180.0 degree rotation about 1. 0. 0. direct lattice direction 1.000 0.000 0.000 0.000 -1.000 0.000 -0.999 0.000 -1.000 Figure of merit 0.11 No reflections omitted 26 Example 2 - Pseudo-Merohedral Twinning
Final XL Results R1 3.17
TITL hnab3 in P2(1) CELL 0.71073 15.4015 5.5240 22.1182 90.000 110.367 90.000 ZERR 4.00 0.0007 0.0005 0.0011 0.000 0.001 0.000 LATT -1 SYMM -X 0.5Y -Z SFAC C H N O UNIT 48 16 32 48 TEMP 32 L.S. 4 ACTA FMAP 2 PLAN 10 TWIN 1 0 0 0 -1 0 -1 0 -1 WGHT 0.029700 EXTI 0.003436 BASF 0.44866 FVAR 0.21356 Final Publication M. A. Rodriquez C. F. Campana A. D. Rae E. Graeber and B. Morosin Acta Cryst. C61 o127-o130 (2005) 27 Example 3 - Merohedral Twinning
58 Example 7 An organic compound exhibiting two types of enantiomeric disorder
Triclinic P-1 Z 8
a 10.1195(5) Å
b 14.1443(7) Å
c 19.3863(10) Å
82.979(3)
84.235(3)
88.777(3)
59 Example 7 An organic compound exhibiting two types of enantiomeric disorder
Problems
R1 18
Many atoms with large U-values strange thermal ellipsoids
Two well-behaved molecules two abnormal molecules
60 Example 7 An organic compound exhibiting two types of enantiomeric disorder
Initial Structure Molecule A
50 Thermal Ellipsoids
61 Example 7 An organic compound exhibiting two types of enantiomeric disorder
Initial Structure Molecule B
50 Thermal Ellipsoids
62 Example 7 An organic compound exhibiting two types of enantiomeric disorder
Initial Structure Molecule C
50 Thermal Ellipsoids
63 Example 7 An organic compound exhibiting two types of enantiomeric disorder
Initial Structure Molecule E
50 Thermal Ellipsoids
64 Example 7 An organic compound exhibiting two types of enantiomeric disorder
Disorder - Molecules C D
65 Example 7 An organic compound exhibiting two types of enantiomeric disorder
Disorder - Molecules E F
Disorder - Molecules E F
66 Example 7 An organic compound exhibiting two types of enantiomeric disorder
Refinement Strategy
Use XP to sort out disorder (PRUN JOIN LINK)
Use restraints (SADI SAME EXYZ EADP etc.) in XL to refine
Final refinement
R1 0.0526 wR2 0.1274 GooF 1.077
Results
Correct structure normal U-values normal weighting scheme no large residual peaks
67 Example 7 An organic compound exhibiting two types of enantiomeric disorder
Final Structure Molecule C
50 Thermal Ellipsoids
68 Example 7 An organic compound exhibiting two types of enantiomeric disorder
Final Structure Molecule D
50 Thermal Ellipsoids
69 Example 7 An organic compound exhibiting two types of enantiomeric disorder
Final Structure Molecule E
50 Thermal Ellipsoids
70 Example 7 An organic compound exhibiting two types of enantiomeric disorder
Final Structure Molecule F
50 Thermal Ellipsoids
71 Example 8 A Commensurately Modulated Carborane Compound
Compound prepared by D.E. Hyatt Lee Todds first graduate student at Indiana U. 1966. No Structure published.
Hyatt D. E. Owen D. A. and Todd L. J. Inorg. Chem. 5 1749-51 (1966).
Recent paper from Durham U. with synthesis spectroscopy etc. No structure published.
Batsanov A.S. Fox M. A. Goeta A. E. Howard J. A. K. Hughes A. K. and Malget J. M. J. Chem. Soc. Dalton Trans. 2624-2631 (2002).
(CH3)3N-CB10H12 72 Example 8 A Commensurately Modulated Carborane Compound
Empirical formula C4H21B10N
Chemical formula (CH3)3N-CB10H12
Formula weight 191.32
Crystal size 0.364 x 0.624 x 0.720 mm
Crystal habit clear colorless prism
Density (calculated) 1.077 Mg/m3
Absorption coefficient 0.05 mm-1
73 Example 8 A Commensurately Modulated Carborane Compound
Early attempts with film and / or scintillation counter methods gave ambiguous unit cells
Small cell Orthorhombic P Z 4 16 Å 10 Å 7 Å
Intermediate cell - Orthorhombic P Z 8 16 Å 10 Å 14 Å
Large cell - Orthorhombic P Z 28 16 Å 10 Å 49 Å
74 Example 8 A Commensurately Modulated Carborane CompoundReciprocal Lattice Viewer
Very strong main reflections (white color)
Weak satellite reflections in between (green color)
h 0 1 2 3 4 5 6 7
75 Example 8 A Commensurately Modulated Carborane Compound Correct Unit Cell Small Cell
Crystal system Orthorhombic
Space group Pnma
Unit cell dimensions a 16.1370(8) Å
b 10.5017(5) Å
c 6.9605(3) Å
Volume 1179.57(10) Å3
Z 4
F(000) 408
Q-vector 0 0 3/7 (0.0000 0.0000 0.42857)
76 Example 8 A Commensurately Modulated Carborane Compound CCD Data Collection
Instrument Used Bruker SMART APEXII
Crystal to Detector Distance 8.926 cm.
Image Width ( or ) 0.5
Maximum 2 angle 68.80
Maximum Resolution 0.63 Å
Total Images Collected 6523
Exposure Time / Image 10.0 sec.
