A Single-Nucleotide Polymorphism in an Endo-1,4-β-Glucanase ...
Polymorphism or Allotropy -...
Transcript of Polymorphism or Allotropy -...
Polymorphism or Allotropy
Many elements or compounds exist in more than one crystalline
form under different conditions of temperature and pressure.
This phenomenon is termed polymorphism and if the material is
an elemental solid is called allotropy.
Example: Iron (Fe – Z = 26)
liquid above 1539 C.
δ-iron (BCC) between 1394 and 1539 C.γ-iron (FCC) between 912 and 1394 C.α-iron (BCC) between -273 and 912 C.
α iron γ iron δ iron912oC 1400oC 1539oC
liquid iron
BCC FCC BCC
Another example of allotropy is carbon.
Pure, solid carbon occurs in three crystalline forms – diamond,
graphite; and large, hollow fullerenes. Two kinds of fullerenes are
shown here: buckminsterfullerene (buckyball) and carbon nanotube.
Crystallographic Planes and DirectionsAtom Positions in Cubic Unit Cells
A cube of lattice parameter a is considered to have a side equal to
unity. Only the atoms with coordinates x, y and z greater than or
equal to zero and less than unity belong to that specific cell.
y
z
x
1,0,1
1,0,0
1,1,1
½, ½, ½
0,0,0
0,0,1 0,1,1
1,1,0
0,1,0
1,,0 <≤ zyx
Directions in The Unit Cell
For cubic crystals the crystallographic directions indices are the
vector components of the direction resolved along each of the
coordinate axes and reduced to the smallest integer.
y
z
x
1,0,1
1,0,0
1,1,1
½, ½, ½
0,0,0
0,0,1 0,1,1
1,1,0
0,1,0A
Example direction A
a) Two points origin coordinates
0,0,0 and final position
coordinates 1,1,0
b) 1,1,0 - 0,0,0 = 1,1,0
c) No fractions to clear
d) Direction [110]
y
z
x
1,1,1
0,0,0
0,0,1
B
C
½, 1, 0
Example direction B
a) Two points origin coordinates
1,1,1 and final position
coordinates 0,0,0
b) 0,0,0 - 1,1,1 = -1,-1,-1
c) No fractions to clear
d) Direction ]111[___
Example direction C
a) Two points origin coordinates
½,1,0 and final position
coordinates 0,0,1
b) 0,0,1 - ½,1,0 = -½,-1,1
c) There are fractions to clear.
Multiply times 2. 2( -½,-1,1) =
-1,-2,2
d) Direction ]221[__
Notes About the Use of Miller Indices for Directions
� A direction and its negative are not identical; [100] is not equal to
[bar100]. They represent the same line but opposite directions. .
� direction and its multiple are identical: [100] is the same direction
as [200]. We just forgot to reduce to lowest integers.
� Certain groups of directions are equivalent; they have their
particular indices primarily because of the way we construct the co-
ordinates. For example, a [100] direction is equivalent to the [010]
direction if we re-define the co-ordinates system. We may refer to
groups of equivalent directions as directions of the same family. The
special brackets < > are used to indicate this collection of directions.
Example:
The family of directions <100> consists of six equivalent directions
00]1[],1[000],1[0[001],[010],[100], >100< ≡
Miller Indices for Crystallographic planes in Cubic Cells
� Planes in unit cells are also defined by three integer numbers,
called the Miller indices and written (hkl).
� Miller’s indices can be used as a shorthand notation to identify
crystallographic directions (earlier) AND planes.
Procedure for determining Miller Indices
� locate the origin
� identify the points at which the plane intercepts the x, y and z
coordinates as fractions of unit cell length. If the plane passes
through the origin, the origin of the co-ordinate system must be
moved!
