Introduction to Crystallography

& Diffraction Techniques

Luca Lutterotti
University of Trento, Italy
X-ray diffraction for the
21st Century
5 days training on the
aspect of Combined
Analysis by X-ray and
Neutron Scattering and
introduction to NAUD
software
WORKSHOP
Combined
Analysis
Using X-ray
and
Neutron
Scattering
July +-8, 2011
Caen (France)
!NEL SAS
Z.A. - C.D. +05
+5+10 Artenay
France
Phone: +33(0)2 38 80 +5 +5
Fax: + 33(0)2 38 80 08 1+
http:ffwww.inel.fr
Email: [email protected]
Registration fees
vAT is not included in the indicated fees (19,6)
!n order to ensure and encourage
individual interaction the number of
participants will be limited to +0.
Registration fees include :
- Admission and participation to the course
- Coffee breaks, lunches, reception and two
conferences dinner
Participants will be required to make their own
accommodation and travelling arrangements to and
from workshop venue. Organizers will send an hotels
list and an access map of the training place. Upon
request organizers can make accommodation
bookings for participants.
Please direct questions or
registration to INEL:
[email protected]
Tel 33{0)2 3S S0 45 45
Fax 33{0)2 3S S0 0S 14
General information
venue
The workshop will be held at Caen, France.
!UT, UCBN, CR!SNAT ENS!CAEN
Access
Caen is located in Normandy at 250 km
west of Paris. Further more details are
available in the registration form.
Organizers
Training summer 2011
900 C 750 C !ndustrial people
900 C 750 C Academic people
500 C +00 C Student
After June
1st, 2011
Until June
1st, 2011
Combined Analysis Using X-ray and Neutron Scattering
X-ray diffraction for the
21st Century
5 days training on the
aspect of Combined
Analysis by X-ray and
Neutron Scattering and
introduction to NAUD
software
WORKSHOP
Combined
Analysis
Using X-ray
and
Neutron
Scattering
July +-8, 2011
Caen (France)
!NEL SAS
Z.A. - C.D. +05
+5+10 Artenay
France
Phone: +33(0)2 38 80 +5 +5
Fax: + 33(0)2 38 80 08 1+
http:ffwww.inel.fr
Email: [email protected]
Registration fees
vAT is not included in the indicated fees (19,6)
!n order to ensure and encourage
individual interaction the number of
participants will be limited to +0.
Registration fees include :
- Admission and participation to the course
- Coffee breaks, lunches, reception and two
conferences dinner
Participants will be required to make their own
accommodation and travelling arrangements to and
from workshop venue. Organizers will send an hotels
list and an access map of the training place. Upon
request organizers can make accommodation
bookings for participants.
Please direct questions or
registration to INEL:
[email protected]
Tel 33{0)2 3S S0 45 45
Fax 33{0)2 3S S0 0S 14
General information
venue
The workshop will be held at Caen, France.
!UT, UCBN, CR!SNAT ENS!CAEN
Access
Caen is located in Normandy at 250 km
west of Paris. Further more details are
available in the registration form.
Organizers
Training summer 2011
900 C 750 C !ndustrial people
900 C 750 C Academic people
500 C +00 C Student
After June
1st, 2011
Until June
1st, 2011 X-ray diffraction for the
21st Century
5 days training on the
aspect of Combined
Analysis by X-ray and
Neutron Scattering and
introduction to NAUD
software
WORKSHOP
Combined
Analysis
Using X-ray
and
Neutron
Scattering
July +-8, 2011
Caen (France)
!NEL SAS
Z.A. - C.D. +05
+5+10 Artenay
France
Phone: +33(0)2 38 80 +5 +5
Fax: + 33(0)2 38 80 08 1+
http:ffwww.inel.fr
Email: [email protected]
Registration fees
vAT is not included in the indicated fees (19,6)
!n order to ensure and encourage
individual interaction the number of
participants will be limited to +0.
Registration fees include :
- Admission and participation to the course
- Coffee breaks, lunches, reception and two
conferences dinner
Participants will be required to make their own
accommodation and travelling arrangements to and
from workshop venue. Organizers will send an hotels
list and an access map of the training place. Upon
request organizers can make accommodation
bookings for participants.
Please direct questions or
registration to INEL:
[email protected]
Tel 33{0)2 3S S0 45 45
Fax 33{0)2 3S S0 0S 14
General information
venue
The workshop will be held at Caen, France.
!UT, UCBN, CR!SNAT ENS!CAEN
Access
Caen is located in Normandy at 250 km
west of Paris. Further more details are
available in the registration form.
Organizers
Training summer 2011
900 C 750 C !ndustrial people
900 C 750 C Academic people
500 C +00 C Student
After June
1st, 2011
Until June
1st, 2011
X-ray diffraction for the
