Bringing Crystal Structures to Reality by 3D Printing
Supporting Information for:
Bringing Crystal Structures to Reality by 3D Printing Philip J. Kitson, Andrew Macdonell, Soichiro Tsuda, HongYing Zang, De-Liang Long and Leroy Cronin* WestCHEM, School of Chemistry, The University of Glasgow, University Avenue, Glasgow G12
8QQ,
UK,
*Corresponding
author
email:
[email protected];
http://www.croninlab.com
S1
Index
Page
Conversion of crystallographic files to 3D CAD models
S3
3D Printing Platforms
S7
3D printing Materials Crystallographic information for {Mo14} and {Mo68}
S2
Conversion of crystallographic files to 3D CAD models
The first stage in the conversion of crystallographic information to a format suitable for 3D printing is the selection of the parts of the X-Ray crystal structure which are required to be converted into a physical model. At this stage any unnecessary information may be deleted from the structure, for example any solvent of crystallization, disordered moieties etc. can be removed. The resulting edited information is then saved in a .pdb file format prior to importing into Blender (See figure S1).
Figure S1: Edited X-Ray crystal structure files are saved in a .pdb format prior to import into Blender. To import .pdb files into Blender, the import option has to first be selected in User Preferences→Addons→Import/Export→Atomic Blender, then the import option will appear under File→Import→Protein Data Bank. When the .pdb file is imported into Blender, a number of options are presented on the lower left side of the import screen. In the first of two boxes, there are options to automatically add a camera and a light for those less familiar with the Blender user interface and a drop-down box which offers a choice between the three different sphere-types Blender offers to represent the atoms. Two scaling factors alter both the distance between all atoms (and the bond length) and the atomic radii and a further drop-down box specifies whether Atomic Blender will use the pre-defined atomic sizes, its own preset atomic radii or the van der Walls radii as the base sphere size. The box beneath this controls the bonding between atoms, which can be turned off and on, allowing you to alter the objects Blender uses to represent the bonds as well as their radii. Once imported, the structure is presented as a single object. In order to separate the individual atoms and bonds into separate objects, the structure is selected (by right clicking on it or pressing the A key) and the command Apply→Make Duplicates Real (or Shift Ctrl A) is used. Now the structure can be manipulated and added to if desired before it is exported for printing (some changes may be necessary to make the structure stable as a physical object). In order to 3D print the structure, it must be exported as an .stl file, which is available under File→Export→Stl. This process is illustrated in Figures S2 – S5 S3
Figure S2: activating the Atomic Blender add-on to allow the import of .pdb files.
Figure S3: preparing to import .pdb files
S4
Figure S4: Selecting the prepared .pdb file
Figure S5: Processing the imported information.
S5
Figure S6: Exporting the 3D model as a STL file.
Once the STL file has been exported it can then be loaded into the platform specific 3D printer software which contains the settings required for the particular material and printer being used.
S6
3D Printing Platforms
The molecular models produced in this work were fabricated on one of four different 3D printers (summarized in Table ST1), using either a Fused Deposition Modeling (FDM) or Stereolithographic approach. Both approaches are based on an additive method whereby solid objects are carved into layers of material which are successively built up by the 3D printer.
Table ST1: 3D printers used for the production of molecular models from crystallographic data. * n/a indicates either the information is not available from the supplier or, in the case of the Reprap printer, the printer was built from a kit by the authors.
3D Printer platform
3D printing methodology
Manufacturer
Form1tm 1
Stereolithographic
FormLabs
Associated software package preformtm
Ultimakertm Original2 3DTouchtm 3
FDM
Ultimaker
Cura
FDM
Axontm
Reprap – modified Prusa i3 model4
FDM
3Dsystems (discontinued) Open-Source
Slicr / other open source compilers
Manufacturer quoted Resolution Layer: 25 μm X / Y:300 μm Layer: ≤ 20 µm X / Y: n/a* Layer: 125 μm X / Y: 200 μm n/a*
Typical Printing materials methacrylate based photopolymer PLA, PET, ABS PLA, PET, ABS PLA, PET, ABS
Each 3D printer requires a specific instruction file which defines the layers from which the solid object will be produced, uniquely defining the specific operations and printing parameters (temperature, speed of motion of printing head etc…) and these files are produced by different software packages for each printer. These software packages are often proprietary products designed uniquely for the printer platform and this was the case for the 3DTouchtm and Form1tm printers used for this work. However, the Reprap platform is an open source project and as such the software used to produce the printer instruction file is also an open source project - in this case, a program called Slicr5 which is freely available. For the Ultimakertm, while the printer is not open source, the compilation software, Cura, is. In the cases where open-source software is used, other freely available software packages are also available. Screenshots of the compilation software for each of the 3D printers used can be seen in Figures S7 – S10.
