Course in Crystal Structure Determination from Single Crystal and Powder Diffraction Data Lars Ehm and Christian

Nther
University of Kiel, Germany Part I: X-Ray Single Crystal Structure Analysis Christian Nther

Content of the course

1. Lecture: Introduction and basics on single crystal structure determination and powder diffraction X-Ray single crystal structure analysis and powder diffraction: What is it? Differences between single crystal structure analysis and powder diffraction Why a lecture on single crystal structure analysis and powder diffraction Information from single crystal structure analysis and powder diffraction How to visualize atoms in crystals Crystals: What they are? The unit cell concept Interference and diffraction, Braggs law, atomic scattering factor 2. Lecture: Symmetry in crystals Symmetry in crystals; symmetry operations and symmetry elements Crystal systems and Laue-symmetry Space groups Determination of the crystal system, the Laue symmetry and the space group

Content of the course

3. Lecture: Determination of a single crystal structure Selecting a crystal Data reduction and absorption correction Structure solution and calculation of the electron density map Structure refinement Judgement of the structure model; reliability factors 4. Lecture: Thermal motion in crystals and absolute structure Thermal motion in crystals Static and dynamic disorder Influence of thermal motion on bond lengths Polar structures Absolute structure Absolute configuration

Content of the course

5. Lecture: Errors and pitfalls in single crystal structure analysis Twinned crystals Wrong lattice parameters Super structures Wrong atoms Disorder Practical examples 6. Lecture: Cambridge Crystallographic Data Centre Introduction: Inorganic Crystal Structure Database (ICSD ) and Cambridge Crystallographic Data Centre (CCDC) Possibilities of the CCDC data base Practical examples

Content of the practical part

1. and 2. Day: Determination of the single crystal structure of Cu2Cl2(4,4-Bipyridine) Starting from the chemical composition, an experimental measured data set and the unit cell parameters: Determination of the Laue-symmetry Determination of the Bravais-type Determination of the space group on the basis of systematic absent reflections Calculation of the number of formula units in the unit cell Structure solution and calculation of the electron density map Generating a first structure model Structure refinement Analysis of the structure concerning the quality of the structure model

What should be learned in the course on single crystal structure analysis

Basic knowledge of this method (theoretical basics, not too much theory and mathematics) How in principle a structure determination is performed ? Possibilities: What can be learned from a single crystal structure ? Limitations: How precise and accurate is this method ? What can be determined ? Critical view onto the results of a structure determination ? How I can judge the result and the quality of a structure determination ? How I can detect possible errors in a structure analysis ?

Definition of X-ray single crystal structure analysis X-ray single crystal structure analysis Determination of the exact three-dimensional arrangement of building blocks (atoms, ions, molecules) in a crystalline chemical compound using X-ray radiation

Wilhelm Conrad Rntgen 1845-1923 Professor for physics Discovered X-rays on 8.11.1895 First Nobel prize winner for physics in 1901

Why a lecture on single crystal structure analysis ?

One of the most common and most precise method for the determination of the three-dimensional structure of crystalline compounds Practically no scientific publication of a new compound without its crystal structure A lot of information on molecular and non-molecular crystals Practically everyone get in contact with this method during his study, master thesis or Ph.D. Thesis The knowledge of the crystal structure of a compound is absolutely necessary for a deeper understanding of its physical properties

Structure-property relationships in solids

Crystal Structure

Reactivity

Physical Properties

Mechanic properties: hardness, fissility Optic properties: polarization refraction / double refraction dispersion optical activity non-linear optical properties (NLO: SHG)

Electric properties piezo- and pyroelectricity conductivity Magnetic properties: ferromagnetism antiferromagnetism ferrimagnetism

Why a lecture on single crystal structure analysis ?

Crystal structure

Co-worker

Information from a single crystal structure determination

Crystal system, Bravais-type, space group, metrics, lattice parameters Crystallographic density and chemical composition Symmetry of molecules Constitution and absolute configuration of a chemical compound Three-dimensional structure and packing of building blocks Precise and sometimes accurate bond lengths Conformation of molecules (torsion angles) Intermolecular bonding parameters Van der Waals radii Volume of molecules Electron distribution Dynamic in crystalline solids Static and dynamic disordering in crystalline solids

Principle of an X-ray single crystal structure determination

N sin2 Fhkl = N j f j exp B 2 exp 2i (hx j + ky j + lz j ) j =1

Single crystal structure analysis versus powder diffraction

Single Crystal Structure Analysis One small single crystal (0.05 -0.8 mm) Information about one crystal Detailed and very precise information

Powder Diffraction Several crystals Information about several crystals Limited information

Single crystal structure analysis versus powder diffraction

Single crystal structure analysis Determination of the crystal structure with high precision and accuracy Information on ordering in crystals Information on thermal motion and dynamics in crystals Very precise bonding parameters

