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Crystallography
• Motif: the fundamental part of a symmetric
design that, when repeated, creates the
whole pattern
• In 3-D, translation defines operations
which ‘move’ the motif into infinitely
repeating patterns
• M.C. Escher’s works are based on these
ideas
Symmetry  Crystallography
• Preceding discussion related to the shape of a
crystal
• Now we will consider the internal order of a
mineral…
• How are these different?
Crystal
Morphology
Growth of crystal is
affected by the
conditions and matrix
from which they grow.
That one face grows
quicker than another is
generally determined by
differences in atomic
density along a crystal
face
Crystallography
• Motif: the fundamental part of a symmetric
design that, when repeated, creates the
whole pattern
• In 3-D, translation defines operations
which ‘move’ the motif into infinitely
repeating patterns
• M.C. Escher’s works are based on these
ideas
Translations
This HAS symmetry, but was GENERATED by translation…
Translations
2-D translations = a net
a
b
Unit cell
Unit Cell: the basic repeat unit that, by translation only, generates the
entire pattern – can you pick more than 1 unit cell?
How differ from motif ??
Translations
Which unit cell is
correct ??
Conventions:
1. Cell edges should,
whenever possible,
coincide with
symmetry axes or
reflection planes
2. If possible, edges
should relate to each
other by lattice’s
symmetry.
3. The smallest possible
cell (the reduced cell)
which fulfills 1 and 2
should be chosen
Unit Cell
• How to choose a unit cell if more than one unit cell
is a possibility…
• Rule: Must represent the symmetry elements of the
whole!
3-D translations
• Operations which ‘move’ a motif create the
lattice – a representation of the ‘moves’
which create the pattern in plane or 3-D
space
• Unit cell is a representation of the crystal
such that it can be repeated (by moving it) to
make that pattern
– If a crystal has symmetry, the unit cell must have
at least that much symmetry
Unit cells have at least as much symmetry
as the crystal (internal order > external
order)
• Here is why there
are no 5-fold
rotation axes! If
the unit cell
cannot be
repeated that way
to make a lattice,
then a crystal
cannot have that
symmetry…
3-D Translations and Lattices
• Different ways to combine 3 non-parallel,
non-coplanar axes
• Really deals with translations compatible
with 32 3-D point groups (or crystal
classes)
• 32 Point Groups fall into 6 categories
Name axes angles
Triclinic a  b  c   90o
Monoclinic a  b  c  = 90
o
90
o
Orthorhombic a  b  c  = 90o
Tetragonal a1 = a2  c  = 90o
Hexagonal
Hexagonal (4 axes) a1 = a2 = a3  c  = 90
o
120
o
Rhombohedral a1 = a2 = a3  90o
Isometric a1 = a2 = a3  = 90o
3-D Lattice Types +c
+a
+b



Axial convention:
“right-hand rule”
Unit cell types
• Correspond to 6 distinct shapes, named after the 6
crystal systems
• In each, representations include ones that are:
– Primitive (P) – distance between layers is equal to the
distance between points in a layer
– Body-centered (I) – extra point in the center
– End-centered (A,B,C) – extra points on opposite faces,
named depending on axial relation
– Face centered (F) – extra points at each face
• Cannot tell between P, I, A, B, C, F without X-ray
diffraction. Can often tell point group, system (or
class), and unit cell shape from xstal morphology
Unit cells – counting motifs (atoms)
• Z represents the number of atoms the unit
cell is comprised of
Z=1
•Atom inside cell
counts 1 each
•Atom at face
counts ½ each
•Atom at edge
counts ¼ each
•Atom at corner
counts 1/8 each
Bravais Lattices
• Assembly of the lattice points in 3-D
results in 14 possible combinations
• Those 14 combinations may have any of
the 6 crystal system (class) symmetries
• These 14 possibilities are the Bravais
lattices
a
b
c
P
Monoclinic
 90o

a b c
a
b
c
I = C
a
b
P
Triclinic

a b c
c
c
a
P
Orthorhombic
  90o
a b c
C F I
b
a1
c
P
Tetragonal
  90o
a1 = a2
c
I
a2
a1
a3
P
Isometric
  90o
a1 = a2 = a3
a2
F I
a1
c
Por C
a2
R
Hexagonal Rhombohedral
90o

