# Presentation: 950932

## Tools for the Solution and Refinement of Problem Structures Charles F. Campana, Ph.D.Bruker AXS Inc. 

- Bruker AXS

## Current Software Tools

_**Bruker Programs**_
**SMART (Chambers)**
**RLATT (Pressprich)**
**CELL_NOW (Sheldrick) [Version 2008/2] **
**XPREP (Sheldrick) [Version 2008/2] **
**SAINT (Chambers) [Version 7.53A] **
**SHELXTL (Sheldrick) [Version 2008/2] **
**SADABS & TWINABS (Sheldrick) [Version 2008/1]**
**APEX2 [Version 2008.2] (Kaercher et al.)**
_**Other Programs**_
**ROTAX (Parsons) [February 2006 Version] **
**PLATON (Spek) [August 2007 Version] **
**JANA2006 (Petricek & Dusek) [March 2008 Version] **
**Mercury (CCDC) [Version 1.4.2]**

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## Recommended Reference for Problem Structures

**Müller, P. *****Crystal Structure Refinement*****. 1st ed. New York, NY: Oxford University Press, 2006. ISBN: 0198570767**

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## 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
- 	Solution – XM or XS
- 	Refinement – XL (BASF + TWIN)
**Modulated Structures**
- 	Diagnosis – SMART, APEX2, RLATT
- 	Processing – SAINT (w/ QVEC inst.), SADABS
- 	Solution – XM or XS
- 	Refinement – JANA 2000(Petricek & Dusek)

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## Introduction and OverviewExamples of Difficult Structures

**Indexing, Unit Cell Determination Problems**
- Split Crystals
- Non-Merohedral (Rotational) Twinning
- Modulated Structures
**Structure Solution Problems**
- Incorrect Space Group
- Pseudo-Merohedral Twinning
- Merohedral Twinning
**Structure Refinement Problems**
- Disordered Structures
- Pseudo-Merohedral Twinning
- Merohedral Twinning

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## Example 1 - Pseudo-Merohedral Twinning

**Background**
**Organometallic Re complex (C****20****H****34****B****6****Cl****2****Re****2****)**
**Monoclinic – P2****1****/n, Z = 4**
**Problems**
**R1 = 20%**
**Many atoms with NPD U-values**
_**Incorrect structure **_**(****3**** Cl atoms per molecule)**

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## Example 1 - Pseudo-Merohedral Twinning

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## Example 1 - Pseudo-Merohedral Twinning

**Other important details**
**330**** violations of systematic absence rules for P2****1****/n**
**1679****  Inconsistent equivalents**
**R(int) = ****0.2042****     R(sigma) = ****0.1212**
**Many significant correlations in refinement**
**Recommended weighting scheme:  WGHT  0.0000 ****920.9722**
**K       ****51.471****   11.087    4.180    2.588**
**Most Disagreeable Reflections **
**	**** ****h   k   l        Fo^2         Fc^2   Delta(F^2)/esd  Fc/Fc(max)  Resolution(A)**
**    ****-8   4   1     **** 16585.63****          7.47       6.25       0.004       1.25**
**   ****-12   2   2     **** 25248.76 ****       151.15       6.16       0.017       0.87**
**     ****8   6   4      ****20892.44****        153.24       6.03       0.017       1.10**
**     ****8   2   8     **** 36143.16 ****       635.95       6.03       0.035       1.01**
**    ****-9   4   2     **** 17985.62 ****       302.20       5.99       0.024       1.12**
**    ****-9   6   3      ****12074.38****         93.03       5.94       0.013       1.07**
**    ****12   2   2      ****18911.99****          2.13       5.93       0.002       0.85**
**    ****12   4   1      ****13717.04 ****        11.69       5.91       0.005       0.85**
** **

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## Example 1 - Pseudo-Merohedral Twinning

**Actual Unit Cell (Unconstrained)**
**	****CELL     10.5146   16.7855   14.3817  **** 89.9607  **** 94.7430  **** 90.0833 ****  2529.575**
**	****CELLSD    0.0011    0.0017    0.0014    0.0019    0.0017    0.0017      0.809**
**XPREP Output**
**	****Option A: FOM = 0.089 deg.   MONOCLINIC   P-lattice   R(sym) = ****0.224 ****[   5389]**
**	****Cell:   10.515  16.785  14.382   89.96   94.74   90.08    Volume:      2529.57**
**	****Matrix: 1.0000  0.0000  0.0000  0.0000  1.0000  0.0000  0.0000  0.0000  1.0000**
**------------------------------------------------------------------------------**
**	****Option B: FOM = 0.000 deg.   TRICLINIC    P-lattice   R(sym) = 0.000 [      0]**
**	****Cell:   10.515  14.382  16.785   89.96   89.92   85.26    Volume:      2529.57**
**	****Matrix:-1.0000  0.0000  0.0000  0.0000  0.0000  1.0000  0.0000  1.0000  0.0000**
**------------------------------------------------------------------------------**
**	****Option A selected (XPREP suggested Option B!!!)**
**	****Systematic absence exceptions:**
**            ****-21-  -a-   -c-   -n- **
**	****N        21   458   458   450**
**	****N I>3s   11   377   358   337**
**	****<I>     ****1.1****  22.0  22.2   ****8.8**
**	****<I/s>   6.9  13.3  12.4  10.0**
**True Space Group is TRICLINIC P-1**

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## Example 1 - Pseudo-Merohedral Twinning

