STUDIAMO LA STRUTTURA

LA DIFFRAZIONE DI RAGGI X.
W. H. Zachariasen X-Ray Diffraction in Crystals
Mermin Aschcroft Solid State Physics cap 6

Maria Grazia Betti

Trattazione semi-classica dell' interazione radiazione materia

Ipotesi: il campo e.m. una perturbazione debole e
e possiamo scrivere l' hamiltoniana come

H= Hs+Hp+Hint
Processi elastici: diffusione elastica e diffrazione
H= Hs+Hp+Hint

Hs rimane invariata E=E' k2=k'2

L'energia e il modulo quadro del vettore k si conservano.

Il vettore momento pu cambiare direzione

Processi anelastici: assorbimento od emissione di un fotone

/
h

Classical approximation: Scattering Amplitude

X-ray scattering cross sections are weak

the intensity of the scattered beam is negligible compared to that of the incident
one.
the incident wave is constant in the whole diffracting volume.
multiple scattering is not considered.
The kinematic approximation of single scattering is valid (1st Born approximation)
Introducing the electron density in the material tot(r), the total scattered amplitude for
elastic scattering is given by the coherent addition of the waves scattered by the electrons:

A(q)
q = k d k i scattering vector,
waves

with

A(q ) = tot ( r ) e iq.r d 3r

ki and kd wave vectors for the incident and scattered

ki = k d = 2 /

 tot ( r ) = j ( r r j )

The material is a collection of j atoms

at positions rj

where j(r) is the electron distribution for atom j

A(q) =

iq.r 3

r
e
d r=
j
j

iq.u 3
(
)

u
e
d ue
j

iq.r j

fj e

iq.r j

Introducing the atomic form factor :

f j0 ( q ) =

i q .u 3
(
)

u
e
d u
j

|q|

Intensity Distribution
Atoms are never residing at fixed lattice sites, they are thermally vibrating around an
average position. If we include a Debye-Waller factor in the structure factor to consider thermal
N1 1 N 2 1N 3 1
vibrations:

A f = Ae F ( q )

exp( iq Rn ) = Ae F ( q )

n1,n 2 ,n 3

n1 = 0 n2 = 0 n3 = 0

exp( iq ( n1a 1 + n2 a 2 + n3a 3 ) )

where Mj is the Debye Waller factor associated to the j-th atom:

Each sum is peaked at 2n/ai and tends in the limit of large Ni value, to a periodic array
of -functions with a spacing of 2/ai.

N 1 q R n = 2 n
n = 0 exp( iq ( n1a1 + n2 a 2 + n3a3 ) ) = 0 q R 2n
n

N1 1

The diffracted intensity from a crystal has the special property of being confined along
specific, well-defined directions and is the product of three orthogonal, periodic -function
arrays. The momentum transfer q has to simultaneuosly meet the three following conditions
for the intensity to be at the maximum:

q a 1 = 2 h

q a 2 = 2 k
q a = 2 l
3

with h, k and l integer values.

The three conditions can be simultaneously satisfied by Q vectors which represent the
reciprocal lattice points. Since the Q vectors are a set of translation vectors in the reciprocal
space corresponding to the real space crystal structure given by Rn, the Laue condition
simply states that the maximum scattered intensity occurs at the reciprocal lattice points of
the real space crystal structure.

Intensity Distribution
Atoms are never residing at fixed lattice sites, they are thermally vibrating around an
average position. If we include a Debye-Waller factor in the structure factor to consider thermal
N1 1 N 2 1N 3 1
vibrations:

A f = Ae F ( q )

exp( iq Rn ) = Ae F ( q )

n1 = 0 n2 = 0 n3 = 0

n1,n 2 ,n 3

exp( iq ( n1a 1 + n2 a 2 + n3a 3 ) )

where Mj is the Debye Waller factor associated to the j-th atom:

F ( q) =

Nc

j= 1

M j = 8

f j ( q ) exp( iq r j ) exp( M j )

2
j

sin
sin
= Bj 2
2

Bragg's law (1913):

Interference pattern of X-rays scattered by long
range ordered structures.

n =2dsin

The path difference is 2dsin where

is the incidence angle

Von Laue
ei(k-k)R=1 se k-k=G
(k-k)R=2m
where R is a Bravais lattice vector
PROBE: ions, electrons, neutrons, protons,
with a wavelength comparable to the distance
between the atomic or molecular structures.

