This work was supported by the National Science Foundation (NSF) under Grant No. CHE-1847583.

1. Preparation of model files for 3D printing
NOTE: The large number of 3D printers and free and commercial printing software make exact directions beyond the scope of this article. General protocol process and recommendations are provided here, with specific considerations given for representative models shown with the listed software and 3D printers (see Table of Materials). Dedicated manufacturer directions specific to a reader&#39;s printer and slicing software combination take precedence over the provided recommendations.
<ol>
	<li>Download the supplementary stereolithography (.stl) files associated with this article (Supplementary Files S1&#8210;S5). Upload these files to the computer with the slicer program.</li>
	<li>Import one of the C_atom_sp3, H_atom, or C-C_bond files into the slicer program. Use millimeter format for the units if an option is available. In the software, either click the Import button of the Models panel of the main window or select the Import Models command under the File pulldown menu. Select the appropriate model file from the resulting file browser.
	<ol>
		<li>Import both H_atom_dual_bottom and H_atom_dual_top files for dual extruder prints of the hydrogen atom. Align, group, and assign the component models to the relevant extruder based on the target filament color.</li>
	</ol>
	</li>
	<li>Scale the imported model to the desired size. For this, double-click either the graphical model in the main display or the listed model in the Models panel of the main window. This action opens a model editing panel that enables translation, rotation, and scaling of the target model. Representative models are presented for 50%, 100%, 200%, and 320% scale for all interconnecting parts.
	<ol>
		<li>Activate support structures for C_atom_sp3 models with scales greater than 100%. Support structures can be used but are generally not necessary for all other models.</li>
		<li>Activate a raft or brim structure for 100% and smaller scale models. Such structures should not be necessary for most larger models as the flat base will have sufficient contact with the bed surface to remain fixed in place. Rafts help provide a well-adhered first layer for a 3D print, so if there are any difficulties in the stability of the first printed layer at any scale, activating a raft structure could lead to more successful prints at the expense of the material needed for the raft structure.</li>
	</ol>
	</li>
	<li>Duplicate models to generate an array of models as desired by selecting the Duplicate Models option from the Edit menu and entering the number of model parts in the resulting dialog box. Arrange the model(s) near the center of the build platform by clicking the Center and Arrange button in the Models panel of the main window, or by selecting the Center and Arrange option under the Edit pulldown menu. 
	NOTE: See Figure 1 for an example arrangement of six C_atom_sp3 models printed with polylactic acid (PLA). It is safest to print a single part at a time, though printing multiple small parts of the same color is usually more time-efficient. The print quality of parts in arrays is often lower because of the need for more filament retraction points between models. Array prints of models also have an increased likelihood of failure as one fallen part during printing can interfere with the printing of other parts.</li>
</ol>
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/61487/61487fig01.jpg" /> 
Figure 1: Like-colored atoms or bonds can be printed as arrays.&#160;To increase printing efficiency at a slight cost in quality, parts of like color are readily printed in arrays. Here, six PLA carbon atoms are printed together, each positioned on a small raft structure with an outlining brim structure. <a href="https://jove.unicartagenaproxy.elogim.com/files/ftp_upload/61487/61487fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<ol start="5">
	<li>Set the appropriate model processing settings for target prints using Add or Edit Process Settings from the Processes panel of the main window. 
	NOTE: The software used has selectable default processing settings for PLA, ABS, and other available thermoplastics when adding a new process or editing a process by respectively clicking the Add or the Edit Process Settings from the Processes panel of the main window. Specific adjustments and rationale for the provided molecular model parts follow.
	<ol>
		<li>Set the model infill value between 15% and 25%. This will use less filament and result in lighter parts, but the final assembled structures will be strong enough to survive physical manipulation.</li>
		<li>Use 100% infill settings for the connector regions of C-C_bond and H_atom model parts if possible or as needed to increase the durability of connector tabs.</li>
		<li>Choose a print layer thickness of 0.2 mm or smaller to maintain print detail.</li>
		<li>Set the First Layer Speed to a value between 25 and 50% in the Layer tab of the process settings. A slowly printed first layer will improve adhesion to the print bed and will result in more successful overall 3D prints.</li>
		<li>Set the printer extruder and printer bed temperatures to values recommended for the chosen printer filament material. The provided temperatures are starting point recommendations.
		<ol>
			<li>For PLA, set Extruder = 215 &#176;C; Bed = No heating.</li>
			<li>For polyethylene terephthalate glycol-modified (PETG) set Extruder = 235 &#176;C, and Bed = 80 &#176;C.</li>
			<li>For acrylonitrile butadiene styrene (ABS) set Extruder = 245 &#176;C and Bed = 110 &#176;C.</li>
		</ol>
		</li>
		<li>For C_atom_sp3 model parts, use two Outline/Perimeter Shells with an &#34;Outside-In&#34; Outline Direction to minimize print distortion at the bottom of the sphere. These options are available from the Layer tab of the Process settings window. For all other parts, the &#34;Inside-Out&#34; Outline Direction is recommended for a cleaner surface finish.</li>
