molecular crystals
DESCRIPTION
Molecular Crystals. Molecular Crystals: Consist of repeating arrays of molecules and/or ions. C 17 H 24 NO 2 + Cl - . 3 H 2 O. Although Z = 2, the unit cell contains portions of a number of molecules. Cl -. Cl -. Cl -. H 2 O. Hydrogen bonds. Cl OH 2. Cl -. H 2 O. - PowerPoint PPT PresentationTRANSCRIPT
![Page 1: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/1.jpg)
Molecular Crystals
![Page 2: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/2.jpg)
Molecular Crystals:
Consist of repeating arrays
of molecules and/or ions.
![Page 3: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/3.jpg)
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C17H24NO2+ Cl- . 3 H2O
![Page 6: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/6.jpg)
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Although Z = 2, the unit cell containsportions of a number of molecules.
![Page 9: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/9.jpg)
Cl-
![Page 10: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/10.jpg)
Cl-
![Page 11: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/11.jpg)
Cl-
H2O
![Page 12: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/12.jpg)
Cl-
H2O
Hydrogen bondsCl OH2
![Page 13: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/13.jpg)
![Page 14: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/14.jpg)
Hydrogen bond
![Page 15: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/15.jpg)
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Model with atoms having VDW radii.
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C17H24NO2+ Cl- . 3 H2O
Although this material is ionic, the + and - chargesare not close enough tocontribute to the formationof the crystal.
![Page 20: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/20.jpg)
Molecular crystals tend to be
held together by forces weaker than
chemical bonds.
van der Waal’s forces are always
a factor.
Hydrogen bonding is often present.
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A layer in an ionic solid with ionsof similar radii.
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Metallic crystal – single layer of like
sized atoms forms hexagonal array.
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Second layer can start at a point designated
b or c.
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At this point, the third layer can repeat the
first and start at a or it can start at c.
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Third layer repeats
first layer.
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Unit Cell
Unit cell volume = V
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Unit Cell
Unit cell volume = V
V = abc 1- cos2 - cos2 - cos2 + 2 cos cos cos
Note: text page 807 may not be correct.
![Page 30: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/30.jpg)
V = abc 1- cos2 - cos2 - cos2 + 2 cos cos cos
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V = abc 1- cos2 - cos2 - cos2 + 2 cos cos cos
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V = abc 1- cos2 - cos2 - cos2 + 2 cos cos cos
cos 90o = 0
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V = abc 1- cos2 - cos2 - cos2 + 2 cos cos cos
cos 90o = 0
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V = abc 1- cos2 - cos2 - cos2 + 2 cos cos cos
cos 90o = 0
V = abc 1 - cos2
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V = abc 1- cos2 - cos2 - cos2 + 2 cos cos cos
cos 90o = 0
V = abc 1 - cos2 sin x = 1 - cos2 x
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V = abc 1- cos2 - cos2 - cos2 + 2 cos cos cos
cos 90o = 0
V = abc 1 - cos2 sin x = 1 - cos2 x
V = abc sin
![Page 37: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/37.jpg)
V = abc 1- cos2 - cos2 - cos2 + 2 cos cos cos
cos 90o = 0
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V = abc 1- cos2 - cos2 - cos2 + 2 cos cos cos
cos 90o = 0
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V = abc 1- cos2 - cos2 - cos2 + 2 cos cos cos
cos 90o = 0
V = abc
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V = abc 1- cos2 - cos2 - cos2 + 2 cos cos cos
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V = abc 1- cos2 - cos2 - cos2 + 2 cos cos cos
a = b
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V = abc 1- cos2 - cos2 - cos2 + 2 cos cos cos
a = b
V = a2c
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V = abc 1- cos2 - cos2 - cos2 + 2 cos cos cos
![Page 44: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/44.jpg)
V = abc 1- cos2 - cos2 - cos2 + 2 cos cos cos
![Page 45: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/45.jpg)
V = abc 1- cos2 - cos2 - cos2 + 2 cos cos cos
V = a3
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V = abc 1- cos2 - cos2 - cos2 + 2 cos cos cos
![Page 47: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/47.jpg)
V = abc 1- cos2 - cos2 - cos2 + 2 cos cos cos
![Page 48: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/48.jpg)
V = abc 1- cos2 - cos2 - cos2 + 2 cos cos cos
![Page 49: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/49.jpg)
V = abc 1- cos2 - cos2 - cos2 + 2 cos cos cos
![Page 50: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/50.jpg)
V = a2c 1- cos2 - cos2 - cos2 + 2 cos cos cos
![Page 51: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/51.jpg)
V = a2c 1- cos2 - cos2 - cos2 + 2 cos cos cos
![Page 52: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/52.jpg)
V = a2c 1- cos2
![Page 53: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/53.jpg)
V = a2c 1- cos2
V = a2c sin
![Page 54: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/54.jpg)
V = a2c 1- cos2
V = a2c sin = a2c sin 120o
![Page 55: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/55.jpg)
Cell volume and cell contents:
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Cell volume and cell contents:
A unit cell will usually contain an
integral number of formula units.
