EXPO2014

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 EXPO2014

Table of contents

General Information ........................................................................................... 3

EXPO2014 installation .................................................................................... 4
Tutorials ....................................................................................................... 8
Preparing input file ....................................................................................... 15
Indexing by EXPO2014 ..................................................................................... 17
Space group determination ................................................................................ 28
Structure solution by Direct Methods .................................................................. 32
All steps of structure solution procedure ......................................................... 42
Extraction of the integrated intensities ........................................................ 42
Normalization of the integrated intensities ................................................... 49
Estimate of structure invariants .................................................................. 50
Application of the tangent formula ............................................................. 53
Crystal structure completion and refinement ................................................ 57
Structure solution by Direct Space methods ......................................................... 64
Direct Methods combined with Simulated Annealing ............................................. 77
Rietveld Refinement .......................................................................................... 81
Commands of EXPO2014 and their use ............................................................... 86
Description of EXPO2014 commands .............................................................. 89
Preparation of data ....................................................................................... 93
Examples ........................................................................................................ 98
Crystal Structure Visualization .......................................................................... 108
How to ...................................................................................................... 109
File ........................................................................................................... 109
Modify ....................................................................................................... 112
Select ........................................................................................................ 113
View ......................................................................................................... 113
Tools ........................................................................................................ 116
Info .......................................................................................................... 121

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 EXPO2014

General Information

EXPO2014
The program EXPO2014 is the evolution of EXPO2009. EXPO2014 performs all
the steps of the ab-initio structure solution by powder data: indexing, space group
determination, estimation of the reflection integrated intensities, structure solution by
Direct/Patterson methods or/and by direct space/hybrid approaches, model refinement by
Rietveld technique.
The program has been designed to:
· require a minimal information as input

· work automatically

· reduce the user intervention and facilitate the interaction by means of a user-friendly
graphic interface.

Program specification

X-ray, synchrotron or neutron diffraction data can be used. There are no limits on the
number of counts in the pattern. The maximum number of reflections is 3000.

The background of system

EXPO2014, the updated version of EXPO2009 is able to solve crystal structures

from unindexed powder diffraction pattern. Its main steps are (select the topic for more
details):
Indexing
An automatic peak search routine generates a list of "d" values corresponding to
the experimental peaks. The values are processed for providing the cell parameters.
Space Group Determination
A statistical analysis is performed by using the experimental diffraction intensities
compatible with the identified crystal system. The procedure is able to provide a list of all
the possible extinction symbols ranked according to their probability value. For each of
them, the corresponding list of compatible space groups is supplied via graphic interface.
Structure Solution
Structure solution can be carried out by the two alternative following methods:

· Direct Methods for phasing the reflections. The electron density map is calculated and
then optimized.

· Direct Space Methods for generating trial structure models (compatible with the
expected molecular geometry) and selecting that one providing the best agreement
with the experimental data.

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Rietveld Refinement
The structure model is refined by Rietveld method.
Files generated by EXPO2014
EXPO2014 creates the following files (in the work directory):
- a direct access file to preserve data and results (name.bin);
- an ascii file containing the Miller indices (hkl) and integrated intensities of the generated
reflections (name.hkl);
- an ascii file to store peak positions if the indexing process has been carried out
(name.pea);
- output file containing information about all the steps of structure determination (name.out).
Authors

A. Altomare(*),C. Cuocci(*), C. Giacovazzo(*), A. Moliterni(*), R. Rizzi(*).

(*)
Institute of Crystallography CNR, (Bari) - Italy
Support
sirmail@ic.cnr.it
http://www.ba.ic.cnr.it/contact
Acknowledgements
The authors are indebted to Giovanni Luca Cascarano and Mariarosaria Mallamo for their
help in the development of the graphic environment.
Main References

If EXPO2014 is used in a publication please include in your citations the reference to

following work:
A. Altomare, C. Cuocci, C. Giacovazzo, A. Moliterni, R. Rizzi, N. Corriero and A.
Falcicchio, "EXPO2013: a kit of tools for phasing crystal structures from powder data", J.
Appl. Cryst. (2013). 46, 1231-1235

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EXPO2014 installation

Hardware and software environment

EXPO2014 is built utilizing OpenGL for three-dimensional molecular visualization and the
GTK for the graphic user interface. All binary packages are pre-compiled by using the Intel

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Fortran Composer XE 2013 and the GNU C++ compiler. Expo2014 runs on the most
popular operating systems: Windows, Apple's Mac OS and some Linux distributions.
On Windows platforms
Both 32- and 64-bit versions of EXPO2014 are available for Windows. They were tested
on Windows 7, Vista, and XP.
To get the 32-bit or 64-bit version of EXPO2014 for Windows, download the file expo-
020513_install.exe or expo-020513-x64_install.exe from
http://www.ba.ic.cnr.it/content/expo2013
Note that the 32-bit version of EXPO2014 can also be used on 64-bit Windows. To install
the software, double click on the downloaded file and follow the instructions.
The program can be launched by double click on the icon of EXPO2014

Mac OS X

The Mac OS X version of EXPO2014 runs on Mac OS X 10.5 (Leopard), Mac OS X

(Snow Leopard), Mac OS X 10.7 (Lion), OS X 10.8 (Mountain Lion) . The program was not
tested on on Mac OS X 10.4 (Tiger) or older.

The Mac OS X version is contained in a file .dmg with a disc image format.

1. Download the file .dmg from

http://www.ba.ic.cnr.it/content/expo2013
2. Double-click the .dmg file to mount it. A new Finder window containing the EXPO2014's
icon should appear.
3. Open a new Finder window and then drag the program EXPO2014 over the
"Applications" in the left side of window.

To do cleaning:
· Close any Finder Windows
· Eject the disk image (not the .dmg file).
· Delete the .dmg file by dragging it to the trash.

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In order to add EXPO2014 to the dock, follow these steps:

· Open up a new Finder window
· Click on "Applications".
· Locate the EXPO2014's icon.
· Drag the icon to your Dock, and drop it wherever you like.

EXPO2014 can be launched by Double click on the icon of EXPO2014.

On Linux platforms
Installing from binary package
Debian and Red Hat RPM packages are available via the download page.
· Install the .deb package typing from the terminal
sudo dpkg -i expo_1.13.05_ubuntu12.10_amd64.deb

· To install RPM package, enter the command:

rpm -i expo-1.13.05.fc18.x86_64.rpm

EXPO2014 can be launched by

1. Double click the icon of the EXPO2014 icon

2. Type the expo command. Read the section command line usage for more details.

Compiling from source

· Install build tools

Most Linux distributions come with the core set of development tools already installed
but if not, you will need to install the following packages via the appropriate package
manager.

Autoconf Program which writes configure scripts

automake Program which writes Makefiles
libtool Generic library support script
g++ C++ compiler from the GNU compiler collection
Fortran compiler compliant with Fortran 95 standard: EXPO has been written and
tested using the Intel Fortran Compilers (IFORT) but if the IFORT is not available, GNU
Fortran (Gfortran) could be also used.

· Install graphic development packages

Expo requires development files for gtk+ library, Mesa OpenGL utility library. The name
of the libraries could be slightly different depending on your GNU/Linux distribution. The
names of the packages is reported for some tested distribution.
o Debian distributions: libgtk2.0-dev, libgl1-mesa-dev, libglu1-
mesa-dev, libcurl4-gnutls-dev
o RedHat distributions: gtk2-devel-....., mesa-libGL-devel-
....., mesa-libGLU-devel-....., libcurl-devel-....
o Mandriva: libgtk+2.0-devel, libmesagl1-devel, libmesaglu1-
devel,libcurl-devel

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o Suse: gtk2-devel, mesa-devel, libcurl-devel

· Download the file expo_1.13.05.tar.gz

Install "expo" using the following commands

tar xvfz expo_1.13.05.tar.gz

cd expo_1.13.05
sh ./autogen.sh
./configure --prefix=destination_directory --
srcdir=expo_source_directory
make clean
make install

Executable files will be stored in

destination_directory/bin
Be sure that the destination_directory/bin is in the PATH
For more information read the file INSTALL in the expo directory.

Command line usage

When typing the expo command, you can supply different types of input file

Type the following command in a command line:

expo merca.exp merca.out
This command will start EXPO2014 running the expo input file merca.exp and
generating the output file merca.out.
The output file may be omitted:
expo merca.exp
or simply
expo
In addition, EXPO2014 can read crystal structures from different types of file (e.g.
*.cif) . You can supply the name of the crystal structure file on the command line, and
EXPO2014 will open the file when it starts, e.g.
expo paracetamol_best1.cif
You can also type the name of a powder diffraxtion data file (e.g. *.xy, *.dat)
expo merca.xy
Use the option -help to displays a brief help message, showing the main command-line
options
expo -help

On a Windows PC to run EXPO2014 simply typing expo, the environmental variable PATH
must be set to include absolute path of the directory where EXPO2014 is placed.

On Linux, if the program has been installed from source files (file expo_1.13.05.tar.gz)
create a symbolic link with 'ln -s' of EXPO2014 in a directory where environment variable
path is set, or declare the path with the shell command `export

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PATH=destination_directory/bin:$PATH`, destination_directory is the

directory where EXPO2014 was installed.

Running examples
Test structures can be found in the folder examples. On Windows platform this folder is
typically located in C:\Users\username\share\expo\examples and on linux
operating system in /home/username/share/examples. To run the program select
the test structures by means of the menu File > Load Examples

Click on on the toolbar to perform the steps of structure solution.

Three test structures are supplied and described in the section Tutorials.

Contact

If you are having trouble during the installation contact corrado.cuocci@ic.cnr.it

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Tutorials
Tutorial 1 - Crystal structure determination of Cimetidine compound

The first tutorial is supplied for carrying out the full pathway of the ab-initio structure solution
process (from indexing up to the structure solution) in case of cimetidine.

The only required information by EXPO2014 is the diffraction data and the chemical
formula (C10H16N6S).
The examples directory contains the necessary files:
· cime.exp: input file for EXPO2014
· cime.dat: a synchrotron X-ray diffraction data file containing the initial 2-theta, the 2-
theta step and the final 2-theta values (in the first line) and the experimental counts (in
the rest of lines).

To access to examples directory:

· Open EXPO2014 by double clicking on Expo2014 icon.
· Click on File > Load Examples

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and select the file cime.exp.

The content of file cime.exp is here reported

%structure cime
%job cimetidine (C10H16N6S) -- Synchrotron data
%data
pattern cime.pow
wavelength 1.52904
synchrotron
%ntreor
%continue

It contains the minimal required information (name of data file, wavelength and type of
radiation used to collect the data if different from X-rays) and commands for the ab-initio
structure solution. This file can be visualized and eventually modified by the 'Edit' button.

More information about the creation of input file can be found in the section Preparing input
file.
Clicking on OK the powder diffraction data will be displayed.

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Selecting Next, an automatic peak search procedure will be applied and the d-values
corresponding to the selected experimental peaks will be automatically supplied to the
indexing procedure. At the end of this process EXPO2014 will provide the indexing results
by graphic interface:

Click on OK to accept the selected plausible cell parameters and to move to the next step:
the space group determination.

The space group determination step, as well as Direct Methods, requires the unit cell
content information. It can be easily derived by taking into account the structure formula and
the cell volume (Vcell) provided by the window above or by the output file of EXPO2014.
The cell content is given by Z multiplied by the structure formula. You can calculate Z as the
ratio between Vcell and the molecular volume (Vmol): Z = Vcell/Vmol.
Vmol can be calculated by one of the two following alternative ways:
1. Using the 18 Å3 rule: counting all the non-hydrogen atoms in the chemical formula and

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multiplying this number by 18 Å3;

2. Using the following approximate atomic volumes: 14 Å3 for C, 12 Å3 for N, 11 Å3 for O,
5 Å3 for H, 26 Å3 for Cl, 25 Å3 for S.
In case of cimetidine compound, the chemical formula is C10H16N6S4 and the cell volume is
1280 Å3. If the fist criterion is applied, the molecular volume is given by: Vmol = 20 x 18 =
360 Å3.
The corresponding Z value is: Z = Vcell/Vmol = 1280/360 = 3.55, that can be approximated
to 4. So 4 molecules of cimetidine are in the unit cell and the unit cell content to be supplied
to EXPO2014 by graphic interface is(C10H16N6S)4 or C40H64N24S4

Click on OK in order to perform the space group determination and then on Next button to
go on continuously. At the end of the procedure a list of the Extinction Groups, compatible
with the lattice symmetry and ranked according to a probability value, is given:

the most plausibile Extinction Group P 1 21/a 1 is automatically selected and by clicking
on OK the space group P 21/a, corresponding to this extinction group, will be chosen.