		<li>If performing a dual extruder print of the aligned H_atom_dual_bottom and H_atom_dual_top models, optionally turn on an ooze shield option. The slicer will then generate a thin wall geometry around the model that will catch any dripping polymer from the inactive, yet still hot, extruder tip.</li>
	</ol>
	</li>
	<li>Slice the model into print layers to generate a G-Code toolpath. Click the Prepare to Print! button on the main window, or select the Prepare to Print option under the Edit pulldown menu.</li>
</ol>
2. Preparation of the printer for printing of parts
<ol>
	<li>Coat the surface of the printer bed with blue painter&#39;s tape for unheated beds. Coat the surface of the printer bed with blue painter&#39;s tape and an underlayer of polyimide tape for heated beds.</li>
	<li>Apply a thin layer of glue stick to the blue painter&#39;s tape. Glue stick polymer will improve print adhesion to the bed surface.</li>
	<li>Place or close a ventilated enclosure over the printer bed. An enclosure minimizes air currents that can disturb print annealing.
	<ol>
		<li>For PLA, open any/all ventilation ports as rapid cooling is preferred. Turn on a bed fan during printing if possible.</li>
		<li>For PETG, open a limited number of ventilation ports as gradual cooling is preferred. A bed fan is unnecessary during printing.</li>
		<li>For ABS, open a minimum number of ventilation ports as very gradual cooling is preferred. Turn off bed fans during printing.</li>
	</ol>
	</li>
	<li>Once the printer is prepared, click the &#34;Begin printing over USB&#34; button to send the G-Code to the connected printer and begin the printing process.</li>
</ol>
3. Finishing and assembly of model structures
<ol>
	<li>Remove parts from the printer bed. In the case of heated bed prints, remove parts after the bed has cooled to avoid distorting the model during separation.</li>
	<li>Remove raft or brim structures from the base of parts if used. Rub the base of the model part with medium to fine grit sandpaper to remove any remaining attached raft filaments.</li>
	<li>Sand the base of the C_atom_sp3 model parts with medium (120 grit) to very fine (320 grit) sandpaper to remove surface defects. Smooth the surface with the very fine grit sandpaper. Polish the surface to desired finish with a polishing cloth or buffer wheel at low revolution per minute setting. 
	NOTE: For example, a Dremel tool with a 0.5-inch diameter buffer wheel set to 10,000 rpm can be used for polishing, taking care to not to overly heat the print and cause surface defects.
	<ol>
		<li>PLA: Prints typically have a slightly glossy finish following printing as shown in the panels of Figure 2. This finish is marred by coarse sanding, but the glossy finish can be restored with polishing.</li>
		<li>PETG: Prints typically have a slightly glossy finish that can be sanded and restored with polishing as with PLA.</li>
		<li>ABS: Prints typically have a matte or only marginally glossy finish following printing (Figure 3A). A high-gloss finish (Figure 3B) can be achieved by separately dipping the parts in an acetone bath for 1&#8210;2 s and placing them in a ventilated area until the acetone has evaporated and the surface has solidified within typically 12&#8210;24 h.</li>
	</ol>
	</li>
</ol>
CAUTION: Acetone is flammable and should be applied sparingly in a fume hood or very well-ventilated area. ABS dissolves in acetone, so parts with layer separation defects due to poor annealing should not be treated with liquid acetone. Acetone will enter models through such defects and dissolve the model infill (Figure 3C). Polishing with acetone vapor is a slower process that will result in a similar effect, though safety precautions should be taken given the flammability of acetone.
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/61487/61487fig02.jpg" /> 
Figure 2: Dual extruder prints can be more visually refined.&#160;(A) Dual extruder model hydrogen atom prints are visually more cohesive than (B) all white model hydrogen atom prints. (C) When connected together to form complete cyclohexane rings, the assembled PLA models are functionally identical. <a href="https://jove.unicartagenaproxy.elogim.com/files/ftp_upload/61487/61487fig02large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/61487/61487fig03.jpg" /> 
Figure 3: ABS models can be chemically processed for a glossy finish.&#160;(A) ABS model prints tend to have a more diffuse or matte appearance, but (B) after chemically treating the parts with a brief dip in acetone they gain a high gloss finish. (C) If acetone enters the interior of the print through layer separation defects, the acetone will dissolve the model from the inside out, causing it to collapse. <a href="https://jove.unicartagenaproxy.elogim.com/files/ftp_upload/61487/61487fig03large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<ol start="4">
	<li>Insert connector ends of C-C_bond and H_atom model parts into sockets on C_atom_sp3 model parts according to desired bonding topology. Squeeze model parts together until an audible click is heard. Once connected, the single bond should freely rotate about this connection without falling apart. 
	NOTE: The connection fit is tight, so this may require significant force for models with scaling greater than 100%. The provided parts are not intended to be separated after connecting them together, but they can be separated with a very significant applied force. Rotation about a connected bond is a desired feature for the provided parts and models. Locking rotation requires an atom model (an sp2 hybridized carbon, for example) with a fixed structure in the connection socket that inserts between the spacings of the tabs on the end of the bond model.</li>
	<li>Assemble all printed parts according to the desired molecular structure. Saturate all C_atom_sp3 model parts by filling any open socket with an H_atom model part. For a ring like cyclohexane, close the ring with a C-C_bond model part between C_atom_sp3 model parts.</li>
</ol>

