Introduction to Crystallography

& Symmetry

Crystallography Short Course

Yangzhou University, May/June 2016

Cora Lind-Kovacs
Department of Chemistry & Biochemistry
The University of Toledo
Toledo, OH 43606, USA
[email protected]
 Crystallography - what and why?
¢ What?
- Determination of the atomic structure of crystalline solids
- Location and type of atoms, bond distances/local environment
- Absolute structure
¢ Why?
- Materials’ properties are intimately related to their structures
> Understanding certain properties requires knowledge of atomic
arrangement, e.g. piezoelectrics
» Structural studies of enzyme active sites can allow the rational selection of
inhibitors
- Impact of crystallography can be seen in the large number of Nobel
Prizes for work related to crystallography or diffraction
»
 Historical development — X-rays
¢ X-rays were discovered by Wilhelm Conrad Rontgen in 1895
- “Interested in the effects of ultra-violet radiation, he covered a cathode-
ray discharge tube with black paper and darkened the room. With the
glow from the tube hidden, Réntgen was surprised to see a fluorescent
screen two metres away light up. For several weeks, Réntgen hid in his
laboratory, finding out more about the mysterious penetrating X' rays,
produced when the cathode rays hit the end of the discharge tube.”
(IUCr history page)
¢ In 1912, Max von Laue discovered that X-rays are diffracted by
crystals
- Coppersulfate, recordedon film
¢ In 1913, Sir William Henry and William Lawrence Bragg
formulated their famous Braggs law
- Birthof “crystallography™
 What was the Big Deal?
¢ Rontgen had shown that X-rays darken photographic film, and
that they are more penctrating than light (c.g., can pass through
the human body).
- Medical use of X-rays for imaging bones developed quickly
¢ It had been proposed that X-rays are electromagnetic radiation
with A wavelength, but there was no direct proof of it!
¢ Mincralogists had classified crystals according to external
symmetry, and had proposed that they are made up of periodic
repeat units, but there was no direct proof of it!
¢ Diffraction of visible light by a grating was known.
 Von Laue’s experiment
¢ Von Laue combined the knowledge of physicists and
mineralogists to propose the first diffraction experiment:
- If crystals are built from regular repeat units...
- If the repeat units in crystals are on the order of A...
- If X-rays are electromagnetic waves of A wavelength...
...then crystals should diffract X-rays in the same manner as
visible light is diffracted by a grating!
¢ Together with Friedrich and Knipping, he collected the first
“Laue pattern” of a CuSO,-5H,0 crystal on film
@ His exneriments nroved both the wave nature of X-ravs and the
 Early crystallography and materials
@ The first crystal structure ever solved was NaCl
¢ Clearly showed equally spaced sodium and chlorine atoms and
thus proved the concept of ions and ionic bonding!
— First proof that not all materials are made up of molecules!
- Admittedly, not everybody was happy to accept this...
¢ Other early crystal structures solved were diamond and graphite
~ Showed that atomic connectivityis at least as important in describing
properties as elemental composition!

Strictire:Mattven! T
 What is possible today?
4 Determination of small molecule structures is routine nowadays
- This was not truze 30 years ago!
- Takes 6-12 h of data collectionin most cases
¢ Crystal structures of macromolecules can be solved from single
crystal data
¢ Synchrotron radiation can in some cases yield single orystal
structures from crystals that.are smaller than 10 pm
¢ Powder methods are becoming more advanced and can in some
cases enable full structure determinations, too
 ti on be fo re the ad ve nt of cr ys tallography
& Historic defini
- A solid with well-defined faces

® Crystallographic definition
structural motif
- A material witha regularly repeating

# The strict definition is more vague

ternwith sharp peaks
- Any material that gives a diffraction pat
vt A1 Famein e the sevetallaoranhic definition in this short
 Repeating motif: The unit cell
4 The repeating structural motif in a crystal is referred to as a
unit cell
- Only the size/shape and contents of one unit cell are necessary to
describe the entire crystal

® Remember to use a right-handed axis system!

