Laboratory Manual 1.0.

7

Background

What is X-ray Diffraction?
X-rays scatter off of electrons, in a process of absorption and re-admission. Diffraction is
the accumulative result of the x-ray scattering of a group of electrons that are spaced in an
orderly array. For an incident X-ray photon of monochromatic wavelength , coherent
waves are produced from the sample at an angle of (2- with respect to the incident x-ray
beam) if the electron groups interact with the x-ray beam and are spaced at a repeat
distance d. The interaction is described by Bragg's law : n=2dsin. The intensity of the
scattered x-ray is proportional to the number of electrons that the x-ray is scattered from.
Why use X-rays?
Normally one would use a microscope to view small objects. For a microscope, light is
scattered by an object and collected using lenses, which in turn magnifies the image of the
object. The limit of the microscope is intrinsic to the nature of the electromagnetic radiation
that is used to probe the object. If we use white light we cannot look at objects smaller
than the wavelength of light, which is about 10
-6
m. Since the atom has dimensions of
about 10
-10
m we cannot image an atom with a photon of white light. X-rays, on the other
hand, have a wavelength of about 10
-10
m and are suitable for imaging objects at the
atomic scale.

What are X-rays
X-rays are electromagnetic radiation of wavelength about 1 (10
-10
m)

which is about the
same size as an atom. They occur in that portion of the electromagnetic spectrum between
gamma rays and the ultraviolet. The discovery of X-rays in 1895 enabled scientists to probe
crystalline structure at the atomic level. X-ray diffraction has been employed in two main
areas: for the fingerprint characterization of crystalline materials and the determination of
their structure. Each crystalline solid has its unique characteristic X-ray powder pattern,
which may be used as a "fingerprint" for its identification. Once the material has been
identified, X-ray crystallography may be used to determine its structure, i.e. how the atoms
pack together in the crystalline state and what the inter-atomic distance and angle are etc.
X-ray diffraction is one of the most important characterization tools used in solid-state
chemistry and materials science.
We can determine the size and the shape of the unit cell for any compound most easily
using the diffraction of x-rays.



Diffraction of X-rays

Given that two parallel rays will strike a grating at an angle theta where the grating
separation is given as d then :
























An interference maximum will be observed when is an integral multiply (n) of .

This leads to the Bragg equation:
n = 2dsin

d
2d




2d

=
= =
= = =
=
=

=
sin 2
) (
' '
' '
sin 2
2
sin
d
difference path BC
BC AB AC then AB B A given
B A AC
d
d
A
B
C
A'
B'
X-ray Sources and Monochromation.
The two sources for in-house or laboratory X-rays are the sealed-tube and the rotating
anode types. The sealed tube is simply a glass or ceramic tube where a tungsten cathode
has been placed above a metallic stationary anode. The tube is then evacuated and current
is applied to the cathode and the anode. A rotating anode is similar to the sealed tube
instrument except for the fact that the metallic anode is now spinning. The spinning anode
spreads the heat of the electron bombardment over a wider area. This allows for higher
wattages, which produces a higher X-ray flux.
For diffraction experiments the X-rays should be monochromatic. To do this we employ
either a crystal monochromator or a metallic filter. The crystal monochromator produces
more monochromatic X-rays at the expense of X-ray flux. The metallic filter is normally
used with powder diffraction and results in high X-ray flux with poor monochromation.
The anode is also rectangular which allows for a line focus (which is broad but has low flux
and a point focus, which is intense but has a narrow illumination area. In practice the line
focus is used with powder diffraction so as to illuminate more sample and the point focus is
used in single crystal and small angle x-ray scattering instruments for higher flux for small
samples.
X-ray Sources
cathode
50kV
anode
e
-

Be window
primary beam
main beam
crystal (graphite)
monochromator
Focus
anode (top view)
line focus
point focus
sealed tube
rotating anode
Normal operation 40kV and 40ma the power =1600 watts

metal filter

anode
rotating anode ~4000rpm
50kV
cathode

e
-

main beam
evacuated
chamber
Normal operation 50kV x 180ma the power =9000 watts
The primary beam is used for
experimentation.
Single crystal work
requires a point focus,
while powder work
employs the line focus
The x-rays that are generated are of two types