21st Century
5 days training on the
aspect of Combined
Analysis by X-ray and
Neutron Scattering and
introduction to NAUD
software
WORKSHOP
Combined
Analysis
Using X-ray
and
Neutron
Scattering
July +-8, 2011
Caen (France)
!NEL SAS
Z.A. - C.D. +05
+5+10 Artenay
France
Phone: +33(0)2 38 80 +5 +5
Fax: + 33(0)2 38 80 08 1+
http:ffwww.inel.fr
Email: [email protected]
Registration fees
vAT is not included in the indicated fees (19,6)
!n order to ensure and encourage
individual interaction the number of
participants will be limited to +0.
Registration fees include :
- Admission and participation to the course
- Coffee breaks, lunches, reception and two
conferences dinner
Participants will be required to make their own
accommodation and travelling arrangements to and
from workshop venue. Organizers will send an hotels
list and an access map of the training place. Upon
request organizers can make accommodation
bookings for participants.
Please direct questions or
registration to INEL:
[email protected]
Tel 33{0)2 3S S0 45 45
Fax 33{0)2 3S S0 0S 14
General information
venue
The workshop will be held at Caen, France.
!UT, UCBN, CR!SNAT ENS!CAEN
Access
Caen is located in Normandy at 250 km
west of Paris. Further more details are
available in the registration form.
Organizers
Training summer 2011
900 C 750 C !ndustrial people
900 C 750 C Academic people
500 C +00 C Student
After June
1st, 2011
Until June
1st, 2011
X-ray diffraction for the
21st Century
5 days training on the
aspect of Combined
Analysis by X-ray and
Neutron Scattering and
introduction to NAUD
software
WORKSHOP
Combined
Analysis
Using X-ray
and
Neutron
Scattering
July +-8, 2011
Caen (France)
!NEL SAS
Z.A. - C.D. +05
+5+10 Artenay
France
Phone: +33(0)2 38 80 +5 +5
Fax: + 33(0)2 38 80 08 1+
http:ffwww.inel.fr
Email: [email protected]
Registration fees
vAT is not included in the indicated fees (19,6)
!n order to ensure and encourage
individual interaction the number of
participants will be limited to +0.
Registration fees include :
- Admission and participation to the course
- Coffee breaks, lunches, reception and two
conferences dinner
Participants will be required to make their own
accommodation and travelling arrangements to and
from workshop venue. Organizers will send an hotels
list and an access map of the training place. Upon
request organizers can make accommodation
bookings for participants.
Please direct questions or
registration to INEL:
[email protected]
Tel 33{0)2 3S S0 45 45
Fax 33{0)2 3S S0 0S 14
General information
venue
The workshop will be held at Caen, France.
!UT, UCBN, CR!SNAT ENS!CAEN
Access
Caen is located in Normandy at 250 km
west of Paris. Further more details are
available in the registration form.
Organizers
Training summer 2011
900 C 750 C !ndustrial people
900 C 750 C Academic people
500 C +00 C Student
After June
1st, 2011
Until June
1st, 2011
X-ray diffraction for the
21st Century
5 days training on the
aspect of Combined
Analysis by X-ray and
Neutron Scattering and
introduction to NAUD
software
WORKSHOP
Combined
Analysis
Using X-ray
and
Neutron
Scattering
July +-8, 2011
Caen (France)
!NEL SAS
Z.A. - C.D. +05
+5+10 Artenay
France
Phone: +33(0)2 38 80 +5 +5
Fax: + 33(0)2 38 80 08 1+
http:ffwww.inel.fr
Email: [email protected]
Registration fees
vAT is not included in the indicated fees (19,6)
!n order to ensure and encourage
individual interaction the number of
participants will be limited to +0.
Registration fees include :
- Admission and participation to the course
- Coffee breaks, lunches, reception and two
conferences dinner
Participants will be required to make their own
accommodation and travelling arrangements to and
from workshop venue. Organizers will send an hotels
list and an access map of the training place. Upon
request organizers can make accommodation
bookings for participants.
Please direct questions or
registration to INEL:
[email protected]
Tel 33{0)2 3S S0 45 45
Fax 33{0)2 3S S0 0S 14
General information
venue
The workshop will be held at Caen, France.
!UT, UCBN, CR!SNAT ENS!CAEN
Access
Caen is located in Normandy at 250 km
west of Paris. Further more details are
available in the registration form.
Organizers
Training summer 2011
900 C 750 C !ndustrial people
900 C 750 C Academic people
500 C +00 C Student
After June
1st, 2011
Until June
1st, 2011
X-Ray Diffraction is used to study
crystalline materials
X-rays scatter off of the
atoms in a sample
If those atoms are
systematically ordered, the
scattered X-rays tell us:
what atoms are present
how they are arranged