� take reciprocals of these intercepts
� clear fractions but do not reduce to lowest integers
� enclose the resulting numbers in parentheses (h k l). Again, the
negative numbers should be written with a bar over the number.
y
z
x
A
Example: Miller indices for plane A
a) Locate the origin of coordinate.
b) Find the intercepts x = 1, y = 1, z = 1
c) Find the inverse 1/x=1, 1/y=1, 1/z=1
d) No fractions to clear
e) (1 1 1)
More Miller Indices - Examples
a
b
c
0.50.5
a
b
c
2/3
1/5
a
b
c
a
b
c
a
b
c
ab
c
Notes About the Use of Miller Indices for Planes
� A plane and its negative are parallel and identical.
� Planes and its multiple are parallel planes: (100) is parallel to the
plane (200) and the distance between (200) planes is half of the
distance between (100) planes.
Certain groups of planes are equivalent (same atom distribution);
they have their particular indices primarily because of the way we
construct the co-ordinates. For example, a (100) planes is
equivalent to the (010) planes. We may refer to groups of
equivalent planes as planes of the same family. The special
brackets { } are used to indicate this collection of planes.
� In cubic systems the direction of miller indices [h k l] is normal
o perpendicular to the (h k l) plane.
� in cubic systems, the distance d between planes (h k l ) is given
by the formula where a is the lattice
constant.
Example:
The family of planes {100} consists of three equivalent planes (100)
, (010) and (001)
222 lkh
ad
++=
A “family” of crystal planes contains all those planes are crystallo-
graphically equivalent.
• Planes have the same atomic packing density
• a family is designated by indices that are enclosed by braces.
- {111}:
)111(),111(),111(),111(),111(),111(),111(),111(
c
(110) = (1100)- -
(100) = (1010)-
a1
a2
a3
(001) = (0001)
(110) = (1100)- -
Two Types of Indices in the Hexagonal System
a1
a2
a3
c
a1
a2
a3
c
Miller: (hkl) (same as before)
Miller-Bravais: (hkil) → i = - (h+k)
a3 = - (a1 + a2)
a1 ,a2 ,and c are independent, a3 is not!
Structure of Ceramics
Ceramicskeramikos - burnt stuff in Greek - desirable properties of
ceramics are normally achieved through a high temperature heat
treatment process (firing).
Usually a compound between metallic and nonmetallic elements
Always composed of more than one element (e.g., Al2O3, NaCl,
SiC, SiO2)
Bonds are partially or totally ionic, can have combination of ionic
and covalent bonding (electronegativity)
Generally hard, brittle and electrical and thermal insulators
Can be optically opaque, semi-transparent, or transparent
Traditional ceramics – based on clay (china, bricks, tiles,
porcelain), glasses.
“New ceramics” for electronic, computer, aerospace industries.
Crystal Structures in Ceramics with
predominantly ionic bonding
Crystal structure is defined by
The electric charge: The crystal must remain electrically
neutral. Charge balance dictates chemical formula (Ca2+ and F-
form CaF2).
Relative size of the cation and anion. The ratio of the atomic
radii (rcation/ranion) dictates the atomic arrangement. Stable
structures have cation/anion contact.
Coordination Number: the number of anions nearest neighbors for a
cation.
As the ratio gets larger (that is as rcation/ranion ~ 1) the coordination
number gets larger and larger.
Holes in sphere packing
Triangular Tetrahedral Octahedral
Calculating minimum radius ratio
for a triangle:
1550
2
330
21
2
1
.
cos
)30=( cos
=
==+
°=
+=
=
a
c
ca
a
ca
a
r
r
rr
r
AO
AB
rrAO
rAB
αα
A C
BO
AC
B
O
4140
2
245
21
2
1
.
cos
)45=( cos
=
==+
°=
+=
=
a
c
o
ca
a
ca
a
r
r
rr
r
AO
AB
rrAO
rAB
αα
for an octahedral hole
C.N. = 2
rC/rA < 0.155
C.N. = 3
0.155 < rC/rA < 0.225
C.N. = 4
0.225 < rC/rA < 0.414
C.N. = 6
0.414 < rC/rA < 0.732
C.N. = 8
0.732 < rC/rA < 1.0
Ionic (and other) structures may be derived from the occupation of
interstitial sites in close-packed arrangements.
