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Diamond 3 操作 認識 cif 檔案及繪製結晶結構

Diamond 3 操作 認識 cif 檔案及繪製結晶結構. Ta-Wei Li NCTU. How to import cif-formated crystal structure data files How to let DIAMOND create a structure picture automatically Hoe to find cif-formated crystal structure data files in ICSD or WWW. Today ’ s Job. How to open a “ cif ” file -- 1.

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Diamond 3 操作 認識 cif 檔案及繪製結晶結構

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  1. Diamond 3 操作認識cif檔案及繪製結晶結構 Ta-Wei Li NCTU

  2. How to import cif-formated crystal structure data files How to let DIAMOND create a structure picture automatically Hoe to find cif-formated crystal structure data files in ICSD or WWW Today’s Job

  3. How to open a “cif” file -- 1 • Start the DIAMOND 3 software • Click on “Open a file” • Set the file type into ”CIF (*.cif)”, and then go to “C:\Program Files\Diamond 3\Tutorial” • Select the file ”c60.cif”

  4. How to open a “cif” file -- 2

  5. How to open a “cif” file -- 3

  6. Phase Data and Atomic Parameters • Structure picture • Tables pane • Phase Data : • Space group • Cell edge : a, b, c • Cell volume. • Atomic Parameters • Relative coordinates of atoms, x/a, y/b, z/c

  7. Tools of investigating crystals

  8. Diamond question 1 • Please find a 6C ring which has bond angle very close to 120.5°. Now, please measure 6 C-C bond distances of any 6C ring on C60 and answer the following questions: (20%) • Are their bond length all the same? • If not, how many C-C bonds are the same? What are their bond length? • Please open and read “pyrene.cif”. What is the chemical formula of “pyrene”. (10%)

  9. Build Body Center Cubic Structure

  10. Crystal Symmetry – Translation Im3m

  11. Crystal Symmetry – InversionIm3m (x & z axes)

  12. Crystal Symmetry – RotationIm3m (y axis)

  13. Create W Crystals with Type in Atomic Positions and Space Group • First, close all the cif file and back to the “START” page of Diamond • Select “Create a new document“ and then select “Create a document and type in structure parameters”

  14. Type in cell parameters • Select “Next” • When you type in cell parameters • First click “Browse” and select the space group : Im-3m (#229) • Type “3.1652” in cell length of a • Click “Next”

  15. Type in Atomic Parameters • Type “W” in Atom • Type “0” in x/a • Type “0” in y/b • Type “0” in z/c • Click “add” and “next” • Click “Finish”

  16. Hexagonal Close Packed Structure

  17. Create Mg Crystals with Type in Atomic Positions and Space Group • Click “File” and then “New • Select “Create a new document“ and then select “Create a document and type in structure parameters”

  18. Type in cell parameters • Select “Next” • When you type in cell parameters • First click “Browse” and select the space group : P63/mmc (#194) • Type “3.2094” in cell length of a • Type “5.2105” in cell length of c • Click “Next”

  19. Type in Atomic Parameters • Add 1st Mg atom • Type “Mg” in Atom • Type “1/3” in x/a • Type “2/3” in y/b • Type “1/4” in z/c • Click “Add” • Add 2nd Mg atom • Type “Mg” in Atom • Type “2/3” in x/a • Type “1/3” in y/b • Type “3/4” in z/c • Click “Add” and then “next” • Click “Finish”

  20. View HCP in the superlattice • Click “Build”, “Fill”, and then “Super Cell” • Select “3x3x3 cells …” • Click “OK” • Click “select” tool and select the second layer of Mg atoms • Click the right button of the mouse and then select “Edit”, “Atom Designs”

  21. View HCP in different atomic models and angles • Then you can change the selected atoms into different color and model, e.g. green and space fill • Click “Rotate Along x- and y- Axis …” to see HCP in different angles

  22. Some Crystal Structures & Parameters

  23. Diamond practice 1 • Please use WebLab to draw Fe crystal and mark the lattice parameter a. Save the file as 「Fe.cif」. (10%) • Please use WebLab to draw Au crystal and mark the lattice parameter a. Save the file as 「Au.cif」. (10%) • Please use WebLab to draw Zn crystal and mark the lattice parameter a. Save the file as 「Zn.cif」. (10%)

  24. Diamond practice 2 • 請利用Diamond 做出氯化鋰，並存成「LiCl.cif」(20%) • 氯化鋰的晶體參數為 • a=5.08, b=5.08, c=5.08 • a=90, b=90, g=90 • Space group:FM3-M (225) • Li 在晶格中的相對位置 0 0 0 • Cl在晶格中的相對位置 0.5 0.5 0.5

  25. Diamond practice 3 • 請利用Diamond 做出硫化鋅，並存成「ZnS.cif」(20%) • 硫化鋅的晶體參數為 • a=5.345, b=5.345, c=5.345 • a=90, b=90, g=90 • Space group: F-43M (216) • Zn 在晶格中的相對位置 0 0 0 • S在晶格中的相對位置 0.25 0.25 0.25

  26. Diamond Homework • Use MS Word to write the answers of “Diamond question 1” and save as「diamond.doc」 • Put diamond.doc, Fe.cif, Zn.cif, Au.cif, LiCl.cif and ZnS.cif all in the same folder “diamond”. Then zip the folder as diamond.zip • Before the midnight of Mar 17, please upload diamond.zip to BB system. • 3月17日午夜十二點以前繳交，滿分100分 • 3月24日午夜十二點以前繳交，滿分80分 • 3月24日午夜十二點以後就不需要繳交，以0分計算

  27. References • G.S. Rohrer, Structure and Bonding in Crystalline Materials. Cambridge University Press, 2001. • U. Müller, Inorganic Structural Chemistry. John Wiley & Sons, Chichester, 1993. • J. Barrett, Structure and Bonding. Royal Society of Chemistry, London, 2001. • M.F.C. Ladd, Symmetry in Molecules and Crystals. Ellis Horwood Ltd., Chichester, 1989. • F. A. Cotton, Chemical applications of group theory (1971) John Wiley & Sons, New York.

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