11-12-2023

5º lesson

• Miller Indices

• Data Collection

• Reciprocal Space

2023 X-ray crystallography (spectroscopic techniques) 1

Summary of the previous lesson

Each reflection is not generated by a single plane but by a family of parallel planes
characterised by a distance d between them

2023 X-ray crystallography (spectroscopic techniques) 2

Miller indices
How to describe the crystallographic planes ?..... ( Diffraction planes each family of planes )

b
O
d(110) Unit cell projection
a

(010) (100)

Family of planes
(001)
d d Set of planes separated by a given d distance

2023 X-ray crystallography (spectroscopic techniques) 3

Crystallographic planes

Example a b c
Intercepts 1 1 ∞
Reciprocal 1/1 1/1 1/∞
Reduction 1 1 0
Miller Indices (110)

Intercepts 1/2
Reciprocal 1/1/2 1/∞ 1/∞
Reduction 2 0 0
Miller Indices (200)

The Miller indexes is the number of times (n) that a given edge (a b or c)
is divided in equal parts. (hkl) ! !
(a), ( )b,
!
(c)
" " "
2023 X-ray crystallography (spectroscopic techniques) 4
Crystallographic planes (cont)
The fractional number can be replaced by their reciprocal numbers are used (1/2, 1/3, 1/4) (234)
(hkl)

Planes parallel
to the unit cell faces

Planes crossing the corners

2023 X-ray crystallography (spectroscopic techniques) 5

Crystallographic planes (cont)

(210)
(230)
h=2, k=1, l=0
h=2, k=3, l=0

2023 X-ray crystallography (spectroscopic techniques) 6

Crystallographic planes (cont)

2023 X-ray crystallography (spectroscopic techniques) 7

Planes shared between families
001 002 003

𝜆
sin 𝜃 =
2𝑑
𝑑$%% 1 𝑑'%% 1
𝑑!"# = =
𝜆= sin 𝜃!"# 𝑑&%% 2 𝑑&%% 3 𝑑(! (" (# 1
𝑛 =
𝑑!"# 𝑛

Hence, (100) planes are a subset of (200) planes

2023 X-ray crystallography (spectroscopic techniques) 8

 Family of planes and hkl reflections

d(110)
Yellow dotes-Lattice
points b
Each family of planes that pass
d(110) through the lattice are diffraction

O
b sources (the atoms/electrons are
d(110) d(110)
a a positioned on crystallographic
planes)
d(110)
Nitrogenase Molybdenum- iron

Each family can be represented by three indices (hkl), which are integers numbers. These numbers
correspond to a reflection.

2023 X-ray crystallography (spectroscopic techniques) 9

Relation between the hkl values and the d distance

012'3$,.,&*)
1
=
(h 2
+ k2 )
d hk 0 2 a2

"#% 𝛼 "#$ a
dhk 0 =
2 1/2
𝛼!!"# (h 2
+k )
"#$
!"#$%$$&#'(')*+,'"+%-$,.,&*)/
cos α = d(a/k)
sen α = d/(a/h4 a
dhkl =
2 1/2
(h 2
+k +l2
)
2023 X-ray crystallography (spectroscopic techniques) 10
Relation between the hkl values and the d distance for other crystal
systems

Cubic Hexagonal

1 h2 + k 2 + l 2 1 4 h2 + k 2 + l 2 l 2
= = ( )+ 2
d 2
a2 d2 3 a2 c

Tetragonal Monoclinic

1 h2 + k 2 l 2 1 1 h 2 k 2 sin 2 β l 2 2hl cos β

= + 2 = ( + + 2− )
d 2
a 2
c d 2 sin 2 β a 2 b2 c ac

Orthorrombic For the triclinic system the formula is quite

complex
1 h2 k 2 l 2
= + +
d 2 a2 b2 c2

2023 X-ray crystallography (spectroscopic techniques) 11

Diffraction pattern for a cubic system

• A single crystal is characterised by an infinite number of planes with different Miller

indexes (family of planes with a dhkl value)

Combining the equation for cubic system with the Bragg’s law:

1 ℎ! + 𝑘 ! + 𝑙 ! !
= 𝜆
𝑑! 𝑎! 𝑠𝑒𝑛! 𝜃 = ! ℎ! + 𝑘 ! + 𝑙 !
4𝑎
𝑛𝜆 = 2𝑑"#$ sin 𝜃"#$

In this equation the value of n in the Bragg´s law is 1

2023 X-ray crystallography (spectroscopic techniques) 12

Diffraction pattern for a cubic system b(cont)

/
𝜆
𝑠𝑒𝑛/ 𝜃 = / ℎ / + 𝑘 / + 𝑙 /
4𝑎

Conclusion: The scatter of X-rays by a crystal yield a large number of

diffraction maxima (reflections). The positions of these spots on the
photographic film depend of unit cell parameters, Miller indexes and value of
Lambda.

