Christoph T. Koch
Max Planck Institut fr Metallforschung Heisenbergstr. 3, 70569 Stuttgart Raum 5N8, Tel: 0711/689-3647 Email: koch@mf.mpg.de
Max-Planck Institut fr Metallforschung Universitt Stuttgart
Background literature
Book: (excellent introduction to reciprocal space and crystallography) Marc de Graef, Introduction to Conventional Transmission Electron Microscopy Cambridge University Press, Cambridge (2003)
Websites: Website for the book by M. de Graef: http://ctem.web.cmu.edu/ More online diffraction simulations: http://emaps.mrl.uiuc.edu/emaps.asp
Universitt Stuttgart
Universitt Stuttgart
Top right: plot of a single top hat aperture function f(x) Bottom right: modulus of FFT of f(x)
http://hrem.mpi-stuttgart.mpg.de/koch/Vorlesung/MatlabScripts/test_XtalFFT.m Max-Planck Institut fr Metallforschung Universitt Stuttgart
Top right: plot of the potential f(x) of small 1D crystal Bottom left: modulus of FFT of f(x)
http://hrem.mpi-stuttgart.mpg.de/koch/Vorlesung/MatlabScripts/test_XtalFFT.m Max-Planck Institut fr Metallforschung Universitt Stuttgart
Top right: plot of the potential f(x) of small 1D crystal Bottom left: modulus of FFT of f(x)
http://hrem.mpi-stuttgart.mpg.de/koch/Vorlesung/MatlabScripts/test_XtalFFT.m Max-Planck Institut fr Metallforschung Universitt Stuttgart
Convolution
f ( x) g ( x) =
Convolution theorem
FT [ f ( x) g ( x)] = FT [ f ( x)] FT [g ( x)] = F (k ) G (k )
The convolution of two functions may be computed by the inverse Fourier transform of the product of their Fourier transforms.
Max-Planck Institut fr Metallforschung Universitt Stuttgart
x
Unit cell potential Reciprocal space: x finite sized lattice
=
= crystal potential
x
Structure factor x crystal shape transform
=
= FT of crystal potential
(Note that the rec. space plots show |F(k)|, which is almost what is seen in diffr. patterns) Max-Planck Institut fr Metallforschung Universitt Stuttgart
0, if x < a f ( x) = 1, if a x b 0, if x > b
F (k ) = = 1 2 1 2
FT[f(x)]:
f ( x)e 2ikx
2ikx
e
a
k=
1 ba
If a=-b:
F (k ) =
2 sin(2ka) 2k
k=
Max-Planck Institut fr Metallforschung
3/ 2 ba
Universitt Stuttgart
Shape transform of interface layer Amorphous interface layer, about 1nm thick
Diffraction pattern
Universitt Stuttgart
x
Infinite lattice x
w shape of crystal
=
= finite sized lattice
x
Reciprocal space lattice x shape transform
=
= continuously sampled reciprocal space
Universitt Stuttgart
k in nm-1 This plot shows the modulus of the Fourier transform of different size arrays of delta functions. For large enough crystals the shape transform vanishes between reciprocal lattice points.
Max-Planck Institut fr Metallforschung Universitt Stuttgart
b*
r a a = 1 a 2
r b b = 1 b 2
r 1 a b* = 2 A a1 b2 r 1 a* = A b1
a*
Unit cell area:
* =
r r A = a b sin( )
Universitt Stuttgart
c b a
The FT of the potential of an infinite crystal may only be non-zero, if h,k, and l are integers.
Max-Planck Institut fr Metallforschung
c b a
Universitt Stuttgart
Universitt Stuttgart
Bravais Lattices
7 crystal systems: {a,b,c,,,} abc; : triclinic or anorthic (a)
{a,b,c,/2,,/2} abc; /2: monoclinic (m) {a,a,c,/2,/2,2/3} a=bc; {a,a,a,,,} a=b=c; /2: {a,b,c,/2,/2,/2} abc: {a,a,c,/2,/2,/2} a=bc: {a,a,a,/2,/2,/2} a=b=c: hexagonal(h) rhombohedral (R) orthorhombic (o) tetragonal (t) cubic (c)
Universitt Stuttgart
1. If the plane intersects the origin, shift it, so that it does not. 2. Determine the points at which the plane intersects each of the unit cell vectors. 3. The Miller indices are the inverse of these values, reduced to the smallest possible integers. 4. Notation: (hkl) Determination of Miller indices (1,2,3) of a plane in real space.
Universitt Stuttgart
10
A plane may be characterized by a single 3D reciprocal space vector, the 3 Miller indices. Since this vector starts at the origin (k=0,0,0), it defines a single point in reciprocal space. The length of the Miller-vector defines the distance between a parallel set of planes in the lattice.
