Introduction to Crystallography Basics
Introduction to Crystallography Basics
Introduction to Crystallography
Diamonds
7.1 periodicity and lattices of crystal structure
7.1.1 The characteristics of crystal structure
1. A few definitions:
• Solids can be divided into two primary categories,
crystalline solids and amorphous solids.
• Crystalline Solids are built from atoms or molecules
arranged in a periodic manner in space, e.g., rock salt and
diamond.
• Amorphous Solids possess short-range order only. They
are not related through symmetry, e.g. glass, rosin, amber
glass.
C.N.:
Si = 4
O=2
No 5-fold axis
is allowed in a
single crystal!
2150 g/mm2
Conductivity
1150 g/mm2
Graphite
570 g/mm2
NaCl
•Definite sharp melting points
T
t
• Symmetry: crystal shape (macroscopic)
lattice arrangement (microscopic)
a)
b)
c)
Structural motif
d)
a is a 1D lattice itself;
b-d are not lattices, but can be represented by a lattice.
a
b
a=b,
=120
ab, =90
Example: 2D-lattice of Graphene
or
T = ma + nb + pc (m, n, p = 0, 1, 2, …)
c. Lattices and its unit in 3D:
T = ma + nb + pc (m, n, p = 0, 1, 2, …)
b
a
c
a b
Structural
motif
Atomic Coordinates: Fractional coordinates
Fractional coordinates:
In this case, the lattice point can be put at the position of either
Cs or Cl atom. Each unit cell contains both a Cs and Cl atom.
aP (Primitive)
• Triclinic crystal system has the lowest symmetry.
• It can be simply represented by a primitive cell.
• Symmetry element: i
A primitive cell contains one lattice point and a
* Monoclinic C-centered unit cell contains two lattice points.
abc Sym. Elements: 90
= =90º i, C2(//b), h, 90
a'
c'
a
90° c b' c
90° 90°
90°
b b
mP (Primitive) mC (C-centered or A-centered)
o
a
o a
c
a c
c
mI ? = mC mF ? = mC
Both I- and F-centered monoclinic are unnecessary and can be
represented by a mC!
• The primitive cell of a C-centred orthor-
* Orthorhombic
hombic lattice is actually monoclinic!
abc
= = =90º
c c b
90°90° O b
O b
a 90° c a
a
oP (Primitive) C-centered or A-centered or B-centered
* Orthorhombic
abc Sym. Elements:
= = =90º 3C2 (//a,b,c), i, 3h (//A,B,C)
oP oC oI oF
or oA or oB (In-centered) (Face-centered)
* Orthorhombic
Face-centered cell (oF) and its primitive cell
90° 90°
O
a 90°
b
tP tI
Does a C- or F-centered tetragonal lattice exist?
• Neither C-centered
tetragonal nor F-centered
tetragonal exists.
tC = tP
a
* Trigonal ---- Rhombohedral
a=b=c
C3
= = 90º
hR
c
b a A rhombohedral lattice can
be represented by a R-
O centered hexagonal lattice!
hP unit cell
* Hexagonal c
a=bc Sym. Elements:
= =90º, C6(//c), i,
=120º h (c, //C) 90°
90°O b
a 120°
Hexagonal 2D lattice
c
O b
a
a. Primitive rhomohedral = b. primitive hexagonal
r-centered hexagonal r-centered rhombohedral
90° 90°
90° b
a
cP cI cF
Is there a c-centered cubic lattice?
• Introducing a C-center eliminates all C3-axes and results in
only one C4 axis. The lattice should be actually tetragonal.
• The primitive cell of a fcc or bcc lattice is rhombohedral,
which does not include the C4–axes of the lattice!
Bravais Lattices: (14)
Unit Cell: the highest symmetry + minimal size
Centered unit cell is thus introduced to contain the
highest symmetry of the lattice.
Crystal P C I F
systems
Triclinic
Monoclinic
Orthorhombic
Trigonal
Tetragonal
Hexagonal
Cubic
Augusta Bravais
Lattices
b (111)
O
a c
(100)
(010) b
(001)c
c O a
(010) Projections
a of crystals
b d010 planes (//c-
(110)
axis) on the
a
b d110 a (001) plane.
b
a d210 ( 2 10)
a b
b (210)
( 1 20)
The spacing between adjacent planes in a family is
referred to as a “d-spacing”
Triclinic:
7.1.5 Real crystals and Crystal defects:
Real crystals are only close approximations of space
lattices
Edge dislocation
Screw Dislocation
• Formed by shear
stress
Tmnp= ma + nb + pc or
m 0 0 a a, b, c: basic vectors!
