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pma 2010
pma 2010
A 2-dimensional Lattice
Pick any position within the 2 dimensional lattice in Fig. 1(a) and note the
arrangement about this point. The chosen position can be indicated by
a point (a lattice point). In view of the repetitive arrangement, there will
be a 2 dimensional array of identical positions and if these are also
marked by a point a 2-dimensional lattice will result if the points are
joined.
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Cubic
Tetragonal
Orthorhombic
Monoclinic
Body
Centred
Cell
I
Face
Centred
Cell
F
End Face Centred
Cell
Triclinic
C
Trigonal
Hexagonal
Primitive Cell
P
Fig. 3
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C - cell
Fig. 4
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P - Cell
C - cell
Orthorhombic
a b c, a = b = = 90
Tetragonal
a = b c, a = b = = 90
a
b
Symmetry Operation
Rotation
Reflection
Inversion
Rotation and reflection
Rotation and inversion
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UNIT CELL
UNIT CELL
Centres of
symmetry
(a)
(b)
Fig. 5
49
19
P
F
I
C and A
P
30
5
9
15
8
Triclinic
Rhombohedral
P and R
25
25
Hexagonal
27
27
Cubic
Tetragonal
Orthorhombic
Monoclinic
Fig. 9
68
59
13
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reflected
beam
B
x
oo
d
m
UNIT
CELL
(a)
x
oo
reflected
beam
B
o
d
UNIT
CELL
(b)
Fig. 11
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In (a) above it is clear that the planes are the (1,0,0) set of planes.
If the path difference is simply one wavelength the Bragg condition
can be stated as
2d (1,0,0 ) sin
This is a first order reflection. If the path difference is
two wave lengths the Bragg condition becomes
2d (1,0,0 ) sin 2
and the reflection is a second order reflection.
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SELECT A SUITABLE
CRYSTAL
A
CRYSTAL SYSTEM
and
UNIT CELL DIMENSIONS
B
FULL DATA SET
COLLECTION
C
BRAVAIS LATTICE
D
SPACE GROUP
E
CONSTRUCT AN
ELECTRON DENSITY
MAP
F
LOCATE ATOM
POSITIONS
G
STRUCTURE
REFINEMENT
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Reflection Analysis
Group
Cond. Op.
All
h00
h=2n+1 21..
18
0k0
k=2n+1
3
00l
l=2n+1
11
0kl
k=2n+1 b..
95
0kl
l=2n+1 c..
0kl
k+l=2n+1 n..
h0l
h=2n+1 .a.
412
h0l
l=2n+1
h0l
h+l=2n+1 .n.
hk0
h=2n+1 ..a
168
hk0
k=2n+1 ..b
hk0
h+k=2n+1 ..n
hkl
k+l=2n+1 A..
hkl
h+l=2n+1 .B.
hkl
h+k=2n+1 ..C
hkl h+k+l=2n+1 I
hkl not all odd/even F
Odd
10
1
6
53
49
40
211
211
212
84
84
86
1591
1638
1651
1637
2440
Cut1
8
1
0
49
43
34
96
1
95
67
76
71
1196
1271
1285
1288
1876
P21/c (14)
CSD Total for all SGs at end of 2006
Cut2
8
0
0
44
40
30
89
1
88
60
69
69
1084
1151
1145
1148
1690
385035
In this case P21/c is the only choice offered by Oscail and this is likely to be correct.
Notice the symmetry operations move to the right when present in the data.
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1
V
F(1,0,0) cos
y
x
z
x y
Direct Methods
After many years of study statistical trends were observed in reflection phases.
It was also observed that some reflections are more important than others.
The Direct Methods approach tries to guess the reflection phases and then
awards a Figure of Merit to the guess. The most popular is the Combined Figure
of Merit or CFOM). It is normal practice to accept solutions with CFOM values
in the range 0.03-0.15 and to try to use these phases to generate an
electron density map.
Charge Flipping
The charge flipping method works well if the data has good resolution.
There is an example in the Oscail tutorials. All non-H atoms are often identified
correctly in the solution.
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Refining a Structure
It should be possible to see atoms in an electron density map if it has good
resolution i.e. at least 1 resolution. The steps in refining a structure are.