1) Characteristic (ejection of electrons from the atom in the anode
2) White Radiation (synchrotron effect)








e
-











The energy of the X-ray is determined from the observed
wavelength and is given by the formula :

Energy (KeV) = 1.2398 / (nm)



M
Characteristic
X-rays
K
alpha
K
beta


White Radiation
Bremsstrahlung
or breaking radiation
Electron strikes the target and
ejects an electron. The cascade of
electrons from higher orbitals
generates X-ray
Electron reaccelerate when
entering the metal and "bend"
their trajectory path. Loss of
momentum results in generation
of X-rays.
Profile of X-rays generated by
electron ejection and
momentum loss. K alpha and
K beta are the characteristic
X-rays from the lowest
electron shells and are
superimposed on the white
radiation.
Energy for K alpha (for Mo) =17.28 KeV
Powder and Single Crystal Diffraction normally employ the K

characteristic
radiation, due to its intensity and monochromatic wavelengths.
Laboratory 1.
Radiation Safety for X-ray Diffractometers

To begin the X-ray Crystallography Laboratory you must complete the on-line
X-ray safety training.

http://xray.tamu.edu/safety_training.php

The following appendix is available for your information and not necessary
reading.

Bibliography

"Procedures Manual for Use of Radioisotopes and Radiation
Producing Devices", Office of Radiological Safety, Texas A & M
University

"A Guide to the Safe Use of X-ray Diffraction and Spectrometry
Equipment", Martin, E., Science Reviews Ltd., Ash Drive, Leeds,
LS 17 8RA U.K.

"A Case History of Severe Radiation Burns from 50 kVC X-rays",
Steidley, K., Stabile, R. & Santillippo, L. Health Physics (1981).
40 399-405.

"Analytical X-ray Hazards: A Continuing Problem" Lubenau, J .,
Davis, J ., McDonald, D. & Gerusky, T. Health Physics (1969). 16,
739-746.

"Occupational Hazards in X-ray Analytical Work" Lindel, B.
Health Physics (1968). 15, 481-486.

"Incidence, Detection and Monitoring of Radiation from X-ray
Analytical Instrumentation" J enkins, R. & Haas, D. X-ray
Spectrom (1975). 4, 33-39.

"Protection Against Radiation Injury" Cook, J . & Oosterkamp, W.
International Tables for Crystallography (1962). 333 -338.
X-ray Diffraction Laboratory 2.
X-RAY ANALYSIS OF SILICON
Warning : This laboratory employs X-rays (~10KeV). X-rays are
hazardous. All necessary safety procedures are in place. Instructors will
mount/dismount samples. The student is not allowed to enter the x-ray
enclosure.

Learning Experiences
Materials Analysis
Qualitative Analysis
Bragg's Law

In this lab you will measure the x-ray powder diffraction pattern from silicon. Your TA
will give you the sample to be measured and show you how to set up the D8 x-ray
diffractometer.

You should measure all the values of 2theta from the chart, and after converting them into
d values calculate the repeat distance in your unit cell. In your lab notebook list all the
2theta values with their corresponding values of n and d.


INSTRUMENTATION
The X-ray diffraction experiment requires an X-ray source, the sample under investigation
and a detector to pick up the diffracted X-rays. Figure 1 is a schematic diagram of a powder
X-ray diffractometer.














Fig. 1. Schematic of an X-ray powder diffractometer


R1

X-ray Tube
X-ray Detector
Receiving Slit
R2

R1 =R2

Sample
The X-ray radiation most commonly used is that emitted by copper, whose characteristic
average wavelength for the K radiation is 1.5418. When the incident beam strikes a
powder sample, diffraction occurs in every possible orientation of 2theta. The diffracted
beam may be detected by using a moveable detector such as a x-ray counter, which is
connected to a computer. In normal use, the counter is set to scan over a range of 2theta
values at a constant angular velocity. Routinely, a 2theta range of 5 to 90 degrees is
sufficient to cover the most useful part of the powder pattern.