First we need some basics
of crystallography
A crystal consists of a periodic arrangement of the unit cell into a
lattice. The unit cell can contain a single atom or atoms in a fixed
arrangement.
a,b and c (length) and , and angles between a,b and c are lattice
constants or parameters which can be determined by XRD.
Crystalline materials are characterized by the
orderly periodic arrangements of atoms.
Parallel planes of atoms intersecting the unit cell are used to define
directions and distances in the crystal.
These crystallographic planes are identified by Miller indices.
The (200) planes
of atoms in NaCl
The (220) planes
of atoms in NaCl
Examples of Miller Planes
a
b
h=1, k=-1
h=1, k=0
h=1, k=-2
h=4, k=-1
h=2, k=1
Note that the 2, 2 and
-2, -2 planes are identical
The diffraction process occurs
when the Braggs law (condition)
is satisfied. It is expressed as:
Where is the wavelength of x-rays
d is the interplanar spacing
is the x-ray angle
n is an integer
Braggs law
Lattices
In 1848, Auguste Bravais demonstrated
that in a 3-dimensional system there are
fourteen possible lattices
A Bravais lattice is an infinite array of
discrete points with identical environment
seven crystal systems + four lattice
centering types = 14 Bravais lattices
Lattices are characterized by translation
symmetry
Auguste Bravais
(1811-1863)
Crystal system
Crystals are grouped into seven crystal systems, according
to characteristic symmetry of their unit cell.
The characteristic symmetry of a crystal is a combination
of one or more rotations and inversions.
Recall that the unit cell of a crystal is the smallest 3-D
geometric figure that can be stacked without rotation to
form the lattice.
The asymmetric unit is the smallest part of a crystal
structure from which the complete structure can be built
using space group symmetry. The asymmetric unit may
consist of only a part of a molecule, or it can contain more
than one molecule, if the molecules not related by
symmetry.
Crystal System External Minimum Symmetry Unit Cell Properties
Triclinic None a, b, c, al, be, ga,
Monoclinic One 2-fold axis, || to b (b unique) a, b, c, 90, be, 90
Orthorhombic Three perpendicular 2-folds a, b, c, 90, 90, 90
Tetragonal One 4-fold axis, parallel c a, a, c, 90, 90, 90
Trigonal One 3-fold axis a, a, c, 90, 90, 120
Hexagonal One 6-fold axis a, a, c, 90, 90, 120
Cubic Four 3-folds along space diagonal a, a, ,a, 90, 90, 90
triclinic
trigonal
hexagonal
cubic
tetragonal
monoclinic
orthorhombic
Specifically 3-D crystals may be
arranged in 7 crystal systems
Rotation axes (by 60, 90, 120, or 180)
Notated: 6, 4, 3, and 2, respectively
Screw Axes (translation and rotation)
Notated: 6
1
, 6
2
, 6
3
, 6
4
, 6
5
; 4
1
, 4
2
, 4
3
; 3
1
, 3
2
; and 2
1
(Translation)
Reflection planes
Glide reflection planes (reflection and translation)
Inversion points
Rotary inversion axes (rotation and inversion)
Proper symmetry elements in 3D
http://www.chem.ox.ac.uk/icl/heyes/structure_of_solids/Lecture1/Bravais.gif
Categories of Space Groups
The combination of all available symmetry operations (32 point
groups), together with translation symmetry, within the all
available lattices (14 Bravais lattices) lead to 230 Space Groups
that describe the only ways in which identical objects can be
arranged in an infinite lattice. The International Tables list those
by symbol and number, together with symmetry operators, origins,
reflection conditions, and space group projection diagrams.
An interactive tutorial on Space Groups can be found on-line in Bernhard Rupps
Crystallography 101 Course: http://www-structure.llnl.gov/Xray/tutorial/spcgrps.htm
Generating a Crystal Structure from its Crystallographic
Description
Using the space group information contained in the International
Tables we can do many things. One powerful use is to generate an
entire crystal structure from a brief description.
Let us consider the description of the crystal structure of NaCl.
Space Group = Fm3m
a = 5.44
Atomic Positions
Using the face centering
generators (0,0,0), (,,0), (,
0,), (0,,) together with the
coordinates of each Wyckoff
site we can generate the
fractional coordinates of all
atoms in the unit cell.
Cl
1:(0.0,0.0,0.0), 2:(0.5,0.5,0.0), 3:
(0.5,0.0,0.5), 4:(0.0,0.5,0.5)
Na
1:(0.5,0.5,0.5), 2:(0.0,0.0,0.5), 3:
(0.0,0.5,0.0), 4:(0.5,0.0,0.0)
With no knowledge of the symmetry diagram we can identify the crystal system
from the space group symbol.
Cubic The secondary symmetry symbol will always be either 3 or -3 (i.e. Ia3,
Pm3m, Fd3m)

