Presentation gives an overview of available open access databases of crystals and crystal structures, as well as discussions of how newly developed 3D printing technologies can be used to teach crystallography at the college level. Offers advice regarding conversion of crystallographic information files to 3D printing files, and shares news from the 3D printing of crystallographic models community

Grazulis, Saulius

International Advisory Board of the Crystallography Open Database

Kaminsky, Werner

Moeck, Peter

Snyder, Trevor J.

Stone-Sundberg, Jennifer

PDXScholar (Portland State University)

Portland State UniversityPDXScholarPhysics Faculty Publications and Presentations Physics20143D Printing & Open Access Databases for CrystallographicCollege EducationPeter MoeckPortland State University, pmoeck@pdx.eduJennifer Stone-SundbergPortland State UniversityTrevor J. Snyder3d Systems CorporationWerner KaminskyUniversity of Washington - Seattle CampusSaulius GrazulisInstitute of Biotechnology, Vilnius, LithuaniaSee next page for additional authorsLet us know how access to this document benefits you.Follow this and additional works at: http://pdxscholar.library.pdx.edu/phy_facPart of the Nanoscience and Nanotechnology Commons, and the Physics CommonsThis Presentation is brought to you for free and open access. It has been accepted for inclusion in Physics Faculty Publications and Presentations by anauthorized administrator of PDXScholar. For more information, please contact pdxscholar@pdx.edu.Citation DetailsMoeck, P.; Stone-Sundberg, J.; Snyder, T.J.; Kaminsky, W.; Gražulis, S.; and all members of the International Advisory Board of theCrystallography Open Database, "3D printing & open access databases for crystallographic college education," IUCr 23rd Congress onCrystallography, Montreal, Canada, 2014.AuthorsPeter Moeck, Jennifer Stone-Sundberg, Trevor J. Snyder, Werner Kaminsky, Saulius Grazulis, andInternational Advisory Board of the Crystallography Open DatabaseThis presentation is available at PDXScholar: http://pdxscholar.library.pdx.edu/phy_fac/2361Peter Moeck1, Jennifer Stone-Sundberg1,2, Trevor J. Snyder3,1, Werner Kaminsky4, Saulius Gražulis5, and all members of the International Advisory Board of the Crystallography Open Database1 Nano-Crystallography Group, Department of Physics, Portland State University, Portland/Oregon2 Crystal Solutions, LLC, Portland/Oregon3 3D Systems Corporation, Wilsonville/Oregon4 Department of Chemistry, University of Washington at Seattle5 Institute of Biotechnology, Vilnius University, Vilnius, LithuaniaFunding: National Science Foundation (most recent NEU: Nano-Science & Engineering: A STE Minor with General Education, EEC-1242197), NorthWest Academic Computing Consortium, Portland State University, Research Council of Lithuania, PANalytical, Crystal Impact, 3D printing & open access databases for crystallographic college education2Outline1. Wikipedia entry and Crystallography Open Database (COD) in its 12th year2. Supporting efforts at Portland State University in their 11thyear3. Converting Crystallographic Information Files (CIF) to 3D printing files (STL, VRML) – a few models to pass around, a selection of materials to print in from Quickparts.com 4. News from the 3D printing of crystallographic models community5. Plans for Bicrystallography Open Database6. Summary3open accessover 293,000 entriesat least 1/3 of all known structure data in open open access4http://www.crystallography.netmirrors worldwidehttp://cod.ibt.lthttp://cod.ensicaen.frhttp://qiserver.ugr.es/codhttp://nanocrystallography.orgweb portal: http://nanocrystallography.netas of Aug. 8, 11:20 am: 293,109entriesAdvisory BoardDaniel Chateigner, Xiaolong Chen, Marco Ciriotti, Robert T. Downs, Saulius Gražulis, Werner Kaminsky, Armel Le Bail, Luca Lutterotti, Yoshitaka Matsushita, Peter Moeck, Peter Murray-Rust, Miguel Quirós Olozábal, Hareesh Rajan, Alexandre F.T. Yokochi Crystallography Open Database5_publ_section_title;Neutron and x-ray structure refinements between 15 and 1083 K ofpiezoelectric gallium arsenate, Ga As O4: temperature and pressurebehavior compared with other $-alpha-quartz materials;loop__publ_author_name'Philippot, E''Armand, P''Yot, P''Cambon, O''Goiffon, A''McIntyre, G J''Bordet, P'_journal_name_full                 'Journal of Solid State Chemistry'_journal_coden_ASTM                JSSCBI_journal_volume                    146_journal_year                      