S7
Figure S7: Curatm software for producing printer instruction files for the Ultimakertm platform.
Figure S8: Axon 2tm software for producing printer instruction files for the 3DTouchtm platform
S8
Figure S9: Preformtm software for producing printer instruction files for the Form1tm platform
S9
Figure S10: Slicr software for producing printer instruction files for the Form1tm platform
The software for individual printers calculates the layer patterns required for a given model along with any supporting material which needs to be laid down to enable the printing of overhanging regions. Once the instruction files have been compiled these are loaded onto the appropriate printer and the printing is begun as per manufacturer’s instructions. Subsequent to printing, any support material used in the printing of the desired structure was mechanically removed. Figures S10 – S13 show each of the printers in-situ in our laboratory and engaged in the printing of molecular models from crystallographic information.
S10
Figure S10: (Left) Form1 printer. (Right) Print bed of Form1 printer while printing.
Figure S11: (Left) Reprap printer. (Right) Print bed of Reprap printer while printing.
S11
Figure S12: Ulitmakertm 3D printer while printing.
Figure S13: (Left) 3DTouchtm printer. (Right) Print bed of 3DTouchtm printer while printing.
S12
3D Printing materials
Photopolymer Resin used for printing with the Form1tm 3D printing platform comprised a clear, colourless methacrylate based resin supplied by FormLabs1 and used without further modification.
Polylactic acid (PLA), Polyethelyne Terephthalate (PET), and Acrylonitrile Butadiene Styrene (ABS) Thermopolymers used with the Ultimakertm, 3DTouchtm and Reprap 3D printers were supplied by Formfutura® 6 as 3mm filament and used without further modification.
S13
Crystallographic information for {Mo14} and {Mo68}
Figure S14: C8Mo14S14O38 cluster ({Mo14}) for 3D printing.
{Mo14}7 has the formula C24H92N4S14Mo14O51 containing a cluster structure {[(Mo2S2O2)(OH)2]7(C4O4)2(H2O)2}8-, C4H12N+ cations and solvent water molecules which crystallizes in the triclinic system with space group P-1 and unit cells a = 13.5218(8) Å, b = 18.4068(11) Å, c = 20.5993(12) Å, α = 113.100(3)˚, β = 96.916(3)˚, γ = 104.268(3)˚, V= 4432.9(5) Å3. The structure of the cluster {[(Mo2O2S2)(OH)2]7(C4O4)2(H2O)2}4- is composed of a tetradecanuclear ring encapsulating two squarate anions with C2v symmetry, while interestingly the coordination geometry of the two squarate anions are orientated differently, 45° rotation related to each other. The cluster has a non-H composition C8Mo14S14O38 that is the object for 3D printing.
Figure S15: C16Mo48S48O184 cluster ({Mo68}) for 3D printing.
{Mo68}8 has the chemical formula C48H534Cs8K12Mo68N4O411S48 consisting of the cluster {[(Mo2O2S2)3(OH)4(C4O4)]8(Mo5O18)4}24- and a number of K+, Cs+ and C4H12N+ cations as counterions. The compound crystallises in triclinic system with space group P-1 and unit cells: a = 19.9865(8), b = 24.6627(11), c = 24.7841(9) Å, α = 88.480(2), β = 71.054(2), γ = 78.984(2) deg, V = 11333.6(8) Å3. The cluster {[(Mo2O2S2)3(OH)4(C4O4)]8(Mo5O18)4}24- has a structure that can be described as two crosses S14
intersecting each other as is found in Figure S15. The cluster is composed of 8 squarate-templated {Mo6} subunits joined by 4 {Mo5} units at the corners. The cluster has a non-H composition C16Mo48S48O184 that is the object for 3D printing.
S15
References 1.
FormLabs, Form1. http://formlabs.com/products/our-printer, (accessed 25/02/14).
2.
Ultimaker BV., https://www.ultimaker.com/, (accessed 25/02/2014).
3.
Bits
from
Bytes
Limited
3DTouch
3D
Printer,
http://www.bitsfrombytes.com/content/3dtouch-3d-printer (accessed 25/02/2014). 4.
Reprapsource Prusa i3 Kit. https://www.reprapsource.com/en/show/6855 (accessed
25/02/14). 5.
Slicr http://slic3r.org/ (accessed 25/02/14).
6.
Formfutura http://www.formfutura.com/ (accessed 25/02/14).
7.
Zang, H.; Miras, H. N.; Yan, J.; Long, D.-L.; Cronin, L., J. Am. Chem. Soc. 2012, 134
(28), 11376-11379. 8.
Zang, H.-Y.; Miras, H. N.; Long, D.-L.; Rausch, B.; Cronin, L., Angew. Chem. Int. Ed.