After the determination of the space group, EXPO2014 starts with the extraction step
which is carried out in the selected space group. Click on Next button continuously. At the
end of the process a list of integrated intensity values, extracted from the experimental
powder pattern, is obtained and automatically supplied to Direct Methods for structure
solution.
The final result will be visualized on JAV Molecular Viewer.

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Some errors in the assignment of carbon or nitrogen atomic species can be easily
recognized and corrected by using the option 'Modify' from JAV menu.

Tutorial 2 - Crystal structure solution of 2-Mercaptobenzoic acid compound

The aim of this example is to guide the user in case of failure of a default run of
EXPO2014.

Open EXPO2014 by double click on Expo2014 icon.

Click on File > Load Examples
Select the input file 'merca.exp'.

%Structure merca
%Job 2-Mercaptobenzoic acid
%Data
Cell 7.885 5.976 14.949 90.0 100.48 90
SpaceGroup p 21/c
Content C 28 O 8 S 4 H 24
Pattern merca.xy
Wavelength 1.54056
%continue

In this example it is assumed that the cell and space group have been already determined

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and the unit cell content corresponds to 4 molecule of C7H6O2S.

Click on Next button to go on continuously.

The final structure model provided by EXPO2014 could not correspond to the correct
crystal structure of 2-Mercaptobenzoic acid. This can occur when the most plausible set of
phases, provided by Direct Methods, is unreliable.
In a default run of EXPO2014, Direct Methods generate several phasing trials; 20 of them
are stored and ranked according to decreasing values of a suitable combined figure of
merit (CFOM). The largest CFOM set of phases is automatically selected for structure
solution. In case of failure, all the rest of stored phasing trials should be explored in order to
find the solution.
This can be automatically performed by graphic interface:
a) Selecting from the top-level menu Solve and then Explore Trials
b) Clicking on the Select all new trials button

c) Clicking on GO

At the end of the procedure, EXPO2014 will rank the phasing trials (and the corresponding
structure models) according to the increasing RF agreement factor values.

The best solution (corresponding to the lowest RF value) will be selected and displayed.

More information about the strategies to apply when Direct Methods fail are described in
the next section of this manual.

Tutorial 3 - Crystal structure solution of paracetamol compound by direct space

methods

The purpose of this tutorial is to guide the user through the crystal structure solution by
direct space methods of paracetamol (form I polymorph) compound.

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Open EXPO2014, select Load Examples and load the input file 'paracetamol.exp'.
Clicking on Next button, the file paracetamol.mol, containing a 3D molecular description of
paracetamol, will be loaded and displayed and the following window will appear:

Select Execute; the Simulated Annealing procedure will be applied performing 10 runs
whose corresponding final structure models can be explored by the button Solutions

References
Cimetidine - Cernik, R.J., Cheetham, A.K., Prout, C.K., Watkin, D.J., Wilkinson, A.P.,
Willis, B.T.M. (1991). J. Appl. Cryst. 24, 222-226.

2-Mercaptobenzoic acid - Florence, A. J., Shankland, N., Shankland, K., David, W. I. F,

Pidcock, E., Xu, X., Johnston, A., Kennedy, A. R., Cox, P. J., Evans, J. S. O., Steele, G.,
Cosgrove, S. D. & Frampton, C. S. (2005). J. Appl. Cryst. 38, 249-259.

Paracetamol (form I polymorph) - Florence, A. J., Shankland, N., Shankland, K., David,
W. I. F, Pidcock, E., Xu, X., Johnston, A., Kennedy, A. R., Cox, P. J., Evans, J. S. O.,
Steele, G., Cosgrove, S. D. & Frampton, C. S. (2005). J. Appl. Cryst. 38, 249-259.

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Preparing input file

Preparing input file in EXPO2014

To run EXPO2014 you need of an input file (*.exp). Two possibilities are available:
1) to create a new input file; 2) to use an already existing input file.
Possibility n.1): creation of an input file by selecting, via graphic interface, the creation of a
new project by the menu "File">"New".

The required information are here listed.

1. You must specify the structure name. This name will be used to create the name of
output file.
2. Load the profile counts file. The following powder diffraction data file can be imported:
ASCII XY files (*.xy), CIF powder files (*.rtv, *.cif), GSAS files (*.qda), CCDC Mercury

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xye (*.xye). Use the extension *.pow to indicate an ASCII xy file or an ASCII file with
2theta min, 2theta step, 2theta max in the first row and counts in free format in the
subsequent lines.
3. Select the 'Range' button if you want to change the 2theta min and/or the 2theta max.
4. Input the wavelength and the type of radiation source (X rays source is the default
choice).
5. To carry out the space group determination it is necessary to activate the check button
'Find Space Group'.
6. For indexing, it is necessary to click on button 'Cell Determination by N-TREOR'.
7. You must provide the content of unit cell. This information is important for the space
group determination and for the structure solution by Direct Methods. A valid molecular
formula for the cell content must meet the following criteria:
o Elements are represented by valid atomic symbols (IUPAC-nomenclature) each
optionally followed by a number.
o It is possible to write the formula in lower-case or upper-case but please note
that 'Sb' will be interpreted as one antimony but 'SB' will be one antimony and
one boron. Spaces are also permitted (eg. 'S B', one antimony and one boron).
We suggest to write the two-letter elements with the second letter in lower-case.
o Valid operators are: ( ) [ ] { }
Examples of valid formula: [C3H5(OH)3]4, C 28 O 8 S 4 h 24
If your formula doesn't follow the required criteria, the input string will appear written in
red.

When you press the button 'Save' (9) an EXPO input file (*.exp) will be created in the same
folder of powder data file and automatically loaded by the program for the indexing. The
button 'Open' (10) is used to open (and possibly modify with a text editor) an already
existing input file.
An already existing *.exp input file can be loaded from menu 'File' > 'Load & Go'.

Format of diffraction data

EXPO2014 recognizes some formats of diffraction data that should be ASCII text files:
1. Files with extension .xy or .xye containing 2theta in the first column and the
intensities in the second one. The format of counts can vary. # could be used for comment

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line.

#This is a comment
4.700 4769.000
4.714 4860.000
4.729 4794.000
4.743 4857.000
4.758 4837.000
4.772 4891.000
4.787 4788.000
4.801 4886.000
4.816 4720.000

Additional column after the second will be ignored. Optionally, the wavelength can be
included in the file as the first line.

2. Files type with extension .dat containing 2theta minimum, 2theta step, 2theta
maximum in the first line. Counts are in the successive lines separated by blanks. The
number of counts for line and the format of counts can vary.

# example 1 for ascii file with start,step,end,intensity

6 0.020 90.0
149. 161. 151. 136. 144. 151. 150. 149. 117. 138.
157. 120. 143. 156. 110. 142. 147. 147. 124. 128.
130. 144. 134. 159. 145. 150. 138. 149. 134. 159.
142. 139. 135. 136. 147. 139. 155. 133. 140. 133.
134. 158. 165. 134. 156. 139. 122. 141. 158. 132.
150. 138. 134. 149. 147. 150. 154. 165. 145. 140.
.................................................

3. Additional readable ASCII file formats are: GSAS ( *.gda ), CIF ( *.rtv, *.cif )

If the file has the extension .pow or the extension is unknown, the program tries to read
according to the format of .xy or .dat file

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Indexing by EXPO2014

Indexing by EXPO2014
In powder diffraction the first necessary step for solving crystal structure is the indexing, i.e.
finding the unit cell parameters and reconstructing the three dimensional lattice from the
one-dimensional information of the powder diffraction pattern. The indexing is performed
by EXPO2014 via the program N-TREOR09 (Altomare et al., 2009), the evolution of the N-
TREOR software (Altomare et al., 2000). In addition EXPO2014 provides a graphical
interface for two popular and freely available indexing program: DICVOL (Boultif & Louër,
2004), McMaille (Le Bail, 2004).

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Starting indexing by EXPO2014

Selecting Peaks for Indexing
Running Indexing in EXPO2014
Indexing from Expo Input File (.exp)
Indexing Using the Command Line
Output of indexing
The indexing directives
Contact and References
Starting indexing by EXPO2014

The simplest method to perform indexing by EXPO2014 is input a powder diffraction data
file by the menu File > Import Diffraction Pattern. Select the appropriate radiation type
and the used radiation wavelength.

In section format of diffraction data the possible formats of the powder diffraction data file
required by EXPO2014 are described. As example you can input the diffraction data
merca.xy which is located in the directory examples and supply wavelength value
1.54056 Å.

Then select the indexing program from Pattern > Indexing. If you choose N-TREOR09 the
dialogue box shown in the following figure opens.

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The user can modify the default values of the maximum cell volume, the maximum cell axial
lengths, the maximum number of allowed impurity lines, the minimum de Wolff figure of
merit (M20). If known you can enter the measured density with the corresponding error.
Molecular weight is not used unless density is not zero.

If you tick DICVOL06 in the frame 'Indexing Programs' you can also activate the interface
for indexing by DICVOL06. In this case EXPO2014 creates a DICVOL06 input file and
automatically will run the program. On Windows operating system the executable file
dicvol06.exe is tipically located in the folder C:\Program Files\Expo2014\bin
and corresponds to the program freely available at http://www.ccp14.ac.uk/ccp/web-
mirrors/dicvol/ . On Linux OS dicvol06.exe is located in expo_install_dir\bin
where expo_install_dir denotes the directory where you have installed the package.
Under Linux OS, the Windows Emulator Wine is required to run DICVOL06. Wine is
available in the software center of the most common linux distributions. You should read
general explanation and suggestions about indexing in the DICVOL06 documentation
available at http://cds.dl.ac.uk/cds/peakquest/dicvol06.html.

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EXPO2014 also provides interface to McMaille version 4.00 (http://www.cristal.org/

McMaille/McMaille-v4.html).

Clicking on Pattern > Indexing > and selecting the indexing program EXPO2014
automatically performs a peak search if peaks have not been already detected. If you think
that the automatically located peaks are correct click on button Run. On the contrary, if you
need to improve the selection of peaks press 'Cancel' and read carefully the next section.

Selecting Peaks for Indexing

Accurate and reliable peak search is a fundamental stage for a correct powder pattern
indexing. EXPO2014 uses the second derivative method in peak recognition. This method
is actually a combination of background subtraction and smoothing, followed by the
calculation of derivatives. The automatic peak search is extremely sensitive to noise and
may suffer from some defects due in particular to the misinterpretation of background that
makes inefficient the algorithm. Moreover, the algorithm usually discards broad peaks at
higher angle and in strong overlap.
In order to check the reliability of the automatic peak search results, use the buttons
to explore the pattern. If the automatic peak search outcome
is not reliable, you can modify the peak search conditions in different ways:
1.By changing the curve describing the background. This is possible adding or removing
background points by clicking on the button and using left mouse click to add points
and right mouse click to delete points. Background function can be also modified by the
button of the 'Pattern' option. When background is changed, the
peak positions are automatically updated.

2.By choosing the tool bar button to add peaks by left click of mouse and remove

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peaks by right click.

3.By the menu Pattern > Modify Peaks > Peak Search Conditions. The button 'Peak
search conditions' opens a window that enables to modify the main search conditions. All
peaks with percentage intensity larger than or equal to '% Int. Threshlod' will be selected.

4.Use the button Pattern > Peak List to access to a list of values associated to each
peak: 2q, d, peak intensity calculated removing the contribution of background, full width at
half maximum (FWHM). This window can be used to edit the 2q or d values and to delete
peaks. If you click on a row in the list, the corresponding peaks will be marked with tick on
the pattern.
5.Use Pattern > Modify Peaks > Load Peaks / Save peaks to load or save peaks as
2theta or d values.