3D reciprocal lattice
In crystallography, the reciprocal lattice of a Bravais lattice is the set of all vectors K
such that

Cella primitiva di Wigner-Seitz

Cella unitaria: puo riempire tutto il cristallo
per operazioni di traslazione.
La cella primitiva la pi piccola cella
unitaria ossia la cella unitaria di volume
minimo.

I vettori di traslazione primitivi vengono

usati per definire gli assi cristallografici,

Fundamentals of Diffraction Techniques in 3D Space

Diffraction techniques require a long-range translational
symmetry of the system giving access to the reciprocal lattice.
The diffraction process satisfies conservation of energy and
momentum but for the addition of any reciprocal lattice vector.
For a 3D-system:

k = (k )
'
k =k +ghkl
2

' 2

Conservation of Energy
Conservation of Momentum

The diffracted beams are characterized by the points of the

points of the reciprocal lattice.
The wavelength of the projectile particle must be of the same
order of magnitude of the interplanar spacings of the solid.

Onda piana

Onda sferica

I(q)

Strategy

I (hkl )

F hkl

2
qFWHM=2/Lc

Lc =2/ qFWHM

Measuring the peak maximum is not reliable

q D =2/qFWHM = Lc

One measures the integrated intensity by

Rocking the sample in front of the detector

De
tec
to

Requirements for a good data set

Diffractometer degrees of freedom

grazing angle
sample rotation axis
Detector in-plane rotation
Detector out of plane rotation
Accurate data normalization
Instrument resolution function
Sample size effects

Building and testing a model

calc
hkl

= f je
j

Mj

2 i ( hx j + ky j + lz j )

q = ha* + kb* + lc*

where h,k are discrete and l continuous variables ; xj yj zj are
the coordinates of atom j in the surface unit cell
Mj is the Debye-Waller factor for atom j related to the thermal vibrations amplitudes
<u2j>
atoms included in the surface cell: all those shifted from ideal bulk location
several atomic layers = more than 20-30 atoms = large number p of free parameters
large number N of independent data (not symmetry related)

Model refinement by least-square methods

Reliability factor

calc
hkl Fobs
hkl F hkl
R=
obs 2
hkl Fhkl

Least-square residue

2 =

Np

(F

obs
hkl

Fcalc
hkl
2
hkl

LA DIFFRAZIONE DI RAGGI X.
Dai sistemi ordinati ai sistemi disordinati e alle proteine

Maria Grazia Betti

SEMINARI
Lunedi 12-14
Mercoledi 14-16
Giovedi 16-18

AULA 4
AULA 4
AULA 4

OTTOBRE
G 10
G 17
G 24
G 31 C. Mariani

Radiazione di sincrotrone, cenni al free electron laser

NOVEMBRE
G 7 C. Mariani
G 14 F. Sciarrino
G 21 A. Polimeni
G 28 M.G. Betti

Applicazioni radiazione di sincrotrone

Laser,tecnologie ottiche per informazione quantistica
Assorbimento e luminescenza nei semiconduttori
La spettroscopia di fotoemissione

DICEMBRE
G 5 N. Saini
Assorbimento dei raggi X
G 12 P. Postorino Diffusione Rayleigh, Spettroscopia Raman
G 19 S. Lupi
Assorbimento nell' infrarosso