![Page 57: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/57.jpg)
Cell volume and cell contents:
A unit cell will usually contain an
integral number of formula units.
The number of formula units in the
cell is often related to the symmetry
of the cell.
![Page 58: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/58.jpg)
The number of formula units in the
unit cell is designated by Z.
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Space group General Positions Z
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Space group General Positions Z
P1 x, y, z 1
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Space group General Positions Z
P1 x, y, z 1
P1 x, y, z 2 -x, -y, -z
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Unit Cell
Unit cell volume = V
V = abc 1- cos2 - cos2 - cos2 + 2 cos cos cos
Note: text page 807 may not be correct.
Triclinic
P1
Z = 2
![Page 63: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/63.jpg)
If Z = 2 then the total mass in the
unit cell is the formula weight x 2.
![Page 64: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/64.jpg)
If Z = 2 then the total mass in the
unit cell is the formula weight x 2.
If the volume is V then the density
of the crystal is formula wt. X 2
V x No
![Page 65: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/65.jpg)
Triclinic cell:
a = 6.8613 Å = 74.746o
b = 9.1535 Å = 81.573o
c = 16.8637 Å = 73.339o
V = 974.45 Å3
C17H24NO2+ Cl- . 3 H2O FW = 363.87 g/mol
![Page 66: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/66.jpg)
V = 974.45 Å3
C17H24NO2+ Cl- . 3 H2O FW = 363.87 g/mol
Z = 2
Density =363.87 g (2)
974.45 Å3 x 6.02 x 1023
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V = 974.45 Å3
C17H24NO2+ Cl- . 3 H2O FW = 363.87 g/mol
Z = 2
Density =363.87 g (2)
974.45 Å3 x 6.02 x 1023
1Å = 1 x 10-8 cm
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V = 974.45 Å3
C17H24NO2+ Cl- . 3 H2O FW = 363.87 g/mol
Z = 2
1Å = 1 x 10-8 cm
Density =363.87 g (2)
974.45 x 10-24 x 6.02 x 1023
Density =363.87 g (2)
974.45 Å3 x 6.02 x 1023
![Page 69: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/69.jpg)
V = 974.45 Å3
C17H24NO2+ Cl- . 3 H2O FW = 363.87 g/mol
Z = 2
Density =727.74 g
5866.19 x 10-1
Density =363.87 g (2)
974.45 x 10-24 x 6.02 x 1023
![Page 70: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/70.jpg)
V = 974.45 Å3
C17H24NO2+ Cl- . 3 H2O FW = 363.87 g/mol
Z = 2
Density =727.74 g
5866.19 x 10-1cm3
Density =363.87 g (2)
974.45 x 10-24 x 6.02 x 1023
= 1.241 g/cm3
![Page 71: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/71.jpg)
Infinitely repeating lattices
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Three possible unit cells; one lattice.
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Crystal lattices include a large number
of repeating sets of planes.
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These sets of planes can act as a
diffraction grating for waves of the
proper wavelength.
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These sets of planes can act as a
diffraction grating for waves of the
proper wavelength.
d
![Page 86: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/86.jpg)
These sets of planes can act as a
diffraction grating for waves of the
proper wavelength.
d = < 1 to 250 Å
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When radiation on the order of
1 ångstöm wavelength interacts
with a crystal lattice having
interplanar spacings on the order
of ångstöms, diffraction occurs.
![Page 88: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/88.jpg)
Where do we find 1 ångstöm
Wavelength radiation?
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1 Å
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What is the source of 1 Å
radiation?
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1 Å
Emission spectrum for hydrogen in visible range
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Electron transitionsfor H atom.
![Page 94: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/94.jpg)
Electron transitionsfor H atom.
Transitions in visibleregion.
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It is possible to cause certain metals
to emit X-rays by temporarily removing
a core electron.