PROCEDURE
**Do not open the enclosure while the alarm red light is on.
1. Obtain a sample from your instructor and place it into the sample holder.
2. Place sample holder in the sample positioner.
3. Record the values of the fixed slits.
4. Close the DOORS. The green ready light should be the only LED displayed
5. Run the COMMANDER program.
6. For RAW-file name type ijkSILICON wher ijk are YOUR initials
7. Add a title under sample identification.
8. Set the instrument at optimum setting as follows
time constant 1 deg/min
range 20 to 90
o
(2)
step size .04
9. Your scan should be complete in about 30 mins.
10. Save the *.raw file when scan is complete.
11. When finished : Close all windows and start EVA
12. Start the EVA program and import your RAW file.

13. Locate all peaks on the chart and corresponding 2theta values and write their values
into your lab notebook. Perform the necessary calculations in the table and calculate the
repeat distance.


14. Use the ZOOM key to zoom out the plot (if necessary).
15. Keep this information for Laboratory 3.
(You can cut and paste the results from the peak list to the notepad)
Use slid bar
append to
list when
finished
type this
tab to get
the peak
list.
16. Find Silicon in the ICCD data base.

17. PLOT the results
23. Print
the results
and be sure
you have
written
down the
peak
positions.
toggle all
unwanted
red all
wanted
green
CHECK
ONLY
THE *
reference
peaks
appear in
red
Laboratory 3. Indexing Powder Patterns


Learning Experiences
o - How to manually index a simple powder pattern.
o - Mathematics involved in pattern indexing

In this lab you will manually index the powder pattern for Silicon. An example of how to
index powder patterns is presented. The mathematics are introduced and the step by step
procedure is presented. You will need a calculator and a pencil.

For the peak positions of Silicon use the values that you determined in Laboratory 2.
or ask your Laboratory assistant for the values.

----------------------------------------------------------------------

Example How to Index the powder pattern for NaCl

Analytical Method : Equations

Given Braggs Law

2
2
2
4
sin
2
sin
sin 2
d
d
n
n d

=
=
=


d
*
can be determined as :

d
*
=1/d =(h
2
a
*
+k
2
b
*
+ l
2
c
*
+ 2hka
*
b
*
cos
*
+ 2hla
*
c
*
cos
*
+ 2klb
*
c
*
cos
*
)
1/2


See "Crystal Structure Determination" by Werner Massa pp 23-25.








For a cubic system a
*
=b
*
=c
*
=1/a and
*
=
*
=
*
=90 cos
*
=0.000 then



Let X =
2
/4a
2
and M =h
2
+k
2
+l
2


Now create a table for M values given h,k and l are integers




Table 1. M
n
=h
2
+ k
2
+ l
2

n h k l M
n

1
1 0 0 1
2
1 1 0 2
3
1 1 1 3
4
2 0 0 4
5
2 1 0
5
6
2 1 1 6
7
2 2 0 8
8
2 2 1 9
9
3 0 0 9
10
3 1 0 10
11
3 1 1 11
12
2 2 2 12
13
3 2 0 13
14
3 2 1 14
15
4 0 0 16
16
3 2 2 17
17
4 1 0 17
18
3 3 0 18
19
4 1 1 18
20
3 3 1 19
21
4 2 0 20
22
4 2 1 21
23
3 3 2 22
24
4 2 2 24
25
4 3 0 25
26
5 0 0 25
27
4 3 1 26
28
5 1 0 26
29
3 3 3 27
30
5 1 1 27
From the X-ray powder pattern we find the peak positions at 2 =38.52, 44.76, 65.14,
78.26, 82.47, 99.11, 112.03 and 116.6
o
Note for cubic systems :

1 0 0 =0 1 0 =0 0 1 2 0 0 =0 2 0 =0 0 2
1 1 0 =1 0 1 =0 1 1 2 2 0 =2 0 2 =0 2 2
etc

some h,k,l values share h
2
+k
2
+l
2
sums e.g. 2,2,1 and 3,0,0 sum
to h
2
+k
2
+l
2
=9

h, k and l must be integers.