Reticolo di Bravais
Un reticolo di Bravais specifica larrangiamento periodico in cui le unit elementari
del cristallo sono disposte.
Tali unit possono essere singoli atomi, gruppi di atomi, molecole, ioni, ecc.
Definizioni:
-Un reticolo di Bravais una schiera infinita di punti discreti con una disposizione e
unorientazione che appare la stessa da qualsiasi dei punti la schiera sia vista.
- Un reticolo di Bravais formato da tutti i punti con vettori posizione della forma:

R = n1a1 + n2 a2 + n3 a3

ai

ni interi

sono detti vettori primitivi

3D crystal structures
CsCl, 2 at/un.cell: (000)a, (1/2,1/2,1/2)a

simple cubic
Li, Na, , Cr, Nb, V, W, 1 at/un.cell

body centered cubic

Cu, Ag, Au,, Ni, Pd, , Ne, Ar, ,1 at/un.cell

NaCl, 2 at/un.cell: (000)a, (1/2,1/2,1/2)a
ZnS 2 fcc : (000)a, (1/4,1/4,1/4)a

face centered cubic

face centered cubic

3D crystal structures

C, Si, Ge 2 fcc : (000)a, (1/4,1/4,1/4)a

GaAs, ZnS 2 fcc : (000)a, (1/4,1/4,1/4)a

a2

a1

Oblique (p) net

|a1||a2| 90

2D Bravais Nets and

Unit Meshes
Rectangular (c) net
|a1||a2| =90
a1

a2
a1

Rectangular (p) net

|a1||a2| =90

a2

a2

a1

Primitive cell

|a1||a2| 90

Unit cell

a1
a2
a2

a1

Square (p) net

|a1|=|a2| =90

Hexagonal (p) net

|a1|=|a2| =120

Cella primitiva di Wigner-Seitz

Cella unitaria con cui si puo riempire tutto il
cristallo per operazioni di traslazione.
La cella primitiva la pi piccola cella
unitaria ossia la cella unitaria di volume
minimo. Per costruzione, contiene un solo
punto reticolare e i soli atomi della base.

I vettori di traslazione primitivi vengono

usati per definire gli assi cristallografici,
A volte si usano assi non primitivi,
quando sono pi convenienti o pi
semplici.

Reticolo di Bravais in 3D:

celle unitarie convenzionali e celle unitarie primitive

real and
reciprocal
space

2D Crystallography: 2D Point Groups

Simmetrie

1 2 3 4 6 m 2mm 3m 4mm 6mm

10 gruppi puntuali
1,2,3,4,6,
2m,3m,4m,4mm,6mm

SIMMETRIE
TRASLAZIONALE
E ROTAZIONALE
120o

THREE-FOLD

Dal solido al liquido

A(q) =

j ( r r j )e
j

iq.r 3

d r=

j ( u) e
j

iq.u 3

d ue

iq.r j

fj e

iq.r j

Dal solido al liquido

A(q) =

j ( r r j )e
j

iq.r 3

d r=

j ( u) e
j

iq.u 3

d ue

iq.r j

fj e

iq.r j

Da sistemi semplicia sistemi complessi

1937 Perutz : Use X-ray diffraction to uncover the biological function of haemoglobin, the
protein in red blood cells responsible for transporting oxygen. No protein structure had been
solved using X-ray crystallography. Perutz's photographs were almost picture perfect, with
characteristic regular arrays of sharp spots indicating a regular, repeating pattern of crystals.

Protein Crystallography:
more than 1000 atoms per unit cell!!!!

