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A.L. (Ton) Spek National Single Crystal Service Facility Utrecht University Amsterdam, 23-10-2007
BLACK BOX
Single Crystals 3D-Structure X-Ray Diffraction Experiment
Some History
The first X-ray structure determination was carried out around 1913 (Bragg). In the sixties, 40 years ago, a small molecule crystal structure determination still took in the order of half a year. Main problems were the time consuming data collection, the solution of the Phase Problem and the the scarce and slow university main frame computing facilities. We received in the late 70th an interesting request from a synthetic chemist interested in the 3D structure of a new compound: .. Can you inject this sample in your diffractometer .., a request that looked nave at the time. In hindsight he was visionary, since
Structure ?
Current Status
Data collection and evaluation procedures have now evolved to a level that a subset of the routine samples can indeed be analyzed automatically in a matter of hours. The problem is that many real world samples still turn out to be non-routine. Thus still a working knowledge is needed of what is in the box in order to get a reliable structure.
Crystal
LNT
X-ray
CCD - Detector
Crystal Goniometer
Data Collection
Diffraction Condition (determines the position of the diffracted beams on the detector): 2 dhkl sin(Q) = n l (Bragg Equation) Result: - Cell Dimensions, a,b,c, a, b, g - Reflection intensities by planes (hkl) in the crystal: I(hkl) (many thousands)
Computation
Data Reduction to hkl I and (I) Correction for absorption effects Determination of the Space Group Solution of the Phase Problem Abstraction of a Parameter Model from 3D-density map Refinement of the Structural Model Analysis of the geometry, intermolecular interactions Structure Validation
Data Reduction
Integration and scaling of the diffraction intensities E.g. with programs (Generally comes with the hardware) DENZO, EVAL-CCD, SAINT
Structure Determination
Experiment Ihkl |Fhkl| = Sqrt(Ihkl) Needed for 3D structure (approximate) Phases: fhkl |Fhkl| + fhkl = Fhkl 3D-Fourier Synthesis
r(x,y,z) = [ Shkl Fhkl exp{-2pi(hx + ky + lz)}] / V x,y,z are fractional coordinates (range 0 1) Example next slide
3D Parameter Model
Extract the 3D Coordinates (x, y, z) of the atoms. Assign Atom Types (Scattering type C, O etc.) Assign Additional Parameters to Model the Thermal Motion (T) of the Atoms. Other Parameters: Extinction, Twinning, Flack x Model: Fhkl = Sj=1,n fj T exp{2pi(hx + ky + lz)} Non-linear Least-squares Parameter Refinement until Convergence. Minimize: Shkl w [(Fhklobs)2 (Fhklcalc)2]2 Agreement Factor: R = S |Fobs Fcalc| / S|Fobs|
Structure Validation
Refinement results in CIF File format. Final Fobs/Fcalc data in FCF File Format IUCr CHECKCIF tool PLATON Validation Tool Check in Cambridge Crystallographic Database for similar structures.
Selected Tools
ADDSYM Detection and Handling of Missed (Pseudo)Symmetry TwinRotMat Detection of Twinning SOLV Report of Solvent Accessible Voids SQUEEZE Handling of Disordered Solvents in Least Squares Refinement (Easy to use Alternative for Clever Disorder Modelling) BijvoetPair Post-refinement Absolute Structure Determination (Alternative for Flack x) VALIDATION PART of IUCr CHECKCIF
ADDSYM
About 1% of the 2006 & 2007 entries in the CSD need a change of space group. Often, a structure solves only in a space group with lower symmetry than the correct space group. The structure should subsequently be checked for higher symmetry. Next slides: Recent examples of missed symmetry
WRONG SPACEGROUP
P-1, Z=2
P1, Z = 8
C C o
Correct Symmetry ?
(Pseudo)Merohedral Twinning
Options to handle twinning in L.S. refinement available in SHELXL, CRYSTALS etc. Problem: Determination of the Twin Law that is in effect. Partial solution: coset decomposition, try all possibilities (I.e. all symmetry operations of the lattice but not of the structure) ROTAX (S.Parson et al. (2002) J. Appl. Cryst., 35, 168. (Based on the analysis of poorly fitting reflections of the type F(obs) >> F(calc) ) TwinRotMat Automatic Twinning Analysis as implemented in PLATON (Based on a similar analysis but implemented differently)
TwinRotMat Example
Originally published as disordered in P3. Solution and Refinement in the trigonal space group P-3 R= 20%. Run PLATON/TwinRotMat on CIF/FCF Result: Twin law with an the estimate of the twinning fraction and the estimated drop in R-value Example of a Merohedral Twin
H
Strong reflection H with theta close to theta of reflection H
STEP # 2 EXCLUDE AN ACCESS RADIAL VOLUME TO FIND THE LOCATION OF ATOMS WITH THEIR CENTRE AT LEAST 1.2 ANGSTROM AWAY
STEP # 3 EXTEND INNER VOLUME WITH POINTS WITHIN 1.2 ANGSTROM FROM ITS OUTER BOUNDS
VOID APPLICATIONS
Calculation of Kitaigorodskii Packing Index As part of the SQUEEZE routine to handle the contribution of disordered solvents in crystal structure refinement Determination of the available space in solid state reactions (Ohashi) Determination of pore volumes, pore shapes and migration paths in microporous crystals
SQUEEZE
Takes the contribution of disordered solvents to the calculated structure factors into account by back-Fourier transformation of density found in the solvent accessible volume outside the ordered part of the structure (iterated). Filter: Input shelxl.res & shelxl.hkl Output: solvent free shelxl.hkl Refine with SHELXL or Crystals Note:SHELXL lacks option for fixed contribution to Structure Factor Calculation.