This statement is valid for any crystal system

2023 X-ray crystallography (spectroscopic techniques) 13

Index the powder diffraction pattern for a cubic systems

Example

Peak 𝜃 Peak 𝜃
1 20.20 5 46.19
2 28.72 6 50.90

3 35.36 7 55.28

4 41.07 8 59.42

M. T. Weller “Inorganic Materials Chemistry”, Oxford Chemistry Primes, 1994

1. Assign the peaks to hkl values

2. Calculate the dimensions of unit cell 5

2023 X-ray crystallography (spectroscopic techniques) 14

 1. Assign the peaks to hkl values

𝜆/
𝑠𝑒𝑛/ 𝜃 = / ℎ / + 𝑘 / + 𝑙 /
4𝑎

4𝑎 /
𝑠𝑒𝑛/ 𝜃 / = ℎ / + 𝑘 / + 𝑙 /
𝜆

Divide 1 by 1 (All peaks are assigned relatively to the first one (like TMS in 1HNMR)

1 = ℎ/ + 𝑘 / + 𝑙/

2023 X-ray crystallography (spectroscopic techniques) 15

Assign the peaks to hkl values (cont)
4𝑎 /
𝑠𝑒𝑛/ 𝜃 / = ℎ / + 𝑘 / + 𝑙 /
𝜆
sin2θn
peak θ sin2θ (hkl)
sin2θ1
1 11.5 0.0397 1 010, 0 -1 0….
2 16.4 0.0703 2 0 11, 101
3 20.2 0.1191 3 111, 1-1 -1
4 23.48 0.1587 4 200, ….
5 26.45 0.1984 5 210,…
6 29.21 0.2382 6 211,…
7 34.30 0.3176 8 220,…

2023 X-ray crystallography (spectroscopic techniques) 16

2. Calculate the dimensions of unit cell

!!"#"#
Sen 2𝜃 = ( $%! ) (1.54)2 = 0.1587

Either the seven peaks can be used to determine the value of a.

2023 X-ray crystallography (spectroscopic techniques) 17

X-ray data collection

The crystal is mounted on a rotating

support, the goniometer, and rotated as
it is exposed to X-rays

Spots are collected on Image Plate or

CCD detector and transferred to the
computer.

2023 X-ray crystallography (spectroscopic techniques) 18

 hkl intensities
A
padrão de difracção
padrão de difracção

diffraction cones h k l Ihkl shkl

8 2 -6 31.86 9.39
8 2 -5 15.79 9.09
8 2 -4 1002.60 20.13
8 2 -2 160.94 6.17
8 2 -1 233.85 6.67
8 2 1 41.78 4.81
The reflections are indexed (assignment of hkl indices) 8 2 2 309.41 7.83
A long list of hkl intensities with the corresponding sigma error 8 2 3 97.07 5.24
8 2 4 14.93 6.18
8 2 5 6.19 8.37
8 2 6 14.06 7.99

2023 X-ray crystallography (spectroscopic techniques) 19

Central Question

How the diffraction pattern of a given compound related with the symmetry
of its crystal?

Nitrogenase Molybdenum- Tremolite Ca2Mg5O22(OH)2

iron
The definite answer to this question involves the evaluation of the x-ray scattered by
the individual atoms in the crystal.
2023 X-ray crystallography (spectroscopic techniques) 20
Diffraction patterns

• The diffraction pattern of both crystals is regular, but the reflections have different intensities and positions.
These features depend on the information present in the unit cell (number and type of atoms, organization-
space group and the unit cell dimensions. The Lambda also affects the position of the peaks-Bragg’s law.
• The positions and intensities of reflections contain the required information for structure determination.
• The intensities depends on the the unit cell’s composition.
2023 X-ray crystallography (spectroscopic techniques) 21
How to relate the content of the unit cell to the crystal
scattering pattern? &5
X-R ay Diff ra ction
X-ray
Tube

High
Voltage
Crystal
X-ray
Beam
Lead Screen
Photographic
Plate

A comparison of the apparatus used for X-ray diffraction and the optical transform experiment and Bragg
diffraction
2023 X-ray crystallography (spectroscopic techniques) 22
X-ray diffraction and optical scattering patterns-An approach to the
understanding of the X-ray.