0o
a1a2c
90o
a1 =a2 =a3
a.k.a. Trigonal
3-D Space
• Possible translations of a lattice point yield
the 6 crystal class shapes by ‘moving’ a
point in space (a, b, c or x, y, z
coordinates)
• Those ‘movements’ have to preserve the
symmetry elements and are thus limited in
the number of possible shapes they will
create.
Symmetry operators, again… but
we save the last ones for a reason
• Must now define 2 more types of
symmetry operators – Space group
operators
• Glide Plane
• Screw Axes
• These are combinations of simple
translation and mirror planes or rotational
axes.
Glide Planes
• Combine translation
with a mirror plane
• 3 different types:
– Axial glide plane (a, b,
c)
– Diagonal glide plane (n)
– Diamond glide plane (d)
• Diagonal and diamond
glides are truly 3-D… Step 1: reflect
(a temporary position)
Step 2:
translate
repeat
Screw Axes
• Combine translation with a rotation
• Can have 2, 3, 4, or 6- fold rotation (360º/n)
and translation of some magnitude (rational
fraction) of t (unit cell edge length)
• Subscripts indicate the magnitude of
translation
– 42 indicates a 4-fold axis translated every 2/4 t
– 43 indicates a 4-fold axis translated every 3/4 t
– 4 indicates a 4-fold axis translated every t
• The screw axes can be either right-handed
(advances away from observer when rotated
clockwise) or left-handed (advances away
from observer when rotated
counterclockwise)
Space Groups
• Atomic structure  Point groups (32 3-D
symmetry combinations) + lattice type (the 14
different Bravais lattices) + glide planes + screw
axes = 230 space groups
• They are represented:
– Start with lattice type (P, I, F, R, A, B, or C) then
symmetry notation similar to what we saw for point
groups, but including the glides and screw axes
– Garnet space group I41/a32/d
Internal – External Order
• We described symmetry of crystal habit (32 point
groups)
• We also looked at internal ordering of atoms in
3-D structure (230 space groups)
• How are they different? – Remember that the
internal order is always equal or greater than the
external order
• All minerals fall into one of 6 crystal systems,
one of 14 Bravais Lattices (variations of those
systems based on 3-D assembly)
Mineral ID
information
• Chapter 14
• Information to
identify minerals:
– Physical
– Chemical
– Optical
– Crystallographic
Why did we go through all this?
• Lattice types and space groups are important in
describing the arrangement of atoms in space
• These arrangements result in planes of atoms
which are spaced at defined intervals, controlled
by the mineral structure, which is described by
crystallography
• They describe possible planes in crystalline
structures where ions are aligned. Light and
high-energy particles interact with those planes,
which yield powerful diagnostic tools!
How does that translate to what we see??
• When a mineral grows in unrestircted space, we
see the external order – the crystal habit
• When a mineral breaks, what defines where it is
likely to break??