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During the peak search remember that the number of peaks must be not too large; and the
indexing problem can be generally solved with the 25 first peaks (even very weak peaks
included). Peaks at low angle not clearly resolved and with an appreciable peak width
should be not included to avoid large errors in peak position.
In case of failure try to improve the indexing by different attempts, gradually eliminating
suspicious Bragg peaks (e.g., the weakest peaks or peaks on a shoulder) and check if it
results in a better indexing solution. The failure could be due to the presence of impurity
peaks and/or to the absence of one or more useful peaks. Sometimes could be very useful
to reduce the intensity threshold when weaker peaks are missed. On the other hand if you
suspect the presence of an impurity and if the impurity phase is a minority phase in the
specimen, it can be useful to reduce the selection to the most intense peaks, e.g. 16-20
peaks may be sufficient. Indexing program as N-TREOR09 and DICVOL06 are able to
successfully index even if some peaks are omitted but they can fail if a lot of dubious peaks
are included.

Submit the selected peaks to a indexing program by click on Run in the window 'Indexing
Settings', accessible by Pattern > Indexing

Running Indexing in EXPO2014

The next step is the automatic refinement of peak positions and profile parameters (a
Pearson VII function is used). At the end of the peak search a file named
structure_name.pea, containing the refined d values associated to the selected
peaks, is automatically created by the program. This file can be used in the future to skip
the peak search procedure (see the directive extefile) if a new indexing process is
performed. Additional input and output files can be found in the working directory:
structure_name.new, condens.out and ntreor.out in case of N-TREOR09;
dicvol_inp, dicvol_out in case of DICVOL06; mcmaille.dat,
mcmaille.imp, mcmaille.mcm in case of McMaille.
At the end of the indexing procedure you can see a list containing, for each solution, the
program used for indexing (N for N-TREOR09, D for DICVOL06, M for McMaille) the cell
parameters and the cell volume, the classical figure of merit M20 (de Wolff, 1968), the
applied zero-shift, the number of unindexed lines, the crystal system. In addition, the figure
of merit FOMnew (Altomare et al., 2009) and the most probable extinction symbol are
available when N-TREOR09 is used. McM20 is displayed in case of indexing performed by
McMaille.

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Sometimes more plausible cells are suggested, they are ranked according to a figure of
merit for each indexing program. When the quality of data is not good, uncertainty in the
indexing procedure is usually manifested by the generation of more than one solution. If
several unit cells are possible, the different solutions should be carefully examined, in
particular if their figures of merit are not encouraging. Clicking on each suggested cell of
the list, the tick marks at the bottom of the experimental pattern indicating the calculated
positions of the Bragg reflections, will be displayed. The tick marks must correspond to
peaks in the pattern. When no experimental peaks are associated to the tick mark, the
corresponding reflection is probably systematically absent. On the other side, if a
diffraction peak in the pattern is not associated to any tick, the peak can be referred to an
impurity phase or the determined cell might be wrong.

The quality and the reliability of indexing, therefore, is routinely characterized by means of
various numerical figures of merit. The figures of merit reported by EXPO2014 are M20,
FOMnew only for N-TREOR09 and McM20 only for McMaille. Consult the output file of the
specific program (Pattern > Indexing > Output) to additional figures of merit (e.g. F20) for
each solution. The more reliable indexing should yield the higher value of figure of merit. In
case of M20, the rule suggested by de Wolff is the following one: if M20 > 10 and the
number of unindexed lines, among the first twenty ones, is not larger than 2 the indexing
process is reliable and substantially correct; exceptions to this rule can be possible. In
case of high quality data (e.g., synchrotron data) the M20 of the correct cell is usually much
larger than 10; in case of laboratory data the correct solution can be characterized by M20
value not so larger than 10.
The correct solution is usually characterize by a high figure of merit and all diffraction peaks
(or most of them) should be indexed.

If a program fails in indexing a powder pattern, it is possible that another program can
succeed. Similar results obtained by different programs strengthen the confidence in the
correctness of the cell. Because N-TREOR09 and DICVOL06 run usually much faster than
McMaille, it is better to apply them first.

N-TREOR09 includes some features in the default strategy: an automatic correction of the
2theta zero-shift is made; it may successfully index powder diffraction patterns containing a
few impurity peaks; starting the search in the cubic system, if an acceptable solution is not
found the program explores all the rest of crystal systems up to triclinic and stops as soon
as a plausible solution has been found and therefore, indexing in the lower symmetry unit
cells will not be performed.
In case of DICVOL06 and McMaille these features are not included in the default strategy
and should be enabled by user in the graphical interface when a preliminary indexing fails.
The search of triclinic cell can take long time depending on the indexing program.

Once the cell parameters calculation step has been carried out, you may perform the
space group determination step by selecting the cell parameters and by clicking on the OK
button. The following dialog window will appear.

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Before clicking OK, in this window you must specify the unit cell content. In the case of the
2-Mercaptobenzoic acid structure the cell volume suggests that the cell can accommodate
4 molecules of C7H6O2S (Z=4) and the cell content may be written as (C7H6O2S)4. For
cimetidine compound the cell content is (C10H16N6S)4
During the editing of the cell content, the program calculates and displays a rough estimate
of the
1. Content Volume: an approximate value of the cell volume calculated as summation of
the average atomic volumes associated to the supplied atoms. Its value is expected to be
close the cell volume calculated directly by cell dimensions and reported in the window
below the cell parameters.
2. Volume per Atom: ratio between the cell volume and number of non-hydrogen atoms. Its
value is expected to be close to 18 Å3 ( 18 Å3 rule) but sensible deviation from this ideal
value can be observed due to the presence of H-bonding or large void space (e.g. zeolites)
in the crystal structure. A reasonable range is 15-22 Å3.
3. Density: is the density calculated by the mass of supplied atoms and the cell volume (g/
cm3). Keep in mind that the density of molecular compound is relatively low and lying to the
range 0.9-2.0 g/cm3.

If more cells are available at the end of indexing they are saved and always accessible
from Pattern> Indexing> Cell List

Indexing from Expo Input File (.exp)

An alternative way to perform indexing by EXPO2014 is to edit a new input file or modify
an existing input file with a text editor and save it with the extension .exp.

An example of input file for indexing of powder pattern of cimetidine is available in the
directory examples (file cime.exp). Its content is the following one:
%structure cime
%job cimetidine (C10H16N6S) -- Synchrotron data
%initialize
%data
pattern cime.dat
wavelength 1.52904
synchrotron
%ntreor
%continue
The command that has to be introduced in the input file for carrying out the indexing

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process by N-TREOR09 is %ntreor. It must be added after command %data. Add %

continue if you want to continue the crystal structure determination process. You can
read the description of the rest of instructions of the input file by looking at the section
commands of EXPO2014 and their use of this manual.
Add the command %dicvol or %mcmaille to activate the indexing by the program
DICVOL06 and McMaille, respectively.
%structure cime
%job cimetidine (C10H16N6S) -- Synchrotron data
%initialize
%data
pattern cime.dat
wavelength 1.52904
synchrotron
%ntreor
%dicvol
%mcmaille
%continue

Once the input file has been created, load the .exp input file from the menu File > Load &
Go.

Use the button in the toolbar to carry out the steps of the indexing procedure.

Indexing Using the Command Line

To execute the indexing procedure from command line, type the name of powder diffraction
data file and add the option -index=indexing program. You can specify the
program(s) to use for indexing with n for N-TREOR09, d for DICVOL06 and m for McMaille
after the argument -index=.
expo merca.xy -index=ndm
the indexing of powder data merca.xy will be performed by using N-TREOR09 (n),
DICVOL06 (d), McMaille (m).
Add -wavel=wavelength to define the wavelength of radiation source. If -wavel is
omitted the default wavelength of Cu K-alpha 1 ( 1.54056 Å) is used.

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expo cime.dat -index=nd -wavel=1.52904

You can also add the option -auto to suppress the interaction with graphical interface and
run the program in automatic mode, -nogui to run the program N-TREOR09 without
graphical interface.
expo cime.dat -index=n -wavel=1.52904 -nogui

Output of indexing

The output file contains details about indexing. Use Info > View output file to
access to the output file or open the file structure_name.out with a text editor or click
on the button from the main menu.

Additional output files are created by the specific indexing programs and are accessible
through the menu Pattern > Indexing > Output

The indexing directives

Directives in data command

The following directives must be added after the command %data in the input file
to activate some specific features useful for the indexing procedure
extefile file_name
This directive is used to supply an external file containing 'd' or '2theta' values of peak
positions. In the latter case the additional 2-theta directive has to be used. An example
of the use of this directive for the indexing of the pattern of structure cime:
%structure cime
%job structure cime
%init
%data

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pattern cime.dat
synchr
wave 1.52904
extefile cime.pea
%ntreor
%continue
cime.pea is an ASCII file containing the observed 'd' values associated to the selected
peaks. In this case peak search and peak refinement will be skipped. When the directive
extefile is omitted the program saves the d values associated to the peaks in a file
with extension .pea before carrying out the indexing process.
2-theta
This directive is used combined with the extefile directive to supply to the indexing
program N-TREOR09 an external file containing 2theta values of the peak positions.
search 2theta-min 2theta-max peak_number threshold
This directive is used to specify the conditions of peak search. The user has to indicate
four parameters: the search range of the peaks in 2theta (2theta-min and 2theta-
max), the number of peaks (peak_number), the intensity threshold (threshold).
Negative or zero values are ignored, it is not necessary to specify all values.
E.g.
To search the 25 most intense peaks in the range 5-80 add the following line after %data
command:
search 5 80 25

To search the 20 most intense peaks:

search 0 0 20

To apply a threshold of 2.5

search 0 0 0 2.5
Directives in ntreor command
The N-TREOR09 directives must be added after the command %ntreor in the
input file to enable some specific features of the indexing procedure
All the directives of the indexing program TREOR (Werner, Eriksson & Westdahl, 1985)
are still valid for the %ntreor command and have to be used with the same syntax (see
the N-TREOR manual for the details).
The default choices can be changed via suitable directives.
An example of application of N-TREOR09 directives is the following one:

%structure diltia
%data
pattern pd_0029.xye
wavelength 1.54056
extefile diltia.pea
%ntreor
CEM = 50,

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CEM = n,is a directive setting to n the maximum allowed cell axis

In a default indexing run, N-TREOR09 searches for cells with a maximum cell volume of
4000 Å3 and a maximum cell axis of 35 Å. Due to this limits the correct cell is not found in a
default indexing run for compounds having larger cell axis values. This is the case of
Diltiazem hydrochloride (diltia) for which one of the maximum axis value is 42.190 Å.
The directive 'CEM = 50' activates N-TREOR09 for a search for a cell having a maximum
axis value of 50 Å.

Contact
For suggestions and bugs contact annagrazia.moliterni@ic.cnr.it.
References
Altomare, A., Campi, G., Cuocci, C., Eriksson, L., Giacovazzo, C., Moliterni, A., Rizzi, R. &
Werner, P.-E. (2009). Advances in powder diffraction pattern indexing: N-TREOR09. J.
Appl. Cryst. 42, 768-775.
Altomare, A., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Rizzi, R. & Werner, P.-E.
(2000). New techniques for indexing: N-TREOR in EXPO. J. Appl. Cryst. 33, 1180-1186.
Boultif, A., Louër, D., (2004). Powder pattern indexing with the dichotomy method. J. Appl.
Cryst. 37, 724-731.
Le Bail, A., (2004). Monte Carlo indexing with McMaille. Powder Diffraction 19, 249-254.
De Wolff, P. M.(1968). A simplified criterion for the reliability of a powder pattern indexing.
J. Appl. Cryst. 1, 108-113
Werner, P.-E., Eriksson, L., & Westdahl, M. (1985). TREOR, a semi-exhaustive trial-and-
error powder indexing program for all symmetries. J. Appl. Cryst. 18, 367-370.
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Space group determination

Space group determination by EXPO2014

In the crystal structure solution process the determination of the space group usually
follows the indexing step. This task is carried out by a careful investigation of the
experimental intensities, aimed at finding the correct extinction group. Because of the
collapse of the experimental data into the Bragg angle one-dimension space, the
experimental pattern suffers by peak overlap and uncertain background definition. As a
consequence, the judge about the 'presence' or 'absence' of the reflections may provide
ambiguous results. A new probabilistic procedure aiming at recognizing the extinction
symbol has been implemented in EXPO2014. It uses the statistics of the normalized z
intensities (as extracted by the Le Bail method) to calculate the probability of each
extinction symbol compatible with the crystal system suggested by N-TREOR09. A suitable
weight w is associated to the intensity of each reflection, depending on the expected
reliability of its estimate. The algorithm provides a probability for each extinction symbol of
the considered crystal system. It has been tested on a large number of test structures and
on all the crystal systems, providing good results (Altomare et al., 2004; Altomare et. al.,
2005; Altomare et al., 2007).

