crystal structure determination and refinement using the bruker axs smart apex ii system
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Crystal Structure Determination Crystal Structure Determination and Refinement Using the and Refinement Using the Bruker AXS SMART APEX II Bruker AXS SMART APEX II
SystemSystem
Charles CampanaBruker AXS Inc.
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.
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
Examples of CrystalsExamples of Crystals
Growing CrystalsGrowing Crystals
Kirsten Böttcher and Thomas Pape
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
What are crystals ?What are crystals ?
Crystallographic Unit CellCrystallographic Unit Cell
Unit Cell Packing Diagram - YLID
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
X-Ray Diffraction Pattern X-Ray Diffraction Pattern from Single Crystalfrom Single Crystal
Rotation Photograph
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
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
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)
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
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.
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!
The Crystallographic Phase The Crystallographic Phase ProblemProblem
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
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
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)
Goniometer HeadGoniometer Head
3-Axis Rotation (SMART)3-Axis Rotation (SMART)
3-Axis Goniometer3-Axis Goniometer
SMART APEX II SystemSMART APEX II System
SMART APEX SystemSMART APEX System
SMART APEX II SystemSMART APEX II System
APEX II detectorAPEX II detector
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
APEX II detectorAPEX II 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 ph.
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
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: gsheldr@shelx.uni-ac.gwdg.defax: +49-551-392582
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 XS XM XE XL XPRO XWAT XP XSHELL XCIF
SHELX (Public Domain)* None SHELXS SHELXD SHELXE SHELXL SHELXPRO SHELXWAT None None CIFTAB
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