Tmnp 0 n 0 b
0 0
p c
a a a
A1 A2 A3 A4
Four lattice points: A1, A2, A3, A4
(m-1)/2 1 m-1 2
Upon an n-fold rotation,
m = 3, 2, 1, 0, -1
A1 B1
cos = 1, 1/2, 0, -1/2, -1
A4 B2
with A1A4 // B1B2. = 2/n = 0º, 60º, 90º, 120º, 180º
B1B2 =a + 2acos = ma n= 1, 6, 4, 3, 2
Twofold axis
Threefold axis 2 3 4 6
Fourfold axis
Rotation axis
Hexagonal lattice
Sixfold axis
General equivalent positions:
i) 2-fold axis (e.g., b axis in monoclinic lattice)
(x, y, z) (-x, y, -z) (Note: in fractional coordinates)
Equivalent upon rotation around a 2-fold axis.
1 0 0 b
R(2) 0 1 0
0 0 1 (-x,y,-z) -z
-x x a
z
(x,y,z)
-y x a
0 1 0 4 fold axis // c axis (cubic lattice)
R(4) 1 0 0 general equivalent positions:
0 0 1 (x,y,z), (-y, x, z), (-x,-y,z), (y,-x,z)
A helical structure is
related to a screw axis!
A 31 screw axis in the crystal of tellurium
31
Screw axes: 31 and 32
Screw 31 Screw 32
31
31
31
32
32
32
61-5
21 31 32 41 42 43
Glide operations: a, b, c, n and d glides
Glide operation: G = T(t)·M Mirror: M (reflection)
t = a/2, b/2, c/2, (a+b)/2, (b+c)/2, (a+c)/2, (a+b+c)/4 etc.
GG = [T(t)M]2 = T(2t), t = 2t (maybe a basis vector of lattice)
a glide
Zig-zag structure
• So far we have
a b c
2. Crystallographic space group
Point groups (32) + translational symmetries = Space groups (230)
Schonflies notation vs. International notation
e.g, D2h16 - P21/n 21/m 21/a C2h5 – P21/c
System directions
1 2 3
Cubic a a+b+c a+b
Hexagonal c a 2a+b
Tetragonal c a a+b
Trigonal (hR) a+b+c a-b -
Trigonal* (hP) c a
Orthorhombic a b c
Monoclinic b - -
How to understand/use Space Group?
Symmetry elements & equivalent positions
1. Each space group can be schematically represented by
using two types of diagrams, i.e., diagrams of symmetry
elements and diagram of general equivalent positions.
2. The physical meaning of general equivalent positions: if
there is an X atom at position (x,y,z), there should a same X
atom at each equivalent position within a unit cell.
Diagram of Symmetry Diagram of general
elements equivalent position
Example: monoclinic point group C2h-2/m
Six space groups belong to C2h point group, denoted:
C2h1-P2/m, C2h2-P21/m, C2h3-C2/m,
C2h4-P2/c, C2h5-P21/c, C2h6-C2/c,
e.g., C2h5 – P21/c (i is always available!)
c glide
at b/4.
41
d glide
plane at
1/8,3/8,
5/8,8/7
• Fcc Sideview topview
• Lattice points: (0,0,0)+, (1/2,1/2,0)+, (0,1/2,1/2)+, (1/2,0,1/2)+
• Structure motif – 2C 0,0,0; 1/4,1/4,1/4
• Totally 8 C atoms within a unit cell.
Note:In this case, the presence of same-type atoms in
structure motif introduces more symmetry elements!
7.2.3 The description and application of crystal structure
Example 1. Crystal of iodine
Crystal System orthorhombic
Space group D2h18-Cmca (or C 2/m 2/c 21/a)
Cell parameters a=713.6 pm b= 468.6 pm c = 987.4 pm
Number of molecules per unit cell Z = 4
Atomic coordinate for I x y z
0 0.15434 0.11741
Lattice points within a unit cell: (0,0,0)+, (1/2, 1/2, 0)+ (C-centered).
General equivalent positions: C 2/m 2/c 21/a
(x,y,z); (-x, -y, -z); (-x, -y+1/2, z+1/2); (x, y+1/2, -z+1/2)
X-ray tube
The wavelengths of X-ray are in the range
of 100-0.01Å
154.439 pm
K2
s0 s
O P
dhkl
3
( r ) exp( 2 iq r / ) d r
Rn
For the crystal structure :
(r ) cell (r Rn )
b
n
c
n1 0 n2 0 n3 0
2iNaq /
N 1
1 e
AN e 2inaq /
2iaq /
n 0 1 e
The intensity:
N
sin 2
a q
I AN
2
AN AN
*
sin 2
Nh
sin a q
2 sin 2
h
30 2
|A|(N=5) 250 |A|2(N=15)
200
20
150
100
10
50
0 h 0 h
-1.0 -0.6 -0.2 0.2 0.6 1.0 -1.0 -0.6 -0.2 0.2 0.6 1.0
In the case of 3-D:
N1 2 N 2 2 N 3
sin
2
a q sin b q sin c q
I Amnp
2
f
2
2 2 2
sin a q sin b q sin c q
Therefore,
aq/=h,bq/=k,cq/=l (h,k,l should be integer)
or aq=h,bq=k,cq=l
----- Laue conditions for X-ray diffraction
I f N N N
2
I Fhkl N N N
2 2 2 2 2 2 2
1 2 3 1 2 3
Fhkl ( x , y , z )e 2i ( hx ky lz )
dxdydz
n Electron density distribution in a unit cell.
