Basics of X-ray diffraction: From symmetry to structure determination
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1 Basics of X-ray diffraction: From symmetry to structure determination T. N. Guru Row Solid State and Structural Chemistry Unit Indian Institute of Science Bangalore Website:
2 Matter : Gases, Liquids and Solids The 3-d world we live in Love of symmetry and Mankind Basic mistake: Joining school Stereographic projection
3 Rubens Aguilon Stereographic Projection
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8 Similar cells can be drawn in all the other repeating (wall-paper) patterns that we saw previously.
9 Crystals are built in a similar manner, with regularly repeating cells. Only now these cells regularly repeat in three dimensions to produce a box called a unit cell.
10 Crystals use (7) different shapes of regular box to build up into a crystal. Actually there are only (5) unique shapes, the other two are special cases of one of the five. The five shapes are: Triclinic Monoclinic Orthorhombic a β γ α c b b β The box has edges of length (a), (b), and (c); and the angles between the edges are (α), (β) and (γ) In triclinic: a b c α β γ 90 o In monoclinic a b c α =γ = 90 o ; β 90 o (A squished book) In orthorhombic a b c α = β = γ = 90 o (A shoe box)
11 Crystals use (7) different shapes of regular box to build up into a crystal. Actually there are only (5) unique shapes, the other two are special cases of one of the five. The five shapes are: Hexagonal Tetragonal A stretched cube Cubic c γ c In tetragonal a=b c α = β = γ = 90 o (a column or pillar) In cubic a=b =c α = β = γ = 90 o Rhombohedral a=b =c α = β = γ 90 o In hexagonal a=b c α = β = 90 o γ =120 o
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13 Miller Indices Take a simple structure, there are an of infinite number of planes that can be constructed through it. d 1 d 2 d 3
14 Miller Indices y x The plane cuts each cell edge once and is the (1,1) plane. This is the (1,2) plane x y This is the (1,0) plane, it never cuts the (y) axis
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17 When there is more than one type of atom in the crystal, each atom forms its own separate array.
18 When there is more than one type of atom in the crystal, each atom forms its own separate array within the crystal.
19 When there is more than one type of atom in the crystal, each atom forms its own separate array and each array separately satisfies the Bragg equation. 2dsinθ=nλ θ θ θ
20 How can we see atoms? supermicroscope via X-ray Microscope X-ray diffraction
21 Single Crystal X-Ray Structure Determination BLACK BOX Single Crystals Crystal structure X-Ray Diffraction Experiment
22 Tabletop Black Box Smart X2S Crystal Structure?
23 One of the several hundreds of CCD images with diffraction spots
24 Determination of the Space Group Cell Dimensions, Laue Symmetry, Intensity Statistics (Centro/Non-Centro), Systematic Extinctions Structure Determination Experiment I hkl F hkl = Sqrt(I hkl ) Needed for 3D structure (approximate) Phases: φ hkl F hkl + φ hkl = F hkl 3D-Fourier Synthesis ρ(x,y,z) = [ Σ hkl F hkl exp{-2πι(hx + ky + lz)}] / V x,y,z are fractional coordinates (range 0 1) Phase problem
25 A typical electron density map
26 Interpreted Structure
27 Structure Completion 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: F hkl = S j=1,n f j T exp{2pi(hx + ky + lz)} Non-linear Least-squares Parameter Refinement until Convergence. Minimize: S hkl w [(F hkl obs ) 2 (F hkl calc ) 2 ] 2 Agreement Factor: R = S F obs F calc / S F obs
28 Refinement of the Structural Model Refinement Steps (Programs SHELXL, Crystals, XTAL etc) 1. Refine positional parameters + isotropic U 2. Refine positional + anisotropic parameters 3. Introduce H-atoms 4. Refine H-atoms with x,y,z,u(iso) or riding on their carrier atoms 5. Refine weighting scheme 6. ORTEP presentation
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30 Analysis of the Geometry and Intermolecular Interactions Programs: PLATON, PARST etc Bond distances, angles, torsion angles, ring (puckering) geometry etc. Intermolecular Contacts 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. Hydrogen Bonds (O-H..O, N-H..O, O-H..π)
31 Technical Problems Poor crystal quality (e.g. fine needle bundles) Determination of the correct Space Group Symmetry Pseudo-Symmetry Absolute Structure of light atom structures Twinning Positional and substitutional disorder of part (or even the whole) molecule Disordered Solvent Incommensurate structures Diffuse scattering, streaks, diffuse layers
32 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.
33 THE CIF DATA STANDARD - Driving Force: Syd Hall (IUCr/ Acta Cryst C) - Early Adopted by XTAL & SHELX(T)L. - Currently: WinGX,Crystals,Texsan, Maxus etc. - Acta Cryst. C/E Electronic Submission - Acta Cryst.:Automatic Validation at the Gate - CIF data available for referees for detailed inspection (and optional calculations). - Data retrieval from the WEB for published papers - CCDC Deposition in CIF-FORMAT.
34 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?