Not all h
2
+k
2
+l
2
sums have integer h, k, l values (i.e. some
h
2
+k
2
+l
2
values are not possible)
2
2
2 2 2
2
2 2 2
2
2
2
2
2 2 2
2
4 ) (
sin
) (
4
sin
) ( 1
a l k h
l k h
a
a
l k h
d

=
+ +
+ + =
+ +
=

Table 2

2 sin
2
/M1 sin
2
/M2 sin
2
/M3 sin
2
/M4 sin
2
/M5 sin
2
/M6 sin
2
/M7 sin
2
/M8 sin
2
/M9 sin
2
/M10 sin
2
/M11
38.52 19.26 0.108805 0.054402 0.036268 0.027201 0.021761 0.018134 0.013601 0.012089 0.01088 0.01088 0.009891
44.76 22.38 0.144969 0.072484 0.048323 0.036242 0.028994 0.024161 0.018121 0.016108 0.014497 0.014497 0.013179
65.14 32.57 0.289799 0.144899 0.0966 0.07245 0.05796 0.0483 0.036225 0.0322 0.02898 0.02898 0.026345
78.26 39.13 0.398265 0.199132 0.132755 0.099566 0.079653 0.066377 0.049783 0.044252 0.039826 0.039826 0.036206
82.47 41.235 0.434477 0.217239 0.144826 0.108619 0.086895 0.072413 0.05431 0.048275 0.043448 0.043448 0.039498
99.11 49.555 0.579165 0.289583 0.193055 0.144791 0.115833 0.096528 0.072396 0.064352 0.057917 0.057917 0.052651
112.03 56.015 0.687546 0.343773 0.229182 0.171887 0.137509 0.114591 0.085943 0.076394 0.068755 0.068755 0.062504
116.6 58.3 0.72388 0.36194 0.241293 0.18097 0.144776 0.120647 0.090485 0.080431 0.072388 0.072388 0.065807
137.47 68.735 0.868462 0.434231 0.289487 0.217115 0.173692 0.144744 0.108558 0.096496 0.086846 0.086846 0.078951


Largest common sin
2
/M value(s) (X) are (see bold values above)

0.036268 =0.036242 =0.036225 =0.036206 = 0.0362 0.001 =X

inserting =0.0362 into the equation affords :

0.0362 =
2
/4a
2
a = (1.54056 )
2
/ 4 (0.0362)
2
= 4.049


From Table 2 we see that 0.0362 is the result for sin
2
/M
3
: M
3
is the result for h =1, k =1
and l =1. Completing the table for the first 4 peaks we now can assign these peaks with
h,k,l values

Table 3. M =h
2
+k
2
+l
2
h k l M
1 1 1 3
2 0 0 4
2 2 0 8
3 1 1 11

Or we can solve Braggs equation for each observed peak. For example for
2

= 38.52 : sin
2
/0.0362 =3.005652 or 3.00. From table 1 we see that M=3
is equivalent to h=1, k=1 and l =1. Therefore the peak at 38.52 is assigned as
the (1,1,1) reflection. Table 4 summarizes the results for all peaks and assigns
their h,k,l values.

Table 4

2 sin
2
/0.0362 M h,k,l
38.52 3.005652 3 1,1,1
44.76 4.004662 4 2,0,0
65.14 8.005491 8 2,2,0
78.26 11.00178 11 3,1,1
82.47 12.00214 12 2,2,2
99.11 15.99904 16 4,0,0
112.03 18.99298 19 3,3,1
116.6 19.99667 20 4,2,0
137.47 23.99066 24 4,2,2





Laboratory Particle: Index the following.

First Task. Fill in Table 1
e.g. for n=1 h=1,k=0,l=0 will afford M
1
=1




Table 1. Table of indices

n h k l M
n
1 1 0 0 1
2 1 1 0 2
3 1 1 1 3
4 4
5 5
6 6
7 8
8 9
9 9
10 10
11 11
12 12
13 13
14 14
15 16
16 17
17 17
18 18
19 19




Note for cubic systems :

1 0 0 =0 1 0 =0 0 1 2 0 0 =0 2 0 =0 0 2
1 1 0 =1 0 1 =0 1 1 2 2 0 =2 0 2 =0 2 2
etc

some h,k,l values share h
2
+k
2
+l
2
sums e.g. 2,2,1 and
3,0,0 sum to h
2
+k
2
+l
2
=9

h, k and l must be integers.

