crystal structure determination and refinement using the bruker axs smart apex system charles...
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Crystal Structure Determination Crystal Structure Determination and Refinement Using the and Refinement Using the
Bruker AXS SMART APEX SystemBruker AXS SMART APEX System
Charles CampanaBruker Nonius
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Flowchart for MethodFlowchart for Method
Interpret the results
Complete and refine the structure
Solve the structure
Data reduction
Measure intensity data
Evaluate crystal quality; obtain unit cell geometryand preliminary symmetry information
Select, mount, and optically align a suitable crystal
Adapted from William Clegg
“Crystal Structure Determination”
Oxford 1998.
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Crystal Growing TechniquesCrystal 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 CrystalsExamples of Crystals
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Growing CrystalsGrowing Crystals
Kirsten Böttcher and Thomas Pape
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Select and Mount the CrystalSelect 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 ?What are crystals ?
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Crystallographic Unit CellCrystallographic Unit Cell
Unit Cell Packing Diagram - YLID
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7 Crystal Systems - Metric 7 Crystal Systems - Metric ConstraintsConstraints
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 X-Ray Diffraction Pattern from Single Crystalfrom Single Crystal
Rotation Photograph
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X-Ray DiffractionX-Ray Diffraction
X-ray beam
1Å(0.1 nm)
~ (0.2mm)3 crystal~1013 unit cells, each ~ (100Å)3
Diffraction pattern onCCD or image plate
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Bragg’s lawBragg’s law
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.
n = 2d sin()
d
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Reflection IndicesReflection Indices
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.
z
y
x
Planes 3 -1 2 (or -3 1 -2)
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Diffraction PatternsDiffraction 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 spaceReciprocal 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 The structure factor FF and and electron density electron density
Fhkl = V xyz exp[+2i(hx+ky+lz)] dV
xyz = (1/V) hkl Fhkl exp[-2i(hx+ky+lz)]
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 The Crystallographic Phase ProblemProblem
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The Crystallographic Phase The Crystallographic Phase ProblemProblem
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 Real Space and Reciprocal SpaceSpace
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 HeadGoniometer Head
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3-Axis Rotation (SMART)3-Axis Rotation (SMART)
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3-Axis Goniometer3-Axis Goniometer
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SMART 6000 SystemSMART 6000 System
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SMART APEX SystemSMART APEX System
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SMART APEX SystemSMART APEX System
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Kappa axes (X8)Kappa axes (X8)
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Kappa RotationKappa Rotation
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Kappa in X8APEXKappa in X8APEX
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Short X-ray beam pathShort X-ray beam path
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Kappa GoniometerKappa Goniometer
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Bruker X8APEXBruker X8APEX
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APEX detectorAPEX detector
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CCD Chip SizesCCD Chip Sizes
Kodak 1K CCD 25x25 mm SMART 1000, 1500
& MSC Mercury
SITe 2K CCD 49x49 mmSMART 2000
4K CCD 62x62 mm
X8 APEX, SMART APEX, 6000, 6500
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APEX detectorAPEX detector transmission of fiber-optic
taper depends on 1/M2
APEX with direct 1:1 imaging 1:1 is 6x more efficient than
2.5:1 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
SMART
setup
sample screening
data collection
ASTRO
data collection strategy
SAINTPLUS
new project
change parameters
SAINT: integrate
SADABS: scale & empirical absorption correction
SHELXTL
new project
XPREP: space group determination
XS: structure solution
XL: least squares refinement
XCIF: tables, reports
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George M. Sheldrick Professor, Director of Institute and part-time programming technician
1960-1966: student at Jesus College and Cambridge University, PhD (1966) with Prof. E.A.V. Ebsworth entitled "NMR Studies of Inorganic Hydrides"1966-1978: University Demonstrator and then Lecturer at Cambridge University; Fellow of Jesus College, CambridgeMeldola Medal (1970), Corday-Morgan Medal (1978)1978-now: Professor of Structural Chemistry at the University of GoettingenRoyal Society of Chemistry Award for Structural Chemistry (1981)Leibniz Prize of the Deutsche Forschungsgemeinschaft (1989)Member of the Akademie der Wissenschaften zu Goettingen (1989)Patterson Prize of the American Crystallographic Association (1993) Author of more than 700 scientific papers and of a program called SHELX Interested in methods of solving and refining crystal structures (both small molecules and proteins) and in structural chemistry
email: [email protected]: +49-551-392582
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SHELXTL vs. SHELX*SHELXTL vs. SHELX*http://shelx.uni-ac.gwdg.de/SHELX/index.htmlhttp://shelx.uni-ac.gwdg.de/SHELX/index.html
SHELXTL (Bruker Nonius) XPREP (space group
det’m) 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