Tetragonal The primary symmetry symbol will always be either 4, (-4), 4

1
, 4
2
or 4
3

(i.e. P4
1
2
1
2, I4/m, P4/mcc)

Hexagonal The primary symmetry symbol will always be a 6, ( 6), 6

1
, 6
2
, 6
3
, 6
4
or
6
5
(i.e. P6mm, P6
3
/mcm)

Trigonal The primary symmetry symbol will always be a 3, ( 3), 3

1
or 3
2
(i.e P3
1
m,
R3, R3c, P3
1
2)
Orthorhombic All three symbols following the lattice descriptor will be either mirror
planes, glide planes, 2-fold rotation or screw axes (i.e. Pnma, Cmc2
1
, Pnc2)
Monoclinic The lattice descriptor will be followed by either a single mirror plane,
glide plane, 2-fold rotation or screw axis or an axis/plane symbol (i.e. Cc, P2, P2
1
/n)
Triclinic The lattice descriptor will be followed by either a 1 or a ( 1).
Summary:
Wyckoff Sites
The Wyckoff positions tell us where the atoms in a crystal
can be found.
Wyckoff position denoted by a number and a letter. Number
is called multiplicity of the site and letter is called Wyckoff
site.
Multiplicity tells us how many atoms are generated by symmetry if we
place a single atom at that position.
The letter is simply a label and has no physical meaning. They are assigned
alphabetically from the bottom up.
The uppermost Wyckoff position (with highest
multiplicity), corresponding to an atom at an arbitrary
position never resides upon any symmetry elements. This
Wyckoff position is called the general position. All of
the remaining Wyckoff positions are called special
positions. They correspond to atoms which lie upon one
of more symmetry elements, because of this they always
have a smaller multiplicity than the general position.
The reciprocal lattice why bother?
The reciprocal lattice is important in all phases of
solid state physics, so an understanding of this
concept is useful in and of itself
Vector algebra is very convenient for describing
otherwise complicated diffraction problems
The reciprocal lattice offers a simple approach to
handling diffraction in terms of vectors
Use of the reciprocal lattice permits the analysis of
diffraction problems that cannot be accessed by
Braggs Law (example: off-peak scattering)
Approaches for placing a reciprocal
lattice point onto the Ewald sphere
move the reciprocal lattice through the
Ewald sphere (the rotating crystal
method)
change the radius of the Ewald sphere
by changing the wavelength (the Laue
method)
Note: S/ used in place of k
The Powder Diffraction Pattern
Powders (i.e., polycrystalline aggregates) are
billions of tiny crystallites in all possible
orientations.
When placed in an x-ray beam, all possible
interatomic planes will be seen