SQUEEZE Algorithm
1. 2.
3. 4.
5.
Calculate difference map (FFT) Use the VOID-map as a mask on the FFT-map to set all density outside the VOIDs to zero. FFT-1 this masked Difference map -> contribution of the disordered solvent to the structure factors Calculate an improved difference map with F(obs) phases based on F(calc) including the recovered solvent contribution and F(calc) without the solvent contribution. Recycle to 2 until convergence.
Fc(model)
Fobs
Solvent Free Fobs
Black: Split Fc into a discrete and solvent contribution Red: For SHELX refinement, temporarily substract recovered solvent contribution from Fobs.
Comment
The Void-map can also be used to count the number of electrons in the masked volume. A complete dataset is required for this feature. Ideally, the solvent contribution is taken into account as a fixed contribution in the Structure Factor calculation (CRYSTALS) otherwise it is subtracted temporarily from Fobs2 (SHELXL) and re-instated afterwards with info saved beyond column 80 for the final Fo/Fc list.
Publication Note
Always give the details of the use of SQUEEZE in the comment section Append the small CIF file produced by PLATON to the main CIF Use essentially complete data sets with sufficient resolution only. Make sure that there is no unresolved charge balance problem.
Friedel Pairs
H,K,L
Selected f - values
f(CuK) Se Cl S O 1.14 0.70 0.56 0.032 f(MoK) 2.23 0.16 0.12 0.006
Flack Parameter
The current official method to establish the absolute configuration of a chiral molecule calls for the determination of the Flack x parameter. Flack, H.D. (1983). Acta Cryst. A39, 876-881. Twinning Model (mixture model and image): Ihklcalc = (1 x) |Fhkl|2 + x |F-h-k-l|2 Result of the least-squares refinement: x(u) Where x has physically a value between 0 and 1 and u the standard uncertainty (esd)
Excellent Correlation
MoKa, P212121
Bayesian Approach
Rob Hooft (Bruker) has developed an alternative approach for the analyses of Bijvoet differences that is based on Bayesian statistics. (Paper under review) Under the assumption that the material is enantiopure, the probability that the assumed absolute structure is correct, given the set of observed Bijvoet Pair Differences, is calculated. An extension of the method also offers the Fleq y (Hooft y) parameter to be compared with the Flack x. Example: Ascorbic Acid, P21, MoKa data
MoKa
Next Slide: This is why the reported density is low and the R and Rw high
235 Ang3
SOLUTION
A solution for the structure validation problem was
pioneered by the International Union of Crystallography - Provide and archive crystallographic data in the computer readable CIF standard format. - Offer Automated validation, with a computer generated report for authors and referees. - Have journals enforce a structure validation protocol. - The IUCr journals and most major journals now indeed implement some form of validation procedure.
VALIDATION QUESTIONS
Single crystal validation addresses three simple but important questions:
1 Is the reported information complete? 2 What is the quality of the analysis? 3 Is the Structure Correct?
ALERT LEVELS
ALERT A Serious Problem ALERT B Potentially Serious Problem ALERT C Check & Explain ALERT G Verify or Take Notice
ALERT TYPES
1 - CIF Construction/Syntax errors, Missing or Inconsistent Data. 2 - Indicators that the Structure Model may be Wrong or Deficient. 3 - Indicators that the quality of the results may be low. 4 - Cosmetic Improvements, Queries and Suggestions.
EXAMPLE OF PLATON GENERATED ALERTS FOR A RECENT PAPER PUBLISHED IN J.Amer.Chem.Soc. (2007)
Properly Validated ?
Example of a PLATON/Check Validation Report: Two ALERTS related to the misplaced Hydrogen Atom
Correct !
ALERT !
QUATERNION FIT
In many cases, an automatic molecule fit can be performed A) Identical atom numbering B) Sufficient number of Unique Atoms C) By manual picking of a few atom pairs
QUATERNION FIT
Tetragonal
Orthorhombic
THE MESSAGE
- Validation should not be postponed to the publication phase. All validation issues should be taken care of during the analysis. - Everything unusual in a structure is suspect, mostly incorrect (artifact) and should be investigated and discussed in great detail and supported by additional independent evidence. - The CSD can be very helpful when looking for possible precedents.
CONCLUSION
Validation Procedures are excellent Tools to: - Set Quality Standards (Not just on R-Value) - Save a lot of Time in Checking, both by the Investigators and the Journals (referees) - Point at Interesting Features (Pseudo-Symmetry, short Interactions etc.) to be discussed. - Surface a problem that only an experienced Crystallographer might be able to Address - Proof of a GOOD structure.
Additional Info
http://www.cryst.chem.uu.nl
(including a copy of this powerpoint presentation)