<

\ )
“Crystal Structure Analysis for Chemists and
Biologists", Olusker, Lewis and Rossi, VCH, 1994,
 The seven crystal systems
Crystalsystem Unit cell edges Unit cell angles
Cubic a=b=c a=p=v1=90°
Hexagonal a=bwc a=pf=90°y=120°
Rhombohedral a=b=c a=p=y#90or120°
Tetragonal a=b=zc a=f=v=90°
Orthorhombic azbzc a=pf=y=90°
Monoclinic azbzc a=7=90°f#900r120°
Triclinic azb=c azp#y#90o0r120°

T e e

Cubic Hexagona! Rbombohedral ~ Tetragomal Orthorhombic Monoclinic Tricknic

“Structure Determination by N-ray Crystaliography”,
A7
~Crystal Structure Analysis for Chemists and 1
Ladd and Palmer. Planum. 1994. Biologists™, Glusker, Lewis and Ross., VCH, 1994,
 Miller indices
@ Any crystal face/planc.can be described by its intersection
points with the three unit cell axes

@ Miller indices are the reciprocal of the intercepts

- integers h, k and | refer to reciprocals of intercepts on a, b and ¢

@ Identify planes adjacent to origin

= planes through the origin cannot be described. as the intercept
would be zero

¢ A planc running parallel to an axis has an intercept of oo,

this carresponds to a Miller index of 0
12
 Examples of lattice planes
-t
O
@Y
OO~
WM
E
MW
=
O

0 4 4 6 B 10

4 Any lattice plane can be described by three integers called

Miller indices h, k and |
 Some examples of Miller indices
“Elernents of X-ray Diffracton”, Cullity '"% Stock, Prentice Hall College Dyv., 3rd edition, 2001,

14
Fig. 2-10 Miller indices of lattice planes. The distance d is the plane spacing.
Imagine...
- having to describe an infinite crystal with an infinite number of atoms
- oreven a finite crystal, with some 10%° atoms

Sounds horrible? Thankfully, there’s symmetry to help you out!

Instead of an infinite number of atoms, you only need to
describe the contents of one unit cell, the structural repeating
motif...
- and life could be even easier, if there are symmetry elements present
inside the unit cell!

- you only need to describe the asyminetric 1t if this is the case 15

@ Lattice symmetry
refers to the unit cell
size and shape
& Without rules, there
would be an infinite
number of different
unit cells to describe
any given lattice
“Crystal Stmcture Analysis for Chemists and
16
Biolopists™, Glusker, Lewis and Rossi, VCH, 1994,
—

# By convention, a unit cell is chosen as

- thesmallest possible repeat unit
= which has the highest symmetry
# This can result in primitive unit cells or centered unit
cells
- notall erystal systems can be ceritered
by this definition
- theseven crystal sy
stems in combinatio
n with the cent ering operations
£IVe Tise 1o fhe 14 Bravaic latinas
 ' * ’
. S

¢ According to our definitions, the centered cell would be preferred

“Crystal Structure Analysis for Chemists and Biologists”, Ghisker. Lewis and Rossi. VCH, 1091, 18
 LA 1
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(IR AR R PRSP i i
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“Elemtents of N-ray Diffiaction”, Culity mnd Stock, Prentice Holl Collage Div,, 3rd edition, 2¢
@ A tetragonal base
centered cell can
always be transformed
into a tetragonal
primitive cell
4 An orthorhombic base centered cell cannot be
transformed into a primitive cell without losing the
orthorhombic symmetry
4 An orthorhombic base centered cell cannot be
transformed into a primitive cell without losing the
orthorhombic symmetry
 Symmetry elements
© When talking about symmetry operations, we must distinguish
- Point symmetry elements
- Translational symmetry
@ Point symmetry clements will always leave at lcast one point
unchanged
- Rotationaxes
- Mirrorplanes
- Rotation-inversion
axes
¢ Translational symmetry clements exist in space groups
- Lattice centering
- Screw axes
- Glide planes
 Rotation axes

v | ¢ Example: A two-fold
- b \“.:; o [
rotation axis
- nochange in handedness
/S - refetorred
as “proper
\a

T syimetry operation”