<ol>
	<li>Pauling, L., Corey, R. B., Branson, H. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+structure+of+proteins:+Two+hydrogen-bonded+helical+configurations+of+the+polypeptide+chain.">The structure of proteins: Two hydrogen-bonded helical configurations of the polypeptide chain.</a> Proceedings of the National Academy of Sciences. 37 (4), 205-211 (1951).</li><li>Claussen, W. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Suggested+Structures+of+Water+in+Inert+Gas+Hydrates.">Suggested Structures of Water in Inert Gas Hydrates.</a> The Journal of Chemical Physics. 19 (2), 259-260 (1951).</li><li>Claussen, W. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Second+Water+Structure+for+Inert+Gas+Hydrates.">A Second Water Structure for Inert Gas Hydrates.</a> The Journal of Chemical Physics. 19 (11), 1425-1426 (1951).</li><li>Watson, J. D., Crick, F. H. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+Structure+of+Nucleic+Acids:+A+Structure+for+Deoxyribose+Nucleic+Acid.">Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid.</a> Nature. 171 (4356), 737-738 (1953).</li><li>Watson, J. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> The double helix: a personal account of the discovery of the structure of DNA. , (1981).</li><li>Cademartiri, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+simple+two-dimensional+model+system+to+study+electrostatic-self-assembly.">A simple two-dimensional model system to study electrostatic-self-assembly.</a> Soft Matter. 8 (38), 9771-9791 (2012).</li><li>Reches, M., Snyder, P. W., Whitesides, G. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Folding+of+electrostatically+charged+beads-on-a-string+as+an+experimental+realization+of+a+theoretical+model+in+polymer+science.">Folding of electrostatically charged beads-on-a-string as an experimental realization of a theoretical model in polymer science.</a> Proceedings of the National Academy of Sciences. 106 (42), 17644-17649 (2009).</li><li>Tricard, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analog+modeling+of+Worm-Like+Chain+molecules+using+macroscopic+beads-on-a-string.">Analog modeling of Worm-Like Chain molecules using macroscopic beads-on-a-string.</a> Physical Chemistry Chemical Physics. 14 (25), 9041-9046 (2012).</li><li>Tricard, S., Stan, C. A., Shakhnovich, E. I., Whitesides, G. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+macroscopic+device+described+by+a+Boltzmann-like+distribution.">A macroscopic device described by a Boltzmann-like distribution.</a> Soft Matter. 9 (17), 4480-4488 (2013).</li><li>Capel, A. J., Rimington, R. P., Lewis, M. P., Christie, S. D. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=3D+printing+for+chemical,+pharmaceutical+and+biological+applications.">3D printing for chemical, pharmaceutical and biological applications.</a> Nature Reviews Chemistry. 2 (12), 422-436 (2018).</li><li>Jones, O. A. H., Spencer, M. J. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Simplified+Method+for+the+3D+Printing+of+Molecular+Models+for+Chemical+Education.">A Simplified Method for the 3D Printing of Molecular Models for Chemical Education.</a> Journal of Chemical Education. 95 (1), 88-96 (2018).</li><li>Paukstelis, P. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MolPrint3D:+Enhanced+3D+Printing+of+Ball-and-Stick+Molecular+Models.">MolPrint3D: Enhanced 3D Printing of Ball-and-Stick Molecular Models.</a> Journal of Chemical Education. 95 (1), 169-172 (2018).</li><li>Pinger, C. W., Geiger, M. K., Spence, D. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Applications+of+3D-Printing+for+Improving+Chemistry+Education.">Applications of 3D-Printing for Improving Chemistry Education.</a> Journal of Chemical Education. 97 (1), 112-117 (2020).</li><li>Robertson, M. J., Jorgensen, W. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Illustrating+Concepts+in+Physical+Organic+Chemistry+with+3D+Printed+Orbitals.">Illustrating Concepts in Physical Organic Chemistry with 3D Printed Orbitals.</a> Journal of Chemical Education. 92 (12), 2113-2116 (2015).</li><li>Au - Da Veiga Beltrame, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=3D+Printing+of+Biomolecular+Models+for+Research+and+Pedagogy.">3D Printing of Biomolecular Models for Research and Pedagogy.</a> JoVE. (121), e55427 (2017).</li><li>Fourches, D., Feducia, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Student-Guided+Three-Dimensional+Printing+Activity+in+Large+Lecture+Courses:+A+Practical+Guideline.">Student-Guided Three-Dimensional Printing Activity in Large Lecture Courses: A Practical Guideline.</a> Journal of Chemical Education. 96 (2), 291-295 (2019).</li><li>Rossi, S., Benaglia, M., Brenna, D., Porta, R., Orlandi, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Three+Dimensional+(3D)+Printing:+A+Straightforward,+User-Friendly+Protocol+To+Convert+Virtual+Chemical+Models+to+Real-Life+Objects.">Three Dimensional (3D) Printing: A Straightforward, User-Friendly Protocol To Convert Virtual Chemical Models to Real-Life Objects.</a> Journal of Chemical Education. 92 (8), 1398-1401 (2015).</li><li>Griffith, K. M., Cataldo, R. d., Fogarty, K. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Do-It-Yourself:+3D+Models+of+Hydrogenic+Orbitals+through+3D+Printing.">Do-It-Yourself: 3D Models of Hydrogenic Orbitals through 3D Printing.</a> Journal of Chemical Education. 93 (9), 1586-1590 (2016).</li><li>Carroll, F. A., Blauch, D. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=3D+Printing+of+Molecular+Models+with+Calculated+Geometries+and+p+Orbital+Isosurfaces.">3D Printing of Molecular Models with Calculated Geometries and p Orbital Isosurfaces.</a> Journal of Chemical Education. 94 (7), 886-891 (2017).</li><li>Van Wieren, K., Tailor, H. N., Scalfani, V. F., Merbouh, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid+Access+to+Multicolor+Three-Dimensional+Printed+Chemistry+and+Biochemistry+Models+Using+Visualization+and+Three-Dimensional+Printing+Software+Programs.">Rapid Access to Multicolor Three-Dimensional Printed Chemistry and Biochemistry Models Using Visualization and Three-Dimensional Printing Software Programs.</a> Journal of Chemical Education. 94 (7), 964-969 (2017).</li><li>Carroll, F. A., Blauch, D. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Using+the+Force:+Three-Dimensional+Printing+a+&#960;-Bonding+Model+with+Embedded+Magnets.">Using the Force: Three-Dimensional Printing a &#960;-Bonding Model with Embedded Magnets.</a> Journal of Chemical Education. 95 (9), 1607-1611 (2018).</li><li>The NIH 3D Print Exchange. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+NIH+3D+Print+Exchange:+A+Public+Resource+for+Bioscientific+and+Biomedical+3D+Prints.">The NIH 3D Print Exchange: A Public Resource for Bioscientific and Biomedical 3D Prints.</a> 3D Printing and Additive Manufacturing. 1 (3), 137-140 (2014).</li><li>Penny, M. R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Three-Dimensional+Printing+of+a+Scalable+Molecular+Model+and+Orbital+Kit+for+Organic+Chemistry+Teaching+and+Learning.">Three-Dimensional Printing of a Scalable Molecular Model and Orbital Kit for Organic Chemistry Teaching and Learning.</a> Journal of Chemical Education. 94 (9), 1265-1271 (2017).</li><li>Nelson, D. J., Brammer, C. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Toward+Consistent+Terminology+for+Cyclohexane+Conformers+in+Introductory+Organic+Chemistry.">Toward Consistent Terminology for Cyclohexane Conformers in Introductory Organic Chemistry.</a> Journal of Chemical Education. 88 (3), 292-294 (2011).</li><li>Anet, F. A. L., Bourn, A. J. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nuclear+Magnetic+Resonance+Line-Shape+and+Double-Resonance+Studies+of+Ring+Inversion+in+Cyclohexane-d11.">Nuclear Magnetic Resonance Line-Shape and Double-Resonance Studies of Ring Inversion in Cyclohexane-d11.</a> Journal of the American Chemical Society. 89 (4), 760-768 (1967).</li><li>Mayes, H. B., Broadbelt, L. J., Beckham, G. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=How+Sugars+Pucker:+Electronic+Structure+Calculations+Map+the+Kinetic+Landscape+of+Five+Biologically+Paramount+Monosaccharides+and+Their+Implications+for+Enzymatic+Catalysis.">How Sugars Pucker: Electronic Structure Calculations Map the Kinetic Landscape of Five Biologically Paramount Monosaccharides and Their Implications for Enzymatic Catalysis.</a> Journal of the American Chemical Society. 136 (3), 1008-1022 (2014).</li><li>Satoh, H., Manabe, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Design+of+chemical+glycosyl+donors:+does+changing+ring+conformation+influence+selectivity/reactivity.">Design of chemical glycosyl donors: does changing ring conformation influence selectivity/reactivity.</a> Chemical Society Reviews. 42 (10), 4297-4309 (2013).</li><li>Allinger, N. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Conformational+analysis.+130.+MM2.+A+hydrocarbon+force+field+utilizing+V1+and+V2+torsional+terms.">Conformational analysis. 130. MM2. A hydrocarbon force field utilizing V1 and V2 torsional terms.</a> Journal of the American Chemical Society. 99 (25), 8127-8134 (1977).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Gaussian 09 v.Revision C.01. , (2010).</li><li>Abraham, M. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=GROMACS:+High+performance+molecular+simulations+through+multi-level+parallelism+from+laptops+to+supercomputers.">GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers.</a> SoftwareX. 1-2, 19-25 (2015).</li><li>Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., Case, D. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Development+and+testing+of+a+general+amber+force+field.">Development and testing of a general amber force field.</a> Journal of Computational Chemistry. 25 (9), 1157-1174 (2004).</li></ol>