**Refinement in P-1 Space Group**
**Unit Cell Parameters**
- 	CELL 0.71073  10.5146  14.3817  16.7855  89.961  89.917  85.257
- 	ZERR    4.00   0.0004   0.0006   0.0007   0.001   0.001   0.001
- 0  Inconsistent equivalents
- R(int) = 0.0267     R(sigma) = 0.0453
- R1 = 0.1342
- Correct structure, but many NPD U-values
- Recommended weighting scheme:  WGHT  0.0000  649.6266
**Most Disagreeable Reflections **
**  ****	**** ****h   k   l          Fo^2          Fc^2  Delta(F^2)/esd Fc/Fc(max)  Resolution(A)**
**     ****7  -7   1      ****11267.14****         18.66       6.84       0.006       1.16**
**    ****-5   4   4      **** 8311.13****        508.36       6.28       0.030       1.61**
**    ****-2   5   3     ****  3458.91 ****         8.18       6.08       0.004       2.23**
**    ****-5   3   3     ****  8537.00 ****         4.83       5.81       0.003       1.77**
**     ****7  -8   3    ****  13399.65****        126.62       5.68       0.015       1.08**
**    ****-3   8   4     ****  6747.74 ****       668.96       5.64       0.034       1.45**
**    ****-5  -3   7    ****   5815.16 ****       320.09       5.63       0.024       1.53**
**     ****7  -3   5    ****  12077.00****        413.54       5.57       0.027       1.29**
**     ****0   4   2    ****   3441.84****        499.71       5.56       0.029       3.30**
**Insert ****LIST 4**** instruction into .INS file and repeat refinement**

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## Example 1 - Pseudo-Merohedral Twinning

**Run ROTAX program from Command Prompt**
**ROTAX output**
**	****180.0 degree rotation about   0.  0.  1. direct lattice direction:**
**	****[  -1.000    0.000    0.002]**
**	****[   0.000   -1.000    0.001]**
**	****[   0.000    0.000    1.000]**
**	****Figure of merit =   0.77 *************
**	****No reflections omitted**
**Insert TWIN and BASF instructions into .INS file and repeat refinement**
**	****PLAN 5**
**	****TWIN -1  0  0  0 -1  0  0  0  1**
**	****BASF 0.5**
**	****WGHT    0.040000**
**Results of twinned refinement**
- BASF   0.23970
- R1 = 0.0329, wR2 =  0.0798, GooF = 1.066
- Correct structure, no NPD U-values, normal weighting scheme

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## Example 1 - Pseudo-Merohedral Twinning

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## Example 2 - Pseudo-Merohedral Twinning

**Background**
**Form III of 2,2’,4,4',6,6'-Hexanitroazobenzene (HNAB-III)**
**Two previous polymorphs (HNIABZ11 & HNIABZ20) characterized and published - E. J. Graeber & B. Morosin, Acta Cryst, B30, 310 (1974).**
**Beautiful orange plate-like crystals obtained (Sandia NL 1977)**
**X-Ray photographs indicated orthorhombic ****C222****1**
**Excellent data collected on Picker FACS-I diffractometer (Sandia NL) & later Syntex P3/F (UNM)**
**No solution after much effort (MULTAN etc.) – 30 years!**
**Hemisphere of data collected on SMART CCD system (Sandia NL 2003)**

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## Example 2 - Pseudo-Merohedral Twinning

**Standard XPREP run (accept default parameters)**
**-------------------------------------------------------------------------------**
**Search for higher metric symmetry**
**Identical indices and Friedel opposites combined before calculating R(sym)**
**------------------------------------------------------------------------------**
**Option A: FOM = 0.008 deg.   ****ORTHORHOMBIC C-lattice****   R(sym) = ****0.046 ****[   3489]**
**Cell:   15.401  41.471   5.524   90.00   90.00   89.99    Volume:      3528.25**
**Matrix: 1.0000  0.0000  0.0000  1.0000  0.0000  2.0000  0.0000 -1.0000  0.0000**
**Option A selected**
**-------------------------------------------------------------------------------**

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## Example 2 - Pseudo-Merohedral Twinning

**Standard XPREP run (accept default parameters)**** **
**	**
**SPACE GROUP DETERMINATION**
**Lattice exceptions:  P      A      B      C      I      F     Obv    Rev    All**
**N (total) =           0   3801   3801      0   3844   3801   5050   5060   7586**
**N (int>3sigma) =      0   2826   2826      0   2903   2826   3754   3734   5596**
**Mean intensity =    0.0    9.1    9.1    0.0   21.4    9.1   18.4   18.0   18.3**
**Mean int/sigma =    0.0    9.8    9.8    0.0   11.2    9.8   10.5   10.5   10.6**
**Crystal system O and Lattice type C selected**
**Mean |E*E-1| =**** ****0.616 ****[expected .968 centrosym and .736 non-centrosym]**
**Chiral flag NOT set**
**Systematic absence exceptions:**
**         ****c--   n--   -c-   -n-   --a   --b  --21 **
**N       229   229    62    62   498   498     7**
**N I>3s  166   166    42    42   373   373     0**
**<I>    14.3  14.3  11.7  11.7   8.5   8.5   0.3**
**<I/s>  12.0  12.0  10.8  10.8   9.9   9.9   0.7**
**dentical indices and Friedel opposites combined before calculating R(sym)**
**Option  Space Group  No.  Type  Axes  CSD  R(sym) N(eq)  Syst. Abs.   CFOM**
**[A] ****C222(1)       **** # 20  chiral   1  **** 155****  0.046   3489  0.7 /  9.9   3.10**
**Option [A] chosen**
**        ****	**

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## Example 2 - Pseudo-Merohedral Twinning

**Standard XPREP run (accept default parameters)**
**-------------------------------------------------------------------------------**
**File hnab.ins set up as follows:**
**TITL hnab in C222(1) **
**CELL 0.71073  15.4015  41.4709   5.5240  90.000  90.000  90.000**
**ZERR    8.00   0.0007   0.0023   0.0005   0.000   0.000   0.000**
**LATT -7**
**SYMM -X, -Y, 0.5+Z**
**SYMM -X, Y, 0.5-Z**
**SYMM X, -Y, -Z**
**SFAC C H N O**
**UNIT 96 32 64 96**
**TEMP 23**
**TREF     **
**HKLF 4**
**END **
**    ****7586 Reflections written to new reflection file hnab.hkl**
**-------------------------------------------------------------------------------**