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Preparing input file for space group determination by EXPO2014

Space group determination by EXPO2013
Output of space group determination
Contact and References

Preparing input file for space group determination in EXPO2014

To run EXPO2014 for space group determination you need to create an input file
(*.exp). You can create an input file for space group determination by graphic interface by
the menu "File" > "New".

You must specify the structure name, the profile counts filename and its format, the type of
radiation source. Click on button 'Find Space Group', fill the frame 'Cell Parameters' and
'Cell Content'. The following picture is an example of input file for the crystal structure
determination in case of cimetidine structure from the indexed pattern.

Once the button 'Save' has been selected, an input file cime.exp will be created and
automatically loaded by the program for the space group determination.
%structure cime
%job structure cime

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%init
%data
pattern cime.pow
filetype counts
wave 1.52904
findspace
cell 10.69808 18.81786 6.82267 90.00000 111.28911
90.00000
cont h 64 c 40 n 24 s 4
%continue
The directive findspace enables the space group determination procedure. It is a
directive of the command %data. The unit cell is assumed to be determined by indexing of
the experimental pattern. To know the meaning of the other lines of the input file, see the
chapter "command and their use" of this manual.
Alternatively you can edit a new input file or modify an exiting input file by a text editor and
save it with extension '.exp'. Once a time the input file has been created, load the exp input
file from menu 'File' > 'Load & Go'.

Space group determination by EXPO2013

The different steps of the algorithm are here schematized.
1) The full pattern decomposition is performed, according to the Le Bail algorithm, in the
space group having the largest Laue symmetry and no extinction conditions (e.g., P 1 2/m
1 in the monoclinic system, P 2/m 2/m 2/m for the orthorhombic, P 4/m mm for the
tetragonal, P 6/m mm for the trigonal-hexagonal, Pm-3m for the cubic systems).
2) The extracted intensities are then normalized, according to the classical Wilson method,
by using the space group mentioned at the point 1).
3) The z statistic is used to define the probability of the extinction symbol.
4) For each crystal system the probability of the different possible extinction symbols is
calculated.
Use the button on the toolbar to carry out to next steps.

At the end of the procedure the following window will be displayed.

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The window contains the extinction symbols ranked according to their calculated
probability. When the user clicks on one of them, the corresponding list of compatible
space groups is supplied. The frequency of the selected space group in the Cambridge
Structural Database (CSD) is reported in terms of number of occurrences in the CSD and
percentage. This information can be useful when different space groups are associated to
an extinction group.
Press the button to access to a list of reflections that, according to the selected
extinction symbol, should be systematically absent. For each reflection the following
specifications are given: the order number of reflection, the Miller index, the symmetry
operator responsible for the extinction and the corresponding extinction condition, the
probability for the extinction, the type of reflection (single or in overlap).
By default the reflections are ordered according to the extinction condition but you can
change the order selecting a different ordering criterion by clicking on the title column. The
selected reflection on a list will be marked on the pattern.
The reflections that are expected to be absent according to the selected extinction symbol
are marked by a vertical bars situated below the observed pattern, just above the set of
bars defining the reflection positions. They have different colors depending on whether the
reflection is single (or belongs to a whole extinct cluster) or in overlapping. By default, a
black vertical bar marks single systematically absent reflections, while the rest of the
absent reflections (those in overlap) are marked with a purple bar. This graphical support
helps the user to discard unreliable extinction symbols even if estimated with large
probability.
Press the 'OK' button to accept the selected space group and continue with the structure
solution process.

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Output of space group determination

The output file contains details about the space group determination procedure.
Use 'Info' > 'View output file' to access to the output file or open the file structure_name.out
with a text editor. At the end of the procedure the new input file, called
structure_name1.exp (e.g. cime1.exp) will be created. This file contains the selected
space group and can be loaded for skip the space group determination and to perform the
structure solution with Direct Methods.
Contact
For suggestions and bugs contact angela.altomare@ic.cnr.it,
annagrazia.moliterni@ic.cnr.it, rosanna.rizzi@ic.cnr.it, corrado.cuocci@ic.cnr.it.

References
Altomare, A., Caliandro, R., Camalli, M., Cuocci, C., da Silva, I., Giacovazzo, C., Moliterni,
A. G. G. & Spagna, R. (2004). Space-group determination from powder diffraction data: a
probabilistic approach. J. Appl. Cryst. 37, 957-966.
Altomare, A., Camalli, M., Cuocci, C., da Silva, I. Giacovazzo, C., Moliterni, A. G. G &
Rizzi, R. (2005). Space group determination: improvements in EXPO2004. J. Appl.
Cryst. 38, 760-767.
Altomare, A., Camalli, M., Cuocci, C., Giacovazzo, C., Moliterni, A. G. G. and Rizzi, R.
(2007). Advances
in space-group determination from powder diffraction data. J. Appl. Cryst. 40, 743-748.
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Structure solution by Direct Methods

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 EXPO2014

Structure Solution in EXPO2014 program

Typical X-ray diffraction experiments provide structure factor moduli, while the relative
phases are lost. Recovery of the phase information is crucial for crystal structure solution
and is referred in crystallography as the phase problem . In EXPO2014 program, the
default strategy used to solve this problem is based on the application of the Direct
Methods (DM) theory (Giacovazzo, 1998). DM are able to estimate phases directly from
the structure factor amplitudes. The application of DM to powder data requires the previous
decomposition of the full pattern to extract single diffraction intensities for each reflection in
the measured 2theta range. Owing to the peak overlap the estimates of the diffraction
moduli will be affected by unavoidable errors: this weakens the efficiency of DM (naively,
wrong moduli will produce wrong phases), and still today makes crystal structure solution
from powder data a challenge.
Load input file for Structure Solution by Direct Methods
When default EXPO2014 fails: strategies
Suggestions
Contact and References
Load input file for Structure Solution with Direct Methods
To run EXPO2014 for structure solution you need to create an input file (*.exp). You
can create an input file accessing by graphic interface by the menu "File" > "New".

You must specify the structure name, the profile count filename and its format, the type of
radiation source. It is supposed that the cell parameters and the space group have been
determined before so fill the frame 'Cell Parameters' and 'Space Group'. Activate the
check button 'Structure Solution' if you intend to perform the crystal structure solution
process with Direct Methods. Otherwise use the button 'Open' to import an existing input
exp, for example you could load the file cime.exp already existing in the directory
'examples'. The following picture is an example of the input file for crystal structure
determination of the cimetidine compound.

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When you press the button 'Save' an input file cime.exp will be created and automatically
loaded by the program for the structure solution process by DM.

%structure cime
%job structure cime
%init
%data
pattern cime.pow
content s 4 c 40 n 24 h 64
wave 1.52904
cell 10.6986 18.8181 6.8246 90.000 111.284 90.000
space p 21/n
sync
filetype counts
%continue

You can known the meaning of lines of the input file by looking at the chapter "command
and their use" of this manual.
Alternatively you can edit a new input file or modify an exiting input file with a text editor and
save it with extension '.exp'. Once a time the input file has been created, load the exp input
file from menu 'File' > 'Load & Go'.

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Press the button in the toolbar and the following steps of the structure solution
process will be automatically performed:
1) Extraction of the integrated intensities from the powder diffraction pattern;
2) The integrated intensities are normalized via Wilson method (Wilson,1942);
3) Triplet invariants are calculated and their phases are estimated via P10 formula
(Cascarano et al., 1984);
4) Phasing process: more plausible sets of phases are generated whose reliability is
assessed via the CFOM figure of merit (Cascarano et al., 1992);
5) Twenty sets of phases with the largest CFOM values are stored and ranked in
decreasing CFOM order. The first set of phases is automatically selected and used for
computing an electron density map via an E-Fourier synthesis (E-map): the most intense
peaks in the E-map are located and chemically interpreted. The obtained structure model
is optimized and completed via the automatic structure model optimization.
More information about the structure solution process by Direct Methods are in the chapter
'The steps of structure solution procedure'.

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When default EXPO2014 fails: strategies

A lot of crystal structures are solved by EXPO2014 by default settings in few

minutes and in completely automatic way.
Unfortunately not always you can obtain the correct structure solution in default. In this
situation two different strategies are suggested and can be applied at the end of the default
run.

Explore trials

In a typical Direct Methods procedure more sets of phases (trials) are generated and
ranked according to the combined CFOM figure of merit (estimating the quality of the trial)
and only the best trial is used to calculate a Fourier map. Because of the unavoidable
errors on the phases, the figure of merit can fail to evaluate the best trial, so it is strictly
suggested to develop the other trials by menu 'Solve' > 'Explore trials'.

The following window will be opened (the procedure has been applied to 2-
Mercaptobenzoic acid compound, whose input file is in the directory 'examples').

and the the CFOM value can be read. The highest CFOM value could not correspond to the
correct solution while subsequent different trials may be successful. This is particularly true
when several nearly equivalent CFOM's are available for different trials as in the picture. If
the trial has been already developed (done='yes'), you can read the RF figure of merit value
that quantifies the agreement between the structure factors extracted from the experimental
pattern and calculated by the model.
Check the button in the first column to decide which trial will be developed and press the

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button If you check the button 'Select all new trials', all the trial not already
explored will be automatically selected and developed.
You can choose three different actions for the structure model optimization (see later):
1)RBM: Resolution Bias Modification is the default action for organic and metal organic
compounds.
2)Fourier: classical Fourier refinement, default choice for inorganic compounds.
3)E-map: the first electron density map calculated directly after the phasing process by
Direct Methods.
4)COVMAP: the covariance principle based completion.

At the end of the procedure, all the trials will appear ordered according to the RF and the
user can also view the model corresponding to each trial by mouse selection.

Alternatively to the graphical option, the use of the command %alltrials in the input file
automatically activate the 'Explore trials' approach. An example of input file is here
reported:

%Structure merca
%Initialize
%Job merca
%Data
Cell 7.885 5.976 14.949 90.0 100.48 90
SpaceGroup p 21/c
Content c 28 O 8 S 4 h 24
Pattern pd_0002.xy
Wavelength 1.54056
%extra
%normal
%invar
%phase
%alltrials

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Structure model optimization

The structure model obtained at the end of the default strategy, generally is a partially
correct representation of the true model: some atoms are in correct positions but other are
incorrectly positioned or completely false. In this situation the user can try to improve the
quality of the Fourier map, as obtained at the end of Direct Methods, by using different
optimization strategies implemented in the EXPO2014 program:
1. suitably weighted least squares (wLSQ) (Altomare et al., 2006), able to compensate
the low accuracy of the intensities of strongly overlapped reflections. The procedure
is automatically applied in case of inorganic compounds.
2. the resolution bias correction algorithm (RBM) (Altomare et al., 2008a, 2008b;
2009, 2010a, 2010b)for reducing, in the electron density map, the errors caused by
the limited experimental resolution: peak broadening, peak shift, intensity distorsion.
The correction has been developed in direct space (it represents the default choice
in case of organic and metal organic compounds), in reciprocal space and in both
direct and reciprocal space;
3. the procedure of electron density modification based on the concept of covariance
between points of the map (COVMAP) (Altomare et al., 2012) The procedure
executes the following strategy: the structural model provided by the RBM procedure
is submitted to COVMAP approach which suitably modifies the electron density
map and successively submits the improved model to wLSQ analysis. The resulting
new model is again modified by COVMAP and cyclically processed in the other two
steps. The number of cycles depends on the structure complexityThe structure
model obtained at the end of the default strategy can be partly correct with some
atoms in correct position but other atoms are incorrectly positioned or completely
false. In this situation the user can try to optimize del model by using different
optimization strategies.

It is possible to graphically choice different RBM procedures for model optimization by the
menu 'Resolution Bias Modification (RBM)', via 'Refine' button from the upper EXPO2014
menu.

Apply the RAMM (RAndom Model based Method) procedure

The new method RAMM (Altomare et al., 2013) has been developed and implemented in
the EXPO2014 computing program for improving the ab initio crystal structure solution
process. When the available information consists of only the experimental powder
diffraction pattern and the chemical formula of the compound under study, the structure
solution classical approach follows two main steps: 1) phasing by Direct Methods (or by
Patterson methods) in order to obtain a structure model (this last is usually uncompleted
and/or approximate); 2) improving the model by structure optimization techniques. The
alternative RAMM approach skips step 1) and supplies a fully random model to step 2).

