For PeppyChains please go here.
See Table 1 for list of materials.
STL files for 3D printingThe 3D printable stereolithography (STL) files of the parts in the model are provided here, along with detailed instructions for assembly to enable anyone to build these models themselves. The STL files can be used for 3D-printing with any color of choice using any 3D printer. The following STL files are provided below for downloading:
1. Amide STL file – amide unit consisting of the hydrogen, nitrogen, carbon (CO) and oxygen atoms
2. cAlpha STL file – alpha carbon unit consisting of the alpha-carbon (Cα) atom and the hydrogen atom
3. methylGroup STL file – the residue (–CH3 group) corresponding to the amino acid Alanine.
These STL files are of acceptable resolution and should provide a smooth surface when printed at the same scale (1x). However, files of higher resolution may be provided upon request.3D printing: We used a Dimension uPrint Plus 3D printer to print the parts using ABS plastic. It uses Fused Deposition Modeling (FDM) technology to build a 3D structure on a layer-by-layer basis using ABS plastic material for the model, and a soluble plastic as a scaffold to support the model structure while it is being printed. Following this, the printed parts were soaked in a sodium hydroxide based solution for 4-6 hours, to dissolve the supporting plastic materials. The parts were then rinsed well with water, and desiccated overnight to make them completely clean and dry. At this point, the dried parts are ready for drilling and assembly. The overall process, from printing to drying, takes about 3-4 days for making a 9-mer model. Printing time varies proportionately depending on quantity.
The Peppytide model can be assembled using the following steps:
Step 1: Part printing. 3D-printing of 3 types of units as described above: amide, alpha-carbon, methyl-group (printing, soaking, drying). See Table 1 for details on magnets, screws, spacers and nuts needed for assembly.
Figure 1: Detailed drilling and assembly plan of Peppytide
Step 2: Amide unit preparation.
a. Installation of the H-bond magnets. Sand the bottom face of the H-bond magnets (3/16" x 1/8") with 220 grit sandpaper to roughen the surfaces for effective adhesion. Next, glue the magnets onto the amides using Epoxy (JB-weld); O with North pole up; H with South pole up (Fig. 2). Leave for 24 hours for setting and drying.
Fig. 2: The 4 atoms of the amide units; the hydrogen-bond.
b. Labeling. Color-code the amide units with red-ring for oxygen, white-ring for hydrogen, and with blue-dot for nitrogen atoms in the amide units (Fig. 2).
c. Drilling dihedral rotational barrier magnet holes. Enlarge the magnet holes by drilling to a depth of 0.074" (drill size #31, 0.120") in the amide units (Fig. 1). This hole-depth will allow each magnet to protrude by ~0.051". Slightly undersized guide holes are provided to minimize the amount of material removed by the drill.
d. Drilling the bond holes. Enlarge the central bond holes (C and N atoms) by drilling to a depth of 0.345" (drill size 0.250”) in the amide units (Fig. 1). This hole-depth will allow the nylon bond spacer to protrude by 1/32". Slightly undersized guide holes are provided to minimize the amount of material removed by the drill.
Step 3: Alpha carbon unit preparation.
a. Drilling the rotational barrier magnet holes. As with the amides, enlarge the magnet holes by drilling to a depth of 0.074" (drill size #31, 0.120") in the alpha carbon units (Fig. 1). This hole-depth will allow each magnet to protrude by 0.051". The final bore diameter of 0.120” is intentionally undersized to allow a press-fit of the 1/8” diameter magnets (see step 4 below).
b. Drilling the bond holes. Drill to a depth of 0.300" (drill size #43, 0.089") on the 3 faces (N-face, C-face and the side-chain-face) of the alpha-carbon units. Guide holes are provided, by design (Fig. 3).
c. Tapping the bond holes. After drilling the central bond holes, tap them with 4-40 threads to their full depth (Fig. 3).
Fig. 3: Alpha carbon bond guide holes
Step 4: Addition of the rotational barrier magnets. Press fit the dihedral magnets (1/8" x 1/8") into alpha carbon units (with North pole up) and in amide units (with South pole up) (Fig. 4).
Fig. 4: Steps of assembly. (Upper) amide unit; (Lower) alpha carbon unit.
Step 5: Bond linkage assembly. Assemble screws, nuts, and spacers for bond linkages (Fig. 5 Left). There are 3 such bonds per monomer unit: Cα–Amide(N), Cα–Amide(C), and Cα–Side-chain.
Fig. 5: Assembled bonds and related parts that need to be linked per repeating monomer unit.
Step 6: Alpha-carbon bond assembly. Assemble bonds into the Cα units by screwing the bonds into the alpha carbon and securely tightening the nut, while leaving a slight gap to allow free rotation of the spacer (Fig. 6).
Fig. 6: Alpha carbon unit with bond linkages
Step 7: Backbone assembly. Push-fit bond linkages from Cα units into amides (Fig. 7). The bonds will bottom out into the amide bores.
Fig. 7: Connecting the alpha carbon unit with the two faces of amide units.
Step 8: Repeat steps 6 and 7 to make the entire backbone chain of alternating amide unit and alpha-carbon unit (Fig. 8).
Fig. 8: Completed backbone assembly of the Peppytide model.
Step 9: Adding side chain residues. Lastly, press-fit the methyl groups onto the 3rd bond linkages of the Cα units in the backbone chain (Fig. 9).
Step 9 gives the final assembled Peppytides chain!
We took care to make the holes and the drilling depths accurate up to 3 decimal places, while correcting for the errors due to the tolerances of the 3D printer and the press-fitting technique. The goal was to have 1/32" of the spacer protruded from the amide N/C faces to get the correct effective bond lengths, and to have the dihedral magnets protrude at most 0.051"-0.054" to avoid collision during rotation, while retaining enough proximity for effectual magnetic attractive forces. We experimented to get the desired drilling depths of holes by using drilling jigs with adjustable heights (Fig. 10). The drilling jig speeds up the time required for assembly by a factor of ~5.
(A) The drill at the top; with ¼" compressed air line to rapidly clear away drilled materials for a smooth hole.
(B) Precision control of drill depth by adjustment of screw stops.
Fig. 10: Drilling jig with adjustable height enables precision depth control.