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## Example 2 - Pseudo-Merohedral Twinning

**XPREP run (****change default parameters****)**
**-----------------------------------------------------------------------------**
**TOLERANCES CHANGED**
**Maximum deviation (deg.) in higher symmetry cell search =  ****1.000**
**Threshold (deg.) for terminating search =  ****0.000**
**R(int) maximum for terminating cell search =  ****0.600**
**R(int) maximum for space group determination =  ****0.300**
**Minimum number of data in group for syst. absence test =   5**
**Maximum mean I/sigma(I) for systematic absences =  2.554**
**Minimum I/sigma gap between absences and rest =  2.109**
**-------------------------------------------------------------------------------**
**        ****	**

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## Example 2 - Pseudo-Merohedral Twinning

**XPREP run (change default parameters) **
**------------------------------------------------------------------------------**
**Option A: FOM = 0.008 deg.   ORTHORHOMBIC C-lattice   R(sym) = 0.046 [   3489]**
**Cell:   15.401  41.471   5.524   90.00   90.00   89.99    Volume:      3528.25**
**Matrix: 1.0000  0.0000  0.0000  1.0000  0.0000  2.0000  0.0000 -1.0000  0.0000**
**------------------------------------------------------------------------------**
**Option B: FOM = 0.000 deg.   MONOCLINIC   P-lattice   R(sym) = 0.032 [   2165]**
**Cell:   15.401   5.524  22.118   90.00  110.37   90.00    Volume:      1764.13**
**Matrix: 1.0000  0.0000  0.0000  0.0000  1.0000  0.0000  0.0000  0.0000  1.0000**
**------------------------------------------------------------------------------**
**Option C: FOM = 0.008 deg.   MONOCLINIC   C-lattice   R(sym) = 0.042 [   2353]**
**Cell:   41.471  15.401   5.524   90.00   90.00   90.01    Volume:      3528.25**
**Matrix:-1.0000  0.0000 -2.0000  1.0000  0.0000  0.0000  0.0000 -1.0000  0.0000**
**------------------------------------------------------------------------------**
**Option D: FOM = 0.008 deg.   MONOCLINIC   C-lattice   R(sym) = 0.042 [   2415]**
**Cell:   15.401  41.471   5.524   90.00   90.00   89.99    Volume:      3528.25**
**Matrix:-1.0000  0.0000  0.0000 -1.0000  0.0000 -2.0000  0.0000 -1.0000  0.0000**
**------------------------------------------------------------------------------**
**Option E: FOM = 0.000 deg.   TRICLINIC    P-lattice   R(sym) = 0.000 [      0]**
**Cell:    5.524  15.401  22.118   69.63   90.00   90.00    Volume:      1764.13**
**Matrix: 0.0000  1.0000  0.0000 -1.0000  0.0000  0.0000  0.0000  0.0000  1.0000**
**Option B selected**
**-------------------------------------------------------------------------------**
**        ****	**

- Bruker AXS

## Example 2 - Pseudo-Merohedral Twinning

**XPREP run (change default parameters) **
**SPACE GROUP DETERMINATION**
**Lattice exceptions:  P      A      B      C      I      F     Obv    Rev    All**
**N (total) =           0   3780   3791   3801   3777   5686   5054   5050   7586**
**N (int>3sigma) =      0   2767   2789   2826   2766   4191   3734   3750   5596**
**Mean intensity =    0.0   17.6   17.1    9.1   17.6   14.6   18.9   18.2   18.3**
**Mean int/sigma =    0.0   10.5   10.6    9.8   10.5   10.3   10.6   10.5   10.6**
**Crystal system M and Lattice type P selected**
**Mean |E*E-1| = ****0.624**** [expected .968 centrosym and .736 non-centrosym]**
**Chiral flag NOT set**
**Systematic absence exceptions:**
**        ****-21-   -a-   -c-   -n- **
**N         7   498   500   496**
**N I>3s    0   373   337   336**
**<I>     0.3   8.5  18.2  18.0**
**<I/s>   0.7   9.9  10.4  10.4**
**dentical indices and Friedel opposites combined before calculating R(sym)**
**Option  Space Group  No.  Type  Axes  CSD  R(sym) N(eq)  Syst. Abs.   CFOM**
**[A] ****P2(1)****          #  4  chiral   1  3543  0.032   2165  0.7 /  9.9   2.29**
**[B] P2(1)/m        # 11  centro   1   402  0.032   2165  0.7 /  9.9  13.08**
**Option [A] chosen**

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## Example 2 - Pseudo-Merohedral Twinning

**XPREP run (****change default parameters – M option****) **
**-----------------------------------------------------------------------------**
**File hnab3.ins set up as follows:**
**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, 0.5+Y, -Z**
**SFAC C H N O**
**UNIT 48 16 32 48**
**TEMP 32**
**FIND    33**
**PLOP    44    55    62**
**MIND 1.0 -0.1**
**NTRY 1000**
**HKLF 4**
**END **
**    ****7586 Reflections written to new reflection file hnab3.hkl**
**----------------------------------------------------------------------------**
**        ****	**

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## Example 2 - Pseudo-Merohedral Twinning

**XM Results **
**-------------------------------------------------------------------------------**
**REM TRY     49   FINAL CC 73.23   TIME      10 SECS**
**REM Fragments: 31 31**
**REM **
**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, 0.5+Y, -Z**
**SFAC C H N O**
**UNIT 48 16 32 48**
**-------------------------------------------------------------------------------**
**        ****	**