1999_journal_page_first                114_journal_page_last                 123_cell_length_a                     4.9940(1)_cell_length_b                     4.9940(1)_cell_length_c                     11.3871(4)_cell_angle_alpha                  90_cell_angle_beta                   90_cell_angle_gamma                  120_cell_volume                       245.9_cell_formula_units_Z              3_symmetry_space_group_name_H-M     'P 31 2 1'_symmetry_Int_Tables_number        152_symmetry_cell_setting             trigonalloop__symmetry_equiv_pos_as_xyz'x,y,z''-y,x-y,1/3+z''y-x,-x,2/3+z''y,x,-z''-x,y-x,1/3-z''x-y,-y,2/3-z'loop__atom_type_symbol_atom_type_oxidation_numberGa3+   3.000As5+   5.000O2- -2.0006Gražulis S. et al. Nucl. Acids Res. 40 (2012) D420-D427, open accessloop_ _refln_index_h _refln_index_k _refln_index_l _refln_F_squared_calc _refln_F_squared_meas _refln_F_squared_sigma _refln_observed_status 1 0 0 88.50 107.46 1.41 o 2 0 0 443.74 483.55 3.27 o 3 0 0 105.70 102.49 1.73 o4 0 0 109.80 97.14 0.68 o5 0 0 61.24 59.93 0.88 o    7much much much less data than COD, emphasis on education89about 950 structures: inorganics, organics, a few  proteins1011Space group P21: A screw axis along the b axis means there are 8 more screw axes parallel to [010], including one through the middle of the unit cell12131415all good open access crystallography resources, e.g. CIFs, space group drawings, history, …http://nanocrystallography.net16prices for 3D printing will come down !Fig.  4 Mid 2012 “expectations versus time” graph of the Gartner group, showing 3D printing at the “peak of inflated expectations” and extrapolating to its “plateau of productivity” in 2017 (to 2022 at the latest).17$2,500 USAn inexpensivemonochrome printer from 3D Systems Corporation (less than $1,000 US), on the basis of their Plastic Jet 3D printing technology.Projet 4500 MultijetTM printer of 3D Systems Corporation, currently the only printer that produces color prints in durable plastics. $69,000 USColorJet Printing (CJP) technology platform and new class of durable VisiJet® C4 Spectrum plastics.one does not need to own a 3D printer, there are professional over-night print shops, e.g. http://www.3dsystems.com/quickparts18http://www.iucr.org/news/newsletter/volume-22/number-1/3d-printing*.cif  to *.stl W. Kaminsky et al., One-click preparation of 3D print files (*.stl, *.wrl) from *.cif (crystallographic information framework) data using Cif2VRML, Powder Diffraction, accepted19designed with a CAD programconverted from CIF to STL with Cif2VRML and WinXMorphP. Moeck et al., Enlivening 300 level general education classes on nanoscience and nanotechnology with 3D printed crystallographic models, J. Mater. Education, accepted20sucrose (with hydrogen bonds)chlorophylldeoxyribonucleic acid(containing a planar phenoxazine-derived bi-functional spectroscopic probe) all printed from CIFs converted to *.wrl (say ‘vormel’) in durable VisiJet® C4 Spectrum plastics with ProJet 450021Tim Herman et al., “Tactile teaching: Exploring protein structure/function using physical models”,Biochemistry and Molecular Biology Education 34 (2006) 241–314, DOI: 10.1002/bmb.2006.4940340426491998Timothy Herman: "I was so intrigued with the technology that I left my position at the Medical College of Wisconsin and opened the … “in Milwaukee.http://cbm.msoe.edu/J. Graber, 3D Printer World,December 9, 2013RP Rasmol,exports STL and VRML Jmol & JSmol (Robert Hanson & coworkers)”Models function as thinking tools that stimulate questions and are a key component of the Next Generation Science Standards”.22232425Biennial Conference on Chemical Education (BCCE), August 4, 2014, Allendale, Michigan26Bicrystallography Open Databasesearchable collection of CIFs for all kinds of simulations and visualizations of grain boundaries to be derived from user inputs and freely modifiable at the atomic level27p21’mn’ - polar physical properties can existp2’mm’ - polar physical properties cannot existtwo color layer group c2’mc’ - a genuine back-white group, polar physical properties can existtwo color layer group c2’mm’ – a gray group, polar physical properties cannot existCeO2 Σ = 5 (310)/[001] 36.9°tilt boundary, dichromatic complex has 3 atoms per lattice point of dichromatic pattern I4/mm’m’CeO2 Σ = 5 (120)/[001] 53.1°tilt boundary viewed down [001]“… disclose generic relations between different interfaces, specify crystallo-graphically equivalent variants of an interface and classify