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X-ray emission
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e-
+-HV
![Page 99: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/99.jpg)
e-
+- HV
If the potential difference is large enough,core electrons will be ejected from the metal.
source ofelectrons
Metal target
![Page 100: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/100.jpg)
hot filament – e- source
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hot filament – e- source
metal target
![Page 102: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/102.jpg)
hot filament – e- source
metal target
+ -
Accelerating potential
![Page 103: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/103.jpg)
![Page 104: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/104.jpg)
1 x 10 mm
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1 x 10 mm
KV = 50
mA = 40
![Page 106: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/106.jpg)
1 x 10 mm
KV = 50
mA = 40
= 2000 watts
![Page 107: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/107.jpg)
hot filament – e- source
metal target
+ -
Accelerating potential
![Page 108: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/108.jpg)
![Page 109: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/109.jpg)
X-ray scattering is due to the interaction ofX-rays and the electron density around atoms.
![Page 110: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/110.jpg)
d = < 1 to 250 Å
![Page 111: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/111.jpg)
d = < 1 to 250 Å
B’
E E’
![Page 112: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/112.jpg)
d = < 1 to 250 Å
B’
E E’
If (B B’)-(E E’) =an integral # ofwavelengths, 100%reinforcement.
![Page 113: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/113.jpg)
B’
E E’
If (B B’)-(E E’) =an integral # ofwavelengths, 100%reinforcement.
2dsin = n
![Page 114: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/114.jpg)
B’
E E’
If (B B’)-(E E’) =an integral # ofwavelengths, 100%reinforcement.
2dsin = nBragg’s Law
![Page 115: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/115.jpg)
B’
E E’
If (B B’)-(E E’) =an integral # ofwavelengths, 100%reinforcement.
2dsin = nBragg’s Law
= wavelengthn = integer (order of diffraction)
![Page 116: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/116.jpg)
2dsin = n
Bragg’s Law= wavelengthn = integer (order of diffraction)
![Page 117: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/117.jpg)
2dsin = n
Bragg’s Law= wavelengthn = integer (order of diffraction)
If d becomes larger, must
decrease.
![Page 118: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/118.jpg)
2dsin = n
Bragg’s Law= wavelengthn = integer (order of diffraction)
If d becomes larger, must decrease.
There is a reciprocal relationship betweenThe crystal lattice and the diffraction pattern.
![Page 119: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/119.jpg)
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2dsin = n
d*
n = 0 1 2 3 4
![Page 123: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/123.jpg)
2dsin = n
d*
n = 0 1 2 3 4
is set by the X-ray target
![Page 124: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/124.jpg)
2dsin = n
d*
n = 0 1 2 3 4
is set by the X-ray target
can be measured by determining the angle between the direct anddiffracted beam.
![Page 125: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/125.jpg)
2dsin = n
d*
n = 0 1 2 3 4
is set by the X-ray target
can be measured by determining the angle between the direct anddiffracted beam.
Unit cell can be determinedfrom this data.
![Page 126: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/126.jpg)
Note that intensities of thediffraction spots vary.
![Page 127: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/127.jpg)
Note that intensities of thediffraction spots vary.
Diffraction intensities tend to decease
as increases.
![Page 128: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/128.jpg)
Note that intensities of thediffraction spots vary.
The derivation of Bragg’s Law is correctbut the conditions are more complicated.Each diffraction spot is the sum of the wavesfrom all atoms in the unit cell.
![Page 129: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/129.jpg)
Note that intensities of thediffraction spots vary.
The derivation of Bragg’s Law is correctbut the conditions are more complicated.Each diffraction spot is the sum of the wavesfrom all atoms in the unit cell. This includesa significant amount of destructive interference.
![Page 130: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/130.jpg)
dd
Each diffraction maximum includes
information on the electron density
in the repeat distance.
![Page 131: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/131.jpg)
Conversion of X-ray intensities to
electron densities is a very complicated
process.
![Page 132: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/132.jpg)
Conversion of X-ray intensities to
electron densities is a very complicated
process.
A major step is determining the atomic
coordinates for a model.
![Page 133: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/133.jpg)
Once the coordinates for a model are
determined, it is possible to calculate
what the intensity data for that model
would look like.
![Page 134: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/134.jpg)
Once the coordinates for a model are
determined, it is possible to calculate
what the intensity data for that model
would look like. The observed intensities
and the model intensities are compared.
![Page 135: Molecular Crystals](https://reader036.vdocuments.site/reader036/viewer/2022081513/56813514550346895d9c67bb/html5/thumbnails/135.jpg)
A least-squares refinement of model
intensities against observed intensities
allows the model structure to become
the actual crystal structure.