f je
2i ( hx j ky j lz j )
Phase difference between
the scattered and incident
j 1
x-ray over atom j.
Sum over all atoms fj: atomic scattering factor defined by
within a unit cell. atomic electron density distribution.
i ( h k l )
f Na ( 1 e ) (f1 = f2 = fNa)
i ( h k l ) ( 2 n 1 )i
i) While h+k+l = 2n+1, e e 1
Fhkl = 0, Systematic absence !
ii) While h+k+l = 2n, ei ( h k l ) 1 Fhkl 2 f Na Strongest!
Body-centered crystal –Two lattice point in a unit cell!
General case: each lattice point contains m different atoms.
• The total number of atoms within a unit cell is 2m;
• For jth atom in a structural motif (a lattice point): (xj,yj,zj)
• Its body-centered equivalent: (0.5+xj, 0.5+yj, 0.5+zj)
2m
Fhkl f i e2i ( hxi kyi lzi )
i 1
m 1 1 1
2i [ h ( x j ) k ( y j ) l ( z j )]
{ f je
2i ( hx j ky j lz j )
fj e 2 2 2
}
j 1
m
] f je
i ( h k l ) 2i ( hx j ky j lz j )
[1 e
j 1
j 1
From translation symmetry of fcc! sum up over all
atoms within a LP!
When h,k,l are neither all even nor all odd, Fhkl = 0, systematic absence!
n
Fhkl 4 f j e
When h,k,l are all even or all odd, 2 πi ( hx j ky j lz j )
diffraction observable! j 1
Example. Unit cell has a 21 screw axis along the c axis.
Equivalent positions: (x, y, z), (-x , -y , z+1/2)
N Each molecule has
Fhkl f j {exp[i 2 ( hx j ky j lz j )] N atoms.
j 1
(x,y,z)
1
exp[ i 2 ( hx j ky j l ( z j ))]}
2
N
F00l [( 1 exp( il )] f j exp( i 2lz j )
j 1
( x , y , z 0.5)
l = 2n+1 F00l 0 Sum over all
atoms of a
systematic absence molecule. Herein two molecules
within a unit cell are
correlated by 21 axis.
How about systematic absence arising from such
screw axes as 31, 41 and 61 ?
2li 4li N/3
• 31||c-axis F00l [ 1 exp( ) exp( )] exp( i 2lzi )
3 3 i 1
l N/3
[ 1 2 cos( l ) cos( )] exp( i 2lzi )
3 i 1
• n1 //c-axis
n
2 ( j 1)li N / n
F00l exp( ) exp( i 2lzi )
j 1 n i 1
Diffraction beam
Powder
sample 2
Incident beam 2 Powder Diffractometer
Detectors
• Film
- poor sensitivity, high background, low dynamic range
• Scintillation counters
- good sensitivity, low background, high dynamic range
• Imaging plates
- good sensitivity, low background, good dynamic range, very
efficient data collection
• CCDs and Multiwire detectors (widely used nowadays)
- fast readout, good sensitivity, low background, good dynamic range,
very efficient data collection
Automated diffractometer method
(2)
2. Applications of X-ray diffraction
a. crystal structure determination
Direction & intensity data collection
Phase problem
A ( x, y , z )
i
Example: Indexing of a cubic system
sin 2 ( / 2a) 2 (h 2 k 2 l 2 )
sin h k l
2 2 2 2 sin 2 1 : sin 2 2 : sin 2 3 : sin 2 4 : ...
3. Get ( h2 k 2 l 2 )1 : ( h2 k 2 l 2 )2 : ( h2 k 2 l 2 )3 ....
I: (hkl) 100, 110, 111, 200, 210, 211, 220, 221, 222, 300, …
(h2+k2+l2) 2, 4, 6, 8, 10, 12, 14, 16 … (1: 2: 3: 4: 5: 6: 7: 8:…)
F: (hkl) 100, 110, 111, 200, 210, 211, 220, 221, 300, 311, 222, ….