Not all h
2
+k
2
+l
2
sums have integer h, k, l values (i.e.
some h
2
+k
2
+l
2
values are not possible)
Table 2. List of sin
2
/ M
n
(n=1,..)

use only observed M
n


From your peak list from Laboratory 2 fill in this table. For example a peak at 26
o
2 will afford =13
o

sin
2
(13) =0.0506 sin
2
(13)/M
1
=0.0506/1 =0.0506 sin
2
(13)/M
2
=0.0506/2 =0.0253
Complete this table for your peaks. (or you may generate a spread sheet in EXCEL to do the same thing)

# 2 sin
2
/M1 sin
2
/M2 sin
2
/M3 sin
2
/M4 sin
2
/M5 sin
2
/M6 sin
2
/M8 sin
2
/M9 sin
2
/M10 sin
2
/M11 sin
2
/M12 sin
2
/M14 sin
2
/M15 sin
2
/M16
1

2

3

4

5

6

7

8

9

10


Continue for M
17
to M
30


sin
2
/M17 sin
2
/M18 sin
2
/M19 sin
2
/M20 sin
2
/M21 sin
2
/M22 sin
2
/M23 sin
2
/M24 sin
2
/M25 sin
2
/M26 sin
2
/M27 sin
2
/M28 sin
2
/M29 sin
2
/M30





















Largest common sin
2
value from Table 2 (value of X) = _________
Remember X =
2
/4a
2

Calculate unit cell a given = 1.54056 _________

Now complete Table 3 from the given information assign the h,k,l value for each peak.

Table 3 List of h, k, l values

Peak # sin
2
sin
2
/A h
2
+k
2
+l
2
=M hkl
1
2
3
4
5
6
7
8
9
10

Laboratory 4. Indexing Complex Patterns

Learning Experiences
o - Use of computer peak picking and indexing programs
o - Programs that you will use
Powder X (C. Dong)
"PowderX: Windows-95 based program for powder X-ray diffraction data processing",
C. Dong, J . Appl. Cryst. (1999), 32, 838-838
Treor (P-E. Werner)
TREOR, a semi-exhaustive trial-and-error powder indexing program for all symmetries.
Werner,P.-E.,Eriksson,L. and Westdahl,M., J.Appl. Cryst.. 18(1985)367-370.

Link to this web site to download POWDERX : www.chem.tamu.edu/xray/pwdx.zip

In this lab you will index a powder pattern from a known and unknown sample. You will
need to use the computers in the X-ray Laboratory. Bring a calculator, your notebook and
a pencil.

The three steps to Indexing and Refined Unit Cell Parameters

1. Peak Picking
- Generation of a list of d
hkl
and their intensities
2. Peak Indexing with the program TREOR
- Choice of unit cell parameters based on the number of
reflections indexed and the figure of merit.
3. Indexing and Cell parameters refinement



1. Peak Picking. Begin the program POWDERX and load the Ascorbic
Acid data.


--- Point to peak and pick simple peak (picking)



Pick show and ok (do not change the tolerances)

Note : The raw data file is in
the BRUKER RAW format.
This is input with the Simens
*.RAW selection.

(Siemens was bought out by
BRUKER in 2000)





Keep the wavelength and save the results.






Caution : If you have
background that has been
choosen as a peak then
click on the ZOOM
feature and ZOOM in on
the area in question.
Then use the add/delete
peak function (right click
on peak) to remove the
unwanted peak. When in
doubt ask the instructor
Point to OK






Example of the Table of peak
positions from the peak Pick
routine
Step 2. Indexing unit cell with the program TREOR

Point to index and Treor




Point to file and use current peaks



















Save (overwrite) the file if prompted.
You should see a
table similar to
this one. This is
the TREOR input
file and can be edit
if necessary..
Point to Start and VBTreor90

Let the program run and examine (print) the output for later study.
(point to file and then print)





Summary of TEROR output

Scroll down the TEROR listing file and find : THIS MAY BE THE
SOLUTION
This is a good sign that you have successfully indexed the cell