line defects in interfaces. The symmetry of a bicrystal imposes constraints on tensor properties of the bicrystal interface, provides classification of the interfacial vibrational modes, discloses possible interfacial transitions etc.”V. Janovec, Th. Hahn and H. Klapper, Twinning and domain structures, International Tables for Crystallography (2006), Vol. D, ch. 3.2, pp. 377-392.Bicrystallography Open DatabaseNo textbook, only a few original papers and book chaptersdiamond, Σ = 5 (310)/[001] 36.9°tilt boundary, viewed down [001], black white (two color) layer group p21’am’R. C. Pond and J. P. Hirth, in Ehrenreich, H., Solid State Physics: Advances in Research and Applications, Volume 47, 1994,  pp. 287-36528Frieze Group     11gSrTiO3Σ = 13a, (510)/[001], 22.6°tilt boundary in [001] projection, sectioned at ¼[510], large disks Sr columns, medium disks pure O columns, small disks mixed O and Ti columnsonly pure O columns are located at interface1 nmP. Moeck et al. Cryst. Res. Technol. 2014, accepted / H. Yang et al., Phil. Mag. 93 (2013) 1219-1229 Aberration-corrected translation-symmetry averaged STEM Z-contrast imaging …primitive cubic lattice, 5 atoms per lattice point of dichromatic pattern P4/mm’m’, zero rigid body shift and expansion for simplicity29some 350,000 – 400,000 CIFs in open access crystallographic databasesCOD in its 12th year, more than 293,000 CIFsEDU-COD in its 11th year, CMD in its 7th year, approx. 1,000 CIFs totalprograms for conversion of CIF (molecule structures, crystal morphologies, grain boundaries, … ) to STL and VRML by Werner Kaminsky http://cad4.cpac.washington.edu/, (color printing only from VRML files)programs are free for individuals, license from UW for all commercial purposes3D printing will come down in price significantly, good for hands-on models in classplans for Bicrystallography Open Databaseopen access crystallography resource portal, nanocrystallography.netsimply google for “open-access crystallography”30related presentationsChemical information presentation in the Crystallography Open Database, Andrius Merkys, … and Saulius Gražulisposter A566, 8/07/2014, 18:30-20:30         CC.P25.A566 (C1710)Launching the Theoretical Crystallography Open Database,Saulius Gražulis …poster A594, 8/07/2014, 18:30-20:30 IT.P14.A594 (C1736)COD at the Software Fayre (Fair), Saulius Gražulis and Andrius Merkys, … 8/8/2014, 11:00 – 11:45, room 519b3D printing of crystallographic models from open access databases, Werner Kaminsky, … and Peter Moeckposter B422, 8/11/2014, 18:30-20:30 MS84.P08.B422 (C1278)31Leroy Cronin: “I don’t want chemistry reduced to plastic trinkets, I want new science to occur as a result of use of ubiquitous 3-D printing and molecular design.”in Halford B. (2014), “3D Models, Without the Kit”, Chemical and Engineering News 92, 32–33.32Merci beaucoup pour vôtre attention!Thank you very much indeed for your attention!3D printing of crystallographic models from open access databases, Werner Kaminsky, … and Peter Moeckposter B422, 8/11/2014, 18:30-20:30 MS84.P08.B422 (C1278)33http://nanocrystallography.research.pdx.edu/media/sugar_molecule_stl.stlhttp://nanocrystallography.research.pdx.edu/media/sugar_morphology_stl.stlour first two 3D print files in open access (April 2014)34access statistics: nanocrystallography.research.pdx.edu, June 1, 2012 to July 31, 2014 35access statistics: nanocrystallography.research.pdx.edu, June 1, 2012 to July 31, 2014 36Caffeine right/large and in Werner’s hand: printed with the so called Z-corp (MIT) technique, dried colored gypsum water mixture dipped into superglue (now ZPrinter series of 3D Systems Corporation, approximately $ 0.25 US per printed cubic centimeter, but models tend to be a bit fragile).left/small printed with a ProJet 4500, the utilized proprietary plastic is much more durable W. Kaminsky et al., One-click crystallographic information framework) data using Cif2VRML preparation of 3D print files (*.stl, *.wrl) from *.cif, Powder Diffraction, accepted37Herapathite, the molecule behind the early fortune of the Kodak companya few 3D printers read *.wrl files (VRML format, say ‘vormel’ )38Biennial Conference on Chemical Education (BCCE), Allendale, Michigan

3D Printing & Open Access Databases for Crystallographic College Education

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3D Printing & Open Access Databases for Crystallographic College Education

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