We know the amplitude, but we do not know the phase: the

undulating cycle of movement from one wave peak to the next
The number of reflections and interactions that occur within
crystals of haemoglobin is so complex that to translate X-ray
patterns into molecular structures requires more than just
knowledge about the intensity of waves. The phase of the wave
could be calculated by knowing the phase angle, the distance
between a point on a wave and a specified reference point..
Researchers called the case of this missing information 'the
phase problem', and at the time solving this was the ultimate
goal for anyone interested in trying to determine protein
structures from X-ray crystallography. Lindo
Patterson creates a contour map that can be used to define the
distances between atoms in a crystal, through knowing only the
position and intensity data.
http://www.nobelprize.org/nobel_prizes/chemistry/laureates
/1962/perutz-lecture.pdf

Phase problem and Patterson map

Maria Grazia Betti

Le mappe di Patterson

In un esperimento di diffrazione si misura la I(q) che e' proporzionale al modulo

quadro | F(q) | 2 . Il fattore di struttura si puo' esprimere come :

F(q)= (r) e-iqr dr

dove la (r) e' la densita' di carica elettronica in tutta la cella.

La funzione di Patterson e' definito come il prodotto di autocorrelazione della

densita' di carica elettronica
P(r')= (r+r') (r) dr

I massimi principali si avranno quando r' e' un vettore di reticolo diretto

P(r')= qq' F(q) F(q') e-iq(r+r') e-iq'r dr

se q'=- q
P(r')= 0
P(r')= q| F(q) | 2 e-iqr'

I coefficienti dello sviluppo in serie della funzione di Patterson sono il modulo

quadro del fattore di struttura

If there is a peak of electron density for atom 1 at position x1 and a peak of electron density
for atom 2 at position x2, then the Patterson map will have peaks at positions given by x2-x1
and x1-x2..

The figure illustrates a Patterson map corresponding to a cell with one molecule. It demonstrates that
you can think of a Patterson as being a sum of images of the molecule, with each atom placed in turn
on the origin. Because for each vector there is one in the opposite direction, the same Patterson map
is also a sum of inverted images of the molecule, as shown in the bottom representation.

Electron Density Map

COMPARISON Microscopy vs. Diffraction

Direct Space
imaging by local probe
microscopy

Reciprocal space
Recording the Diffraction Pattern
X-rays

Metallic tip STM

Si tip

AFM

non-interacting probe
top layer
STM ~ []2
charge density topography
lateral resolution 0.1nm

Electrons

E=h=hc/
()=12398/E(eV)
=1 , E=12,4 keV
interacting probe

E=p2/2m = (h/)2/2m
()=12,265/E0.5(eV)
=1 , E=150 eV LEED
interacting probe

Abs.length > 100m

Abs.length 1 nm (LEED)

a ~ Z2barn

a ~ 108 barn

resolution 0.001nm

resolution 0.01nm

n = 1- : GIXD

DE BROGLIE
c
E = h = h

c
E = h = h

h
=
mv

DAVISSON E GERMER
Le particelle si comportano come onde
con =h/mv e vengono diffratte

hk2/2m

electrons

Sonda

Massa (g)

Velocit (m/s)

(m)

e- lento

9 x 10-28

1.0

7 x 10-4

Inelastic Mean Free Path (nm)

10

Inelastic Mean Free Path

of Electrons vs. Kinetic
Energy

5
1.0
0.5
50 100 500 1000 5000 1000

Kinetic Energy (eV)

The inelastic mean free path of excited electrons in

solids is very short with respect to the inter-atomic
distance.

How the emission of

elastically scattered
electrons decays as a
function of depth (z)

Excited Electron

Solid Surface

1-st

z3

2-nd
3-rd
4-th
5-th

Excited Atom

Solid

LEED
Thereby:
I = I0 + I0 exp[-z1/sin] + I0 exp[-z2/sin] +
+ I0 exp[-z3/sin] + .=
= I0 {1 + exp[-d/sin] + exp[-2d/sin] +
+ exp[-3d/sin] + }
where I is the total emission of electrons which did
not undergo inelastic scattering and I0 is the emission
from the surface plane.
Thereby only electrons created in the near-surface
region can escape into the vacuum with no energy

Fundamentals of Diffraction Techniques

Ewald Sphere Construction in 2D Reciprocal Space
Notice that the
reciprocal lattice is now
replaced by infinite
reciprocal lattice rods
perpendicular to the
surface and passing
through the reciprocal
net points