0 LI NES ARE UNI NDEXED. <- number of peaks not indexed 0 is good
M- TEST= 27 UNI NDEXED I N THE TEST=0
THI S MAY BE THE SOLUTI ON ! ! !
THE REFI NEMENT OF THE CELL WI LL NOWBE
REPEATED
THREE CYCLES MORE. - - - GOOD LUCK !
. . . .
The predicted unit cell
NUMBER OF SI NGLE I NDEXED LI NES = 24
TOTAL NUMBER OF LI NES = 40
A = 17. 288210 0. 001634 A ALFA= 90. 000000
0. 000000 DEG.
B = 6. 353682 0. 000787 A BETA= 102. 102612
0. 009219 DEG.
C = 6. 410086 0. 000446 A GAMMA= 90. 000000
0. 000000 DEG.
The predicted volume. Does is make sense based on the
chemical formula?
UNI T CELL VOLUME = 688. 46
The first few indexed peaks. Is the DELTA value small?
H K L SST- OBS SST- CALC DELTA 2TH- OBS 2TH- CALC D- OBS FREE
PARAM.
2 0 0 0. 008335 0. 008306 0. 000029 10. 476 10. 458 8. 4373 211
0 0 1 0. 015096 0. 015105 - 0. 000009 14. 115 14. 119 6. 2695 72
3 0 0 0. 018689 15. 715 6. 2695 82
3 0 0 0. 018689 15. 715 6. 2695 82
- 2 0 1 0. 018708 0. 018714 - 0. 000006 15. 723 15. 725 5. 6317 82
1 0 1 0. 019581 0. 019530 0. 000051 16. 088 16. 067 5. 5048 79
2 1 0 0. 023014 0. 023005 0. 000010 17. 451 17. 448 5. 0776 318
- 1 1 1 0. 029661 0. 029531 0. 000130 19. 834 19. 790 4. 4727 510

Final Figures of Merit
NUMBER OF OBS. LI NES = 40
NUMBER OF CALC. LI NES =62
M( 20) = 26 AV. EPS= 0. 0000304
F20 = 44. ( 0. 009199, 50)
M( 30) =27 AV. EPS= 0. 0000290
F30 = 51. ( 0. 007849, 0)
M( 40) =23 AV. EPS= 0. 0000293
F40 = 52. ( 0. 007162, 109)




How interpret the Figures of Merit

The main rule is that if all the first twenty lines are indexed and the De
Wolff figure of merit M(20) [J. Appl. Cryst. (1972). 5, 243] is greater
than 9, then the indexing problem is in principle solved.

Comments
a. If the De Wolff figure of merit M(20) is less than 10 or more
than one line is un-indexed within the 20 first observed lines,
the solution is probably meaningless.

b. Hexagonal and Tetragonal cells are sometimes indexed as ortho-
rhombic.

c. Observe that the De Wolff figure of merits are derived from the assumption
that no systematic extinctions occur and all lines are indexed.
Warning. a high figure of merit has no meaning unless the lines are indexed.

d. If possible, use the density and formula weight to check that
the unit cell contains an integral number of formula units.

e. If a cell axis is more than 20 a....be very suspicious!
The De Wolff figure of merit test may fail in such cases.

f. If one cell edge is much shorter than the others, be suspicious!
It may cause a dominant zone problem.

g. If a table starts with....not refined unit cell...
then two parameters are probably almost identical (the symmetry may
be higher) and the trial cell parameters are used to print the
list.


Is this the correct unit cell?


Proceed to the next window for refinement and point to CALCULATE



Exam the DHKL results and look for unassigned peaks. If none then
point to
PEAK MATCH. You should see something like this





Zoom in on the first few peaks with the zoom command
















Notice all of the peaks (save the one near 13.48
o
) are labeled. You did
not select the 13.48 peak at the peak picking stage so it is not labeled
now. Add this peak with the TASK/ADD remove peak command and
type finish. For the wavelength box point to OK Goto to
INDEXING/DHKL and recalculate the PEAK MATCH. Now when
you ZOOM you will see the peak labeled.



CAUTION : Care must be taken when manually picking the peak. You
could be off and assign the peak as 100 which would be WRONG!


Finally Point to the REFINE CELL button and you will refine the cell.






Report your results.