Universitt Stuttgart
11
Constructive interference
Destructive interference
Constructive interference
n = 2d sin( )
Max-Planck Institut fr Metallforschung
n = d sin( )
Universitt Stuttgart
Structure factor
Superposition of the scattering at each individual atom i Consists of the phase shifts caused by the different positions ri=(xi, yi, zi) of the atom the scattering factor fi() of the atoms
F ( g ) = f j (| g |)e
j
rr 2ig r j
F(q) is called the structure factor and is important to calculate the scattering amplitude at different angles (diffraction pattern) Destructive interference can lead to zero intensity in the diffraction pattern
Universitt Stuttgart
12
c b a
=
Potential of crystalline specimen
Universitt Stuttgart
k=
1 t
Relrods are 1-dimensional objects for specimen that are infinitely large in x- and y-diections. Reciprocal Lattice Rod (relrod)
Max-Planck Institut fr Metallforschung Universitt Stuttgart
13
Reciprocal lattice rods (relrods) Reciprocal lattice is convoluted with the specimen shape transform. Thin specimen produce extended crystal truncation rods in the direction normal to the specimen surface
Max-Planck Institut fr Metallforschung Universitt Stuttgart
k=k+q q
kx Reciprocal lattice
Max-Planck Institut fr Metallforschung Universitt Stuttgart
14
|k|-|kinel|h-1(2mE)1/2
Energy lost in inelastic scattering event
k q kinel
Reciprocal lattice
Max-Planck Institut fr Metallforschung Universitt Stuttgart
Kinematic Diffraction
A kinematic diffraction pattern is the modulus squared of the crystal potential in reciprocal-space at its intersection with the Ewald sphere. If the reciprocal space plane normal to the momentum vector of the incident electron is called zone axis. First order Laue zone (FOLZ)
-k
K=(0,0,0)
kx
-kz
Diffraction spots may appear, even if the Laue condition is only roughly satisfied. For infinitely thick crystals no ZOLZ reflection appears under exact zone axis conditions.
Max-Planck Institut fr Metallforschung Universitt Stuttgart
15
kz
K=(0,0,0)
kx
Relative tilting between Ewald sphere and reciprocal lattice may position certain reciprocal lattice points on the Ewald sphere (in diffracting condition).
Max-Planck Institut fr Metallforschung
Universitt Stuttgart
Example: Graphite
Modulus of the scattering potential U(gx,0,kz) for a 2-dimensional Graphite crystal (a=2.46A, c=6.7A) which has a thickness of one unit cell, i.e. two graphene sheets. (Note: the kz-axis is on a much finer scale than the kx-axis)
Max-Planck Institut fr Metallforschung Universitt Stuttgart
16
Universitt Stuttgart
Diffraction plane
17
U (r ) =
2me 2m0 e V (r ) = V (r ) 2 h h2
In reciprocal space:
Ug =
Universitt Stuttgart
Ewald sphere
sg
Shape transform at distance sg away from g
2
s r rg 2 r r 2 2 g + 2g k k (k + g ) sg = = 2k 2k
Ig = Ug
sin 2 (ts g )
Universitt Stuttgart
18
Mott-Bethe Formula
The Mott-Bethe formula relates electron scattering factors to X-ray scattering factors:
f e (q) =
|e| 16 2 0 q
2
[Z f X (q)]
Note, that fe(q) is proportional to q-2. This means that for low scattering angles (small q) electron scattering factors are much stronger than X-ray scattering factors.
These charge density maps of CuO2 were obtained by combining (low-resolution) electron diffraction and (high resolution) X-ray diffraction data.
Universitt Stuttgart
V (r , t ) = V (r + u (t )) = V (r ) + u (t ) dV (r ) u (t ) 2 d 2V (r ) + + ... dx u =0 dx 2 u =0 2!
V (r , t ) = V (r ) +
u 2 d 2V (r ) + ... 2! dx 2 u =0
This leads to an attenuation of the atomic scattering factor fe(q) by the Debye-Waller factor B:
f e (q) = f e (q) e
2 2 u 2 q 2
= f e (q ) e 0.25 Bq
Universitt Stuttgart
19
Notation
Coordinates in square brackets such as [100] denote a direction (in real space). Coordinates in angle brackets or chevrons such as <100> denote a family of directions which are equivalent due to symmetry operations (e.g. in a cubic system this could mean [100], [010], [001] or the negative of any of those directions). Miller indices in parentheses such as (100) denote a plane, in a cubic system the normal to the (hkl) plane is the direction [hkl]. Indices in curly brackets or braces such as {100} denote a family of plane normals which are equivalent due to symmetry operations. Negative indices are denoted by a horizontal line above _ them (e.g. [1-10] = [110]).