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Such model is then submitted to important structure optimization tools present in EXPO:
wLSQ , RBM and COVMAP which are able to lead to correct structure. RAMM is based on
a cyclic process generating several random models which are then optimized. The process
stops automatically when recognizes the correct structure.

Click 'RAMM' on the menu 'Solve' to activate this alternative strategy for structure solution
at the end of the default run of EXPO2014. The following pictures are related to 2-
Mercaptobenzoic acid whose input file is in the directory 'examples'.

The procedure can take from some minutes to several hours depending on the complexity
of problem (number of atoms, quality of data, data resolution). If more than one plausibile
solution is found they will be ordered according to the R-structure factor in an interactive
list.

The selected model will be visualized on the molecular viewer. Press 'OK' to accept the
selected model.
When Direct Methods procedure fails, the RAMM approach can be a very useful tool to find
the correct solution.
The use of the command %randomsolve in the input file automatically activate the
'Explore trials' approach. An example of input file is here reported:
%Structure merca
%Initialize
%Job merca
%Data
Cell 7.885 5.976 14.949 90.0 100.48 90
SpaceGroup p 21/c
Content c 28 O 8 S 4 h 24

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Pattern pd_0002.xy
Wavelength 1.54056
%randomsolve

Suggestions
The number of options in the program is quite large. The optional strategies regard the
improvement of both the decomposition process for carrying out more reliable reflection
intensities and the Direct Methods performances. We give some other secondary
strategies.

About the improvement of the decomposition process

· It is important to provide good quality diffraction pattern. For example, it is

recommended to reduce the pattern range in case of high noise signal at large 2theta
values. Use the directive range in the command '%data' to select a portion of pattern
or select 'Pattern' > 'Range' by the graphical interface.
· If a partial structure fragment has been located by the default run, it may be recycled in
the extraction process (a graphic option must be selected). Click on 'Restart' >
'Recycle in extra'.
· The use of the 'RANDOM' directive in the EXTRACTION module activates the
procedure for overcoming the Le Bail method tendency to equipartition the intensity of
a group of strongly overlapped reflections. Based on a Monte Carlo approach, it may
provide a set of more statistically meaningful intensities.
· If the default run has revealed pseudo symmetry effects and, in particular, if the
percentage of electron density affected by pseudo is large, it may be very useful to
exploit that information in the extraction process (a graphic option activates the
procedure).

About the optimization of Direct Methods procedure

· Magic integers procedure is an effective and simple way for starting a multi-solution
process.
A random approach may be alternatively chosen in the phasing process (directive
'RANDOM' in the PHASE module).
· Second representation formula for triplet invariants proved much more powerful than
first representation formula therefore it is used as a default for estimating triplets. In
case of failure, the user can choose P3 formula (directive 'COCHRAN' in the
INVARIANT module) and/or conveniently increase the number of symbols in the
phasing step (directive 'SYMBOLS' followed by the number of symbols to be used in
the 'PHASE' module).
· A check for possible pseudotranslational symmetry is always made by EXPO2014: if
PSEUDO keyword is not activated the information is given but not used in the
normalization routine and in the phasing process. The user can decide to use it
(directive 'PSEUDO' in the NORMAL module).

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 EXPO2014

· the value of NREF (number of reflections actively used in the phasing process) is fixed
by EXPO2014. For some special structures the ratio "number of active triplets/NREF"
is too small (less than 10). Larger values of NREF may improve the phasing
procedure (directive 'NREFLECTIONS' followed by the number of reflections in the
NORMAL module).
· High (or low) resolution reflections may occasionally play a too important role in the
first steps of convergence and divergence process. Fixing a thermal factor lower (or
larger) than that automatically provided by the normalization routine may successfully
change convergence and divergence process (directive 'BFACTOR' followed by the
isotropic thermal factor in the NORMAL module).
· An alternative space group should be carefully considered (directive 'SPACEGROUP'
in the DATA module).
· Sometimes the structure model is partial. Successive combined Fourier map
calculations (Fo-Fc, 2Fo-Fc or Fo) and Rietveld refinements may be conveniently
selected by graphical options.

Contact
For suggestions and bugs contact:
angela.altomare@ic.cnr.it
annagrazia.moliterni@ic.cnr.it
rosanna.rizzi@ic.cnr.it
corrado.cuocci@ic.cnr.it

References
Altomare, A., Cuocci, C., Giacovazzo, C., Moliterni, A.G.G., Rizzi, R. (2006.) Powder
diffraction: the new
automatic least-squares Fourier recycling procedure in EXPO2005. J. Appl. Cryst. 39
(2006) 558-562.
Altomare, A., Cuocci, C., Giacovazzo, C., Kamel, G. S., Moliterni, A. & Rizzi, R. (2008a).
Minimally
resolution biased electron-density maps. Acta Cryst. A64, 326-336.
Altomare, A., Cuocci, C., Giacovazzo, C., Moliterni, A. & Rizzi, R. (2008b). Correcting
resolution bias in electron density maps of organic molecules derived by direct methods
from powder data. J. Appl. Cryst. 41, 592-599.
Altomare, A., Cuocci, C., Giacovazzo, C., Moliterni, A., Rizzi, R. (2009) Correcting
electron-density
resolution bias in reciprocal space. Acta Cryst. A65, 183-189.
Altomare, A., Cuocci, C., Giacovazzo, C., Moliterni, A., Rizzi, R. (2010a) The dual-space
resolution bias
correction algorithm: applications to powder data. J. Appl. Cryst. 43, 798-804.
Altomare, A., Cuocci, C., Giacovazzo, C., Moliterni, A., Rizzi, R. The dual-space resolution
bias
correction in EXPO2010. Z. Kristallogr. 225, 548-551.
A. Altomare, C. Cuocci, C. Giacovazzo, A. Moliterni and R. Rizzi (2012). Covariance and

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 EXPO2014

correlation estimation in electron-density maps. Acta Cryst. A68, 244-255.

A. Altomare, C. Cuocci, C. Giacovazzo, A. Moliterni and R. Rizzi (2013). RAMM: a new
random-model-based method for solving ab initio crystal structure using the EXPO
package. J. Appl. Cryst. 46,
Cascarano, G., Giacovazzo, Camalli, M., Spagna, R., Burla, M. C, Nunzi, A. & Polidori, G.
(1984). The method of representations of structure seminvariants. The strengthening of
triplet relationships. Acta Cryst. A40, 278-283.
Cascarano G., Giacovazzo C. & Guagliardi A. (1992). Improved figures of merit for direct
methods. Acta Cryst. A48, 859-865.
Giacovazzo, C. (1998). Direct Phasing in Crystallography. Oxford: IUCr/Oxford University
Press.
Wilson, A. J. C. (1942). Determination of Absolute from Relative X-Ray Intensity Data.
Nature, Load.
150, 152.
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All steps of structure solution procedure

The steps of structure solution procedure

Using the command %continue, the program runs in default conditions carrying out the
commands

%extraction
%normal
%invar
%phase
%fourier
%menu
%end

and each command corresponds to a step in the structure solution with Direct Methods. All
the following steps are described.

1)Extraction of the integrated intensities (%extraction command)

2)Normalization of the integrated intensities (%normal command)
3)Estimate of structure invariants (%invariants command)
4)Application of the tangent formula (%phase command)
5)Crystal structure completion and refinement (%fourier command)

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Extraction of the integrated intensities

Extraction of the integrated intensities ('extraction' command)

To calculate the integrated intensities, the program uses the Le Bail algorithm (Le
Bail et al., 1988) and combines it with a least squares procedure minimizing the quantity:

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 EXPO2014

(1)

The summation in (1) goes over all the data points,

wi = 1 /yi2
yoi = observed intensity at the i-th step
yci = calculated intensity at the i-th step
(
2
)
The summation over h includes neighbouring Bragg h reflections,

s = scale factor

LPh = Lorentz - polarization factor

mh = reflection multiplicity

Fh = structure factor

P = profile function

A = asymmetry function
background intensity at the i-th
ybi =
step.

The background in (2) is automatically estimated and is described by the polynomial

function (Young, 1993)

N, the polynomial degree, is automatically defined by the program as the number which
provides the best fit of the background interpolation points.

is the associated to the minimum intensity in the range in which the background is
estimated.
From the pattern a standard peak is automatically selected. The standard peak fitting is
performed to provide the starting values of the variables to refine in the least squares
procedure.
The full pattern is automatically divided into intervals. The refined parameters derived by
the fitting of each interval will be taken into account for the final full pattern fitting.
The following profile shape functions are available for user choice:

Pearson
VII

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 EXPO2014

Gaussian

Lorentzian

P
s
e
u
d
o
-
V
o
i
g
t

where

The default is the Pearson VII function. In this case

44 / 126
 EXPO2014

otherwise

The peak shape, the asymmetry, the cell and the background parameters are all refined by
the program. To overcome the tendency of the Le Bail algorithm to equipartition the
intensities of strongly overlapping reflections, a new approach was introduced. It is based
on the random variation of the reflection intensities belonging to a given cluster and on the
subsequent selection of the good fit feasible trials.
After a first default run of EXTRA, it is possible to run it again starting from the refined
variables in the previous run. In this case the preliminary standard peak procedure and the
interval by interval extraction procedure are skipped. The related command is %
RECYCLE.
Directives in extraction command
The following directives must be added after the command '% extraction' in the
input file to activate some specific features of the procedure
ALL

To activate the procedure of selection of the profile function type (among Pearson VII,
Gaussian, Lorentzian, Pseudo-Voigt) from the best fit of each interval.

DAMPING x

x is the damping factor used in the least squares routine (default value 0.1). (It is convenient
to use a small x value).

FAST

This directive is used if the graphic interface has been requested by the "window"
command. In this case, the user graphic interaction in a default run is avoided.

FIRST

To activate the procedure of selection of the profile function type (among Pearson VII,
Gaussian, Lorentzian, Pseudo-Voigt) from the best fit of the first interval .

FRECYCLE filename.ext

If the "filename" is available from a previous run of EXPO2014 (or EXTRA), or from any
source containing hkl and the corresponding F-squared values, Le Bail algorithm is started
again for obtaining new estimates.

GAUSSIAN

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 EXPO2014

To use only if the gaussian function is preferred.

INTERVAL n

n is the number of intervals in which the powder pattern is divided (max 8). n is only given if
the user wants to change the automatic division of the pattern.

LORENTZIAN

To use only if the lorentzian function is preferred.

LOWB

To reduce the background by a constant factor equal to the minimum value observed count.

NCYCLE n

n is the number of cycles for each interval (default value is 60).

NOBA

To not refined the background

NOCELL

To skip the cell refinement.

NOSINGLE

This directive is used if the preliminary fitting of the standard peak (automatically selected
by the program) is omitted. In this case a preliminary fitting of the first interval is carried out.

OPTI

To continue the refinement procedure for each interval.

POLYNOMIAL k

k is the background polynomial degree (max 10). k is given if the user wants to use a fixed
degree in each interval and not the degree automatically selected by the program.

PVOIGT

To use only if the Pseudo-Voigt function is preferred.

RANDOM p

To activate the random procedure in the integrated intensity extraction step. p is the
coefficient for the reflection overlapping definition. Default value = 0.5

SMOO

To activate the procedure for calculating the background by following (Brückner, 2000). In
this case the background is not refined.

STANDARD

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 EXPO2014

To activate the procedure of selection of the profile function type (among Pearson VII,
Gaussian, Lorentzian, Pseudo-Voigt) from the best fit of the standard peak.

SLOW

This directive can be used if the graphic interface has been requested by the "window"
command. In this case the program stands by after some relevant calculations and waits
for the user graphic interaction to go on.

VERBOSE

This directive is used to have a more detailed print in the output file. In this case, the Rp
and Rwp values and the values of the refined variables are printed interval by interval.

WIDTH x

x is the factor which, multiplied by the FWHM of each peak, gives the total peak width. (In
this case the automatic calculation of x is not taken into account).