The authors have nothing to disclose.

The primary aim of this study is to report a protocol for the crafting of dynamic molecular models with commodity 3D printers. These printers are increasingly accessible, often even free to use in libraries, schools, and other venues. Getting started involves making choices about both the models to print and the materials to use and deciding from these options may require some inspiration regarding what creative additive manufacturing can do for research and instruction. To address these issues, we provide some practical material recommendations, suggested model parts, a 3D printing protocol, and an example application, each of which warrant further discussion.
There are many choices of thermoplastic for use in 3D printing. We highlight three in the presented protocol as these three materials are currently the most widely available for do-it-yourself 3D printing. The choice may depend on what material is supported by an available 3D printer, for example many open access facilities will only print with PLA because of environmental constraints. PLA is a biodegradable and compostable material that has a printing protocol with mild temperature settings. Both ABS and PETG are less environmentally friendly and not generally recyclable, though PETG is based on highly recyclable polyethylene terephthalate (PET) and may eventually see wider spread reprocessing like PET. Sustainable printing practices would involve printing few parts at a time to ensure both print quality and print success, this while using as little discarded material (support structures, rafts, ooze shields, etc.) as possible. PLA can be brittle, so if available, ABS and PETG thermoplastics can result in prints that are more mechanically resilient and have improved layer adhesion, respectively. These properties could be desirable for an interactive molecular model that will see regular manipulation in a laboratory or classroom setting.
The models presented here take these considerations into account, though they are firstly engineered to work together to enable dynamic molecular model construction. At the default scale, they will assemble successfully into interactive molecular structures. They can readily be scaled up to large models, though assembly will require more force as the connection prongs are less easy to distort at larger size. In shrinking the components, a 50% reduction in size will still work with minor modifications, such as shrinking the carbon atom model to 48&#8210;49% while keeping the bond and hydrogen atom at 50% to enable tighter connections between parts in PLA prints. Models this small are more delicate and often require raft structures to successfully print, but they are still functional as dynamic molecular models.
The thermoplastic material and chosen models to print are the two most critical aspects of a 3D printing protocol. The chosen thermoplastic will dictate the temperature, adhesion, annealing, and finishing considerations and options. If the available 3D printer does not have a heated bed, PLA is the only one of the presented thermoplastic choices that will print parts reproducibly. While the provided parts are designed to reproducibly print with different thermoplastics and hold up to dynamic manipulation, prints will degrade with use and crack, often between print layers, when placed under increasing stress. In such situations, it is easy and relatively cost effective to print a replacement part.
The dynamic functionality of molecular assemblies printed from the provided models differentiates this work from other available and 3D printable models that primarily highlight connectivity and bonding types. The dynamical aspects are presented in small part with the example cyclohexane structure. The configuration landscape of cyclohexane is directly accessible by hand using these models, and the topologies of these landscapes are in general agreement with computational investigations. Much of this comes from a respect for the specifics of molecular geometry and degrees of freedom in these physical modeling components. In Linus Pauling&#39;s commentary on their success in discovering the structure of the &#945;-helix1, they claimed that their contemporaries faced difficulties coming from idealistic integral assumptions and adopting &#34;...only a rough approximation to the requirements about interatomic distances, bond angles, and planarity of the conjugated amide group, as given by our investigations of simpler substances.&#34; More quantitative insight along these lines requires more specific detail than the considerations taken in building these model parts, but these models and recommendations provide a foundation for general interactive physical investigation of molecular systems. These models are an extension of 3D printable model kits we have been producing for research and outreach activities for several years prior to this report, and additional component parts that are compatible with both these models and the described protocol are available from the authors to enable more diverse bonding arrangements and dynamical action.

Molecular structure building has long been a critical aspect for discovery and validation of our understanding of the shape of and interactions between molecules. Physical model building was a motivating aspect in the determination of the &#945;-helix structure in proteins by Pauling et al.1, the primary clathrate hydrate structures of water2,3, and the double-helix structure of DNA by Watson and Crick4. In James Watson&#39;s published account of the DNA structure, he details many of the struggles faced in such model building, such as wrapping a copper wire around model carbon atoms to make phosphorus atoms, precariously delicate suspensions of atoms, and making cardboard cutouts of bases while waiting on tin cutouts from the machine shop5. Such struggles in model building have largely been remedied with computational modeling augmenting or entirely supplanting physical approaches, though physical models remain an essential aspect in chemical education and experimentation6,7,8,9.
Since around 2010, 3D printing has seen a significant growth in adoption as a tool for creative design and manufacturing. This growth has been driven by competition and availability of a variety of Fused-Deposition Modeling (FDM) printers from a series of new companies focused on broad commercialization of the technology. With the growing accessibility, there has been a concurrent growth in application of these technologies in chemistry education and experimental laboratory settings10,11,12,13,14,15,16,17,18,19,20,21. During this time period, both commercial and open community repositories for 3D models, such as the NIH 3D Print Exchange22, have made model systems for 3D printing more accessible, though many of these models tend to be centered on specific target molecules and provide simple static structures with an emphasis on bond connectivity and type. More general atomic and molecular groups can enable more creative constructions12,23, and there is a need for models that can enable general structure creation with tactile, dynamic, and force sensitive feedback for molecular structures.
Here, we present molecular model structure components that can be readily printed and assembled to form dynamic molecular models of saturated hydrocarbons. The component structures are part of a wider kit we have developed for extension and outreach activities for our laboratory and university. The parts provided have been engineered to be printable with a variety of polymer filament types on commodity FDM 3D printers. We present model results using different polymers and finishing techniques from both single and dual extruder FDM printers. These components are scalable, enabling model manufacturing suitable for both personal investigation and demonstration in larger lecture settings.
The primary aim of this report is to aid other researchers and educators in translating chemical structure details and knowledge in more physical ways with 3D printing. To this end, we highlight an example application by assembling and manipulating cyclohexane at different scales. Six-member ring system conformations are a core topic in introductory Organic Chemistry courses24, and these conformers are a factor in the reactivity of ring and sugar structures25,26,27. The printed models flexibly adopt the key ring conformers24, and the force needed for ring interconversion pathways can be directly explored and qualitatively evaluated by hand.