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Applied Biochemistry

  • 1.
  • 2. Crystallography • Motif: the fundamental part of a symmetric design that, when repeated, creates the whole pattern • In 3-D, translation defines operations which ‘move’ the motif into infinitely repeating patterns • M.C. Escher’s works are based on these ideas
  • 3. Symmetry  Crystallography • Preceding discussion related to the shape of a crystal • Now we will consider the internal order of a mineral… • How are these different?
  • 4. Crystal Morphology Growth of crystal is affected by the conditions and matrix from which they grow. That one face grows quicker than another is generally determined by differences in atomic density along a crystal face
  • 5. Crystallography • Motif: the fundamental part of a symmetric design that, when repeated, creates the whole pattern • In 3-D, translation defines operations which ‘move’ the motif into infinitely repeating patterns • M.C. Escher’s works are based on these ideas
  • 6. Translations This HAS symmetry, but was GENERATED by translation…
  • 7. Translations 2-D translations = a net a b Unit cell Unit Cell: the basic repeat unit that, by translation only, generates the entire pattern – can you pick more than 1 unit cell? How differ from motif ??
  • 8. Translations Which unit cell is correct ?? Conventions: 1. Cell edges should, whenever possible, coincide with symmetry axes or reflection planes 2. If possible, edges should relate to each other by lattice’s symmetry. 3. The smallest possible cell (the reduced cell) which fulfills 1 and 2 should be chosen
  • 9. Unit Cell • How to choose a unit cell if more than one unit cell is a possibility… • Rule: Must represent the symmetry elements of the whole!
  • 10. 3-D translations • Operations which ‘move’ a motif create the lattice – a representation of the ‘moves’ which create the pattern in plane or 3-D space • Unit cell is a representation of the crystal such that it can be repeated (by moving it) to make that pattern – If a crystal has symmetry, the unit cell must have at least that much symmetry
  • 11. Unit cells have at least as much symmetry as the crystal (internal order > external order) • Here is why there are no 5-fold rotation axes! If the unit cell cannot be repeated that way to make a lattice, then a crystal cannot have that symmetry…
  • 12.
  • 13. 3-D Translations and Lattices • Different ways to combine 3 non-parallel, non-coplanar axes • Really deals with translations compatible with 32 3-D point groups (or crystal classes) • 32 Point Groups fall into 6 categories Name axes angles Triclinic a  b  c   90o Monoclinic a  b  c  = 90 o 90 o Orthorhombic a  b  c  = 90o Tetragonal a1 = a2  c  = 90o Hexagonal Hexagonal (4 axes) a1 = a2 = a3  c  = 90 o 120 o Rhombohedral a1 = a2 = a3  90o Isometric a1 = a2 = a3  = 90o 3-D Lattice Types +c +a +b    Axial convention: “right-hand rule”
  • 14. Unit cell types • Correspond to 6 distinct shapes, named after the 6 crystal systems • In each, representations include ones that are: – Primitive (P) – distance between layers is equal to the distance between points in a layer – Body-centered (I) – extra point in the center – End-centered (A,B,C) – extra points on opposite faces, named depending on axial relation – Face centered (F) – extra points at each face • Cannot tell between P, I, A, B, C, F without X-ray diffraction. Can often tell point group, system (or class), and unit cell shape from xstal morphology
  • 15. Unit cells – counting motifs (atoms) • Z represents the number of atoms the unit cell is comprised of Z=1 •Atom inside cell counts 1 each •Atom at face counts ½ each •Atom at edge counts ¼ each •Atom at corner counts 1/8 each
  • 16. Bravais Lattices • Assembly of the lattice points in 3-D results in 14 possible combinations • Those 14 combinations may have any of the 6 crystal system (class) symmetries • These 14 possibilities are the Bravais lattices
  • 17. a b c P Monoclinic  90o  a b c a b c I = C a b P Triclinic  a b c c c a P Orthorhombic   90o a b c C F I b
  • 18. a1 c P Tetragonal   90o a1 = a2 c I a2 a1 a3 P Isometric   90o a1 = a2 = a3 a2 F I a1 c Por C a2 R Hexagonal Rhombohedral 90o  0o a1a2c 90o a1 =a2 =a3 a.k.a. Trigonal
  • 19.
  • 20. 3-D Space • Possible translations of a lattice point yield the 6 crystal class shapes by ‘moving’ a point in space (a, b, c or x, y, z coordinates) • Those ‘movements’ have to preserve the symmetry elements and are thus limited in the number of possible shapes they will create.
  • 21. Symmetry operators, again… but we save the last ones for a reason • Must now define 2 more types of symmetry operators – Space group operators • Glide Plane • Screw Axes • These are combinations of simple translation and mirror planes or rotational axes.
  • 22. Glide Planes • Combine translation with a mirror plane • 3 different types: – Axial glide plane (a, b, c) – Diagonal glide plane (n) – Diamond glide plane (d) • Diagonal and diamond glides are truly 3-D… Step 1: reflect (a temporary position) Step 2: translate repeat
  • 23. Screw Axes • Combine translation with a rotation • Can have 2, 3, 4, or 6- fold rotation (360º/n) and translation of some magnitude (rational fraction) of t (unit cell edge length) • Subscripts indicate the magnitude of translation – 42 indicates a 4-fold axis translated every 2/4 t – 43 indicates a 4-fold axis translated every 3/4 t – 4 indicates a 4-fold axis translated every t • The screw axes can be either right-handed (advances away from observer when rotated clockwise) or left-handed (advances away from observer when rotated counterclockwise)
  • 24. Space Groups • Atomic structure  Point groups (32 3-D symmetry combinations) + lattice type (the 14 different Bravais lattices) + glide planes + screw axes = 230 space groups • They are represented: – Start with lattice type (P, I, F, R, A, B, or C) then symmetry notation similar to what we saw for point groups, but including the glides and screw axes – Garnet space group I41/a32/d
  • 25. Internal – External Order • We described symmetry of crystal habit (32 point groups) • We also looked at internal ordering of atoms in 3-D structure (230 space groups) • How are they different? – Remember that the internal order is always equal or greater than the external order • All minerals fall into one of 6 crystal systems, one of 14 Bravais Lattices (variations of those systems based on 3-D assembly)
  • 26. Mineral ID information • Chapter 14 • Information to identify minerals: – Physical – Chemical – Optical – Crystallographic
  • 27. Why did we go through all this? • Lattice types and space groups are important in describing the arrangement of atoms in space • These arrangements result in planes of atoms which are spaced at defined intervals, controlled by the mineral structure, which is described by crystallography • They describe possible planes in crystalline structures where ions are aligned. Light and high-energy particles interact with those planes, which yield powerful diagnostic tools!
  • 28. How does that translate to what we see?? • When a mineral grows in unrestircted space, we see the external order – the crystal habit • When a mineral breaks, what defines where it is likely to break??