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.