Title: Crystal Structure Determination and Refinement Using the Bruker AXS SMART APEX II System
1Crystal Structure Determination and Refinement
Using the Bruker AXS SMART APEX II System
- Charles Campana
- Bruker AXS Inc.
2Flowchart for Method
Adapted from William Clegg Crystal Structure
Determination Oxford 1998.
3Crystal Growing Techniques
- Slow evaporation
- Slow cooling
- Vapor diffusion
- Solvent diffusion
- Sublimation
http//laue.chem.ncsu.edu/web/GrowXtal.html http/
/www.as.ysu.edu/adhunter/YSUSC/Manual/ChapterXIV.
pdf
4Examples of Crystals
5Growing Crystals
Kirsten Böttcher and Thomas Pape
6Select and Mount the Crystal
- Use microscope
- Size 0.4 (0.2) mm
- Transparent, faces, looks single
- Epoxy, caulk, oil, grease to affix
- Glass fiber, nylon loop, capillary
7What are crystals ?
8Crystallographic Unit Cell
- Unit Cell Packing Diagram - YLID
97 Crystal Systems - Metric Constraints
- Triclinic - none
- Monoclinic - ? ? 90?, ? ? 90?
- Orthorhombic - ? ? ? 90?
- Tetragonal - ? ? ? 90?, a b
- Cubic - ? ? ? 90?, a b c
- Trigonal - ? ? 90?, ? 120?, a b
(hexagonal setting) or ? ? ? , a b c
(rhombohedral setting) - Hexagonal - ? ? 90?, ? 120?, a b
10X-Ray Diffraction Pattern from Single Crystal
11X-Ray Diffraction
X-ray beam
? ? 1Å (0.1 nm)
(0.2mm)3 crystal 1013 unit cells, each
(100Å)3
Diffraction pattern on CCD or image plate
12Braggs law
n? 2d sin(?)
?
?
d
- We can think of diffraction as reflection at
sets of planes running through the crystal. Only
at certain angles 2? are the waves diffracted
from different planes a whole number of
wavelengths apart, i.e. in phase. At other angles
the waves reflected from different planes are out
of phase and cancel one another out.
13Reflection Indices
z
y
- These planes must intersect the cell edges
rationally, otherwise the diffraction from the
different unit cells would interfere
destructively. - We can index them by the number of times h, k
and l that they cut each edge. - The same h, k and l values are used to index
the X-ray reflections from the planes.
x
Planes 3 -1 2 (or -3 1 -2)
14Diffraction Patterns
- Two successive CCD detector images with a
crystal rotation of one degree per image
For each X-ray reflection (black dot) indices
h,k,l can be assigned and an intensity I F 2
measured
15Reciprocal space
- The immediate result of the X-ray diffraction
experiment is a list of X-ray reflections hkl and
their intensities I. - We can arrange the reflections on a 3D-grid based
on their h, k and l values. The smallest repeat
unit of this reciprocal lattice is known as the
reciprocal unit cell the lengths of the edges of
this cell are inversely related to the dimensions
of the real-space unit cell. - This concept is known as reciprocal space it
emphasizes the inverse relationship between the
diffracted intensities and real space.
16The structure factor F and electron density ?
Fhkl ? V ?xyz exp2?i(hxkylz) dV
?xyz (1/V) ?hkl Fhkl exp-2?i(hxkylz)
F and ? are inversely related by these Fourier
transformations. Note that ? is real and
positive but F is a complex number in order
to calculate the electron density from the
diffracted intensities I F2 we need the PHASE
(? ) of F. Unfortunately it is almost impossible
to measure ? directly!
17The Crystallographic Phase Problem
18 The Crystallographic Phase Problem
- In order to calculate an electron density map, we
require both the intensities I F 2 and the
phases ? of the reflections hkl. - The information content of the phases is
appreciably greater than that of the intensities. - Unfortunately, it is almost impossible to measure
the phases experimentally !
This is known as the crystallographic phase
problem and would appear to be insoluble
19Real Space and Reciprocal Space
- Real Space
- Unit Cell (a, b, c, ?, ?, ?)
- Electron Density, ?(x, y, z)
- Atomic Coordinates x, y, z
- Thermal Parameters Bij
- Bond Lengths (A)
- Bond Angles (º)
- Crystal Faces
- Reciprocal Space
- Diffraction Pattern
- Reflections
- Integrated Intensities I(h,k,l)
- Structure Factors F(h,k,l)
- Phase ?(h,k,l)
20Goniometer Head
213-Axis Rotation (SMART)
223-Axis Goniometer
23SMART APEX II System
24SMART APEX System
25SMART APEX II System
26APEX II detector
27CCD Chip Sizes
X8 APEX, SMART APEX, 6000, 6500
4K CCD 62x62 mm
Kodak 1K CCD 25x25 mm SMART 1000, 1500 MSC
Mercury
SITe 2K CCD 49x49 mm SMART 2000
28APEX II detector
- transmission of fiber-optic taper depends on 1/M2
- APEX with direct 11 imaging
- 11 is 6x more efficient than 2.51
- improved optical transmission by almost an order
of magnitude - allowing data on yet smaller micro-crystals or
very weak diffractors. - original SMART 17 e/Mo photon APEX
170 e/Mo ph.
29project database
default settings
detector calibration
30 31SHELXTL vs. SHELXhttp//shelx.uni-ac.gwdg.de/SHE
LX/index.html
- SHELXTL (Bruker Nonius)
- XPREP
- XS
- XM
- XE
- XL
- XPRO
- XWAT
- XP
- XSHELL
- XCIF
- SHELX (Public Domain)
- None
- SHELXS
- SHELXD
- SHELXE
- SHELXL
- SHELXPRO
- SHELXWAT
- None
- None
- CIFTAB