1) Researchers have used 3D printing to create molecular structures for teaching inorganic chemistry. They convert crystallographic files into 3D printable file formats and print structures like metal complexes and inorganic compounds. 2) To facilitate sharing of 3D printable molecular structures, the Royal Society of Chemistry has created an online repository containing over 30,000 structures converted from crystallographic data files. 3) 3D printing allows visualization of complex molecular structures and is gaining popularity for teaching, research, and hobbyist interests in chemistry.

1. 1
Accessing 3D Printable Structures Online
Vincent F. Scalfani, Antony J. Williams, Robert M. Hanson, Jason E. Bara,
Aileen Day, and Valery Tkachenko
Science and Engineering Librarian, The University of Alabama
vfscalfani@ua.edu
248th ACS National Meeting
San Francisco, CA
August 13, 2014

2. 2
...so Chemists build tangible models to overcome this challenge. We have
used commercial and/or do-it-yourself techniques for many decades.
Visualizing Molecules/Solids in 3D Has Always Been Challenging...
Chuang, C. et al. J. Chem. Educ. 2012, 89, 414.; Siodłak, D. J. Chem. Educ. 2013, 90, 1247.
Molymod kits Beads
Bottle caps!

3. 3
More Recently, Researchers have used 3D Printing
Scalfani, V. F. and Vaid, T. P., J. Chem. Educ. 2014, ASAP. DOI: 10.1021/ed400887t
3D printing is an additive manufacturing process capable of producing
objects with very high complexity! It is well suited to create any molecular
structure.
Manufacture object
layer by layerconvert to slices (tool path)computer 3D model
many different techniques and wide variety of materials available (e.g.
thermoplastics (ABS/PLA), UV resins, glued powders, metals, and more)

4. 4
How to Create 3D Printable Molecular Structure Files?
3D printers only understand specific 3D file formats. Two common formats are
STL (triangulated mesh surface) and WRL (modeling language text file).
STL = single color
WRL = full color
Scalfani, V. F. and Vaid, T. P., J. Chem. Educ. 2014, ASAP. DOI: 10.1021/ed400887t

5. 5
Many Different Workflows Possible...Here is One
Repaired STL file
Netfabb
Crystallographic
information file (.cif)
VRML file (.wrl) STL file (.stl)
VRML 2.0 file (.wrl)
MicroMouse
AccuTrans 3D
We have also used many variations of this
workflow with UCSF Chimera, Python
Molecular Viewer and Crystal Impact Diamond
with great success...
Scalfani, V. F. and Vaid, T. P., J. Chem. Educ. 2014, ASAP. DOI: 10.1021/ed400887t

6. 6
We have used 3D Prints for Teaching Inorganic Chemistry
3D printing has allowed us to create many unique molecular models for
teaching inorganic chemistry.
Pb3
C6
S6
P6/mmm
alkene
porphyrin
(R = p-tolyl)
C1
Scalfani, V. F. and Vaid, T. P., J. Chem. Educ. 2014, ASAP. DOI: 10.1021/ed400887t

7. 7
We have used 3D Prints for Teaching Inorganic Chemistry
Cd
N
N N
N
N
N
2
Cd
N
N N
N
N
N
2
Fe
H2N
Cl NH2
Cl Fe
Cl
H2N NH2
Cl
Λ-[Cd(en)3
]2+
D3
Δ-[Cd(en)3
]2+
D3
[FeCl2
(C6
H8
N2
)2
]
trans
C2h
cis
C2
Scalfani, V. F. and Vaid, T. P., J. Chem. Educ. 2014, ASAP. DOI: 10.1021/ed400887t

8. 8
Many Others Have Also Been Preparing 3D Printable Files
Tim Herman and staff at the MSOE have been creating biomolecular 3D
printed models for many years.
www.cbm.msoe.edu

9. 9
Many Others Have also been Preparing 3D Printable Files
Kitson, P. J. et al. Crystal Growth & Design 2014, 14 (6), 2720.; Chen, T.-H. et al. CrystEngComm 2014, 16 (25), 5488.
Amar Flood (Indiana University Bloomington)
Ognjen Miljanic (University of Houston)
Leroy Cronin (University of Glasgow)
Peter Moeck (Portland State University)
Marvin Hackert (UT Austin)
Henry Rzepa (Imperial College London)
...and many other researchers, teachers, and
hobbyists!

10. 10
3D Printing Crystallography Community
We started a Listserv [3DP-XTAL] and wiki hosted at UA Libraries for
those interested in 3D printing Crystal Structures, http://apps.lib.ua.edu/
blogs/3dp-xtal/

11. 11
3DP-XTAL Community Works Together at IUCr 2014
and last week in
Montreal...
3DP-XTAL
community for
puts together a
great display of
3D prints at the
IUCr 2014, 23rd
Congress on
Crystallography
Meeting, Montreal,
Canada.

12. 12
Where do we Store Files? How to Access Online?
• The 3D printing crystallography
community is growing rapidly. Many
are now starting to generate 3D
structure files from crystal structures,
where do we store these files? How
can we access this information?
• There is a learning curve with software
used to generate 3D printable files.
Repositories overcome this limitation.
• Current popular 3D model repositories such as Thingiverse and Trimble
3D Warehouse are not designed for chemical structures — can not search
for chemicals via structure, formula, SMILES, and InChI key, etc.