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## Example 2 - Pseudo-Merohedral Twinning

**XM Results**

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## Example 2 - Pseudo-Merohedral Twinning

**XL Results – R1 = 17%**

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## Example 2 - Pseudo-Merohedral Twinning

**XL Results – R1 = 17%**

** ****Most Disagreeable Reflections (* if suppressed or used for Rfree)**
**          ****h   k   l        Fo^2         Fc^2   Delta(F^2)/esd  Fc/Fc(max)  Resolution(A)**
**    ****-2   1  12        ****555.54****         17.30       7.18       0.025       1.74**
**    ****-1   0  11        ****233.91****          7.52       5.90       0.017       1.96**
**    ****-2  -1  12        ****619.16****         17.35       5.89       0.025       1.74**
**   ****-13   0  11        ****403.33****         28.87       5.54       0.032       1.15**
**     ****5   0   2       ****1820.13****        310.96       5.31       0.107       2.56**
**     ****8   3   5       **** 262.33 ****         5.53       5.12       0.014       1.15**
**     ****5   0   6        ****735.08****        138.45       5.11       0.071       1.91**
**     ****2   3  10        ****151.73 ****         7.99       4.84       0.017       1.30**
**    ****-9   0  11        ****269.03****          7.10       4.77       0.016       1.51**
**    ****-4   1   5        ****371.20****         74.39       4.74       0.052       2.87**
**   ****-11   0  12        ****265.56****         28.40       4.74       0.032       1.28**
**     ****2  -1  13        ****270.30****         24.35       4.71       0.030       1.41**
**    ****-1   0  19        ****419.68****         61.03       4.70       0.047       1.12**
**    ****-5   0  10        ****487.22****         72.29       4.62       0.051       2.06**
**    ****-1   0  21        ****241.18****          7.45       4.59       0.016       1.01**
**     ****4   3   3        ****163.01****         20.78       4.59       0.028       1.54**
**   ****-11   0   3        ****236.22****         19.83       4.51       0.027       1.38**
**     ****4   3   5        ****214.44 ****        39.52       4.44       0.038       1.45**
**    ****-4   3   6        ****185.38****          9.78       4.43       0.019       1.58**
**     ****2   1  13        ****253.70****         24.36       4.40       0.030       1.41**
**    ****-8   1  11        ****165.49****         17.43       4.38       0.025       1.55**
**    ****11   0   2        ****178.01****          5.94       4.28       0.015       1.25**
**    ****-2   1  16        ****210.01****         14.64       4.24       0.023       1.32**
** **

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## Example 2 - Pseudo-Merohedral Twinning

**ROTAX Results**

**  **
**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**

- Bruker AXS

## 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, 0.5+Y, -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)**
** **

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## Example 3 - Merohedral Twinning

**Background**
**CELL 0.71073  16.5617  16.5617  15.4439  90.000  90.000 120.000**
**ZERR    6.00   0.0023   0.0023   0.0031   0.000   0.000   0.000**
**Hexagonal / Trigonal unit cell, Z = 6**
**Organometallic Ru complex (C****30****H****24****N****6****Ru) -Ru(bipy)****3**
**Problems**
**Excellent quality data**
**	****R(int) = 0.0307     R(sigma) = 0.0179**
**Ambiguous space group, structure could not be solved**

- Bruker AXS

## Example 3 - Merohedral Twinning

**XPREP Output**
**	****------------------------------------------------------------------------------**
**	****Option A: FOM = 0.000 deg.   HEXAGONAL    P-lattice   R(sym) = ****0.025 ****[   6448]**
**	****Cell:   16.562  16.562  15.443   90.00   90.00  120.00    Volume:      3668.43**
**	****Matrix: 1.0000  0.0000  0.0000  0.0000  1.0000  0.0000  0.0000  0.0000  1.0000**
**	****Option A selected**
**	****-------------------------------------------------------------------------------**
**	****Systematic absence exceptions:**
**        ****	****61/65 62=31  63    -c-   --c **
**	****N        22    18    12   710   475**
**	****N I>3s    9     9     0     7   279**
**	****<I>   140.0 171.1   ****0.3   0.9****  39.0**
**	****<I/s>  10.9  13.3   ****0.3   0.6****   9.2**
**	****Option  Space Group  No.  Type  Axes  CSD  R(sym) N(eq)  Syst. Abs.   CFOM**
**	****[A] P-3c1          #165  centro   1    28  0.028   8263  0.6 /  9.2   8.91**
**	****[B] P3c1           #158  non-cen  1    11  0.028   8263  0.6 /  9.2  23.27**
**	****[C] P6(3)cm        #185  non-cen  1     2 **** 0.031****   9328  0.6 /  9.2  44.75**
**	****[D] P6(3)/mcm      #193  centro   1     1  ****0.031****   9328  0.6 /  9.2  51.94**
**	****[E] P-6c2          #188  non-cen  1     0  ****0.031 ****  9328  0.6 /  9.2 111.42**
**	****Option [A] chosen**
**True Space Group is ****TRIGONAL P-3c1**** ****(No solution possible in any hexagonal space group)**

- Bruker AXS

## Example 3 - Merohedral Twinning

**Solution in ****P-3c1**** ****Space Group with XS Program**
- Two independent Ru(bipy)3 molecules – one on D3 site and one on C3 site
**Refinement in ****P-3c1**** ****Space Group**
- 0  Systematic absence violations
- 0  Inconsistent equivalents
- R(int) = 0.0305     R(sigma) = 0.0179
- R1 =  0.2542
- Correct structure, but some NPD U-values & very large residual peaks in map
**Most Disagreeable Reflections**
- 	h   k   l        Fo^2         Fc^2   Delta(F^2)/esd  Fc/Fc(max)  Resolution(A)
-     -2   6  10      12249.62          7.38       4.69       0.006       1.34
-     -3   5  10      12390.42          8.50       4.55       0.007       1.40
-     -1   4  14       5660.73         13.56       4.45       0.009       1.06
-     -5   7   2       6912.71         25.24       4.37       0.012       2.20
-     -1   4  10      14770.25        301.41       4.33       0.041       1.44
-      0   5  10      11512.03          3.27       4.22       0.004       1.36
-     -6  11  10       4414.28         42.68       4.19       0.016       1.08
-     -8   9  10      11256.75        375.46       4.15       0.046       1.14
**Insert ****LIST 4**** instruction into .INS file and repeat refinement**