2013, 52 (27), 6903-6906.
S16
Bringing Crystal Structures to Reality by 3D Printing Philip J. Kitson, Andrew Macdonell, Soichiro Tsuda, HongYing Zang, De-Liang Long and Leroy Cronin* WestCHEM, School of Chemistry, The University of Glasgow, University Avenue, Glasgow G12
8QQ,
UK,
*Corresponding
author
email:
[email protected];
http://www.croninlab.com
S1
Index
Page
Conversion of crystallographic files to 3D CAD models
S3
3D Printing Platforms
S7
3D printing Materials Crystallographic information for {Mo14} and {Mo68}
S2
Conversion of crystallographic files to 3D CAD models
The first stage in the conversion of crystallographic information to a format suitable for 3D printing is the selection of the parts of the X-Ray crystal structure which are required to be converted into a physical model. At this stage any unnecessary information may be deleted from the structure, for example any solvent of crystallization, disordered moieties etc. can be removed. The resulting edited information is then saved in a .pdb file format prior to importing into Blender (See figure S1).
Figure S1: Edited X-Ray crystal structure files are saved in a .pdb format prior to import into Blender. To import .pdb files into Blender, the import option has to first be selected in User Preferences→Addons→Import/Export→Atomic Blender, then the import option will appear under File→Import→Protein Data Bank. When the .pdb file is imported into Blender, a number of options are presented on the lower left side of the import screen. In the first of two boxes, there are options to automatically add a camera and a light for those less familiar with the Blender user interface and a drop-down box which offers a choice between the three different sphere-types Blender offers to represent the atoms. Two scaling factors alter both the distance between all atoms (and the bond length) and the atomic radii and a further drop-down box specifies whether Atomic Blender will use the pre-defined atomic sizes, its own preset atomic radii or the van der Walls radii as the base sphere size. The box beneath this controls the bonding between atoms, which can be turned off and on, allowing you to alter the objects Blender uses to represent the bonds as well as their radii. Once imported, the structure is presented as a single object. In order to separate the individual atoms and bonds into separate objects, the structure is selected (by right clicking on it or pressing the A key) and the command Apply→Make Duplicates Real (or Shift Ctrl A) is used. Now the structure can be manipulated and added to if desired before it is exported for printing (some changes may be necessary to make the structure stable as a physical object). In order to 3D print the structure, it must be exported as an .stl file, which is available under File→Export→Stl. This process is illustrated in Figures S2 – S5 S3
Figure S2: activating the Atomic Blender add-on to allow the import of .pdb files.
Figure S3: preparing to import .pdb files
S4
Figure S4: Selecting the prepared .pdb file
Figure S5: Processing the imported information.
S5
Figure S6: Exporting the 3D model as a STL file.
Once the STL file has been exported it can then be loaded into the platform specific 3D printer software which contains the settings required for the particular material and printer being used.
S6
3D Printing Platforms
The molecular models produced in this work were fabricated on one of four different 3D printers (summarized in Table ST1), using either a Fused Deposition Modeling (FDM) or Stereolithographic approach. Both approaches are based on an additive method whereby solid objects are carved into layers of material which are successively built up by the 3D printer.
Table ST1: 3D printers used for the production of molecular models from crystallographic data. * n/a indicates either the information is not available from the supplier or, in the case of the Reprap printer, the printer was built from a kit by the authors.
3D Printer platform
3D printing methodology
Manufacturer
Form1tm 1
Stereolithographic
FormLabs
Associated software package preformtm
Ultimakertm Original2 3DTouchtm 3
FDM
Ultimaker
Cura
FDM
Axontm
Reprap – modified Prusa i3 model4
FDM
3Dsystems (discontinued) Open-Source
Slicr / other open source compilers
Manufacturer quoted Resolution Layer: 25 μm X / Y:300 μm Layer: ≤ 20 µm X / Y: n/a* Layer: 125 μm X / Y: 200 μm n/a*
Typical Printing materials methacrylate based photopolymer PLA, PET, ABS PLA, PET, ABS PLA, PET, ABS
Each 3D printer requires a specific instruction file which defines the layers from which the solid object will be produced, uniquely defining the specific operations and printing parameters (temperature, speed of motion of printing head etc…) and these files are produced by different software packages for each printer. These software packages are often proprietary products designed uniquely for the printer platform and this was the case for the 3DTouchtm and Form1tm printers used for this work. However, the Reprap platform is an open source project and as such the software used to produce the printer instruction file is also an open source project - in this case, a program called Slicr5 which is freely available. For the Ultimakertm, while the printer is not open source, the compilation software, Cura, is. In the cases where open-source software is used, other freely available software packages are also available. Screenshots of the compilation software for each of the 3D printers used can be seen in Figures S7 – S10.