Powder diffraction Identification of compounds or mixtures of different compounds Investigations on homogeneity Information on stress, strain and crystal size Quantitative phase analysis Determination of the crystal structure (Usual not as precise as from single crystal structure analysis)

Diffraction pattern

Single Crystal

Crystalline Powder

Characteristics of a powder pattern

Intensity
8

Reflections Position Intensity Width Shape

10

12

14

16

18

20

22

24

26

28

30

Bragg angle 2-Theta /

Characteristics of a crystal

Characteristics of Crystals: Symmetry Habit Beauty Crystal [Grecian. Ktystallos Ice, rock crystal], a crystalline solid which is composed of a three-dimensional regularly repeated arrangement of building blocks (atoms, ions, molecules) 3-dimensional periodically arrangement of the building blocks

Crystals that show habit, symmetry and beauty: halit (NaCl)

Crystals that show habit, symmetry and beauty: pyrite (FeS2)

Crystals that show habit, symmetry and beauty: vanadinit (Pb5[Cl(PO4)3])

Crystals that show habit, symmetry and beauty: quartz (SiO2)

Visualizing the internal regularity of crystals by electron microscopy Electron micrographs copper phthalocyanine hepadnavirus

Visualizing the internal regularity of crystals by STM

Scanning tunneling microscope image of gallium arsenide Ga Ga Ga Ga Ga Ga

As

As

As

As

As

As

Periodical arrangement in crystals

The unit cell concept

Characteristics of the unit cell

By convention the unit cell is characterized by three vectors: the three axis (a, b, c), the interaxial angles between the unit cell: (, , ) = angle between b and c = angle between a and c = angle between a and b Right-handed axial system Selection of a unit cell (done by a program): Small unit cell if possible Axial repeat lengths as short as possible Interaxial angles as near to 90 as possible

Characteristics and advantages of the unit cell Characteristics of the unit cell: Imaginary building block that helps to appreciate the internal periodicity of crystals (Crystal contains atoms or molecules not unit cells) Is useful for an easier description of the periodicity in crystals Advantages of the unit cell concept: The crystal is divided into small identical units For the description of the whole structure only a few parameters are needed The problem of determining the structure is reduced to that of determining the structure of the content of only one unit cell; any other unit cell will be like the first Only the position of the atoms in the unit cell must be determined Numbers of Unit Cells in a Crystal of 1 mm3 (10 6 3) NaCl D-xylose-isomerase 1019 Unit Cells 1015 Unit Cells

Selection of an unit cell

Selection of the unit cell: Each contains the same number of sulfur molecules

Crystal structure of orthorhombic sulfur

How the position of a building block in the unit cell is described ?

The position of the building blocks (atoms, ions, molecules) in the unit cell is defined by their positional parameters xyz (atomic coordinates). They are each measured as a fraction of the distance along the appropriate unit cell edge (fractional coordinates). Only values between 0 and 1 are possible. Position: xyz: Outgoing from the origin of the cell (000) x a, y b and z c a = length of the a-axis b = lengths of the b-axis c = lengths of the c-axis

Atomic coordinates

1,1,1 = 0,0,0

1,0,0 = 0,0,0 1/2,1/2,1/2 1/2,0,0 x,y,z 1/2,1,1 = 1/2,0,0

a c 0,0,0 b 0,y,0 X,0,z

How to visualize atoms ?

Relation between resolution and wavelength

The details of an object can only be visualized if the these details are separated by at least half of the wavelengths of the radiation used for observation

visible light 25 24 23 22 21 20 19 18 17 16 15 14 13 12 11 10 9 8 7 6 5 4
microwaves radiowaves

3 2 1 log [Hz]
alternating current

-7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 log []
1 10 1 10 100

1 10 100 1000

1 1 1 10 100 10

infrared

cosmic rays

x-rays

ultraviolet

> /2

1 1 10 100 1 10 100 1000 10 100 1000 104 10

C-C: 1.40 1 100 pm

femtometres picometres micrometres millimetres

metres

kilometres

Can we use a microscope for visualizing atoms ?

Light microscope

Can we use a microscope for visualizing atoms ?

Electron microscope

Can we use a microscope for visualizing atoms ?