1)

At surfaces 2D translational symmetry holds thereby only the wave vector

parallel to the surface is conserved with the addition of a reciprocal net
vector

2) The procedure of Ewald sphere construction is similar to the 3D case

3) The dashed scattered wave vectors propagate into the solid and are not
observable

Fundamentals of Diffraction Techniques in 2D Space

k = (k )
2 2 ' 2 ' 2
k
k
k|| +
k
|| +
=

Conservation of Energy

'
k || =k|| +ghk

Conservation of Momentum

' 2

is not conserved since the translational

symmetry normal to the surface is now broken

The indexing of the diffracted beams is, by convention, referenced to

the substrate real and reciprocal net.
If the selvedge or adsorbate structures have larger periodicities, the
surface reciprocal net is smaller than that of the substrate alone.
The extra reciprocal net points and associated diffracted beams are
dnoted by fractional rather than integral indices.

LEED: How the Surface Meshes in the Real Space and in

the Reciprocal Space Correspond Each Other
Laue Conditions
a1 (s - s0) = n1
a2 (s - s0) = n2
s00

s0

s01

a1
a2

b1

b2

s11

s01

s / = n1 b1 + n2 b2

(ai bj = ij)

LEED: A Series of Observations

To a first approximation, the single scattering formalism (kinematical
approximation) is adopted.
The incident electron is described as a plane wave and the amplitude
of the outgoing electron is given by the coherent sum of scattering
from each atom

A
e
x
p
i
kA
fj e
x
p
i
kr
(
)
(

k=
j)
n m

A k

A
fj

rj

Amplitude of the outgoing electron

Real surface net vector
Atomic scattering factor
Position vector within a surface unit mesh

n, m Indices of surface meshes

LEED: A Series of Observations

1) The atomic scattering cross section (fj) involves a phase shift (also
dependent on k) and is thus complex
2) the incident wave is exponentially attenuated in the solid
3) Since atom-electron scattering cross sections can be very large (
1 2, i.e. 1010 times larger than in X-ray diffraction), multiple
scattering must be included. This means that each incident electron is
treated a a superposition of the primary wave and the scattered
waves

A
expi
kA
F
(
)

k=

k
n m

Fk =
fj expi
(krj )
j

Geometrical structure factor

Calculated Diffraction Intensities

Spot Separation Halfwidth
(relative to 2/a)
One atom

Two atoms
(distance a)

1/2

1/N

N atoms in a row
(regular distance a)
Several (M) groups of N atoms
each (regularly spaced)
[distance of group centers
(N+1/2)a]
Several groups of varying size
(arranged as in (d))

N atoms randomly distributed

over 2N regular sites

1/[N+(1/2)]

1/{M[N+(1/2)]}

dependening on
spot size and
mixture
1

1/(2N)

GRAFENE: Super-reticoli in 2D

LEED
Examples of spot profiles as a function of the primary
beam energy
Spot profile
analysis reveals
the inadequacy
of the simple
scattering
approach.
Multiple
scattering plays
a major role and
it must be
included in the
theory.

Grazing Incidence X-ray Diffraction

n

n = 1 - - i
and are related to the polarisability and absorption

e2

e 10 5
2 mc 2

Boundary conditions

kt , // = ki cos( i ) =
kt , =

kt2 kt2, // =

10 6
4

2
kt = n

For small incidence angle

kt ,

2
i

2 2i

cos (i) = n cos(t )

i < c with cosc = n
Total reflexion

2
cos( i ) with

n 2 cos 2 i =

n=1 i

The refraction index for X-rays is expressed as:

