Crystal Structure Determination and Refinement Using the Bruker AXS SMART APEX System

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Crystal Structure Determination and Refinement
Using the Bruker AXS SMART APEX System

• Charles Campana
• Bruker Nonius

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Flowchart for Method
Adapted from William Clegg Crystal Structure
Determination Oxford 1998.
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Crystal 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
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Examples of Crystals
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Growing Crystals
Kirsten Böttcher and Thomas Pape
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Select 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

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What are crystals ?
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Crystallographic Unit Cell

• Unit Cell Packing Diagram - YLID

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7 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

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X-Ray Diffraction Pattern from Single Crystal

• Rotation Photograph

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X-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
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Braggs 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.

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Reflection 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)
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Diffraction 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
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Reciprocal 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.

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The 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! F(h,k,l)
A iB
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The Crystallographic Phase Problem
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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
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Real Space and Reciprocal Space

• Real Space
• Unit Cell (a, b, c, ?, ?, ?)
• Electron Density, ?(x, y, z)
• Atomic Coordinates x, y, z
• Thermal Parameters Bij or Uij
• Bond Lengths (A)
• Bond Angles (º)
• Crystal Faces

• Reciprocal Space
• Unit Cell (a, b, c, ?, ?, ?)
• Diffraction Pattern
• Reflections h,h,l
• Integrated Intensities I(h,k,l)
• Structure Factors F(h,k,l)
• Phase ?(h,k,l)

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Goniometer Head
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3-Axis Rotation (SMART)
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3-Axis Goniometer
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SMART 6000 System
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SMART APEX System
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SMART APEX System
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Kappa axes (X8)
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Kappa Rotation
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Kappa in X8APEX
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Short X-ray beam path
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Kappa Goniometer
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Bruker X8APEX
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APEX detector
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CCD 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
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APEX 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
  photon

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project database
default settings
detector calibration
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SHELXTL vs. SHELXhttp//shelx.uni-ac.gwdg.de/SHE
LX/index.html

• SHELXTL (Bruker Nonius)
• XPREP (space group detm)
• XS (structure solution)
• XM
• XE
• XL (least-squares refinement)
• XPRO
• XWAT
• XP (plotting)
• XSHELL (GUI interface)
• XCIF (tables, reports)

• SHELX (Public Domain)
• None
• SHELXS
• SHELXD
• SHELXE
• SHELXL
• SHELXPRO
• SHELXWAT
• None
• None
• CIFTAB