1. Use whatever atoms you have that look OK to generate an electron density
map.
2. The known atoms are subtracted from this to generate a difference map.
3. Any atoms that have been missed should be in the difference map.
4. The refinement process minimises the difference between observed and
calculated reflection intensities.
5. In the final difference map there should be no peaks larger than a H atom
i.e. > 1e/3. (A H atom has a volume of about 13 and has 1 e.)
Resolution The resolution of a crystal structure is usually quoted in
Angstroms, . Standard small molecule structures should always be at least
of 1 resolution to give accurate bond lengths. Resolution can be related to
Bragg angle at any wavelength through the Bragg equation n = 2d sin.
Using the value of the reflection with the largest Bragg angle in a data set
then d = /2sin gives the resolution. The pattern shown on slide 15 has a
resolution of 0.98 at the edge.
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1
d ( h, k , l )
h2
a
k2
b
l2
c2
1
d ( h,k ,l )
(h 2 k 2 )
a
l2
c2
1
d ( h,k ,l )
(h 2 k 2 l 2 )
a2
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Cl1
0
12/4
0
4
In the CsCl structure both ions have coordination numbers of 8 and the structure
is a simple primitive one with no centring.
Formula Cs at centre = 1
8 x 1/8Cl = 1 = CsCl
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pma 2010
n 2d sin
to
2
2
sin
2
4d
If the value of 1/(dh,k,l)2 in the cubic system equation above is inserted into
this form of the Bragg equation you have
2 2
sin 2 (h k 2 l 2 )
4a
2
sin 2 A(h 2 k 2 l 2 )
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2d
The ccp lattice is an F type lattice and the only reflections observed are those
with all even or all odd indices.
Thus the only values of sin2 in
sin 2 A(h 2 k 2 l 2 )
are 3A, 4A , 8A, 11A, 12A,16A and 19A for the first eight reflections.
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Insert the values into a table and compute sin and sin2.
Since the lowest value of sin2 is 3A and the next is 4A the first
Entry in the Calc. sin2 column is (0.10854/3)*4 etc.
d/
Sin
Sin2
2.338
0.32945
0.10854
2.024
0.38056
0.14482
0.14472
(2,0,0)
1.431
0.53826
0.28972
0.28944
(2,2,0)
1.221
0.63084
0.39795
0.39798
(3,1,1)
1.169
0.65890
0.43414
0.43416
(2,2,2)
1.0124
0.76082
0.57884
0.57888
(4,0,0)
0.9289
0.82921
0.68758
0.68742
(3,3,1)
0.9055
0.85063
0.72358
0.72360
(4,2,0)
Calc. Sin2
(h, k, I)
(1,1,1)
Calculation of a
For the first reflection (for which h2 + k2 + l2 = 3)
sin2 = 3A = 3 ( 2 / 4a2 )
a2 = 32 / 4sin2
a = 4.04946 = 4.04946 x 10-8 cm.
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Since values are available sin2 values can be calculated and inserted
in a table.
2
Sin2
Calc. Sin2
27.80
13.90
0.0577
32.20
16.10
0.0769
0.07693
46.20
23.10
0.1539
0.1539
54.80
27.40
0.2118
0.2116
57.45
28.73
0.2310
0.2308
67.45
33.73
0.3083
0.3077
Density of AgCl
Since sin2 = 2(h2 + k2 + l2)/4a2
a2 = (1.54)2.(16)/4(0.3083) using the largest (most accurate) 2
a2 = 30.7692
a = 5.547 (1 = 10-8 cm)
Formula wt. of unit cell = 4AgCl = 573.284g
This is the weight of 4 moles of AgCl.
The weight of 4 molecules is 573.284 / (6.02 x 1023)
Density = 573.284 / (6.02 x 1023)(5.547 x 10-8)3
A is in thus the answer should be multiplied by 1 / 10-24
Density = 5.580 g/cm3
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Nifedipine
Calculated pattern
Observed pattern
There are no preferred orientation effects here as all reflections have their
expected intensity.
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Benzoic acid
Calculated pattern
002
Observed pattern
004
Preferred orientation effects are often observed for needles and plates.
pma 2010