35 IUCr CHECKCIF WEB-Service reports the outcome of: IUCr standard tests Consistency, Missing Data, Proper Procedure, Quality etc. + Additional PLATON based tests Missed Symmetry, Twinning, Voids, Geometry, Displacement Parameters, Absolute Structure etc. ALERT A Serious Problem ALERT B Potentially Serious Problem ALERT C Check & Explain ALERT G Verify or Take Notice
36 EXAMPLE OF PLATON GENERATED ALERTS FOR A RECENT PAPER PUBLISHED IN J.Amer.Chem.Soc. (2007) Attracted special attention in Chemical and Engineering News Properly Validated?
37 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 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.
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39 1. Sample preparation 2. Method - λ used (Source) 3. Mode of Data Collection 0.02 in 2θ ~5000 Data Points in the Range in 2θ ~20,000 Data Points in the Range 1-100
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41 SrBi 4 Ti 4 O 15
42 X-ray powder pattern X-ray powder pattern after decomposition
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44 Profile functions Examples Function [C o 1/2 / H k π 1/2 ] exp(-c o (2θ i - 2θ k ) 2 /H k2 ) Gaussian (G) (C 1 1/2 /πh k ) 1/ [1+C 1 (2θ i - 2θ k ) 2 /H k2 ] 2 Lorentzian (L) (2C 2 1/2 /πh k ) 1/ [1+C 2 (2θ i - 2θ k ) 2 /H k2 ] 2 Mod 1 Lorentzian (C 3 1/2 /2H k ) 1/ [1+C 3 (2θ i - 2θ k ) 2 /H k2 ] 3/2 Mod 2 Lorentzian η L + (1-η)G pseudo-voigt The mixing parameter η can be refined as a linear function of 2θ wherein the refinable variables are NA and NB. η= NA + NB * 2θ
45 Refinable Parameters Structural parameters Profile parameters 2θ-Zero Instrumental profile Profile asymmetry Background Crystallite size and microstrain(through profile parameters) Specimen-profile breadth parameters Lattice parameters Specimen displacement Specimen transparency Absorption
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47 Crystal structure of α-nabi 3 V 2 O 10 New phase - NaBi 3 V 2 O 10 in Na 2 O-Bi 2 O 3 -V 2 O 10 system (D C Sinclair et.al, J Mater. Chem. 1998, 8 (2), ) Oxide ion conductor, conductivity = 1.5mS cm -1 at 675 C Synthesized at 600 C from Na 2 O, Bi 2 O 3, V 2 O 5
48 NaBi 3 V 2 O 10 (single phase) 700 C NaBi 3 V 2 O 10 + minor phase 775 C NaBi 3 V 2 O 10 (melts) cool two phases Phase transition at 575 C -DTA analysis -High temperature powder XRD 575 C NaBi 3 V 2 O 10 phase transition NaBi 3 V 2 O 10
49 Crystal Data for α-nabi 3 V 2 O 10 Formula NaBi 3 V 2 O 10 Formula weight Color Yellow Space group P 1 Z 1 λ ( Å ) θ o Number of Structural parameters 41 Profile function Pseudo-Voigt a(å) (4) b(å) (3) c(å) (2) α (3) β (2) γ (2) V(Å 3 ) (2) R wp 13.14% R p 9.91% R(I,hkl) 8.68%
50 Results of the EXTRA pattern decomposition module 2θ = 3.00 to º 498 reflections generated R p = 11.55% R wp = 15.80% Result of the SIRPOW97 structure solution module Positional parameters of two Bismuth atoms and one Vanadium atom were found Difference Fourier analysis was used to locate remaining atoms GSAS was used for Rietveld refinement
51 Difference Fourier map
52 Difference Fourier map
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55 Methods and Strategy * Traditional approach -pattern decomposition (Pawley,Le Bail method) -structure solution -structure completion (difference Fourier technique) -Rietveld refinement * Direct Space approach model (Direct,Patterson method) -trial structures are generated independent of powder pattern, -compare calculated pattern with experimental powder pattern ( Monte Carlo, simulated annealing, grid search)
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58 Direct Space approach The most preferred approach for organic compounds- Drugs The methodology 1. Trial crystal structures need to be generated in direct space 2. Calculated powder pattern compared with observed powder pattern 3. R and R wp give guidelines How and Why? 4. Aim is to identify the trial structure with lowest R value 5. Any technique for global optimization may be used Monte Carlo Simulated annealing grid search genetic algorithm 6. Cell dimensions and experimental pattern are prerequisites 7. Unit cell contents are known ( structural formula) 8. Molecular dimensions are optimized and known partly or fully
59 Solving a structure from powder diffraction data chemical information whole profile equipartitioning FIPS/triplets multiple datasets overlap treatment method of solution crystal structure model based methods Reci.lattice methods direct space methods Genetic algorithm structure completion Le Bail Pawley space group intensity extraction polycrystalline sample indexing Rietveld refinement radiation source data collection laboratory X-rays synchrotron X-rays neutrons
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61 A. R. Choudhury, K. Islam, M. T. Kirchner, G. Mehta, T. N. Guru Row, J. Am. Chem. Soc.(communication), 2004, 126(39), In situ cryo-crystallization of diphenyl ether
62 Motor Silicone oil bath Furnace A B C D E F G Sample Holder Vacuum pump mm/hg
63 Acknowledgements: My students, post-docs and project assistants IISc and DST for funding
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