investigate zeolite synthesis in search of new ways to separate and purify air. They discovered the new types of synthetic zeolites A, X and Y – which were then commercialised by Union Carbide.

The great thing about zeolite A is that you probably have some in your house right now, it has been extensively used as a water softener in detergent (those pore sizes are just the right size to exchange limescale causing calcium for sodium).

So to the print!

Armed with a crystallographic information file (cif) from the brilliant International Zeolite Association website:
http://europe.iza-structure.org/IZA-SC/material_tm.php?STC=LTA (accessed May 2019)

It was pretty easy to load it up into crystalmaker, however from experience I know that the ball and stick model doesn’t print too well so with a little help from the guys at
http://crystalmaker.com/crystalmaker/video-tutorials/index.html (their video tutorials are great – to do this I used the ‘building massive polyhedra’ video). I managed to create the following model:

Massive polyhedra view of zeolite A, sodalite beta cages in pink, and d4r (double 4 ring) in grey

If you are not used to working in 3D with zeolites, this doesn’t quite get across how they are formed of pores and channels connected by secondary or composite building blocks (the sodalite beta cage and d4r) so I’ve produced a little gif below to help.

Rotation movie of zeolite A massive polyhedra

Much better, these pores and channels are what make zeolites so useful and special, they can trap things (like gases or radioactive isotopes), sieve things (different sized and shaped molecules) and carry out ion exchange.

As this structure is fairly simple I could convert it into a stl and load it into snapmaker with no problems.

Scaled up to 300 %

A good 7 and a half hour print, so time to go to some friends for lunch and go for a walk in a forest..

Ta da!

Looking good – sorry for the mess around it.
After a quick clean up

Success! One out of around 50 done (depends which other synthetic zeolites I print..) Printed really well and easily, a little trouble with the overhangs on the sodalite cages but otherwise I’m very happy.

STL file:
https://www.thingiverse.com/thing:3623903

[1] H. de St. Claire Deville, Comptes Rendus Acad. Sci, 1862, 54, 324

[2] R. M. Barrer, J. Soc. Chem. Ind., 1945, 64, 130

[3] R. M. Barrer, J. Chem. Soc., 1948, 2158

[4] R. M. Barrer, J. Chem. Soc., 1948, 127

P-1

One down, only 229 to go. Gulp. Eventually, bar a minor filament failure and raft adhesion issues P1 seemed to work ok. So lets go through the same process with P-1. It’s important to remember that this is still a primitive triclinic system (a ≠ b ≠ c , α ≠ β ≠ γ or for the unit cell, the sides a,b and c are not equal, the angles α, β and γ are not equal) and the P-1 space group is related by inversion (hence the ‘-1’) to the P1 space group. But not just a simple inversion, check out; http://pd.chem.ucl.ac.uk/pdnn/symm3/sgtricl.htm for more information.

To the print! Again from the wonderful people at: https://crystalsymmetry.wordpress.com/230-2/

We the get the example:

Chalcanthite CuSO4 • 5(H2O)

http://webmineral.com/data/Chalcanthite.shtml

CIF can be found here:
http://rruff.geo.arizona.edu/AMS/minerals/Chalcanthite

I’m using the one from neutron diffraction data by: ‘G. E. Bacon, D. H. Titterton, Zeitschrift fur Kristallographie, 1975, 141, 330-341′

With the same process of open the CIF in crystal maker and tweak it so we have polyhedra and a thick unit cell line (10 pixels) we get the following structure: (see
https://crystalprint.home.blog/2019/05/06/beginnings-p1/ for a more detailed run through of the process)

Chalcanthite viewed down c. Copper and sulphur polyhedra are blue and yellow respectively. Oxygen and deuterium, red and grey. Extra water molecules and stranded atoms hidden.

Looking pretty good, although I doubt those deuterium (grey, an isotope of hydrogen) positions will print and will cause havoc with my scaffolding. I’ve bumped the relative size of the bonds up to 80 % of the atomic radii of deuterium (remember this is about 3D printing, sometimes sacrifices will have to be made on the chemistry convention – a thicker bond is more representative of the probable electron position anyway..)

The .stl loaded into snapmaker, scaled up by 750 %

Ah. So even with those bonds bumped up to 80 %, and the model scaled up by 750 % we get floating hydrogen atoms. Crystalmaker will only let you increase bonds to 90 % of the atomic radii but even then, they are still not getting picked up by the snapmaker software. I then fiddled with the atomic radii of deuterium (usually 0.04 angstroms) but even having it the same as oxygen (1.2 angstroms), still no bonds!

Right, I’m going to have to slightly off-piste with this one – my number one objective is to print the unit cell of this space group, as faithfully as possible. So I’m going to make some changes to the atomic radii to do this. Firstly I changed the deuterium radii to 0.75 angstroms (it looked silly as 1.2 as well as being very, very wrong). Next in the ‘model>model inspector’ menu I changed entire ball-stick atomic radii to 65 % of actual. Don’t forget, those ball and stick models you see of crystals are not true representative models of the structure, actually there is very little space between the atoms and the spheres (in reality ellipsoids but that is another story), they are shrunk for convenience.

Chalcanthite viewed down c, this time with deuterium (grey) atomic radii set to 0.75 angstroms and then all ball radii scaled to 65 % of actual. Extra water molecules and stranded atoms hidden.

Boom. This looks much better. What about in snapmaker?

Scaled up to 750 %

Looking good, with a raft everywhere and standard snapmaker settings to normal, we’re looking at 30 hours and about 50 m of filament! Looking back at P1 we are printing out at just shy of 100 mm in the largest direction so I think P-1 can be shrunk a tiny bit.. At 550 % scale up we’re getting dimensions of 58.6 x 92.1 x 77.4 mm and a print time of 15 hours. Lets give this a shot, tune in later to find out what happens!

P1 failure

Half the fun in science, engineering or life in general really, is getting it wrong. The entire point of the maker movement is the ideal that ‘making is the process, not the end result’.

I believe in this fully. It is why problem based learning is the core of our internal offer at Winchester Science Centre. We need to show people it is OK to fail, and quite often more interesting!

So, soap-box moment over. My first print for this project? Failed:

The filament snapped about 4 hours into the print. Now I’ve noticed the prima value PLA I’m using is a bit more brittle than I’m used to, but it wasn’t the culprit..

The spool was a bit too big for the Snapmaker spool holder, and so after I left for work with the spool balancing on the end, the filament feeder tugged it closer, and closer and closer to the enclosure until it caught on a protruding screw and stuck.

Tug. Tug.

Snap.

Ah well, now I know and I’ve come up with an ingenious way to fix it:

Yup, a washie-tape washer. Here goes attempt number two!

Edit1:

Turns out attempt number two went a bit further but another problem, good old physics, rose its head:

When the model gets to about 60 mm in height the force of the print head moving around is enough to knock it off the raft – doh!

I’ll rotate the model in Snapmaker so there is more contact with the raft and try that next..

Edit2:

Damn, in my attempt to make the overall structure stronger, I forgot the lesson I learnt from printing tactile planets: ‘spheres do not like to stay on rafts’.. See if you can spot where it went wrong..

Beginnings part 2: P1

It’s done, the stl code has been sliced (put in a format the 3D printer understands) and all I need to do now is wait..

Of course there was the minor hurdle of the filament getting stuck on its feeder. The Snapmaker filament holder is just a little too short to handle Primia 1 kg filament but I think I caught it in time..

Whatever happens I’ll post about it and when I have a successful stl file it will be shared on the space group print project page!

Raft is down for the first P1 print, it’s not perfect due to the filament feeder getting stuck, but let’s try it out!