Max-Planck Institut fr Metallforschung Universitt Stuttgart
[001]
Max-Planck Institut fr Metallforschung
[111]
[011]
Universitt Stuttgart
(*WEBEMAPS: http://emaps.mrl.uiuc.edu/emaps.asp)
20
Universitt Stuttgart
animation of a Si (001) pattern tilted from zone axis up to 5 about the y-axis
Universitt Stuttgart
21
Universitt Stuttgart
Laue center
22
Atomic vibrations may be decomposed into phonon modes with characteristic wavelengths.
Max-Planck Institut fr Metallforschung
Universitt Stuttgart
Deficiancy line
Max-Planck Institut fr Metallforschung
Excess line
Universitt Stuttgart
23
24
Stereographic projection
Universitt Stuttgart
Stereographic projection
The stereographic projection, as used in crystallography, projects the point of intersection of a given crystallographic direction (relative to the direction defining the pole of the projection) with the unit sphere on its equatorial plane. Directions in the northern (southern) hemisphere are projected towards the south pole and are represented by solid (empty) circles.
S
Max-Planck Institut fr Metallforschung Universitt Stuttgart
25
Universitt Stuttgart
Tilting the (001) crystallographic direction to the north pole shows its fourfold symmetry
Universitt Stuttgart
26
Symmetry
Most crystal structures have symmetry. This means that if one performs certain mathematical operations (e.g. flipping, rotating, shifting) on any of the atomic positions within the unit cell, one obtains the atomic coordinates of another atom (of the same kind) in the same unit cell. A crystal structure has a given symmetry, if this symmetry operations is valid for all atoms of the unit cell simultaneously. Henn-egg white lyzozyme (PDB entry: 5LYZ) Space group: P43212
Max-Planck Institut fr Metallforschung Universitt Stuttgart
27
Universitt Stuttgart
28
Symmetry operations
Operations of the first kind: Rotation (n-fold symmetry: =2/n, [n=1,2( ),3( ),4( ),6( )]) Translation Operations of the second kind: Pure reflection (about a given mirror plane) Inversion (about a given point, r -r) Combinations of above operations Rotoinversion: rotation + inversion Screw axis: rotation + translation Glide plane: reflection + translation
Max-Planck Institut fr Metallforschung Universitt Stuttgart
A given combination of all possible symmetry operations for a crystal structure also identifies the crystal system. _ Examples: - If the point symmetry is 1 or 1, the crystal system is triclinic (a). Any other crystal system would have higher symmetry. - If the point symmetry contains a rotation axis of order 6, the crystal system must be hexagonal (h).
_ 3
Max-Planck Institut fr Metallforschung
_ 2
Universitt Stuttgart
29
a,b,c: n: d:
x1 ' = D11 x1 + D12 x2 + D13 x3 + u1 x2 ' = D21 x1 + D22 x2 + D23 x3 + u2 x3 ' = D31 x1 + D32 x2 + D33 x3 + u3
D11 D W = 21 D 31 0 D12 D22 D32 0 D13 D23 D33 0 u1 u2 , then u3 1
If r=(x1,x2,x3,1) and
r r r ' = Wr
Max-Planck Institut fr Metallforschung
Universitt Stuttgart
30
Forbidden reflections
In Si (face-centered cubic): Why are only diffraction spots with even indices visible in the (001) zone axis ?
Universitt Stuttgart
F ( g hkl ) =
f ( g )e
i hkl
Translational symmetry operations may be combined into a single phase factor when computing the structure factor: Structure factor computed from atom positions in asymmetric unit + translational symmetry operations: N asym N trans 2i ( hx j + ky j + lz j ) 2i ( hxi + kyi + lzi ) hkl i hkl j =1 i =1
F (g ) =
f (g
)e
Universitt Stuttgart
31
Definition of the fcc symmetry operations generates the remaining atomic positions: x x x+0.5 x+0.5 y y+0.5 y y+0.5 z z+0.5 z+0.5 z (no operation) (translation) (translation) (translation)
Alternatively: Define only one atom position and apply the diamond structure symmetry operations (see homework).
Universitt Stuttgart
f ( g )e
i hkl
2 i ( hxi + kyi + lz i )
[1 + e
i ( h + k )
+ ei ( h +l ) + ei ( k +l )
FCC symmetry operations: In the (001) Zone axis: l=0 h arbitrary k arbitrary x x x+0.5 x+0.5 y y+0.5 y y+0.5 z z+0.5 z+0.5 z
[1 + e
i ( h + k )
+ ei ( h ) + ei ( k )
32
1. Sketch the configuration (see examples to the right) used to produce the stereographic projection of the outline of the earths continents shown above. 2. What is the space group symbol of the diamond structure (as in silicon)
Universitt Stuttgart
33