<table>
	<tbody>
		<tr>
			<td>ABS: Black 1.75 mm filament spool, 1 kg</td>
			<td>MakerBot</td>
			<td>MP01969</td>
			<td>Obtained from reseller (B&#38;H and/or Amazon).</td>
		</tr>
		<tr>
			<td>ABS: Dark Gray 1.75 mm filament spool, 1 kg</td>
			<td>Amazon</td>
			<td>B07T6W8TRF</td>
			<td>Obtained from reseller (B&#38;H and/or Amazon).</td>
		</tr>
		<tr>
			<td>ABS: White 1.75 mm filament spool, 1 kg</td>
			<td>Hatchbox</td>
			<td>B00J0H6NNM</td>
			<td>Obtained from reseller (B&#38;H and/or Amazon).</td>
		</tr>
		<tr>
			<td>Crown Acetone, 1 Gallon</td>
			<td>Crown</td>
			<td>206539</td>
			<td>Obtained from a hardwares store (Lowes).</td>
		</tr>
		<tr>
			<td>MakerGear M2</td>
			<td>MakerGear</td>
			<td></td>
			<td>This printer is more costly than inexpensive FDM printers obtainable on Amazon or other sites, but it is engineered for more consistent performance.</td>
		</tr>
		<tr>
			<td>MakerGear M2 Dual</td>
			<td>MakerGear</td>
			<td></td>
			<td>This model printer is no longer available for purchase. It has been replaced with a new model that has independent dual extruders.</td>
		</tr>
		<tr>
			<td>Multi-Surface 1.88-in Painters Tape</td>
			<td>3M</td>
			<td>116480</td>
			<td>Obtained from a hardwares store (Lowes).</td>
		</tr>
		<tr>
			<td>PETG: Pink 1.75 mm filament spool, 1 kg</td>
			<td>Amazon</td>
			<td></td>
			<td>Obtained from reseller (B&#38;H and/or Amazon). No longer available from this company.</td>
		</tr>
		<tr>
			<td>PETG: White 1.75 mm filament spool, 1 kg</td>
			<td>Amazon</td>
			<td></td>
			<td>Obtained from reseller (B&#38;H and/or Amazon). No longer available from this company.</td>
		</tr>
		<tr>
			<td>PLA: Black 1.75 mm filament spool, 2 lb</td>
			<td>MakerBot</td>
			<td>MP05775</td>
			<td>Obtained from reseller (B&#38;H and/or Amazon).</td>
		</tr>
		<tr>
			<td>PLA: Cool Gray 1.75 mm filament spool, 2 lb</td>
			<td>MakerBot</td>
			<td>MP05784</td>
			<td>Obtained from reseller (B&#38;H and/or Amazon).</td>
		</tr>
		<tr>
			<td>PLA: White 1.75 mm filament spool, 2 lb</td>
			<td>MakerBot</td>
			<td>MP05780</td>
			<td>Obtained from reseller (B&#38;H and/or Amazon).</td>
		</tr>
		<tr>
			<td>POLYIMIDE TAPE (2&#34; ROLL)</td>
			<td>MakerGear</td>
			<td></td>
			<td>Provided with the printer from MakerGear, though obtainable from a variety of sources.</td>
		</tr>
		<tr>
			<td>Simplify3D</td>
			<td>Simplify3D</td>
			<td></td>
			<td>Slicer softward used in prints. This software can be purchased from the company, or it can be purchased from MakerGear and other 3D printer makers.</td>
		</tr>
	</tbody>
</table>

interactive molecular model assembly with 3d printing

With the growth in accessibility of 3D printing, there has been a growing application of and interest in additive manufacturing processes in chemical laboratories and chemical education. Building on the long and successful history of physical modeling of molecular systems, we present select models along with a protocol to facilitate 3D printing of molecular structures that are able to do more than represent shape and connectivity. Models assembled as described incorporate dynamic aspects and degrees of freedom into saturated hydrocarbon structures. As a representative example, cyclohexane was assembled from parts printed and finished using different thermoplastics, and the resulting models retain their functionality at a variety of scales. The resulting structures show configurational space accessibility consistent with calculations and literature, and versions of these structures can be used as aids to illustrate concepts that are difficult to convey in other ways. This exercise enables us to evaluate successful printing protocols, make practical recommendations for assembly, and outline design principles for physical modeling of molecular systems. The provided structures, procedures, and results provide a foundation for individual manufacture and exploration of molecular structure and dynamics with 3D printing.