ZEROPROFILE x

x is the 2q shift value supplied by the user (to be substracted from the 2q observed
positions). In this case the automatic calculation of the 2q shift using the preliminary fitting
of the standard peak is skipped by the program).
EXAMPLES
Example 1
A Pseudo-Voigt function will be used and the background in each interval will be described by a constant.
The counts file format is not the default one and the graphic window is suppressed.
%structure mes
%job MES - data from home diffractometer
%initialize
%data
pattern mes.pow
cell 8.588 9.931 11.105 90.0 93.754 90.0
content C 24 N 4 O 20 S 4 H 52
spacegroup p 21/c
wavelength 1.5406
filetype double
%extraction
pvoigt
polynomial 0
%end

Example 2
The starting values of the integrated intensities in the extraction step are supplied by the user in the file
"yono.ext" and the number of least-square cycles is set to 40.
%structure yono
%job YONO - Synchrotron data
%initialize
%data
pattern yono.pow
cell 9.385 16.394 3.627 90.000 101.067 90.000

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 EXPO2014

content Y 8 O 26 N 2 H 18
spacegroup p 21
wavelength 1.2323
synchrotron
%extraction
fstarting yono.ext
ncycle 40
%end

Example 3
The preliminary fitting of the standard peak is skipped and the starting 2q shift value is supplied by the user
(the program refines it).
%window
%structure agpz
%job AGPZ - data from home diffractometer
%init
%data
pattern agpz.pow
cell 6.526 20.059 6.464 90.000 90.000 90.000
spacegroup p b c a
content Ag 8 N 16 C 24 H 24
wavelength 1.54056
%extraction
nosing
zeroprof 0.02
%continue

Example 4
Neutron data and a deuterium atom in the cell content are used. Fast graphic interaction for the integrated
intensities extraction process is activated.
%structure baco
%job BACO - Neutron data
%initialize
%data
neutron
isotope H 0.67
pattern baco.pow
cell 10.0632 7.9330 6.8487 90.0 122.3423 90.0
spacegroup C 2/m
content Ba 4 C 8 O 20 H 8
wavelength 1.909
%extraction
fast
%continue

References

Le Bail, A., Duroy, H., Fourquet, J.L. (1988). Ab-initio structure determination of LiSbWO6
by X-ray
powder diffraction. Math. Res. Bull. 23, 447-452.
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 EXPO2014

Normalization of the integrated intensities

Normalization of the integrated intensities ('% normal' command)

In this module diffraction intensities are normalized using the Wilson method.
Statistical analysis of the intensities is made in order to suggest the presence or absence
of the inversion center, to identify the possible presence and type of pseudotranslational
symmetry (Cascarano et al. 1988 a,b; Fan, Yao et al. 1988) and to detect preferred
orientation effects (Altomare et al. 1994; Altomare et al. 1996). Possible deviations (of
displacive type) from ideal pseudotranslational symmetry are also detected. All the above
information is used as prior information in the integrated intensities extraction process,
unless the directive NOPSEUDO is given to the program.
When some additional prior information, besides positivity and atomicity of electron
density, is available, then a suitable renormalization of structure factors is made.
Directives in normal command
The following directives must be added after the command '% normal' in the input
file to activate some specific features of the procedure
BFACTOR x
Temperature factor if the user wants to supply it. (The scale factor is assumed equal to 1).
NOPREFERRED
If this directive is given the program does not apply the correction for preferred orientation.
NOPSEUDO
If this directive is given the program does not recycle the PSEUDO information in a new
extraction process.
NREFLECTIONS n
Number of active reflections with largest E-values subject to a minimum value of E(obs) =
1.0.
Default = 4 * number of independent atoms + 50 if centrosymmetric + 50 if triclinic + 150 to
a maximum of 499. If PSEUDO directive is on, the program tries to use all the E's down to
1.0.
NZRO n
Number of smallest E-values (maximum E-value 0.3) to calculate psi-zero triplets. The
default (and the maximum) is 1/3 of the strong reflections. (The directive allows to decrease
that number).
NPLA n
n is the number of candidate planes for preferred orientation analysis (default 10; maximum
30)
The number includes the equivalent planes which will not be considered.
PLANE h k l G
Preferred orientation direction supplied by the user; G is the correction factor.
PSEUDOTRANSLATION n(1,1) n(2,1) n(3,1) n(4,1) n(1,2) . . . n(4,3)
If parameters are equal to zero, or omitted, the normalization routine performs statistics for
the pseudotraslation effects and renormalizes the reflections on assuming the most

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 EXPO2014

probable pseudotranslation as prior information.

If user wants to supply a specific pseudotranslational symmetry, and this corresponds to a
class given in Table 1 the n(1,1) can be set to the class number and the other values must
be omitted.
If the pseudotranslation is more complex, it should be specified by up to 3 sets of 4 values
n(i,j) so that

( n(1,j)*h + n(2,j)*k +n(3,j)*l = n(4,j)*m ) j=1,..,3

where m is an integer number.

THRP x
Threshold value of the mean fractionary scattering power (M.F.S.P.) to recycle the pseudo-
translational symmetry information in a new extraction process.
EXAMPLE

Example 1
Use of the pseudotranslational symmetry (if it is present) as prior information for a new extraction process is
inhibited.
%structure agpz
%job AGPZ - data from home diffractometer
%initialize
%data
pattern agpz.pow
cell 6.526 20.059 6.464 90.000 90.000 90.000
spacegroup p b c a
content Ag 8 N 16 C 24 H 24
wavelength 1.54056
filetype xy
%extraction
%normal
nopseudo
%continue

References
Cascarano G., Giacovazzo C. & Luic' M. (1988a). Acta Cryst. A44, 176-183.
Cascarano G., Giacovazzo C. & Luic' M. (1988b). Acta Cryst. A44, 183-188
Fan H., Yao J. & Qian J. (1988). Acta Cryst. A44, 688-691.
Altomare A., Burla M.C., Cascarano G., Giacovazzo C., Guagliardi A., Moliterni, A.G.G. &
Polidori, G. (1996). J. Appl. Cryst. 29, 341-345.
Altomare A., Cascarano G., Giacovazzo C., Guagliardi A., Burla M.C., Polidori G. &
Camalli M. (1994). J. Appl. Cryst. 27, 435 - 436.
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Estimate of structure invariants

Estimate of structure invariants ('% invariants' command)

Up to 10000 triplets relating reflections with normalized E values greater than a
given threshold (strong triplets) are stored for active use in the phasing process. Also
triplets (PSI-ZERO triplets) relating two reflections with large E and one with E close to zero
are generated: they are used to define a special figure of merit (PSCOMB). Special types

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 EXPO2014

of triplets (PSI-E triplets) based on two strong and one intermediate reflections (just below
the threshold of strong reflections) are calculated and used in the FOURIER/LEAST-
SQUARES module in order to extend phase information (Altomare et al. 1991).
Negative quartets are generated by combining the psi-zero triplets in pairs, and those with
cross-magnitudes smaller than a given threshold are estimated by means of their first
representation, as described by Giacovazzo (1976). These quartets are used to provide an
important contribution to the CPHASE FOM.
Active triplets may be estimated according to Cochran's (1955) P3 distribution: the
concentration parameter of the von Mises distribution is then:

(
3)

Triplets can also be estimated according to their second representation (i.e. P10 formula,
as described by Cascarano et al., 1984). The concentration parameter of the new von
Mises distribution is given by

G = C (1 + q) (4)

where q is a function (positive or negative) of all the magnitudes in the second

representation of the triplet. The G values are rescaled on the C values and the triplets are
ranked in decreasing order of G. The top relationships represent a better selection of
triplets with phase value close to zero than that obtained when ranking according to C.
These triplets will be actively used in the phase determination process.
Triplets characterized by a negative G represent a sufficiently good selection of
relationships close to 180 degrees, to be used for the calculation of a powerful FOM
(CPHASE). Triplets with G close to zero are expected to have values widely dispersed
around 90 or 270 degrees and are used to compute an enantiomorph sensitive FOM. A
similar FOM is also computed using quartets estimated with a very small concentration
parameter.
As a default, triplets are estimated according to P10 formula.
The parameter C of the Cochran distribution (say P3) is suitably modified when the pseudo
information in the section 'NORMAL module' is available. Then triplet phases are no longer
expected to be around zero (see quoted references) and may lie anywhere between 0 and
2p.
The method of the joint probability distribution functions (Cascarano et al., 1991;
Carrozzini et al., 1997) can be applied to obtain an estimate of normalized structure
factors, that will be used as a source of supplementary prior information in the extraction
process (if directive ESTIMATION is used).
Directives in invariants command
The following directives must be added after the command '% invariants' in the
input file to activate some specific features of the procedure

GMIN x
Positive triplets with G < x are not actively used.
Default value x=0.6 (in any case 0.2 < x < / = 1.0 is accepted range of value.

COCHRAN

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 EXPO2014

To use the P3 formula. (By default P10 formula is used).

CORRECTION x
If a PSEUDOTRANSLATION procedure is on, a correction factor depending on x is
applied to the probabilistic argument of weak-weak-weak triplets when they are present.
The default value is calculated by program.
x = -1 eliminates weak-weak-weak triplets,
x = 1 corresponds to the largest confidence in them.

EMAX x
Maximum value of E for the weak reflections for the psi-zero search (up to a maximum of
NRPSIZERO reflections). x > 0.3 not accepted.
Minimum value for the normalized structure factors in the sigma2 search. x < 1.0 not
accepted.
Default = minimum value of E for the strongest reflections selected by normalization
routine.

ESTIMATION
To run the procedure which estimates the |E|'s for all the reflections and use them as a prior
information in a new extraction process.
The procedure will not be applied if PSEUDOTRANSLATIONAL information has been
recycled.

NPSI0
To not calculate PSI-0 triplets (Default uses them).

NRPSIZERO n
The number of weakest reflections for the psi-zero search.
Default = number computed by normalization routine.
The value will substitute the default one in the direct access file.

NRTRIPLETS n
The number of strongest reflections for the sigma2 search. ( Up to Emin = 1.0 )
Default = number computed by normalization routine (nstrong).
The value will substitute the default one in the direct access file.
Value less than nstrong/2 is not accepted.

NLARGE n
To supply the number of largest reflections for the psi-zero search ( default = number of
strongest reflections used for sigma2 search).
nlarge > nrtriplets is not accepted.

NQUARTETS
To not calculate negative quartets (Default uses them).

NUMK n
The number of free-vectors used by P10 formula.
Default value is provided by EXPO according to the structural complexity:
n = min ( natom / msym + 30, 70 )
where natom is the number of atoms in the cell and msym is the number of symmetry
operators of the space group.

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 EXPO2014

YPSIE
To calculate PSI-E triplets (Default doesn't use them).

EXAMPLE
Example 1
Use of the triplets estimation as prior information for a new extraction process.
%structure mes
%job MES - data from home diffractometer
%initialize
%data
pattern mes.pow
cell 8.588 9.931 11.105 90.0 93.754 90.0
content C 24 N 4 O 20 S 4 H 52
spacegroup p 21/c
wavelength 1.5406
filetype double
%extraction
%normal
nopseudo
%invariants
estimation
%continue

References
Altomare A., Cascarano G., Giacovazzo C. & Viterbo D. (1991). Acta Cryst. A47, 744-748.
Carrozzini B., Giacovazzo C., Guagliardi A., Rizzi R., Burla M.C. & Polidori G. (1997). J.
Appl. Cryst. 30, 92-97
Cascarano G., Giacovazzo C., Burla M.C., Nunzi A. & Polidori G. (1984). Acta Cryst. A40,
389-394.
Cascarano, G., Giacovazzo, C., Guagliardi, A. & Steadman, N. (1991). Acta Cryst. A47,
480-484.
Cochran W.(1955). Acta Cryst. 8, 473-478.
Giacovazzo C. (1976). Acta Cryst. A32, 958-966.
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Application of the tangent formula

Application of the tangent formula ('% phase' command)

In the EXPO2014 program the most reliable one-phase s.s. are treated as known
phases. Besides triplets, also the most reliable negative quartets and two-phase s.s. may
be actively used.
Each relationship is used with its proper weight: the concentration parameter of the first
representation for quartets and two-phase s.s., and C or G for triplets.
- CONVERGENCE/DIVERGENCE PROCEDURE -
The convergence procedure (Germain et al. 1970) is a convenient way of defining an
optimum starting set of phases to be expanded by the tangent formula or by any other
algorithm.
When the P10 formula is used, as a default, a special convergence process is devised
which chooses the starting set according to

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 EXPO2014

(
5
)

as suggested by Giacovazzo (1979-a,b) and by Burla et al. (1987), with

(
6
)

I1 and I0 represent modified Bessel functions of order one and zero respectively. The
summation in (5) is over all relationships defining the reflection h. If P3 formula is used the
default choice is

(7)

Once the starting set has been defined, a good pathway for phase expansion is
determined by a divergence procedure. In the divergence map, starting from the reflections
in the starting set, each new reflection is linked to the preceding ones with the highest value
of < a >.
- PHASE EXTENSION AND REFINEMENT -
The starting set defined by the preceding step is usually formed by the origin (and
enantiomorph) fixing reflections, a few one phase s.s. and a number of other phases which
may be obtained:
a) by magic integer permutation (White et al. 1975; Main, 1978),
b) by a random approach (Baggio et al. 1978; Burla et al. 1992).
The option a) is the default, b) runs if the directive RANDOM is used. In this last case a
large number (depending on the available computer time) of trials can be requested.
Directives SYMBOLS, SPECIALS, MAXTRIAL may be used to change default values.
Phase expansion and refinement are carried out by means of a tangent formula using
triplets, negative quartets, psi-zero triplets and the most reliable two-phase structure
seminvariants. In the weighting scheme the experimental distributions of the alpha
parameters are forced to match with the theoretical ones (Burla et al. 1987).
For each phase set, several FOM's are computed using all invariants and seminvariants
estimated by means of the representation method. Their meaning and an optimized way of
combining all the computed FOM's to give a highly selective combined figure of merit
(CFOM) is described in the papers by Cascarano et al. (1987, 1992).
All FOM's, as well as the combined CFOM, are expected to be equal to 1.0 for correct
solutions. CFOM larger than 0.5 can be considered encouraging.
If pseudotranslational symmetry is present then CFOM > 0.3 may characterize the correct
solution.