(h2+k2+l2) 3, 4, 8, 11, 12, 16, 19, 20 …
Example for the indexing of cubic system and its applications
FCC: (hkl) 100, 110, 111, 200, 210, 211, 220, 221, 300, 311,222, ….
(h2+k2+l2 ) 3, 4, 8, 11, 12, 16, 19, 20 …
(7) Index and calculate h2+k2+l2
Peak Positions
Crystal system, cell parameters, qualitative phase identification
Peak Intensities
Unit cell contents, quantitative phase fractions
• Quantitative Analysis:
The peak intensities are proportional to the weight percentage of
the corresponding phase.
(ii) Changes of lattice parameters―Solid solution, doping
Using high-angle diffraction data or applying least square method.
2dhklsin =
Why use high angle values?
Maximal
minimal d/
0° 90°
(ii) Changes of lattice spacing along specific
directions―residue stress
stress 2dhklsin =
d sin = /(2dhkl)
d d d
d
I Fhkl N N N Fhkl A
2 2 2 2 2 2
1 2 3
[001]
XRD pattern of ZnO nanowires
晶格的畸变(不均匀应变、微观应变、内应力)
d1
=d /d
d4 d5
2(d+d)sin(+)=
d2 d3
or 2d(1+)sin(+)=
and are very small,
d
d1 d2 and hence ,
2=-2tg or
= 2tg
Separation of the effects of Crystallite size and Lattice
Distortion
K
i '
2tg
D cos
i
cos sin K
2
D
2
sin a S
m
sin 2 ns
f p ( s ) K P ( n)
n 1 sin (s )
2
B0 (B)
h( s ) g (t ) f (s t )dt
or h( s) g ( s) f ( s)
25.0k
20.0k
Intensity a.u.
15.0k
10.0k
5.0k
(103) (004)
0.0
30 40 50 60 70 80 90
2-Theta degree
ZnO nano-arrays
140.0k (201)
120.0k
100.0k
Intensity
80.0k
60.0k
40.0k
(002)
20.0k
0.0
30 40 50 60 70 80
2-Theta degree
b. Applications of powder diffractions
Applications
Qualitative Analysis
Quantitative Analysis
Lattice Parameter Determination
Crystallite size / size distribution & Lattice Distortion
Analysis (Non-uniform microstrain)
Crystallinity Analysis
Residue Stress Analysis
Texture analysis
Structure Solution and Refinement
Radical distribution function (for amorphous materials)
7.3.5 Electron Diffraction and Neutron Diffraction
1. Electron Diffraction
de Brogli wave length
of electron in a field V:
h
=
2meeV
Atom-level resolution!
a) TEM image of the tip part of one TeO2 nanorod. (b)
Enlarged TEM image. (c) The corresponding electron
2. Neutron Diffraction diffraction pattern.
7. The term quasicrystal was first used in print shortly after the
announcement of Shechtman's discovery, in a paper by Steinhardt and
Levine. (Phys. Rev. Lett. 1984, 53,2477)
I Fhkl N N N Fhkl A
2 2 2 2 2 2
1 2 3
Scherrer formula K K
Dhkl
(size: 1-100nm) coshkl ( B B0 ) coshkl
c) Deformation of lattice—broadening of diffraction peaks
d
d1 d4 d5 d1 d2
d2 d3
In the diffraction direction, the difference between the
incident and the diffracted beam through any two lattice
points must be an integral number of wavelengths.
2D lattices:
3 parellelograms
Inversion center:
(0,0,0); (1/2,1/2,1/2)
(0,0,1/2), (1/2,0,0),
(0,1/2,0);
(1/2,1/2,0),(0,1/2,1/2),
(1/2,0,1/2)
Crystal Characteristic Unit cell Choice of Lattic
systems symmetry parameters axis Point
elements Group
Monoclinic C2, i,h abc b // C2 C2h
==90 ac//h
2D lattices:
1 parellelogram
2 rectangles.
Crystal Characteristic Unit cell Choice of Lattic
systems symmetry parameters axis Point
elements Group
Orthorhombic 3C2,3h a≠b≠c a,b,c // 3C2 D2h
===90
2D lattices:
3 rectangles.
Tetragonal C4 a=bc c // C4 D4h
===90
2D lattices:
1 square
2 rectangles.
Cubic 4C3 a=b=c Four C3 axes are parallel Oh
===90 to the body diagonals
of the cube.
2D lattices:
3 squares
Hexagonal C6,h a=bc c // C6 D6h
==90
=120
C6
c b
a
aO b
2D lattices:
1 hexagon + 2 rectangles.
Trigonal C3 Rhombohedral D3d
a=b=c, ==<12090
Hexagonal D6h
a=bc, ==90, =120
C3
c
b a
O
Rhombohedral