6%&&*#+ 7

8%&&*#+$9

2023 X-ray crystallography (spectroscopic techniques) 23

 :-'(*,$";$$<=$))

2023 X-ray crystallography (spectroscopic techniques) 24

 0#.,&%-$,6%3* >*3'6#"3%-$,6%3*

!"#$%&'(")*+,%*
-"(+*#%../'*'(0%

1$23**4*+2*
5

!"#$%&$%'(")'*$&('
+),,'#$%,)

6.(7%*8.&"% ?*#+%#.$%@',$

2023 X-ray crystallography (spectroscopic techniques) 25

 0#.,&%-$,6%3*$ >*3'6#"3%-$,6%3*$

!"#$%&'(")*+,%*
-"(+*#%..*
7(3%"'(2"'

-$&('+),,./''#$%,)'+"#$%)'

2023 X-ray crystallography (spectroscopic techniques) 26

 0#.,&%-$,6%3* >*3'6#"3%-$,6%3*
1$23**4*+2*
&*5*-"(+*#%..

?*#+%#. %@',
A-'(*$6-%+*

2023 X-ray crystallography (spectroscopic techniques) 27

DNA double-helix

• Crystals and X-ray data were obtained by

Rosalind Franklin.
• The symmetry of diffraction pattern suggested
the DNA structure.

2023 X-ray crystallography (spectroscopic techniques) 28

Reciprocal space
• Interpretation of the geometrical features of X-ray
diffraction (photos)
J.D. Bernal (1926) “On the interpretation of Xray, Single Crystal,
Rotation Photographs” Proceedings of the Royal Society 113:117.

BC(!
BC("

(! ("

nl
D%3E ;%)'-. "; 6-%+*,$', (*;'+*( 2. %$F*3&"# G'&E -*+HE& "; BC( d=
2senq
2023 X-ray crystallography (spectroscopic techniques) 29
Relationship between crystallographic space (crystal) and reciprocal space
@

.
BII
JII
BBI (KJII4$L$BCJ(KBII4

JBI

2023 X-ray crystallography (spectroscopic techniques) 30

Reciprocal lattice at 3-D

Rotating the crystal

'()*+",-./01!-2,1.+3

?E*$#*3'6#"3%-$-%&&'3*$',$3")6",*($2.$%--$(';;#%3&'"+$,6"&,
2023 X-ray crystallography (spectroscopic techniques) 31
Relationship between unit cell parameters in real space and in reciprocal space

Stout & Jensen (1989) X-Structure Determination. A practical guide. 2nd ed. John Wiley & Sons, New York

2023 X-ray crystallography (spectroscopic techniques) 32

Relationship between unit cell parameters in real space
and in reciprocal space

2023 X-ray crystallography (spectroscopic techniques) 33

Examples of direct and reciprocal lattices

Figures from Jensen and Stout “X-Ray structure determination.

A pratical guide”)

Monoclinic direct and reciprocal cells

Orthorhombic direct and

reciprocal cells

Triclinic direct and reciprocal cells

2023 X-ray crystallography (spectroscopic techniques) 34
Properties of reciprocal space: Summary

• A vector in the reciprocal space represents a series of crystallographic

planes (family of planes) and the length of the vector is inversely
proportional to the distance between planes of a given family.

• An infinite number of crystallographic planes (family of planes) are

described through a single vector (in the reciprocal space they are
represented by a point).

• The reciprocal lattice is "connected" to the crystal lattice. When crystal

moves the reciprocal lattice moves together with the crystal lattice

2023 X-ray crystallography (spectroscopic techniques) 35

Properties of reciprocal space: Summary

• The diffraction pattern is the reciprocal image of the crystal.

• A large separation between diffraction planes (eg (100) and

(001)) yields a small separation between the corresponding spots
in the reciprocal space and vice versa. Proteins have larger unit
cells than smaller molecules and smaller reciprocal cells.

• The diffraction pattern of a crystal has the same symmetry of the

crystal, revealing how the atoms are organized in the crystal

structure.
2023 X-ray crystallography (spectroscopic techniques) 36
 Question
Why proteins are measured with copper radiation and not with
molybdenum one ?...

𝜆
sin 𝜃 =
2𝑑

M+$#*($&E*$(',&%+3*$;#")$&E*$(*&*3&"#$&"$&E*$3#.,&%-
Increasing the lambda value a better resolution of the reciprocal
space is obtained.
2023 X-ray crystallography (spectroscopic techniques) 37