By systematically changing the experimental
angle, we will produce all possible diffraction
peaks from the powder
Geometric relationship between the 2D reciprocal lattice
[d*(hk) vector] and its 1D projection |d*| = 2sinq/l
Indexing: Determination of hkl indices for each
peak and lattice parameters evaluation, i.e.,
reconstruction of the 3-D geometry
We do not need to collect the rings from cones but
just the ring intersection on an equatorial film
If the scattering power is low, the integration of
intensity in the cones may be required.
In the early times this was done with a
Debye-Scherrer camera
The relationships between a film intensity and
ordinary powder diffraction pattern
Film
Film is the oldest, and in some cases, still the best method
(certainly the least expensive) for recording X-ray
intensities
optical density:
light X-rays
log E
D
E
D
light -- requiries many photons to
transform one AgI grain (D log E)
X-rays -- one photon transforms
many AgI grains (D E)
gamma
Which Wavelength to Use in the home lab?
Generally use Cu 1.5418 or Mo 0.71073
The longer the wavelength the farther apart
the diffraction spots (lines) are in space. For
large unit cells like macromolecules biologists
should prefer Cu.
Cu produces x-rays efficiently and the
detectors have a higher efficiency in
measuring them.
Mo is not as absorbed as Cu. Best for heavy
element problems. However metals have in
general small unit cells.
Powder diffractometers working in the Bragg-
Brentano (/2) geometry utilize a parafocussing
geometry to increase intensity and angular
resolution
Small crystallite size and large lattice strain affect the peak broadening
The elementary cell size determines peak densification in the diffraction space
(according to reciprocity laws, small dimension determines large separation)
Atom position within the unit cell affects the relative peak intensities
The lattice simmetry determines the diffraction peaks sequence.
Reciprocity rules and atoms in the unit cell
Diffraction analyses
Phase identications (crystalline and amorphous)
Crystal structure determination
Crystal structure renements
Quantitative phase analysis (and crystallinity determination)
Microstructural analyses (crystallite sizes - microstrain)
Texture analysis
Residual stress analysis
Order-disorder transitions and compositional analyses
Thin lms
McCusker maze
The issue of indexing a
powder pattern
was treated in a monograph
2002
By the International
Union of Crystallography
To which programs should we address (the list is not
so numerous) ???
We had a period of productivity in the past 12-16
years
Von Dreele, R.B., Stephens, P.W., Smith, G.D., Blessing, R.H.
The first protein crystal structure determined from high-resolution X-ray powder
diffraction data: a variant of T3R3 human insulin-zinc complex produced by grinding.
Acta Crystallogr., Sect.D v56 pp.1549-1553 , 2000
In Maud
Ab initio structure solution
Indexing
Structure solution
Structure databases
Search match
Crystal structure databases
ab-initio structure solution
Collection of a very good experimental pattern
accurate peak positions
low noise, good intensities, sharp peaks
Indexing (to determine symmetry, cell parameters and
possible space groups)
Atoms location
usual:
structure factors extraction
structure solving by specialized programs
direct:
atoms location from tting
Structure renement (Rietveld)
Structure validation (Platon?)
Indexing and solution in Maud
Indexing:
smoothing, background subtraction and peak locations
peak list export for classical indexing programs (Dicvol, Treor
etc.)
or genetic indexing or full pattern indexing (when no one else
program succeed)
Dicvol indexing results import and space group sorting (space
group identication)
Le Bail tting for cell renement and structure intensities extraction
(with export for structure solution programs)
Structure solutions:
Genetic algorithm
Electron density maps
Export to other programs (superip, sir20xx, shelx....)
Le Bail or Pawley fitting
monoclinic
Rw(%)=7.5
a=19.87820(5)
b=8.19454(2)
c=11.24154(3)
=106.0656(2)
Space groups sorting
Atom locations
Direct methods (Shelx, Sir2004...):
Some algorithms are used to solve the phase problem
They work best with single crystal structure factors
Electron density maps, difference electron density maps and Patterson maps
using Fourier transform or maximum entropy methods
from electron density maps atom should then be located (not easy)
Charge ipping algorithm: special technique to obtain electron density maps,
as for the previous lot of reections are required (ex. superip)
Direct atom locations:
genetic algorithms
simulated annealing
Montecarlo methods
Special methods were developed for particular cases: envelopes, energy
principles....
Texture can be used for
structure solution (better
extraction for overlapped
peaks)
Structure solution: when?
First use the search-match (next)
Check for every similar compound
Check literature and structural databases
Repeat the experiment in case
If nothing similar is found then go for the ab initio structure
solution
After indexing better to do the search again
Search match
OPEN DATA and
Crystallography Databases
Open access on the Web :
PDB (proteins)
NDB (nucleic acids)
AMCSD (minerals)
COD (small/medium crystal structures, based on donations)
Toll databases :
CSD (organic, organometallic)
ICSD (inorganic, minerals)
CRYSTMET (metals, intermetallics)
ICDD (powder patterns)
Other structure Databases
For all metallic/intermetallic phases: The Pearson books (in
paper format)
For some simple structures: Wyckoff, Crystal Structures
(book)
Literature: all IUCr journals like Acta Cryst., J. Appl.
Cryst. etc.
Searching the COD
http://www.crystallography.net/
Databases in Maud
Maud has a small structure database that can be expanded
by the user
Phases, Instruments can be stored in the databases in CIF
format
The CIF format is the Crystallographic Information Format
developed by the IUCr
Maud can import from any le containing phases or
instruments in CIF format
A special function can submit a solved or rened structure
directly to the COD database online