- Bruker AXS

## Example 3 - Merohedral Twinning

**Run ****ROTAX**** program from Command Prompt**
**ROTAX output**
**	****180.0 degree rotation about  -1.  1.  0. direct lattice direction****:**
**	****[   0.000   -1.000    0.000]**
**	****[  -1.000    0.000    0.000]**
**	****[   0.000    0.000   -1.000]**
**	****Figure of merit =   0.00 *************
**XPREP output - test for merohedral twinning**
-  	**[1] -3 / -31m: R(int) 0.028(9795)/0.017(1907), <|E^2-1|> 1.063/1.070**
** ****	****TWIN  0 -1 0  -1 0 0  0 0 -1****   **
**   ****	****BASF  0.414 [C]  or  0.390 [NC]**
**Insert TWIN and BASF instructions into .INS file and repeat refinement**
**	****PLAN 5**
**	****TWIN  0 -1 0  -1 0 0  0 0 -1 **
**	****BASF 0.5**
**	****WGHT    0.040000**
**Results of twinned refinement**
- BASF   0.49628 (perfect twinning)
- R1 =  0.0259, wR2 =  0.0725, GooF = 1.066
- Correct structure, no NPD U-values, normal weighting scheme, no large residual peaks

- Bruker AXS

## Example 3 - Merohedral Twinning

- Bruker AXS

## Example 4 – Non-Merohedral Twinning

**Simple Monoclinic Structure**
**	****Formula – C****4****N****4****S****4****Cl****4**
**	****Space Group – P2****1****/c, Z = 2**

- Bruker AXS

## Example 4 – Non-Merohedral Twinning

**Refinement Output**
- 	0  Systematic absence violations
- 	1611  Inconsistent equivalents
- 	R(int) = 0.4518     R(sigma) = 0.1179
- 	K       68.634   14.563    4.282    2.946    1.865    1.905
- 	R1 =  0.2550, wR2 =  0.4532,  GooF = 3.031
- 	WGHT      0.1768     87.8417
-  Most Disagreeable Reflections (* if suppressed or used for Rfree)
-          h   k   l         Fo^2          Fc^2  Delta(F^2)/esd Fc/Fc(max) Resolution(A)
-      9   2   3        664.82         58.18       7.24       0.045       0.62
-     10   3   2        447.64         40.77       7.19       0.038       0.60
-     -7  17   3        251.81          0.62       5.95       0.005       0.62
-      9   1   2        123.93         20.71       5.33       0.027       0.66
-      8   0   2        540.63        161.71       4.29       0.076       0.73
-     -8  17   2        219.59         20.52       3.93       0.027       0.59
-      8   3   4        124.35         19.64       3.79       0.026       0.62
-      7  17   1        156.00          7.77       3.68       0.017       0.58
-      9   2   2        142.45          0.03       3.49       0.001       0.66
-     -6   4   2       1270.72        142.27       3.42       0.071       1.15
-      8   4   2        187.78          1.51       3.39       0.007       0.72

- Bruker AXS

## Example 4 – Non-Merohedral Twinning

**ROTAX **OUTPUT
- 180.0 degree rotation about   1.  0.  0. reciprocal lattice direction:
- [   1.000    0.000    0.955]
- [   0.000   -1.000    0.000]
- [   0.000    0.000   -1.000]
- Figure of merit =   1.59 ***********
- Non-Integer Matrix Element – We cannot use a simple TWIN instruction- we must use **CELL_NOW**

- Bruker AXS

##   Example 4 – Non-Merohedral TwinningCELL_NOW Output

**Cell for domain  1:    7.388   13.144    6.182    89.96   113.68    90.06**
** **
**  ****1517 reflections within 0.250 of an integer index assigned to domain  1,**
**  ****1517 of them exclusively;    46 reflections not yet assigned to a domain**
** ****------------------------------------------------------------------------------**
** ****Cell for domain  2:    7.388   13.144    6.182    89.96   113.68    90.06**
** **
** ****Rotated from first domain by ****179.2 ****degrees about**
** ****reciprocal axis -0.484  0.006  1.000  and real axis ****-0.004  0.001  1.000**
** ****Twin law to convert hkl from first to     -0.996   0.006  -0.967**
** ****this domain (SHELXL TWIN matrix):         -0.028  -1.000  -0.001**
**                                           ****-0.007   0.002   0.996**
** **
**  ****1350 reflections within 0.250 of an integer index assigned to domain  2,**
**    ****46 of them exclusively;     0 reflections not yet assigned to a domain**