13. 13
Current 3D Model Repositories – NIH 3D Print Exchange
New NIH 3D Print Exchange is great — target audience and data is for
biomedical applications (e.g., anatomy, labware, protein and macromolecular
structures, bacteria, cells).
http://3dprint.nih.gov/
Searchable by names and phrases. This
seems to work well for the target data.

14. 14
We Need an Online Repository for Molecules and Solids
We need a 3D printable structure database for molecules and extended
solids that has robust chemical search tools. (e.g., searchable by structure,
formula, SMILES, and InChI. Solution? Host 3D printable files on The Royal
Society of Chemistry’s (RSC) Crystal Data Repository.

15. 15
RSC Crystal Data Repository
RSC Crystal Data Repository (http://api.beta.rsc-us.org/Crystals/v1/cod/)
1 One of four planned new RSC repositories (crystals, compounds, reactions,
and spectra)
2 Currently contains: the entire Crystallography Open Database (COD) of
289,395 .cif and 48,022 .hkl files of molecules and extended solids; 3D
Printable Files – 31,239 .wrl files (color printing) and 11,732 .stl files.
3 Still in beta mode, can manually browse through files. Repository will
soon have user interface that is fully searchable (name, structure, formula,
SMILES, InChI, and others) with deposition and crowd-source curation/
annotation platform.

16. 16
RSC Crystal Data Repository – A Closer Look at the Beta

17. 17
How to Create > 30,000 3D Printable Structures...A bit Tricky
We used Jmol Scripting to batch convert COD .cif files into .wrl files. Let’s
start with molecules, we need to remove unwanted counter ions and solvent
molecules first.
CHCl3
Cyclic Oligo(p-
phenylene oxide) +
chloroform
Usually not
interested in
3D printing any
solvent or counter
ions.
COD ID: 4022031

18. 18
Jmol Script Can Auto Delete Solvent and Counter Ions
Counter ions and solvent molecules can be deleted with Jmol scripting:
load “G:4022031.cif”
info = getProperty(“moleculeInfo”)
nmax = getProperty(info,”nAtoms”).max
m = getProperty(info,”[select number where
nAtoms = nmax]”)[1]
print {molecule=m}
select on molecule=m
delete molecule !=m
Selects largest molecule, deletes
everything else, then you can export as
a WRL file. Cool!

19. 19
Quality of Current Data is“Pretty Good”
Selecting only the molecule with greatest # of atoms works in majority of
cases. One scenario it will fail is if counter ions/solvent molecules are larger
than the compound of interest. Will need to manually curate these:
COD ID: 2011077
NBu4
+
(53 atoms)
acetyl butyrolactonate
(16 atoms)

20. 20
How to Create > 30,000 3D Printable Structures...A bit Tricky
What about the extended solids? Well, only the asymmetric unit loads by
default (unique atom positions). Need to tell software to pack the unit cell.
load “G:1010311.cif” {1 1 1} PACKED
Bi2
O3
Bismuth Oxide
COD ID: 1010311

21. 21
Once We had the WRLs, the STLs are Easy to Prepare
Repaired STL file
Netfabb
Crystallographic
information file (.cif)
VRML file (.wrl) STL file (.stl)
VRML 2.0 file (.wrl)
MicroMouse
AccuTrans 3D
Has excellent batch
conversion tools built in.

22. 22
Results–Examples From the RSC Crystal Data Respository
(3-Methoxyphenyl)
(2,4,6-triisopropylphenyl)
methanone
Printed on
MakerBot 5th
Generation
COD ID: 2003038

23. 23
Results–Examples From the RSC Crystal Data Respository
COD ID: 2007214
natural product,
ryanoid derivative.

24. 24
Results–Examples From the RSC Crystal Data Respository
Chloro Borazinediamine
COD ID: 2237358
Shapeways.com
Color Sandstone, $7 dollars
Manganese complex
COD ID: 2205559
MakerBot 5th Generation
PLA Clear

25. 25
Take Home Messages
1 The 3D printing crystallography community is growing rapidly. Scientists
are using models for teaching and research. General population has a
hobbyist interest in 3D molecules too (Great!).
2 In response to growing community, RSC has started to host 3D files on the
RSC Crystal Data Repository – currently contains over 30,000 STL and WRL
3D printable molecules and extended solids.
3 Go 3D print some chemical structures! You can create your own or simply
download one from the RSC repository (soon...). No 3D printer? Find a 3D
printing service website such as shapeways.com.

26. 26
Acknowledgements
Collaborators
Antony J. Williams (RSC)
Valery Tkachenko (RSC)
Aileen Day (RSC)
Robert M. Hanson (St. Olaf College)
Jason E. Bara (University of Alabama)
Funding and Support
Royal Society of Chemistry
UA Libraries
UA Department of Chemistry
UA Engineering 3D Lab
Slides
Will be posted on 3DP-XTAL Wiki
http://apps.lib.ua.edu/blogs/3dp-xtal/
How to Contact Me
Vincent F. Scalfani
Science and Engineering Librarian
The University of Alabama
vfscalfani@ua.edu