¢ An n-fold rotation axis

I & will rotate the object by
Y ¥ fi e 360/n°

/(_. rpotation @ Symbol: n (e.g.. 2. 3,4, 6)

twofold sos

*Crystal Saretum: Amysis for Chemmsts and Biologists™, Glusker, Lewts and Rossi, VCH. 1994, 22
-
 & A mirror plane ¢hanges
the handedness of the
object it is operating on
- cannot exist in crystals of
). -
“I

—F% - W i ;
an enantiomerically pure
&
- - substance
T Ethe (kg
- referred toas “improper
symmetry operation”
el hasd waht Hand
x ¢ Symbol: m
J-" s “Cryshl Structure Anlysis for Chemists and
Biologists”, Glusker, Lewss and Rosst, VCH, 1904,
 Inversion centers
¢ “Turning an object inside

¢ Equivalent to a “point

ny.x ;}\ reflection™ through the

o mooca; . inversion center
N o Ps'i= .

E gt - similar to focal pointof a

lense
kel ight haod - changes handedness

&g % ¢ Symbol: i
conter of symmey “Crystal Strocture Amalysis for Chemists and 2
Biologists”, Glusker, Lewis and Rossi, VCH, 1994,
 Rotation-inversion centers
o~

/ !
el
s
Ly im
> @ Rotation
2
followed by
s hasd
i1 inversion
ngh basd F ;
; ¢ An inversion center can
’L > be regarded as a “one-fold
R rotation” followed by an
/4 . .
inversion
ks ,0 Siep 3 Exe
L —
et o ey ¢ Symbol: -n or 7

) “Crystal Structure Analysis for Chemists and 26

Biologists”, Glusker, Lewis and Rossi. VCH, 1994,
 axes
& Crystallographers work with rotation-inversion
ject
+ Ifyou take a class in Group Theory or another sub
involving symmetry operations. your teacher may -not
consider rotation-inversion axes a synmuetry operation
- theyuse rotation-reflectionaxes (svmboi: 5,)

- rtotation-inversion and rotaticn-reflection aves are NOT the same!

- gninversion cenlercorresponds to s =1 axis™. but to an $; axis!

- however. any compound that has 2 —4 axis will also possess an 5 axis
bar
 trazlation af2

===

\ A derrw
ey
« 7. \\ ’
A\
Ay5 i
p 74 v /
’ D
i/
/- = 7
[

@ A 2, screw axis translates an object by halfa unit cell in the

direction of the screw axis, followed by a 180° rotation
“Crysial Structure Amlysis for Chemists and Biologists™, Glusker, Lewis and Rossi, VCH, 1004,
 “Stricture Determination by X«
Ladd and Palmer, Plepum. 1594

PEN
tromisgtion
T Unek mavia ton | O

i -
L
Flgure 3.20. Screw axis 2, Figere 321, Screw w3,
. N_

¢ A C, screw axis translatesan object by the unit cenr aimensic

multiplied by n/C along the direction of the screw axis, follo
a C-fold rotation
 Glide planes
¢ A glide plane corresponds to a reflection-translation operation
- reflectionthrough the glide plane
- ftranslationparallelto the glide plane
- exact translationdepends on type of glide
@ There are a, b, ¢, n and d glide planes
- a,bandc glides correspondto translationsof Y2 a, 2 band %z ¢
respectively
- called “axial glide planes™
- nglide correspondstoa translationof Y2a + ' b, Y2a+ Y2 c.or's b+ Yac
- called “diagonal glide plane”
- deglide correspondstoa translationof Y% a + % b, Yaa+ Yac,ora b+ Yic
- called “diamond glide plane™ 3
 —
translation af2

g“d.n plane
 Combining symmetry operations
@ An object can possess several symmetry clements
@ Not all symmetry clements can be combined arbitrarily
- for example, two perpendicular two-fold axes imply the existence of
third perpendicular two-fold
¢ Translational symmetry in 3D imposes limitations
- only2, 3, 4 and 6-fold rotation axes allow for space filling
translational symmetry
¢ The allowed combinations of symmetry elements are called
point groups
- there are 32 point groups that give rise to periodicity in 3D