- Bruker AXS

##    Example 4 – Non-Merohedral Twinning.P4P File from CELL_NOW

**FILEID SAINT        V7.06A        4.00        04/27/04 14:25:12 NSF2**
**SITEID Administrator                       ?**
**TITLE  Integration**
**CHEM   C4N4S4Cl4**
**CELL      7.3884   13.1436    6.1822   89.9643  113.6805   90.0630    549.797**
**CELLSD    0.0015    0.0026    0.0012    0.0300    0.0300    0.0300     0.275**
**ORT1        0.035939306    -0.056865178    -0.082636222 **
**ORT2        0.017559534     0.049863208    -0.112305790 **
**ORT3        0.142276525     0.008283437     0.108424976 **
**ZEROS   0.0000000 -0.0178117 -0.0247456    0.0883    0.1712    0.3467          **
**ADCOR       -6.3043     -0.1071     -0.0043      0.1575      0.1081     -0.0209**
**CELL2     7.3884   13.1436    6.1822   89.9643  113.6805   90.0630    549.797**
**CELLSD2   0.0015    0.0026    0.0012    0.0300    0.0300    0.0300     0.275**
**ORT12      -0.036804073     0.056372143    -0.118583880 **
**ORT22      -0.015264848    -0.050249487    -0.127575904 **
**ORT32      -0.142320156    -0.009261458    -0.029318471 **
**ZEROS2  0.0000000 -0.0178117 -0.0247456    0.0883    0.1712    0.3467          **
**ADCOR2      -6.3043     -0.1071     -0.0043      0.1575      0.1081     -0.0209**
**SOURCE MO     0.71073   0.70930   0.71359   2.00000    0.00    0.00**
**Read this .P4P file into SAINT Integration Program**

- Bruker AXS

## Example 4 – Non-Merohedral TwinningHKLF 5 format file from TWINABS

**   ****0   9   3  801.97    7.43   1**
**   ****0  -9  -3  805.63    4.71   1**
**   ****3   9  -3  861.66    6.32  -2**
**   ****0  -9  -3  861.66    6.32   1**
**  ****-3   9   3  851.29    8.22  -2**
**   ****0  -9   3  851.29    8.22   1**
**  ****-3   9   3  796.70    7.03  -2**
**   ****0  -9   3  796.70    7.03   1**
**   ****3  -9  -3  779.89    7.47  -2**
**   ****0   9  -3  779.89    7.47   1**
**   ****3  -9  -3  841.68    7.58  -2**
**   ****0   9  -3  841.68    7.58   1**
**   ****3   9  -3  839.86    8.11  -2**
**   ****0  -9  -3  839.86    8.11   1**
**  ****-3  -9   3  862.09    6.34  -2**
**   ****0   9   3  862.09    6.34   1**
**   ****3   9  -3  872.52    8.36  -2**
**   ****0  -9  -3  872.52    8.36   1**
**   ****0  -9  -3  202.50    3.03   2**
**   ****0   9  -3  177.75    3.10   2**
**   **

- Bruker AXS

##    Example 4 – Non-Merohedral TwinningFinal Refinement

**FMAP 2**
**PLAN 5**
**WGHT    0.023000**
**EXTI    0.002298**
**BASF   0.18207**
**FVAR       0.65985**
**CL1   4    0.807182    0.420776    0.495285    11.00000    0.01294    0.01349 =**
**      ****0.01087    0.00096    0.00272    0.00102**
**C2    1    0.711815    0.368499    0.035413    11.00000    0.01049    0.00888 =**
**         ****0.01396    0.00045    0.00539    0.00048**
** ...****..**
**HKLF ****5**
** **
**REM  NSF2 in P2(1)/c**
**REM R1 =  ****0.0241**** for   9786 Fo > 4sig(Fo)  and  0.0302 for all  12385 data**
**REM     75 parameters refined using      0 restraints**

- Bruker AXS

## Example 4 – Non-Merohedral TwinningFinal Structure

- Bruker AXS

## Example 5 – Whole Molecule Disorder

**Background**
- Sample from UCSD Summer School
- Prof. Michael Richmond et al. (U. of North Texas)
- NMR indicated dynamic equilibrium between two isomers
**Structure was easily ‘solved’, but could not be refined**
- R1 = 16%
- Many NPD atoms
- Three very large difference peaks (‘Star of David’)

- Bruker AXS

## Example 5 – Whole Molecule Disorder

**Preliminary structure – Chelating Phosphine Ligand**

- Bruker AXS

## Example 5 – Whole Molecule Disorder

**Three Large Difference Peaks**

- Bruker AXS

## Example 5 – Whole Molecule Disorder

**FVAR      0.15477   ****0.8500**
**OS1   5   1.38180   0.36327   0.23664  ****21.00000 ****  0.01306**
**OS2   5   1.16037   0.44356   0.29321  ****21.00000****   0.01737**
**OS3   5   1.22802   0.46498   0.16310  ****21.00000 ****  0.01676**
**C1A   1   1.22737   0.29544   0.22637  ****21.00000****   0.01424**
**O1A   3   1.14724   0.25371   0.21696  ****21.00000****   0.01327**
**C2A   1   1.53166   0.43473   0.24515  ****21.00000****   0.02705**
**O2A   3   1.61483   0.47245   0.24881  ****21.00000****   0.01637**
**C3A   1   1.00907   0.38885   0.25481  ****21.00000****   0.02644**
**O3A   3   0.91212   0.35992   0.23556  ****21.00000 ****  0.03082**
**C4A   1   1.33420   0.49045   0.32785  ****21.00000****   0.02520**
**O4A   3   1.42200   0.51620   0.35349  ****21.00000****   0.02519**
**C5A   1   1.13429   0.40796   0.37402  ****21.00000****   0.01968**
**O5A   3   1.11507   0.38537   0.42076  ****21.00000****   0.04168**
**C6A   1   1.03019   0.51972   0.29063  ****21.00000****   0.02206**
**O6A   3   0.94876   0.56097   0.28462  ****21.00000****   0.04682**
**C7A   1   1.12667   0.38230   0.13189  ****21.00000  **** 0.02768**
**O7A   3   1.06313   0.34129   0.11120  ****21.00000   ****0.02261**
**C8A   1   1.33629   0.53964   0.20167  ****21.00000  **** 0.02088**
**O8A   3   1.39946   0.58535   0.21995  ****21.00000 ****  0.02206**
**C9A   1   1.34144   0.46478   0.08771  ****21.00000 ****  0.02607**
**O9A   3   1.39311   0.47459   0.04379  ****21.00000 ****  0.02768**
**C10A  1   1.07098   0.52231   0.13931  ****21.00000   ****0.02470**
**O10A  3   0.98114   0.55458   0.12305  ****21.00000 ****  0.04529**
**P1    4   1.49269   0.30401   0.31810  11.00000   0.01685**
**P2    4   1.51235   0.30162   0.16667  11.00000   0.02253**
**C1    1   1.64848   0.25992   0.21803  11.00000   0.02086**
**C2    1   1.64668   0.26068   0.28099  11.00000   0.02963**
**C3    1   1.77319   0.22528   0.30686  11.00000   0.03008**