The protocol provided covers a variety of potential options for interactive molecular model construction. As a basic and unifying example for a molecular assembly using these model parts, we have chosen to assemble interactive cyclohexane structures at a variety of scales. Figure 2 shows the parts necessary for this structure: six C atoms, six C-C bonds, and twelve H atoms. These specific prints were crafted using both printers listed in the Table of Materials. The more costly dual extruder printer enables the production of dual color components; here the two-colored hydrogen atom structures with the color change at the midpoint of the bond (Figure 2A). The mono-colored hydrogens in Figure 2B print in about 50&#8210;60% less time due to the lack of an ooze shield structure and lack of polymer retractions in switching between active extruders. The assembled cyclohexane structures (Figure 2C) are functionally equivalent, though the dual extruder prints tend to look moderately more refined.
The PLA models in Figure 2 have reasonably nice finish&#160;that is more refined than ABS models straight off the printer (Figure 3A). Chemical treatment of ABS models with acetone gives a smooth and high gloss finish that almost gives the surface a wet look (Figure 3B). Such finishing can be troublesome, particularly if ABS models are not annealed well. Large models printed with ABS are prone to layer separation defects. Layer separation defects happen when the previous layer cools before the extruder can traverse over to lay down the next layer. It is critically important for large ABS prints that the environment around the heating bed of the printer remain at an even and warm temperature to slow down the cooling rate. If a print with a layer defect is submerged in acetone, the acetone will enter the model and dissolve the interior support structure. This will collapse the model from the inside as shown in Figure 3C.
A visually distinct appearance is secondary to functionality of the model structures. The connectors were designed to enable free rotation about single bonds. To test their utility in different systems, four different sets of part sizes were printed, with the carbon atom diameter running from 17.5 mm, 35 mm, 70 mm, and 112 mm. The assembled cyclohexane structures (Figure 4) were all able to flex, distort, and adopt relevant conformers in the same manner. The smallest of these models was the most prone to print flaws, making this size potentially too small and not recommended without tweaking the relative size of the parts. One of the primary benefits to the smaller prints is the speed of printing. An array of six of the smallest carbon atoms printed in around 2 h, as compared to the 10 h required for a single carbon atom of the largest size. While slow to print, large models are potentially more effective for communication in lecture settings where it would be difficult to see the motion of a small structure from a distance.
<img alt="Figure 4" class="xfigimg" src="/files/ftp_upload/61487/61487fig04.jpg" /> 
Figure 4: Models are functional at a variety of scales.&#160;To illustrate how the models can be printed for different purposes, cyclohexane models were assembled at four different scales and all retain the same functionality. The carbon atoms of the largest are larger than a softball (112 mm diameter) while the assembled cyclohexane of the smallest could fit within a softball. <a href="https://jove.unicartagenaproxy.elogim.com/files/ftp_upload/61487/61487fig04large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
The dynamic aspect is one of the key attributes that separate these structures from other printable molecular models. Since the atoms can readily rotate relative to one another, the structures can be distorted to snap into the different representative conformers of cyclohexane. Figure 5 shows the chair, boat, and the transition state structure for interconversion between their respective configuration spaces. This transition state point has four labeled carbon atoms in a nearly planar geometry24,28, the same transition state structure that one achieves doing B3LYP/6-311+G(2d,p) calculations29. Following the same transition state imaginary frequency motion, slightly twisting 2 up and 3 down will snap the model into the boat conformer landscape, while slightly twisting 2 down and 3 up will return the structure to the chair conformer.
<img alt="Figure 5" class="xfigimg" src="/files/ftp_upload/61487/61487fig05.jpg" /> 
Figure 5: Conformers of cyclohexane are fully accessible.&#160;As the atoms can rotate about their bonds, the models can adopt the sterically locked chair and more conformationally free boat forms. The transition state between these forms involves four nearly coplanar carbon atoms in the ring. Lightly twisting 2 up with 3 down will slip the model to the boat conformer, while twisting 2 down with 3 up will return the model to the chair conformer. <a href="https://jove.unicartagenaproxy.elogim.com/files/ftp_upload/61487/61487fig05large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
The state point free energy estimates (Supplementary Table S1) from B3LYP/6-311+G(2d,p) calculations of optimized state points (Supplementary Files S6&#8210;S9) give a gap between the twist-boat and boat conformers of 0.8 kcal/mol, which is very close to thermal energy at 298.15 K. This suggests that conversion between these should sample nearly freely. The gap between the chair conformer and interconversion transition state is more than ten times this value, indicating that the chair should be conformationally locked in comparison. This is illustrated in Figure 6, which shows estimated average conformer energy when each carbon atom location relative the ring plane is latitudinally projected onto a sphere over the course of a gas phase molecular dynamics calculation30,31. In the chair conformer on the left, the energy is low when the carbon atoms are displaced above or below the ring plane, but it ramps up dramatically if they displace to align with the ring plane. In the boat conformer, the conformer energy is relatively low when carbons are in the ring plane (twist-boat state), and the more highly displaced boat conformer is not at a drastically higher energy. These configuration landscapes can be explored with the 3D printed cyclohexane models, with the chair conformer only being able to locally vibrate while the boat conformer can smoothly undulate from one pair of opposite carbon atoms to the next.
<img alt="Figure 6" class="xfigimg" src="/files/ftp_upload/61487/61487fig06.jpg" /> 
Figure 6: Model behavior matches calculations.&#160;In the chair and boat conformer states, the latitudinal displacement of carbon atoms about the ring plane over the course of a Molecular Dynamics calculation can be projected onto the surface of an enclosing sphere. While the chair form is most energetically stable, it is locked and can only interconvert to the inverted form by passing through a high energy transition state. Both calculations and printed model flexibility indicate that the boat and twist-boat conformers are separated by close to 1 kBT at 298.15 K, allowing nearly free latitudinal displacement of carbon atoms in this form. <a href="https://jove.unicartagenaproxy.elogim.com/files/ftp_upload/61487/61487fig06large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
Supplementary Table S1: State point free energy estimates. <a href="https://cloudflare.jove.com/files/ftp_upload/61487/Table_S1.xlsx" target="_blank">Please click here to download this table.</a>
Supplementary File 1. <a href="https://cloudflare.jove.com/files/ftp_upload/61487/File_S1_C_atom_sp3.stl" target="_blank">Please click here to download this file.</a>
Supplementary File 2. <a href="https://cloudflare.jove.com/files/ftp_upload/61487/File_S2_C-C_bond.stl" target="_blank">Please click here to download this file.</a>
Supplementary File 3. <a href="https://cloudflare.jove.com/files/ftp_upload/61487/File_S3_H_atom.stl" target="_blank">Please click here to download this file.</a>
Supplementary File 4. <a href="https://cloudflare.jove.com/files/ftp_upload/61487/File_S4_H_atom_dual_bottom.stl" target="_blank">Please click here to download this file.</a>
Supplementary File 5. <a href="https://cloudflare.jove.com/files/ftp_upload/61487/File_S5_H_atom_dual_top.stl" target="_blank">Please click here to download this file.</a>
Supplementary File 6. <a href="https://cloudflare.jove.com/files/ftp_upload/61487/File_S6_Chair_B3LYP.pdb" target="_blank">Please click here to download this file.</a>
Supplementary File 7. <a href="https://cloudflare.jove.com/files/ftp_upload/61487/File_S7_Boat_B3LYP.pdb" target="_blank">Please click here to download this file.</a>
Supplementary File 8. <a href="https://cloudflare.jove.com/files/ftp_upload/61487/File_S8_TwistBoat_B3LYP.pdb" target="_blank">Please click here to download this file.</a>
Supplementary File 9. <a href="https://cloudflare.jove.com/files/ftp_upload/61487/File_S9_TransitionState_B3LYP.pdb" target="_blank">Please click here to download this file.</a>

Watch this Scientific Journal Video about Interactive Molecular Model Assembly with 3D Printing at JoVE.com

Interactive Molecular Model Assembly with 3D Printing

Physical modeling of microscopic systems helps obtain insights that are difficult to gain by other means. To facilitate the construction of physical molecular models, we demonstrate how 3D printing can be used to assemble functional macroscopic models that capture qualities of molecular systems in a tactile way.

With the growth in accessibility of 3D printing, there has been a growing application of and interest in additive manufacturing processes in chemical ...

interactive-molecular-model-assembly-with-3d-printing

Research

Education

JoVE Journal

JoVE Core

Chemistry

Molecules, Compounds, and Chemical Equations

SCIENTISTS IN ACTION

9.8K Views.  Oklahoma State University. Physical modeling of microscopic systems helps obtain insights that are difficult to gain by other means. To facilitate the construction of physical molecular models, we demonstrate how 3D printing can be used to assemble functional macroscopic models that capture qualities of molecular systems in a tactile way.