33
 Space filling repeat patterns

‘ma

#0nly 2, 3, 4 and 6-fold rotz

fel &
can produce space filling pat
e
“Strocture Determimation . by X-ray Crystallograph
Ladd and Pahner, Plenum, 1994,
 Symeol masing. sppeopres for poion coapeed

Syttem Shivt oo Fina pocition Secomdposition Thind porition

Téds B] Ome symbed pewtion wely, demiriing 8t Sevciions
e O

4 Show 3D repeat Mosactioic™ 3, m 3 fm

Ortborhowbie 222.m2.
o&wm&—\md-lm,
Jandier] 2edfor} 3 ondieedsbangr
mm- wlong v Nong ¥
pattern Tetsoost 4. 4,4fm - -
aAdem e :u::-l Tandlor
S 4y
. l =
lh‘;n— Lo 24 i
4 Contain symmetry
Trigomt” %) })u,d—. = =
32 3m A 2 Daedfeed -
clements alowg b
Heopondl 6,54, 6 adion & — -
mb—:l. Wong 2 Tendled Fandiee 03T
@ 32 point groups exist L35 RUP
-
wooy
xye
ok y. 0 i the
"y pleve
“Cabic nm Pasdiord | dordm -
wong x Y. Ry
. e -
HL B, tandjoed 2 antior Tl
mim somg 1.3 Arnnyr
r B oy, vz and
2x planet
* I €0 R by, (00 5 S0 B ke 4 £50 aoic 3 or 3 aa B Do e 1 0 ahmg
150 plane prenented by fhe Aaree ol s e posat rown el in prpenicater ie ) The beves
ettt iy Srastiy admndic bs shoe crywead prvimmd. {15 b best 48 Wiy O aemtadinn o ¢ pliee
‘b,»nu--m-fl
“Structure Determination by X-ray Crystallography"', - . 19 8 o o e
Ladd and Palmer, Plenum. 1994, .:L_'__"",'" ::M"‘:mi*flhmp‘m <
4 Assatyess 010 KL
 Space groups
© When talking about crystal structures, people will usually
report the space group of a crystal
4 Space groups are made up from
- lattice symmetry (translational)
- pointsymmetry (not translational)
- glide and/or screw:axes (same translational component)
¢ There are 230 space groups

7 crystal 14 Bravais 32 point 23(

systems lattices groups grc
 Interpretation of Space Group Symbols
@ All space group symbols start with a letter corresponding to the lattice
centering, followed by a collectionof symbols for symmetry operationsin the
three lattice directions
- For symmetry “directions”, see point group table 2 slides ago!
4 There are sometimes short notations for space group symbols
- P121isusually wriltenasP2
- primitive monoclinic cell that has a two-fold rotation along the b axis
- P2,2,2, (cannot be abbreviated)
- primitive cell that has a 2y screw along each axis, orthorhombic
- Cmma (full symbol: C2/m 2/m 2/a)
- C-centered cell with a mirror plane perpendicular to a and b and an a glide plane
perpendicular 10¢
- also has implied symmetry elements (e.g., the 2-fold rotations)
 hflfl“%'
g;w-fluflu o
vector of 2 tilhi.-lnrlfid& h
plfli-ll elemen
rew rotation m wnils tor @ parenthesety
GHFMPW“‘H. \barest Tattice franslation yec
Gymmetry A1l of symmeLTY point paralicl 10 the
1
Nomt
None '3
demtey
Nome
T'walohd rofation sai []
Twofold roatia}n poun! .
two dimenion }
a2d b I )
rwa aw o
scrl
None k]
Mhreciold rotation axis 'y
Threcfold rotation point 3
wo dimenusons} ]
A
Threelold screw sun=')wb 1 i 3,
Y
Threctold screw anv:"} wb T
Foufold folation v w Nove 41
Fourfold rotation point *
1w dupcmsoni} 1 4,020
'*' LS 4' (":
Fourfold screw mn tdwb I ¢ x I
Fowsrfold sorew axis:8 b ¥ o
. 4, (2,1
Fourfold screw avis "4 sub T +
H
m rolar roatfon niki 6 (32)
i pd None
o dimensiont ] #* i
6120200
Soctobd borew anic 6 suk 1° .
: 7
6 swb » 8, (3s.2)
SikloM serew ane i
Sixfiodd scr ew axn : 6 wh ¥ ]
i 6,132 L1
ixfold sczew axia "6 wh & & 6, (3,0
* i
ixfold screw axia; 6 wh § { 6, th2)
 Graphical symbols (2)
“Internntionnl Tables for Crystallogruphy, Vol. A”, Khnwer, 1903,
Cemre of symmrtry, mvenian
Noow 1
Nooe iah
Nene I
oked