- Bruker AXS

## Example 5 – Whole Molecule Disorder

**FVAR       0.14765   ****0.84986**
**PART  1**
**ANIS   3**
**OS1   5    1.381809    0.363269    0.236644    21.00000    0.01398**
**OS2   5    1.160375    0.443563    0.293216    21.00000    0.01832**
**OS3   5    1.228021    0.464972    0.163111    21.00000    0.01769**
**PART  2**
**ANIS   3**
**OS4   5    1.279201    0.372329    0.290337   -21.00000    0.01897**
**OS5   5    1.356916    0.404339    0.165486   -21.00000    0.01516**
**OS6   5    1.132255    0.478575    0.221611   -21.00000    0.02121**
**PART  1**
**C1A   1    1.227149    0.295498    0.226379    21.00000    0.01463**
**O1A   3    1.147208    0.253766    0.216857    21.00000    0.01437**
**C2A   1    1.531363    0.434503    0.245167    21.00000    0.02786**
**O2A   3    1.614757    0.472385    0.248824    21.00000    0.01766**
**...**
**C9A   1    1.341290    0.464934    0.087821    21.00000    0.02657**
**O9A   3    1.392650    0.474727    0.043766    21.00000    0.02908**
**C10A  1    1.071073    0.522226    0.139298    21.00000    0.02516**
**O10A  3    0.981357    0.554645    0.123065    21.00000    0.04658**
**PART  0**
**ANIS   2**
**P1    4    1.492683    0.304015    0.318087    11.00000    0.01777**
**P2    4    1.512382    0.301606    0.166718    11.00000    0.02357**
**C1    1    1.648401    0.259913    0.218106    11.00000    0.02206**
**C2    1    1.646876    0.260442    0.280954    11.00000    0.03039**

- Bruker AXS

## Example 5 – Whole Molecule Disorder

**Remaining Carbonyl Atoms Revealed in Difference Map**

- Bruker AXS

## Example 5 – Whole Molecule Disorder

**Superposition of both isomers**

- Bruker AXS

## Example 5 – Whole Molecule Disorder

**Chelating Phosphine Ligand (85%)**

**Bridging Phosphine Ligand **
**(15%)**

- Bruker AXS

## Example 5 – Whole Molecule Disorder

**Crystallographic restraints (SADI, ISOR, SIMU, EADP) were used in initial refinement**
**Final refinement converged at R1 = 5.2%**

- Bruker AXS

## Example 6 – Urea Host : Guest Complex

**Background**
- Prof. Mark Hollingsworth et al. (Kansas State U.)
- Urea host lattice with long-chain carboxylic acid in channels
**Structure of urea lattice was ‘solved’, but carboxylic acid molecules could not be located**
**Apparent unit cell**
- Orthorhombic P212121
- _a_ = 8.3096 Å , _b_ = 10.9591 Å , _c_ =  13.6330 Å
- 12 Urea molecules, 4 carboxylic acid molecules per cell

- Bruker AXS

## Example 6 – Urea Host : Guest Complex

- Projection down _b_-axis

- Bruker AXS

## Example 6 – Urea Host : Guest Complex

- Projection down _a_-axis

- Bruker AXS

## Example 6 – Urea Host : Guest Complex

**Analysis of Q-peaks**

- Bruker AXS

## Example 6 – Urea Host : Guest Complex

**Analysis of Q-peaks**

- Bruker AXS

## Example 6 – Urea Host : Guest Complex

**N2C   3    0.662814    0.937759    0.024542    11.00000    0.02028**
**AFIX  93**
**H2CA  2    0.626060    1.006875    0.048581    11.00000    0.05118**
**H2CB  2    0.753628    0.936746   -0.008654    11.00000    0.05692**
**AFIX   0 **
**PART  -1**
**C1S   1    0.047758    0.093743    0.256429    ****10.33333****    0.02221**
**O1S   4   -0.065938    0.059457    0.208123    ****10.33333****    0.03123**
**O2S   4    0.147213    0.019479    0.303494    ****10.33333 ****   0.03285**
**AFIX   3**
**H2S   2    0.117603   -0.055411    0.292184    ****10.33333****    0.05883**
**AFIX   0**
**C2S   1    0.090446    0.226023    0.271096    ****10.33333****    0.02369**
**AFIX  23**
**H2SA  2    0.196427    0.240424    0.240008    ****10.33333****    0.03582**
**H2SB  2    0.103898    0.240028    0.342366    ****10.33333****    0.05245**
**AFIX   0**
**....**
**C10S  1    0.080032    1.122110    0.284898    ****10.33333****    0.02266**
**AFIX  23**
**H10A  2    0.095393    1.108073    0.356020    ****10.33333   **** 0.03019**
**H10B  2    0.185537    1.108980    0.252859    ****10.33333****    0.07844**
**AFIX   0**
**C11S  1    0.034726    1.252421    0.270929    ****10.33333****    0.02477**
**O3S   4   -0.087391    1.287204    0.233376    ****10.33333****    0.03143**
**O4S   4    0.147522    1.327757    0.305089    ****10.33333   **** 0.03101**
**AFIX   3**
**H4S   2    0.123082    1.402847    0.301909    ****10.33333****    0.66676**
**PART   0**

- Bruker AXS

## Example 6 – Urea Host : Guest Complex

- Anisotropic refinement of dicarboxylic acid

- Bruker AXS

## Example 6 – Urea Host : Guest Complex

**Final refinement**
- R1 = 3.83%
- Temperature factors on hydrogen atoms refined

- Bruker AXS

## Example 7 – An organic compound exhibiting two types of enantiomeric disorder

**Example 7 – An organic compound exhibiting two types of enantiomeric disorder**

- 4,8a-dimethyl-2-phenyl-4a,5,6,7,8,8a-hexahydro-4*H*-benzo[d] [1,3]oxazine
- C16H21NO
- Hemant Yennawar et al. (Pennsylvania State U.)