Directives in phase command

The following directives must be added after the command '% phase' in the input
file to activate some specific features of the procedure

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 EXPO2014

ENANTIOMORPH n

Code of the reflection chosen by the user to fix the enantiomorph (by default the
enantiomorph is chosen by the program ).

LIST n

The number of reflections at the top of the divergence map for which a list of the map is
obtained. Default = no printout of the map.

MAXTRIALS n

Maximum number of trials when random approach is used. (Default 100). Only if RANDOM
directive is on.

MINFOM x n

x: the program automatically stops when a solution is found with CFOM > x . Default value =
1.00.

n: is the maximum number of phase sets (with the largest combined figure of merit -
CFOM) to retain (default value = 10).

NOREJECT

Used to retain equivalent sets of phases.

ORIGIN n(i) phi(i)

Codes and phases of the reflections chosen by the user to fix the origin. The total number
of reflections (max 3) needed to fix the origin must be given (by default the origin is chosen
by the program).

PERMUTE n(i)

Codes of the permuted reflections chosen by the user (i.e. included in the number of
required symbols, max 12).

PHASE n(i) phi(i) wt(i)

Codes, phases and weights of reflections with known phase (max 200).
If one card is not sufficient, the directive PHASE must be repeated in the other card(s).

RANDOM n

To use random phases starting sets.

n: is the number of random phases. If n is omitted, it is equal to one half of the strong
reflections (nstrong).

Maximum value allowed for n = nstrong - 4

Minimum value allowed for n = nstrong / 4

Default value for random generation seed is 67543.

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 EXPO2014

(Not consistent with SYMBOLS directive)

SEED n

Random generation seed. n must be an integer large value and must be odd.

SPECIALS n

The number of reflections with restricted phase to be permuted (i.e. included in the number
of required symbols, max 12).

SYMBOLS n

The number of permuted phases (max 12). Default = 5.

(Not consistent with RANDOM directive)

TABLE

To print the table of alpha values (at the beginning of PHASE procedure).

TEST

To restart the random number generator using the default seed. Only if RANDOM directive
is on.

TRIAL n

To print the final phases for the specified trial n .

YNEG

To actively use negative triplets in the phasing process. (Default does not use them).

YNGQ

To actively use negative quartets in the phasing process. (Default does not use them).

EXAMPLE
Example 1
The program restarts from the PHASE procedure.
A random approach is used and the best 100 sets of phases, over 250 trials, are retained in the direct
access file. No Fourier is required.
%structure nizr
%job nizr structure
%init
%data
pattern nizr.pow
cell 12.388 8.9269 8.8449 90.0 90.550 90.0
cont zr 8 p 12 o 48 ni 4

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space p 21/n
wave 1.0302
filetype double
synch
%extraction
%normal
%invar
%phase
random
maxtrials 250
minfom 1.0 100
%end

References
Baggio R., Woolfson M.M., Declerq J.P. & Germain G. (1978). Acta Cryst. A34, 883-892.
Burla M.C., Cascarano G., Giacovazzo C., Nunzi A. & Polidori G. (1987). Acta Cryst. A43,
370-374.
Burla M.C., Cascarano G. & Giacovazzo C. (1992). Acta Cryst. A48, 906-912.
Cascarano G., Giacovazzo C. & Viterbo D. (1987). Acta Cryst. A43, 22-29.
Cascarano G., Giacovazzo C. & Guagliardi A. (1992). Acta Cryst. A48, 859-865.Germain
G., Main P. & Woolfson M.M. (1970). Acta Cryst. B26, 274-285.
Main P. (1978). Acta Cryst. A34, 31-38.
White P.S. & Woolfson M.M. (1975). Acta Cryst. A31, 53-56.
Created with the Personal Edition of HelpNDoc: Free EPub producer

Crystal structure completion and refinement

Crystal structure completion and refinement ('% fourier' command)

The sets of phases generated by the tangent routine are first expanded through psi-
E relationships and then passed to the fast fourier transform routine written by L.F.Ten Eick
(1977) and subsequently modified by the MULTAN team (Main, 1978; Main et al. 1980).
Several additional features have been introduced in the present version:
a) From the solution with the highest CFOM value a Fourier map may be calculated by
involving a supplemental number of reflections which are phased through the so-called psi-
E triplets (Altomare et al. 1991)
b) Special positions are handled, peaks very close to symmetry elements are moved onto
symmetry elements, the site symmetry is defined and the atomic occupancy factor is
calculated; key numbers for designating free, coupled or fixed positional parameters for
least-squares subroutines are also calculated together with symmetry conditions on the
thermal ellipsoid.
c) Cycles of structure factor calculation -least squares- (2Fo -Fc) Fourier synthesis are
automatically performed in order to provide a more complete and refined crystal structure.
Due to reflection overlapping the results of the refinement must carefully be considered by
the user who will take always into account the ratio 'number of parameters to refine/number
of independent observations'.
The program provides the following R-factors which can be used as reliability parameters:

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(8)

(9)

(10)

An alternative approach, based on real space techniques (Altomare et al. 2002) originally
used for phase extension and refinement of proteins (Giacovazzo & Siliqi, 1997; Burla et
al. 2000), has been introduced in EXPO and modified to improve the phasing process
from powder data. It combines an Electron Density Modification procedure with Fourier
map calculations.
Directives in fourier command
The following directives must be added after the command '% fourier' in the input
file to activate some specific features of the procedure
COORDINATION El dmin dmax n

The minimum and maximum value of the bond distance are assigned to element El. n is the
coordination type.

Allowed values for bond angles are:

n=1 55 - 180 Degrees
n=2 85 - 145 Degrees
EDMO

This directive is used to enable a direct space procedure consisting of an Electron Density
Modification (EDM) process followed by successive Fourier maps using (2Fobs -Fcalc)
coefficients. Except for the Fourier directive 'set', all the rest of Fourier recycling directives
are not valid for EDM procedure.

2EOEC

This directive enables to use (2Eobs-Ecalc) as Fourier coefficients in the Fourier step (if
EDM procedure is applied).

EOBS

This directive enables to use the observed normalised structure factors (Eobs) as Fourier
coefficient in the Fourier step (if EDM procedure is applied).

FRAGMENT string

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Used to supply a known fragment to be completed. String is the name of the file in which,
for each atom, are stored: Element X, Y, Z, isotropic thermal factor.

FWHM D

This directive is used in order to change the value of D that is the parameter for the
condition 2q1 - 2q2 < D*FWHM.
Default value is approximately 0.9 depending on the ratio between the number of
observations and the number of parameters to refine.

GRID x

The grid on which the Fourier-map is evaluated will have a spacing of approximately x
angstroms. The default spacing is computed by the program (1/3 Å).

INTEGRATION x n

x is the radius of integration in the peak search routine. (Default value 0.5). n may be 1 to
use the gaussian fitting of the fourier peak in the map or 2 to use the peak average density.
(Default value 2).

LAYX

This directive can be used only if MAP directive is given. The Fourier-map will be printed in
section of constant x.

LAYY

This directive can be used only if MAP directive is given. The Fourier-map will be printed in
section of constant y.

LAYZ

This directive can be used only if MAP directive is given. The Fourier-map will be printed in
section of constant z.

LEVEL n

All numerical values in the E-map greater than n will be underlined with **** in the lineprinter
output to facilitate contouring.

The default is 100. The map is automatically scaled between ± 999 (approximately) at the
grid points at which it is calculated.

Note, however, that it is printed between ± 99. (This directive can be used only if
associated to MAP directive).

LIMITS x1 x2 x3

The E-map will be printed from 0 to x1 along x, from 0 to x2 along y, from 0 to x3 along z.
(This directive can be used only if associated to MAP directive).

MAP

If MAP is specified, the E-map will be printed on the lineprinter. The printing of the E-map
is rarely used.

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The output is in sections of constant y with x across the page and z running down it on a
grid of about three points per angstrom.

The maximum number of grid points across the page is 36 ( i.e. about 12 angstroms in
length). If more are needed, a new page is started.

PEAKS n

The number of peaks to be searched for in the map. The default is the number of peaks
which

å(occ(i)*m) = 1.3 * n

where occ is the crystallographic site occupancy factor, m is the number of symmetry
operators, n is the number of non-hydrogen atoms in the unit cell.

PSE

To actively use PSI-E triplets in these procedures (Default doesn't use them). (This
directive can be used only if associated to YPSIE directive of INVARIANTS routine).

RADIUS El x

The value x of the radius used to compute the connectivity is assigned to element El.

RECYCLE n

Used to stop the recycling procedure after cycle number n. If n is equal to zero only the E-
map will be calculated.

SET n

The serial number of the set from which to calculate the E-map. If 'SET n' is not specified,
the set with the highest combined figure of merit will be used, and then if FOURIER routine
is re-run, the set with the next highest combined FOM will be used.

SOGF x

The percentage of the largest |F| value reflections actively used in the Fourier recycling
routine.
The reflections with the smallest |F| values corresponding to the rejected percentage have
a zero weight value in the refinement process. (Default value 100.0).

SOGI x

The percentage of the most intense groups of overlapping reflections actively used in the
Fourier recycling routine. (Default value 91.0).

STOPF x

This directive enables to stop the Fourier step at the cycle number x (if EDM procedure is
applied). The default value of x is 10 (the maximum allowed value).

THRE x

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x is the threshold for the E value of the reflections actively used in the Electron Density
Modification step. The default value is 0.8.

THRM x

x is the fraction of the Fourier map points actively used in the Electron Density Modification
step. The default value is 0.025.

THRW x

x is the threshold of the Bessel weight of the reflections actively used in the Fourier step (if
EDM procedure is applied). The default value is 0.5.

EXAMPLES
Example 1
Only the E-map corresponding to the set number 7 and the complete FOURIER/LEAST-SQUARES
procedure for set number 10 are requested by the user. The binary file "vfi.bin" must exist.
%structure nbpo
%fourier
set 7
recyc 0
%fourier
set 10
%continue

Directives in label command

Direct methods applied to powder diffraction data often provide electron density maps of
which the quality is usually affected by systematic and/or random phase errors, by
amplitude truncation effects in the series representation of the electron density, etc. The
frequent incorrect labelling of the peaks can strongly affect the efficiency of the procedures
used for crystal structure refinement. An algorithm has been introduced in EXPO aiming at
using the crystal chemical information that is usually available a priori to improve the peak
labelling (Altomare et al., 2001)
The following directives must be added after the command '% label' in the input file
to activate some specific features.

DLIGHT d tol

d is the expected heavy atom to light atom distance;

tol is the tolerance around the ideal distances. Default value = 0.5.