None 6 =iim
Teobold retwivom wxih with wentre Nane Umil)
of symmetry
Twokold
screw axis with cemra of symmetry 1 2m (1)
Fouricld rorarion ssw with evaue L Nooe 4w td21)
of symametry
“dwd T sorew auis with contre
of ymmenry 6 & 1 4 /m3n
Sanbold rotation anis with cenire o Mo wim (613210
of symmetry
% sub T aceww
aen it ceniee [ H 6/m 83927
of symmetry
Reflection plane. mirede ’lw}
Reflection bine, wmrror e Neme -
(reo dimeeuom)
“Anial’ ghide plane | lattee wecme whong llew m progecton plear a“boore
Gisde Fime fiwo dimensions) | e wrent slong liee in plane
“Aual ghdc plaoe —— § oommal be prajection plane “hkooee

"Dogbie” . .
(= mn:‘:lm) !Mr:mwzu—m

*Disgonal’ ghide plane - flide vecior with fwo camposcsts: L]

Inonllm-nluw:::mum

“Dismond ghde plame! - 1 aloog liw paratiel bo projpection planc.

.Jluln in conired -————— cominoed with | morml ko peopc iow 39
plane urrow indicatey Jirection
paralict ta the proyectson plane fo
which the pormal companant
i posiliv)
Symmetry elements parallel to plane of projection
“Intermational Tables for Crystallography, Vol A™, Khuwer, 1993,

Symmetry plane Graphieal rymbol® G ot e o e crion plane Prioted symbol

Reflection plane, mirror plane r /— Noae -

“Axial ghide plane I~ r‘ | tarnce vectoe in the direcon of the srvow aboce

“Double’ | in cithee of:the

Tiwo gide vectons .
(h«mv'::'llr-:;) r. fixfi‘d*l‘m

“Disgosal” ghde plane |'-_ i’:fl"wunm -

T
a
i
|hhm:.t:um.hfll
A
“Diamond" glide plane!
e .- conventional celt

Screw vector af & nght-handed Printed symbol

Symmeery anis Graphical symboit mwlhmnd& (:nhhk-—)-
paralic]
10 the axis
Twolold totation sns - - [ ] Nove 2
Twolold screw axi: 2 awb I -_—- ! ? ] 2,
Fourfold rotation sus .- T4 None 40
Fourfold screw a4 wh I 4 = o= E $ 4,2)
Fourfold screw axis. ‘4 mub T | S i ! 4@
Fourfold screw axi:*4 sab ¥ 4 7T - 3] 4,20
taversion axie:*4 bar" s 4 T g % Nore im 40
Tverion poat 08 ‘4 bar"ais 4 d = 3 potm
 1) Svmmtey plimes inclised bo the plame =l prwjrctios (1 swble (pocs provpm of stss dhe sed sde sody

Oommast byl . e pims

s Citice
o woe| v 1wt eo Jebsice beuenty.
aeraite Prstad
Sywmetry plone e o v
O amaa0T) mmd (10F)
(19 1610)and(01}) [01]mae(rol)
Bl = = -
worsare (1 () MR OESEE e
weonnss (T ) e, Ly
“Deabis” 5 plome* -~ g " e Tew M

gres (D) O T T
s iw 1% W= Velong |190) end | wicoy

Dagerr pcpiom
(VR
(1T sk
ePlids T
drrm (b gl socmr o

comrpaigme (17 D Lehlye fmepilme

= (R A X
{0 Ermmrrry o binal b e o of goviocion o exhle spave grmeps smiv) [ & ‘Laeglipe bemim-