o/t fcc(ccp) hcp
all oct. NaCl NiAs
all tetr. CaF2 (ReB2)
o/t (all) (Li3Bi) (Na3As)
½ t sphalerite (ZnS) wurtzite (ZnS)
(½ o CdCl2 CdI2)
Comparison between structures with filled octahedral and tetrahedral holes
Location and number of tetrahedral
holes in a fcc (ccp) unit cell
- Z = 4 (number of atoms in the unit cell)
- N = 8 (number of tetrahedral holes in the
unit cell)
Crystals having filled Interstitial Sites
NaCl structure has Na+ ions
at all 4 octahedral sites
Octahedral, Oh, Sites
Na+ ions
Cl- ions
Ionic Crystals prefer the NaCl
Structure:
• Large interatomic distance
• LiH, MgO, MnO, AgBr, PbS,
KCl, KBr
Crystals having filled Interstitial Sites
Both the diamond cubic structure
And the Zinc sulfide structures
have 4 tetrahedral sites occupied
and 4 tetrahedral sited empty.
Tetrahedral, Th, Sites
Zn atoms
S atoms
Covalently Bonded Crystals Prefer
this Structure
• Shorter Interatomic Distances
than ionic
• Group IV Crystals (C, Si, Ge, Sn)
• Group III--Group V Crystals
(AlP, GaP, GaAs, AlAs, InSb)
• Zn, Cd – Group VI Crystals
(ZnS, ZnSe, CdS)
• Cu, Ag – Group VII Crystals
(AgI, CuCl, CuF)
Rock Salt Structure (NaCl)
Cl NaCoordination = 6
NaCl, MgO, LiF, FeO, CoO
NaCl structure: rC = rNa = 0.102 nm,
rA = rCl = 0.181 nm rC/rA = 0.56
AX Type Crystal Structures
Cesium Chloride Structure (CsCl)
CsClCoordination = 8
Is this a body centered cubic structure?
CsCl Structure: rC = rCs = 0.170 nm,
rA = rCl = 0.181 nm → rC/rA = 0.94
Zinc Blende Structure (ZnS)
ZnSCoordination = 4
radius ratio = 0.402
ZnS, ZnTe, SiC have this crystal structure
AmXp-Type Crystal StructuresIf the charges on the cations and anions are not the same, a compound
can exist with the chemical formula AmXp , where m and/or p ≠ 1. An
example would be AX2 , for which a common crystal structure is
found in fluorite (CaF2).
Fluorite CaF2
Fluorite (CaF2): rC = rCa = 0.100 nm, rA= rF = 0.133 nm ⇒ rC/rA = 0.75
From the table for stable geometries we
see that C.N. = 8
Other compounds that have this crystal
structure include UO2 , PuO2 , and ThO2.
AmBnXp-Type Crystal Structures
It is also possible for ceramic compounds to have more than one
type of cation; for two types of cations (represented by A and B),
their chemical formula may be designated as AmBnXp . Barium
titanate (BaTiO3), having both Ba2++++ and Ti4+ cations, falls into this
classification. This material has a perovskite crystal structure and
rather interesting electromechanical properties
Perovskite -
an Inorganic Chameleon
ABX3 - three compositional variables, A,
B and X
• CaTiO3 - dielectric
• BaTiO3 - ferroelectric
• Pb(Mg1/3Nb2/3)O3 - relaxor
ferroelectric
• Pb(Zr1-xTix)O3 - piezoelectric
• (Ba1-xLax)TiO3 – semiconductor
• (Y1/3Ba2/3)CuO3-x -
superconductor
• NaxWO3 - mixed conductor;
electrochromic
• SrCeO3 - H - protonic conductor
• RECoO3-x - mixed conductor
• (Li0.5-3xLa0.5+x)TiO3 - lithium ion
conductor
• LaMnO3-x - Giant magneto-
resistance