Total Data Collection Time 21.74 hours
Temperature 100(2) K
Total Reflections Measured 21978
Independent Reflections 2492
R(int) 4.81
R(sig) 2.54
Reflections gt 2sigma(I) 1965
77 Example 8 A Commensurately Modulated Carborane Compound Integration of satellite reflections with SAINT
New features of SAINT (Version 7.53A)
allows the input and refinement of up to three QVEC instructions for up to 6-dimensional modulated structures. The following input .P4P file was used for this integration
FILEID SAINT V7.09A 4.00 07/08/04 142534 carborane
78 Example 8 A Commensurately Modulated Carborane Compound Integration of satellite reflections with SAINT
When the SAINT program encounters a QVEC instruction in the .P4P file it automatically produces output files with the .ram extension instead of the normal .raw extension.
Note The SAINT.INI file must be edited to include a MAXSATIND 2 parameter to the INTEGRATE section (to integrate both first and second-order satellite reflections)
79 Example 8 A Commensurately Modulated Carborane Compound SADABS output formats
.hkl file SHELX-compatible files for normal solution and refinement (main reflections only)
-1 -6 0 0.19 0.40
-1 -6 0 -0.02 0.35
1 -6 0 0.12 0.32
-2 -6 0 218.05 7.44
-2 6 0 222.14 8.67
-2 -6 0 222.34 8.49
2 -6 0 215.54 7.41
-2 -6 0 221.98 10.43
2 6 0 211.25 8.64
2 -6 0 203.46 10.39
-3 -6 0 0.17 0.36
-3 -6 0 -0.03 0.39
3 6 0 -0.03 0.50
80 Example 8 A Commensurately Modulated Carborane Compound SADABS output formats
.hk6 file JANA2006-compatible files for modulated structure refinement with JANA2006
-2 -5 -8 0 0 0 8.98 0.66 7
-2 -6 0 0 0 0 215.66 7.41 7
-2 -6 0 2 0 0 20.74 7.31 7
-2 -6 0 -1 0 0 0.76 7.29 7
-2 -6 0 1 0 0 1.66 7.29 7
-2 -6 0 -2 0 0 8.67 7.29 7
2 -6 0 0 0 0 218.17 7.44 7
2 -6 0 1 0 0 2.09 7.30 7
2 -6 0 -1 0 0 0.79 7.29 7
2 -6 0 -2 0 0 6.14 7.29 7
2 -6 0 2 0 0 18.14 7.31 7
-2 -6 -1 2 0 0 29.00 3.36 7
-2 -6 -1 1 0 0 95.42 3.42 7
-2 -6 -1 0 0 0 104.30 3.41 7
-2 -6 -1 -1 0 0 0.60 3.31 7
81 Example 8 A Commensurately Modulated Carborane Compound Absorption correction for modulated structure data with SADABS
The SADABS (Version 2008/2) scaling and absorption program has been modified to include the following new features
When files with the .ram extension are read into SADABS the program uses the main reflections to optimize the absorption correction model in the normal manner. The correction is then applied to all reflections including satellite reflections.
82 Example 8 A Commensurately Modulated Carborane Compound Solution and refinement - small cell
Small Cell Refinement (.hkl file main reflections only)
Space Group Pnma Z 4
Modeled as 2-fold disorder with Ratio 43 (PART 1 PART 2)
R1 7.9
83 Example 8 A Commensurately Modulated Carborane Compound- Supercell Structure 84 (No Transcript) 85 (No Transcript) 86 (No Transcript) 87 (No Transcript) 88 (No Transcript) 89 (No Transcript) 90 (No Transcript) 91 (No Transcript) 92 (No Transcript) 93 (No Transcript) 94 (No Transcript) 95 (No Transcript) 96 (No Transcript) 97 (No Transcript) 98 (No Transcript) 99 (No Transcript) 100 (No Transcript) 101 (No Transcript) 102 (No Transcript) 103 (No Transcript) 104 (No Transcript) 105 (No Transcript) 106 (No Transcript) 107 (No Transcript) 108 (No Transcript) 109 (No Transcript) 110 (No Transcript) 111 (No Transcript) 112 (No Transcript) 113 (No Transcript) 114 (No Transcript) 115 (No Transcript) 116 (No Transcript) 117 (No Transcript) 118 (No Transcript) 119 (No Transcript) 120 (No Transcript) 121 (No Transcript) 122 (No Transcript) 123 (No Transcript) 124 (No Transcript) 125 (No Transcript) 126 Example 8 A Commensurately Modulated Carborane Compound Modulated structure refinement - JANA2006
Superspace Group Pnma (00) 0s0
Refinement model whole molecules distributed over two symmetrically related positions described by the crenel-like modulation one molecular harmonic used for additional positional and ADP modulations
127 Example 8 A Commensurately Modulated Carborane Compound Summary commensurate structure analysis
Determine unit cell and q-vector(s)
Integrate data (including satellite reflections) write .ram files
Perform absorption correction and scaling write .hkl and .hk6 files
Solve and refine basic structure SHELXTL
Determine superspace group refine modulated structure JANA2006
Analysis and presentation of results
128 Application of Advanced Tools to Problem Structures
Non-Merohedral Twins
Diagnosis CELL_NOW RLATT ROTAX
Processing SAINT (w/ multiple OM) TWINABS
Solution XM or XS (HKLF 4 data)
Refinement XL (BASF HKLF 5)
Pseudo-Merohedral Twins
Diagnosis XPREP ROTAX
Processing SAINT SADABS
Solution XM or XS
Refinement XL (BASF TWIN)
Merohedral Twins
Diagnosis XPREP ROTAX
Processing SAINT SADABS
Solution XM or XS
Refinement XL (BASF TWIN)
Inversion (Racemic) Twins
Diagnosis XPREP ROTAX
Processing SAINT SADABS
129
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