- Bruker AXS

## 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)****°**

- Bruker AXS

## 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**

- Bruker AXS

## Example 7 – An organic compound exhibiting two types of enantiomeric disorder

**Initial Structure – Molecule A**

**50% Thermal Ellipsoids**

- Bruker AXS

## Example 7 – An organic compound exhibiting two types of enantiomeric disorder

**Initial Structure – Molecule B**

**50% Thermal Ellipsoids**

- Bruker AXS

## Example 7 – An organic compound exhibiting two types of enantiomeric disorder

**Initial Structure – Molecule C**

**50% Thermal Ellipsoids**

- Bruker AXS

## Example 7 – An organic compound exhibiting two types of enantiomeric disorder

**Initial Structure – Molecule E**

**50% Thermal Ellipsoids**

- Bruker AXS

## Example 7 – An organic compound exhibiting two types of enantiomeric disorder

**Disorder - Molecules C & D**

- Bruker AXS

## Example 7 – An organic compound exhibiting two types of enantiomeric disorder

**Disorder - Molecules E & F**

**Disorder - Molecules E & F**

- Bruker AXS

## 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

- Bruker AXS

## Example 7 – An organic compound exhibiting two types of enantiomeric disorder

**Final Structure – Molecule C**

**50% Thermal Ellipsoids**

- Bruker AXS

## Example 7 – An organic compound exhibiting two types of enantiomeric disorder

**Final Structure – Molecule D**

**50% Thermal Ellipsoids**

- Bruker AXS

## Example 7 – An organic compound exhibiting two types of enantiomeric disorder

**Final Structure – Molecule E**

**50% Thermal Ellipsoids**

- Bruker AXS

## Example 7 – An organic compound exhibiting two types of enantiomeric disorder

**Final Structure – Molecule F**

**50% Thermal Ellipsoids**

- Bruker AXS

## Example 8 – A Commensurately Modulated Carborane Compound 

**Compound prepared by D.E. Hyatt – Lee Todd’s 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).**

**(CH****3****)****3****N-CB****10****H****12**

- Bruker AXS

## Example 8 – A Commensurately Modulated Carborane Compound 

**Empirical formula****	****	****C****4****H****21****B****10****N**
**Chemical formula****	****	****(CH****3****)****3****N-CB****10****H****12**
**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**

- Bruker AXS

## 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**** **

- Bruker AXS

## Example 8 – A Commensurately Modulated Carborane CompoundReciprocal Lattice Viewer

**Very strong main reflections (white color) **
**Weak satellite reflections in between (green color)**
**h =     *****0   1   2   3   4   5   6   7******	***

- Bruker AXS

## 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) Å****3**
**Z****	****	****	****	****	****	****4**
**F(000)****	****	****	****	****	****408**
**Q-vector****	****	****	****	****	****0, 0, 3/7 (0.0000, 0.0000, 0.42857)**

- Bruker AXS

## 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 > 2sigma(I)****	****	****1965**

- Bruker AXS

## 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 14:25:34 carborane
- SITEID Administrator                       ?
- TITLE  Integration
- CHEM   (Ch3)3N-CB10H12
- CELL     16.1418   10.5087    6.9644   90.0000   90.0000   90.0000   1181.365
- CELLSD    0.0011    0.0007    0.0005    0.0000    0.0000    0.0000     0.131
- ORT1    -9.6469503e-003  6.6842519e-002 -9.9723525e-002
- ORT2    -5.8215410e-002  1.0598534e-002  4.6428315e-002
- ORT3     1.8862667e-002  6.6895336e-002  9.2288941e-002
- ZEROS   0.0000000 -0.0264180  0.0316215   -0.5332   -0.8447   -0.9388
- QVEC     0.00000   0.00000   0.43194
- SOURCE MO     0.71073   0.70930   0.71359   2.00000    0.00    0.00
- LIMITS    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
- MORPH  Prism
- DNSMET ?
- CCOLOR clear

- Bruker AXS

## 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):
**VOLTARGET=1.00000**
**BGQSCALE=6**
**MAXSATIND=2**
**IBATNO=1**
**ESD_SCALE=1.00000**
**PARNAME=C:\Frames\guest\carborane\work\carborane_0m.p4p**

- Bruker AXS

## 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

- Bruker AXS

## 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

- Bruker AXS

## 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.**

- Bruker AXS

## 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 4:3 (PART –1, PART –2)
- R1 = 7.9%

- Bruker AXS

## Example 8 – A Commensurately Modulated Carborane Compound- Supercell Structure

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## 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

- Bruker AXS

## 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**

- Bruker AXS

## 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
- 	Solution – XM or XS
- 	Refinement – XL (BASF + TWIN)
**Modulated Structures**
- 	Diagnosis – SMART, APEX2, RLATT
- 	Processing – SAINT (w/ QVEC inst.), SADABS
- 	Solution – XM or XS
- 	Refinement – JANA 2000(Petricek & Dusek)

- Bruker AXS

- www.bruker-axs.com

- Bruker AXS