Video: Interactive Molecular Model Assembly with 3D Printing

Origami Inspired Self-assembly of Patterned and Reconfigurable Particles

There are numerous techniques such as photolithography, electron-beam lithography and soft-lithography that can be used to precisely pattern two dimensional (2D) structures. These technologies are mature, offer high precision and many of them can be implemented in a high-throughput manner. We leverage the advantages of planar lithography and combine them with self-folding methods1-20 wherein physical forces derived from surface tension or residual stress, are used to curve or fold planar structures into three dimensional (3D) structures. In doing so, we make it possible to mass produce precisely patterned static and reconfigurable particles that are challenging to synthesize.
In this paper, we detail visualized experimental protocols to create patterned particles, notably, (a) permanently bonded, hollow, polyhedra that self-assemble and self-seal due to the minimization of surface energy of liquefied hinges21-23 and (b) grippers that self-fold due to residual stress powered hinges24,25. The specific protocol described can be used to create particles with overall sizes ranging from the micrometer to the centimeter length scales. Further, arbitrary patterns can be defined on the surfaces of the particles of importance in colloidal science, electronics, optics and medicine. More generally, the concept of self-assembling mechanically rigid particles with self-sealing hinges is applicable, with some process modifications, to the creation of particles at even smaller, 100 nm length scales22, 26 and with a range of materials including metals21, semiconductors9 and polymers27. With respect to residual stress powered actuation of reconfigurable grasping devices, our specific protocol utilizes chromium hinges of relevance to devices with sizes ranging from 100 &mu;m to 2.5 mm. However, more generally, the concept of such tether-free residual stress powered actuation can be used with alternate high-stress materials such as heteroepitaxially deposited semiconductor films5,7 to possibly create even smaller nanoscale grasping devices.

We describe experimental details of the synthesis of patterned and reconfigurable particles from two dimensional (2D) precursors. This methodology can be used to create particles in a variety of shapes including polyhedra and grasping devices at length scales ranging from the micro to centimeter scale.

There are numerous techniques such as photolithography, electron-beam lithography and soft-lithography that can be used to precisely pattern two ...

Synthesis of Zeolites Using the ADOR (Assembly-Disassembly-Organization-Reassembly) Route

Zeolites are an important class of materials that have wide ranging applications such as heterogeneous catalysts and adsorbents which are dependent on their framework topology. For new applications or improvements to existing ones, new zeolites with novel pore systems are desirable. We demonstrate a method for the synthesis of novel zeolites using the ADOR route. ADOR is an acronym for Assembly, Disassembly, Organization and Reassembly. This synthetic route takes advantage of the assembly of a relatively poorly stable that which can be selectively disassembled into a layered material. The resulting layered intermediate can then be organized in different manners by careful chemical manipulation and then reassembled into zeolites with new topologies. By carefully controlling the organization step of the synthetic pathway, new zeolites with never before seen topologies are capable of being synthesized. The structures of these new zeolites are confirmed using powder X-ray diffraction and further characterized by nitrogen adsorption and scanning electron microscopy. This new synthetic pathway for zeolites demonstrates its capability to produce novel frameworks that have never been prepared by traditional zeolite synthesis techniques.

Synthesis of Zeolites Using the ADOR Assembly-Disassembly-Organization-Reassembly Route

A protocol for the preparation of novel zeolites by the ADOR (Assembly-Disassembly-Organization-Reassembly) synthetic route is presented.

Zeolites are an important class of materials that have wide ranging applications such as heterogeneous catalysts and adsorbents which are dependent on ...

Direct Imaging of Laser-driven Ultrafast Molecular Rotation

We present a method for visualizing laser-induced, ultrafast molecular rotational wave packet dynamics. We have developed a new 2-dimensional Coulomb explosion imaging setup in which a hitherto-impractical camera angle is realized. In our imaging technique, diatomic molecules are irradiated with a circularly polarized strong laser pulse. The ejected atomic ions are accelerated perpendicularly to the laser propagation. The ions lying in the laser polarization plane are selected through the use of a mechanical slit and imaged with a high-throughput, 2-dimensional detector installed parallel to the polarization plane. Because a circularly polarized (isotropic) Coulomb exploding pulse is used, the observed angular distribution of the ejected ions directly corresponds to the squared rotational wave function at the time of the pulse irradiation. To create a real-time movie of molecular rotation, the present imaging technique is combined with a femtosecond pump-probe optical setup in which the pump pulses create unidirectionally rotating molecular ensembles. Due to the high image throughput of our detection system, the pump-probe experimental condition can be easily optimized by monitoring a real-time snapshot. As a result, the quality of the observed movie is sufficiently high for visualizing the detailed wave nature of motion. We also note that the present technique can be implemented in existing standard ion imaging setups, offering a new camera angle or viewpoint for the molecular systems without the need for extensive modification.

We present a protocol for creating a real-time movie of a molecular rotational wave packet using a high-resolution Coulomb explosion imaging setup.

We present a method for visualizing laser-induced, ultrafast molecular rotational wave packet dynamics. We have developed a new 2-dimensional Coulomb ...

Grafting Multiwalled Carbon Nanotubes with Polystyrene to Enable Self-Assembly and Anisotropic Patchiness

We demonstrate a straightforward protocol to graft pristine multiwalled carbon nanotubes (MWCNTs) with polystyrene (PS) chains at the sidewalls through a free-radical polymerization strategy to enable the modulation of the nanotube surface properties and produce supramolecular self-assembly of the nanostructures. First, a selective hydroxylation of the pristine nanotubes through a biphasic catalytically mediated oxidation reaction creates superficially distributed reactive sites at the sidewalls. The latter reactive sites are subsequently modified with methacrylic moieties using a silylated methacrylic precursor to create polymerizable sites. Those polymerizable groups can address further polymerization of styrene to produce a hybrid nanomaterial containing PS chains grafted to the nanotube sidewalls. The polymer-graft content, amount of silylated methacrylic moieties introduced and hydroxylation modification of the nanotubes are identified and quantified by Thermogravimetric Analysis (TGA). The presence of reactive functional groups hydroxyl and silylated methacrylate are confirmed by Fourier Transform Infrared Spectroscopy (FT-IR). Polystyrene-grafted carbon nanotube solutions in tetrahydrofuran (THF) provide wall-to-wall collinearly self-assembled nanotubes when cast samples are analyzed by transmission electron microscopy (TEM). Those self-assemblies are not obtained when suitable blanks are similarly cast from analogous solutions containing non-grafted counterparts. Therefore, this method enables the modification of the nanotube anisotropic patchiness at the sidewalls which results into spontaneous auto-organization at the nanoscale.

A procedure for the synthesis of polystyrene-grafted multiwalled carbon nanotubes using successive chemical modification steps to selectively introduce the polymer chains to the sidewalls and their self-assembly via anisotropic patchiness is presented.

We demonstrate a straightforward protocol to graft pristine multiwalled carbon nanotubes (MWCNTs) with polystyrene (PS) chains at the sidewalls through a ...

