Diamond 3 操作 認識 cif 檔案及繪製結晶結構 Ta-Wei Li NCTU. Today ’ s Job How to...
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Transcript of Diamond 3 操作 認識 cif 檔案及繪製結晶結構 Ta-Wei Li NCTU. Today ’ s Job How to...
Diamond 3 操作認識 cif檔案及繪製結晶結構
Ta-Wei Li
NCTU
Today’s Job
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
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”
How to open a “cif” file -- 2
How to open a “cif” file -- 3
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
Tools of investigating crystals
測量距離
測量角度
測量旋轉角
繞著x 或 y
軸旋轉
繞著z 軸旋轉
平移 放大
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%)
Build Body Center Cubic Structure
Atom W
Space Group Im3m (#229)
Cell Dimensions
a = 3.1652Å
Atomic Positions:
(0,0,0)
Crystal Symmetry – Translation Im3m
Crystal Symmetry – InversionIm3m (x & z axes)
Crystal Symmetry – RotationIm3m (y axis)
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”
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”
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”
Hexagonal Close Packed Structure
Atom Mg
Space GroupP63/mmc (#194)
Cell Dimensions
a=b= 3.2094Å
c = 5.2105Å
Atomic Positions:
(1/3, 2/3, 1/4)
(2/3, 1/3, 3/4)
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”
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”
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”
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”
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
Some Crystal Structures & Parameters
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%)
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
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
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
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.