(1

)2

cos 2

Grazing Incidence X-ray Diffraction

kt ,

2
i

2 2i =

2
i

2
c

2 i

By introducing the critical value c : cos c = Re(n) = 1-

2 10 3 rad

The expression for the crystal wave which is the true incident wave
For further diffraction processes is :

i ( k t , // .r // + Re( k t , ) z ) Im ( k t , ) z

For i < c kt , is purely imaginary the cristal wave is evanescent in z ( for =0)

A thorough treatment is given in Vineyard, Phys. Rev.B (1982)

Grazing Incidence X-ray Diffraction

L=

Penetration depth

Profondeur de pntration

L ()
1000

ht pe d noit art e ne P

2 Im ( kt , ) 4 Im 2
i

2
c

2i

Cu
15 keV
= 7,6 10-6
= 4,4 10-7
c = 0.22

100

i :
10

i/ c

0.1 c

L () : 15

c
100

2 c
1000

Collecting Grazing Incidence X-ray Diffraction Data

De
te c
to

be
am

te

nt be
a

Di
ffr
ac

Inci
de

eam
b
d
acte
r
f
f
i
D

Specular beam

q = kd - ki

I(q)

ion
t
c
e
j
pro

Case of a semi-infinite crystal = bulk truncated at the surface

(z ) = 1
(z ) = 0

for z < 0

(x,y)=1

for z > 0

z
( q) =
2

The Fourier transform of (r) = (z) (x,y) * :

1
( q // )
2
q

Each reciprocal node is infinitely narrow in-plane and broadened with a 1/q 2
dependence along the surface normal
One derives the resulting intensity distribution in reciprocal space

F ( q)

1

(
)
I ( q) =

//
//
s 2 2 sin ( l ) G //

As
Ga

_
X [110]

Intensity distribution in
reciprocal space

I(l)

1x1
100000

Y [110]

10000

2/sin2(l)

1000
100
10

1/l2

1
0,1
0,01

Truncation Rod for a rough surface

Cu (001)

1000

Structure factor

(2,0, l) volume

100

10

Optimal sensitivity in anti-bragg position:

used to monitor layer by layer growth through
pseudo-periodic oscillations
After I. K. Robinson Phys. Rev. B33, 3830 (1986).

_
X [110]

1x1

Y [110]

Intensity distribution
From a 2D layer:
Peaks in-plane
Diffuse rods out-of
plane

Intensity distribution from a surface layer

_
X [110]

1x1

Y [110]

Intensity distribution
from a surface layer on a
semi-infinite bulk:
Bulk Bragg
peaks
Intensity
distribution
From
2D layer: Rods
Diffusea Truncation
Peaks in-plane
interfering
without-of
the surface
Diffuse rods
plane
rods

Influence of surface relaxation on truncation rod scattering

dilation or contraction of the interplanar spacing
1000

Cu(001) Surface :
rod (2,0, l)

d/d = +10%

Struture Factor

+
d
+
+
+
-

d/d = -10%

100

10

Truncations rods

After B. Croset et al. PRL 88, 56103 (2002

Truncations rods :
bare Cu (001) and saturated N-Cu (001)
4

10
cuivre nu
Exprience
Calcul

cuivre satur en N
Exprience
Calcul

10

100

10

Amplitude diffracte (u. a.)

Amplitude diffracte (u. a.)

10

cuivre nu
Exprience
Calcul

cuivre satur en N
Exprience
Calcul

10

100

10
0

0,5

1,5

1,5

rod (2,0,L)

rod (1,1,L)

bare Cu
Relaxation d12
Relaxation d23

0,5

-3,16%
-0,54%

N saturated Cu ( =1)
+13,54%
+1,46%

Reconstruction or adsorption

_
X [110]

1x1

Y [110]

Larger direct unit cell

ex c(2x2)

Additional half-order
surface rods

_
X [110]

reconstructed surface or
adsorbed layer on a semiinfinite bulk

1x1

Y [110]

Bulk Bragg peaks

Diffuse Crystal Truncation
Rods (CTR) interfering with
the 1x1 surface rods
Pure surface rods