X-ray microscope

Alternative to a microscope

No X-ray lens system available (refractive index is practically 1) ---> Alternative Principle: Diffraction of electromagnetic radiation by crystals Radiation: X-rays, synchrotron radiation, neutrons Results of the analysis: Three-dimensional arrangement of the building blocks Kind of information: Atomic coordinates and displacement parameters Atomic coordinates: Position of the atoms in a repeating unit (unit cell)

Calculation of interatomic parameters (distances, angles, torsion angles)

Displacement parameters: Measure of the atomic motion and ordering

Discovering of X-ray diffraction Max Felix Theodor von Laue Discovered X-ray interference at crystal lattices and proved the wave nature of X-rays in 1912 1879-1960 together with Walther Friedrich and Paul Knipping Professor for physics For this he became a Nobel prize winner in physics in 1914

Diffraction pattern of a crystal on a photographic film

Characteristics of electromagnetic radiation Electromagnetic radiation: transversal wave motion Displacement perpendicular to the direction of the wave front

Phase relative to the origin

Amplitude

Nonpolarized

polarized

Direction of wave front

Origin Wavelength Velocity of the wave front Wavelength = frequency

Intensity: proportional to the square of the amplitude

Diffraction Change of the direction of a wave front from the straight-line path

Size of object >>>>> wavelength: Straight-line path Mac-Light

Size of object = wavelength: Diffraction Mac-Light

er d r o 2. er 1. ord

0. order
-1. ord er -2. o rder

Double slit

Interference

er d r o 2.

in phase
Surfer

er 1. ord 0. order
-1. ord er -2. o rder

Out on phase Path difference

Partially out of phase

Relation between structure and intensity: Structure factor equation

2 sin B 2 exp 2i ( hx j + ky j + lz j ) = f j exp j =1 N

Fhkl

Ihkl

The diffraction intensities contain all information on the position of the atoms in the unit cell. They have to be measured completely and as precise as possible

Examples of diffraction patterns from a variety of masks spacing between the spots is inversely proportional to the distances between the holes

Increasing size of the holes

At which position diffraction spots can be expected ?

Founder of X-Ray structure analysis: father and son Bragg

Developed a method for the determination of the wavelength of X-ray radiation Developed the rotating crystal method Constructed a diffractometer for crystal structure analysis using X-rays (Bragg method, Goniometer method)

Sir William Henry Bragg 1862-1942 Professor for physics 1915 Nobel prize winner in physics

Sir William Lawrence Bragg 1890-1971 Professor for physics 1915 Nobel prize winner in physics

Net planes

Crystal faces and netplanes as well as indexing of crystal faces and net planes

Crystal faces and indexing of crystal faces (100) (1-10) (110)

(0-10)

(001) (001)

(010)

(-1-10) (-100)
001 0 0 -1

(-110)

001
1 0 -1 110 1-10 010 110 1-1 0

-1 0 1 0 -1 1 -1 0 0

0 -1 -1 -1 0 -1
101

Braggs Law

Crystal Net plane hkl

inc om ing

dhkl

dif fra cte db ea m

be am

plane hkl

plane hkl

= wave length d = d-spacing (spacing between the net planes) = Bragg angle (angle of diffraction) n = 0, 1, 2, 3, 4,....

n = 2 d sin

am be ing m tco ou

Intensity measurement

Intensity measurement

X-ray tube

b 2-Theta

Refl.: 100 200 300 400 110 210 310 410 120 220 320 etc.

Counter 2-Theta

Which reflections can be measured ? Number of reflections which can be measured up to the first order l: h; k; l (Its called: measuring of the complete sphere) hkl -h -k -l h k l -h k -l h k -l -h k l -h k l h k -l
100 010 001 110 101 011 111 -1 0 0 0 1 0 0 0 1 -1 1 0 -1 0 1 0 1 1 -1 1 1 0 1 1 1 1 1 0 1 1 -1 1 -1 1 1 -1 -1 -1 1 -1 1 1 1 -1 -1 1 1 0 -1 1 0 1 0 -1 -1 0 1

Note: The order of the reflections measured increases with increasing Braggangle and in the same direction the structure becomes more precise Which reflections are absolutely necessary for structure determination depend on the Laue-symmetry !

Too what Bragg angle reflections should be measured ?: Resolution

With increasing Bragg-angle the structure becomes more precise

n = 2 d sin

Resolution: sin /
Resolution: 2-Theta (): 5.00 8.2 3.50 11.7 2.50 16.3 2.00 20.5 1.70 24.1 1.50 27.4 1.40 29.4

Resolution: 2-Theta ():

1.30 31.7

1.20 34.5

1.10 37.7

1.00 41.6

0.90 46.5

0.80 52.7

The atomic scattering factor

The atomic scattering factor is a measure for the contribution of some sort of atoms to the diffraction intensity as function of the Bragg-angle. They were derived by theory and are listed in International Tables for Crystallography The Atomic Scattering Factor depends on 1. The number of electrons (Z) 2. The distribution of the electron density Path difference

X-ray diffraction versus neutron diffraction

X-rays

X-ray diffraction: Diffraction by the electrons Neutron diffraction: Diffraction by the nucleus (10 4 times smaller) Atomic scattering factor is not a simple function of Z Atomic scattering factor depends on: 1. Atomic mass (A) A1/3 2. Energy of the interaction between neutron and nucleus Consequences: Practically no decrease of diffraction intensity with increasing diffraction angle

Neutrons