S7
Figure S7: Curatm software for producing printer instruction files for the Ultimakertm platform.
Figure S8: Axon 2tm software for producing printer instruction files for the 3DTouchtm platform
S8
Figure S9: Preformtm software for producing printer instruction files for the Form1tm platform
S9
Figure S10: Slicr software for producing printer instruction files for the Form1tm platform
The software for individual printers calculates the layer patterns required for a given model along with any supporting material which needs to be laid down to enable the printing of overhanging regions. Once the instruction files have been compiled these are loaded onto the appropriate printer and the printing is begun as per manufacturer’s instructions. Subsequent to printing, any support material used in the printing of the desired structure was mechanically removed. Figures S10 – S13 show each of the printers in-situ in our laboratory and engaged in the printing of molecular models from crystallographic information.
S10
Figure S10: (Left) Form1 printer. (Right) Print bed of Form1 printer while printing.
Figure S11: (Left) Reprap printer. (Right) Print bed of Reprap printer while printing.
S11
Figure S12: Ulitmakertm 3D printer while printing.
Figure S13: (Left) 3DTouchtm printer. (Right) Print bed of 3DTouchtm printer while printing.
S12
3D Printing materials
Photopolymer Resin used for printing with the Form1tm 3D printing platform comprised a clear, colourless methacrylate based resin supplied by FormLabs1 and used without further modification.
Polylactic acid (PLA), Polyethelyne Terephthalate (PET), and Acrylonitrile Butadiene Styrene (ABS) Thermopolymers used with the Ultimakertm, 3DTouchtm and Reprap 3D printers were supplied by Formfutura® 6 as 3mm filament and used without further modification.
S13
Crystallographic information for {Mo14} and {Mo68}
Figure S14: C8Mo14S14O38 cluster ({Mo14}) for 3D printing.
{Mo14}7 has the formula C24H92N4S14Mo14O51 containing a cluster structure {[(Mo2S2O2)(OH)2]7(C4O4)2(H2O)2}8-, C4H12N+ cations and solvent water molecules which crystallizes in the triclinic system with space group P-1 and unit cells a = 13.5218(8) Å, b = 18.4068(11) Å, c = 20.5993(12) Å, α = 113.100(3)˚, β = 96.916(3)˚, γ = 104.268(3)˚, V= 4432.9(5) Å3. The structure of the cluster {[(Mo2O2S2)(OH)2]7(C4O4)2(H2O)2}4- is composed of a tetradecanuclear ring encapsulating two squarate anions with C2v symmetry, while interestingly the coordination geometry of the two squarate anions are orientated differently, 45° rotation related to each other. The cluster has a non-H composition C8Mo14S14O38 that is the object for 3D printing.
Figure S15: C16Mo48S48O184 cluster ({Mo68}) for 3D printing.
{Mo68}8 has the chemical formula C48H534Cs8K12Mo68N4O411S48 consisting of the cluster {[(Mo2O2S2)3(OH)4(C4O4)]8(Mo5O18)4}24- and a number of K+, Cs+ and C4H12N+ cations as counterions. The compound crystallises in triclinic system with space group P-1 and unit cells: a = 19.9865(8), b = 24.6627(11), c = 24.7841(9) Å, α = 88.480(2), β = 71.054(2), γ = 78.984(2) deg, V = 11333.6(8) Å3. The cluster {[(Mo2O2S2)3(OH)4(C4O4)]8(Mo5O18)4}24- has a structure that can be described as two crosses S14
intersecting each other as is found in Figure S15. The cluster is composed of 8 squarate-templated {Mo6} subunits joined by 4 {Mo5} units at the corners. The cluster has a non-H composition C16Mo48S48O184 that is the object for 3D printing.
S15
References 1.
FormLabs, Form1. http://formlabs.com/products/our-printer, (accessed 25/02/14).
2.
Ultimaker BV., https://www.ultimaker.com/, (accessed 25/02/2014).
3.
Bits
from
Bytes
Limited
3DTouch
3D
Printer,
http://www.bitsfrombytes.com/content/3dtouch-3d-printer (accessed 25/02/2014). 4.
Reprapsource Prusa i3 Kit. https://www.reprapsource.com/en/show/6855 (accessed
25/02/14). 5.
Slicr http://slic3r.org/ (accessed 25/02/14).
6.
Formfutura http://www.formfutura.com/ (accessed 25/02/14).
7.
Zang, H.; Miras, H. N.; Yan, J.; Long, D.-L.; Cronin, L., J. Am. Chem. Soc. 2012, 134
(28), 11376-11379. 8.
Zang, H.-Y.; Miras, H. N.; Long, D.-L.; Rausch, B.; Cronin, L., Angew. Chem. Int. Ed.
2013, 52 (27), 6903-6906.
S16