Combustion Chemistry of Fuels: Quantitative Speciation Data Obtained from an Atmospheric High-temperature Flow Reactor with Coupled Molecular-beam Mass Spectrometer

This manuscript describes a high-temperature flow reactor experiment coupled to the powerful molecular beam mass spectrometry (MBMS) technique. This flexible tool offers a detailed observation of chemical gas-phase kinetics in reacting flows under well-controlled conditions. The vast range of operating conditions available in a laminar flow reactor enables access to extraordinary combustion applications that are typically not achievable by flame experiments. These include rich conditions at high temperatures relevant for gasification processes, the peroxy chemistry governing the low temperature oxidation regime or investigations of complex technical fuels. The presented setup allows measurements of quantitative speciation data for reaction model validation of combustion, gasification and pyrolysis processes, while enabling a systematic general understanding of the reaction chemistry. Validation of kinetic reaction models is generally performed by investigating combustion processes of pure compounds. The flow reactor has been enhanced to be suitable for technical fuels (e.g. multi-component mixtures like Jet A-1) to allow for phenomenological analysis of occurring combustion intermediates like soot precursors or pollutants. The controlled and comparable boundary conditions provided by the experimental design allow for predictions of pollutant formation tendencies. Cold reactants are fed premixed into the reactor that are highly diluted (in around 99 vol% in Ar) in order to suppress self-sustaining combustion reactions. The laminar flowing reactant mixture passes through a known temperature field, while the gas composition is determined at the reactors exhaust as a function of the oven temperature. The flow reactor is operated at atmospheric pressures with temperatures up to 1,800 K. The measurements themselves are performed by decreasing the temperature monotonically at a rate of -200 K/h. With the sensitive MBMS technique, detailed speciation data is acquired and quantified for almost all chemical species in the reactive process, including radical species.

An investigation of the oxidative combustion chemistry of novel biofuels, fuel components, or jet fuels by comparison of quantitative speciation data is presented. The data can be used for kinetic model validation and enables fuel assessment strategies.This manuscript describes the atmospheric high-temperature flow reactor and demonstrates its capabilities.

This manuscript describes a high-temperature flow reactor experiment coupled to the powerful molecular beam mass spectrometry (MBMS) technique. This ...

Stereolithographic 3D Printing with Renewable Acrylates

The accessibility of cost-competitive renewable materials and their application in additive manufacturing is essential for an efficient biobased economy. We demonstrate the rapid prototyping of sustainable resins using a stereolithographic 3D printer. Resin formulation takes place by straightforward mixing of biobased acrylate monomers and oligomers with a photoinitiatior and optical absorber. Resin viscosity is controlled by the monomer to oligomer ratio and is determined as a function of shear rate by a rheometer with parallel plate geometry. A stereolithographic apparatus charged with the biobased resins is employed to produce complex shaped prototypes with high accuracy. The products require a post-treatment, including alcohol rinsing and UV irradiation, to ensure complete curing. The high feature resolution and excellent surface finishing of the prototypes is revealed by scanning electron microscopy.

A protocol for additive manufacturing with renewable photopolymer resins on a stereolithography apparatus is presented.

The accessibility of cost-competitive renewable materials and their application in additive manufacturing is essential for an efficient biobased economy. ...

Light-driven Molecular Motors on Surfaces for Single Molecular Imaging

The design and synthesis of a synthetic system that aims for the direct visualization of a synthetic rotary motor at the single molecule level on surfaces are demonstrated. This work requires careful design, considerable synthetic effort, and proper analysis. The rotary motion of the molecular motor in solution is shown by 1H NMR and UV-vis absorption spectroscopy techniques. In addition, the method to graft the motor onto an amine-coated quartz is described. This method helps to gain more insight into molecular machines.

The manuscript describes how to synthesize and graft a molecular motor on surfaces for single molecular imaging.

The design and synthesis of a synthetic system that aims for the direct visualization of a synthetic rotary motor at the single molecule level on surfaces ...

Inkjet Printing All Inorganic Halide Perovskite Inks for Photovoltaic Applications

A method for synthesizing photoactive inorganic&#160;perovskite quantum dot inks and an inkjet printer deposition method, using the synthesized inks, are demonstrated. The ink synthesis is based on a simple wet chemical reaction and the inkjet printing protocol is a facile step by step method. The inkjet printed thin films have been characterized by X-ray diffraction, optical absorption spectroscopy, photoluminescent spectroscopy, and electronic transport measurements. X-ray diffraction of the printed quantum dot films indicates a crystal structure consistent with an orthorhombic room temperature phase with (001) orientation. In conjunction with other characterization methods, the X-ray diffraction&#160;measurements show high quality films can be obtained through the inkjet printing method.

A protocol for synthesizing inorganic-lead-halide hybrid perovskite quantum dot inks for inkjet printing and the protocol for preparing and printing the quantum dot inks in an inkjet printer with post characterization techniques are presented.

A method for synthesizing photoactive inorganic&#160;perovskite quantum dot inks and an inkjet printer deposition method, using the synthesized inks, are ...

Reactive Inkjet Printing and Propulsion Analysis of Silk-based Self-propelled Micro-stirrers

In this study, a protocol for using reactive inkjet printing to fabricate enzymatically propelled silk swimmers with well-defined shapes is reported. The resulting devices are an example of self-propelled objects capable of generating motion without external actuation and have potential applications in medicine and environmental sciences for a variety of purposes ranging from micro-stirring, targeted therapeutic delivery, to water remediation (e.g., cleaning oil spills). This method employs reactive inkjet printing to generate well-defined small-scale solid silk structures by converting water soluble regenerated silk fibroin (silk I) to insoluble silk fibroin (silk II). These structures are also selectively doped in specific regions with the enzyme catalase in order to produce motion via bubble generation and detachment. The number of layers printed determines the three-dimensional (3D) structure of the device, and so here the effect of this parameter on the propulsive trajectories is reported. The results demonstrate the ability to tune the motion by varying the dimensions of the printed structures.

This protocol demonstrates the ability to utilize reactive inkjet printing to print self-motile biocompatible and environmentally friendly micro-stirrers for use in biomedical and environmental applications.

In this study, a protocol for using reactive inkjet printing to fabricate enzymatically propelled silk swimmers with well-defined shapes is reported. The ...

Assembly and Characterization of Polyelectrolyte Complex Micelles

Polyelectrolyte complex micelles (PCMs), core-shell nanoparticles formed by self-assembly of charged polymers in aqueous solution, provide a powerful platform for exploring the physics of polyelectrolyte interactions and also offer a promising solution to the pressing problem of delivering therapeutic oligonucleotides in vivo. Developing predictive structure-property relationships for PCMs has proven difficult, in part due to the presence of strong kinetic traps during nanoparticle self-assembly. This article discusses criteria for choosing polymers for PCM construction and provides protocols based on salt annealing that enable assembly of repeatable, low-polydispersity nanoparticles. We also discuss PCM characterization using light scattering, small-angle X-ray scattering, and electron microscopy.

We provide protocols and representative data for designing, assembling, and characterizing polyelectrolyte complex micelles, core-shell nanoparticles formed by polyelectrolytes and hydrophilic charged-uncharged block copolymers.

Polyelectrolyte complex micelles (PCMs), core-shell nanoparticles formed by self-assembly of charged polymers in aqueous solution, provide a powerful ...