The program uses only one value of 'd' for all types of light atoms.

DWEIGHT d tol

d is the expected heavy atom to heavy atom distance;

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tol defines the tolerance around the ideal distances. Default value = 0.5.

The program uses only one value of 'd' for all types of heavy atoms.

LABEL n1 El1 n2 El2

n is the number of peaks to relabel using El element;

El is the atomic species to assign to the peaks.

Only two combination (n, El) can be used.

COORD xi

x specifies the expected number of heavy atoms surrounding each i-th heavy atom (the
coordination type) (i = 1,2).

EXAMPLE
Example 1
Use of the label change procedure to relabel the peaks of an electron density map obtained by applying the
FOURIER procedure. The binary file "vfi.bin" must exist.

% window

% structure vfi

% job VFI - Synchrotron data

% changelab

label 3 al 3 p

coord 4 4

dwei 3.1 0.5

dlig 1.9 0.5

% continue

Directives in polyhedra command

The following directives must be added after the command '% polyhedra' in the
input file to activate some specific features of the polyhedra procedure

MISSING n1 n2 El tetrahedron (octahedron) d tol1 tol2

n1 and n2 are the two order numbers (taken from an external file or from a Fourier map) of

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the cations between which the missing cation must be located;

El is the missing cation label tetrahedron (octahedron): the type of coordination of the
missing cation. (The procedure can only handle octahedron and tetrahedron);
d is the expected cation-anion distance;
tol1, tol2 are the tolerance parameters for the distance and the tetrahedron (octahedron)
angle respectively. Default values are 0.3.

OCTAHEDRON El d tol1 tol2

d is the expected octahedral coordination distance around the El element;

tol1 and tol2 are the tolerance parameters for distances and angles respectively.

TETRAHEDRON El d tol1 tol2

d is the expected tetrahedral coordination distance around the El element;

tol1 and tol2 are the tolerance parameters for the distances and angles respectively.

EXAMPLES
Example 1
The POLPO1 procedure is applied to locate the light atoms around each specified heavy atoms. The crox.fra
file contains the cations coordinates.
The binary file 'crox.bin' must exist.
% window
%structure crox
%job CROX - home diffractometer data
%polyhedra
fragment crox.fra
octahedron 1 1.92 0.2 0.2
tetrahedron 2 1.75 0.2 0.2
tetrahedron 3 1.75 0.2 0.2
tetrahedron 4 1.75 0.2 0.2
%continue

Example 2
The POLPO2 procedure is applied to locate one or more missing cations and surronding anions. The
sapo.fra file contains the located cations coordinates.
The binary file 'sapo.bin' must exist.
% window
%structure sapo
%job SAPO - data from home diffractometer
%polyhedra
fragment sapo.fra
tetrahedron Si 1 1.6 0.2 0.2
tetrahedron Si 2 1.6 0.2 0.2
missing 1 2 Si tetrahedron 1.6 0.2 0.2

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missing 1 2 Si tetrahedron 1.6 0.2 0.2

%continue
Directives in Patterson command

The following directives must be added after the command '% patterson' in the
input file to activate some specific features of the patterson procedure.

E**2 (or E*E)

Coefficients to be used in the Patterson synthesis. This is the default.

E*F (or F*E)

Coefficients to be used in the Patterson synthesis.

F**2 (or F*F)

Coefficients to be used in the Patterson synthesis.

INVERSE

To activate the procedure of calculating the |F| values from an inverted suitably modified
Patterson map to use as starting point for the Le Bail algorithm in the extraction routine.

MAP, LAYX, LAYY, LAYZ, PEAKS, LIMIT, GRID: See FOURIER directives.

NPAT n

The number of cycles of successive inversions of the Patterson map.( Default values: 6 for
X-ray data, 5 for neutron data

References
Altomare A., Cascarano G., Giacovazzo C. & Viterbo D. (1991). Acta Cryst. A47, 744-748.
Main P. (1978). Acta Cryst. A34, 31-38.
Main P., Fiske S.J., Hull S.E., Lessinger L., Germain G., Declercq J.P. & Woolfson M.M.
(1980) - MULTAN80, a system of computer programs for the automatic solution of crystal
structures from x-ray diffraction data - Univ. of York, England.
Ten Eick L.F. (1977). Acta Cryst. A33, 977-979.

Created with the Personal Edition of HelpNDoc: Easy EBook and documentation generator

Structure solution by Direct Space methods

Direct Space algorithms in EXPO2014

Direct space methods for crystal structure determination from powder diffraction
data have become widely available and popular in recent years and have successfully

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been applied to solve the structures of organic, inorganic and organometallic materials.
Different but similar procedures can be realized: grid search, Monte Carlo, Simulated
Annealing (SA), parallel tempering, genetic algorithm. Each method involves the
generation of a random sequence of trial structures starting from an appropriate 3D model
and moving it until a good match between the calculated and the observed pattern is found.
The information about chemical knowledge of molecules is actively used to reduce the
number of parameters to be varied: bond distances and angles are usually known and kept
fixed while only the torsion angles are varied during the procedure.
Two Direct Space algorithms are now available in the EXPO2014 program, for
crystal structure solution.
They are:
1) a classical Simulated Annealing (SA) approach;
2) the Hybrid Big Bang Big Crunch (HBB-BC) algorithm (Altomare et al., 2013). It results
from an appropriate combination of BB-BC approach with SA and relies on one of the
evolutionary theory of the universe consisting of two successive phases: 1) the Big Bang,
corresponding to an energy dissipation procedure for creating a completely random initial
population; 2) the Big Crunch, corresponding to a contraction procedure for converging to
a global optimum point.
The procedure is supported by the same graphic interface of Simulated Annealing and is
automatically applied by the program for compounds described by less than 6 internal
degrees of freedom (torsion angles) and constituted by less than 3 fragments. In all other
cases the classical SA approach is used.

Preparing Input file

Graphic Interface of Simulated Annealing
Output file
When Direct Space approach fails
The directives in Simulated Annealing
Contact and References

Preparing Input file

To run EXPO2014 for structure solution by Direct Space approaches, first you need to
create the input file. It is supposed that the cell parameters and the space group have been
determined before so, fill the frame 'Cell Parameters' and 'Space Group'. Activate the
check button 'Structure Solution', select 'Simulated Annealing' and import the starting
model from 'fragment filename'. The following picture is an example for the crystal structure
determination of the paracetamol molecule. The profile counts file (paracetamol.xy) is in the
directory 'examples'.

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When you press the button 'Save' an input file paracetamol.exp (shown below) will be
created and automatically loaded by the program for the structure solution process by
Simulated Annealing.
%Structure paracetamol
%Initialize
%Job paracetamol
%Data
Cell 7.100 9.380 11.708 90.0 97.42 90.0
SpaceGroup p 21/n
Pattern paracetamol.xy
Wavelength 1.54056
%fragment paracetamol.mol
%sannel

Otherwise you can import an existing input file by the button 'Open' on the 'New Project'
dialog window or selecting 'File' > 'Load & GO' in the main menu. For example you
could load the file paracetamol.exp already existing in the example folder.

%sannel is a command to access to the Simulated Annealing graphic interface.

%fragment paracetamol.mol is the command to import the starting structural

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model for Simulated Annealing in MDL Molfile format (*.mol). This command can be
repeated several times to import more than one fragment (see the section Usage of
command %fragment). Some other file types can be imported in the same way:
MOPAC file (*.mop), Tripos Sybyl file (*.mol2,*.ml2), C.I.F. file (*.cif), Protein Data
Bank file (*.pdb), Fenske-Hall Z-matrix (*.zmt), EXPO fragment or Free Fractional
Format (*.frac), XYZ format (*.xyz), Tripos SYBYL (*.mol2, *.ml2), Shelx File (*.ins). A
complete list of the supported input file can be find in section Import of this document.
Instead of command %fragment name_starting_model.ext, with ext=mol,
frac, cif etc, you can import the starting structural model directly by the graphic
interface from the menu File > Import.

Modify > Add fragments to add fragment to an existing partial structural model.
Instead of command %sannel, you can access directly to the graphic interface from menu
"Solve" > "Simulated Annealing".

Press the button in the dialog window to run the Simulated Annealing

procedure.

Consider the following two strategies on the preparing starting model for direct-space
solution.

1) The user is strongly advised to check for similar molecules in the Cambridge Structure
Database (CSD) (organics & organometallics) or in the Inorganic Crystal Structure

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Database (ICSD) (inorganics, elements, minerals & intermetallics) or in the

Crystallography Open Database (COD: http://www.crystallography.net/) or in the literature. If a new struc

Some free database where look up molecules are:

1. NIST Chemistry WebBook: http://webbook.nist.gov/chemistry/
2. Drugbank: http://www.drugbank.ca/
3. PubChem: https://pubchem.ncbi.nlm.nih.gov/
Calculated 3D molecules in sdf, pdb, mol format can be find in these database and
imported in EXPO2014. Computed Simplified Molecular-Input Line-Entry System
(SMILES), when available, can be converted in 3D by File > Import Fragment > From
SMILES or Modify > Add Fragments > From SMILES

2) Starting molecular model can be created by geometry optimization using quantum-

chemistry package, e.g., MOPAC, Gaussian, Gamess, NWChem. Some free available
software that can be used to sketch molecules, optimize the geometry by force field
method and create input file for the quantum-chemistry calculations are:
1. Avogadro: http://avogadro.cc/wiki/Main_Page
2. Gabedit: http://gabedit.sourceforge.net/
3. ACD/ChemSketch: http://www.acdlabs.com/resources/freeware/chemsketch/
4. MarvinSketch: https://www.chemaxon.com/products/marvin/marvinsketch/
See the section Geometry Optimization for more information about the support provided
by EXPO2014 for theoretical calculations.

Graphic Interface of Simulated Annealing

The dialog window of Direct Space algorithms in EXPO2014 is composed by 4
pages.
The first page contains the general settings of:
Simulated Annealing algorithm:

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or HBB-BC algorithm:

Cost function: 2 cost functions can be selected: R weighted profile (default cost
function), R-Bragg intensities.
Resolution: defines the maximum resolution used by Simulated Annealing procedure.
Random seed: selects the value determining the sequence of random numbers used
from the algorithm. When is set to 0 the random seed will be calculated by the system
clock.
Nr. of runs: select the number of Simulated Annealing runs. At the beginning of each
run a new value of random seed is calculated.
Starting temperature: selects the starting temperature. Check on 'automatic' and the
program automatically will find the starting temperature at the beginning of the
procedure.
Number of cycles: the number of moves for each step of temperature is Np*N*20

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where Np is the number of refined parameters and N is a number set by the user in the
entry box. Choosing 'automatic' the program automatically will determine the value of N
by taking into account the external and internal DOFs and the flexibility of the molecule.
This number can be modified also by directive niter (see above).
Temperature reduction factor: the reduction factor applied to the temperature at
each step in the annealing schedule. The default value is 0.90. Increasing this value,
the chance to find the global minimum can be improved even if a longer execution time
will be taken by the procedure.
Solutions: browse the best solutions saved at the end of each run.

The second page External DOF contains information about the external degrees of
freedom (DOFs):

Select fragment: selects the fragment and visualizes the corresponding structure
information.
Atoms: list of the atoms in the selected fragment.
Parameter for fragment: list of the external DOFs for the selected fragment. Check
the parameters to refine, enter the lower and upper bounds of the parameters.
The third page Internal DOF contains information about the internal degrees of
freedom (DOFS):

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Internal DOFs: list of the torsions associated to each refinable internal DOF. Check
the parameters to refine, enter the lower and upper bounds of parameters.

Press the button 'Atomic parameters' to access to the following dialog window:

Thermal parameters: check the buttons on column 'B[iso]' to refine the thermal
parameters of atoms. Click on label 'B[iso]' to select all checks in the column. If the
thermal parameters are not indicated in the imported fragment file, the program
assigns the default values of B=3.0 for non-hydrogen atoms and B=6.0 for hydrogen
atoms. These default values can be changed editing the new values in the
column. The refinement of the thermal parameters is discouraged because usually
doesn't improve the results.
X Y Z: check the buttons on column 'Shift on xyz' to refine the atom positions, in this

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case the fragment is not rigid but the atom positions are shifted respect to the
barycentre. Click on label 'Shift on syz' to select all checks in the column. The
positions refinement (x,y,z) is generally discouraged because can considerably
increase the time to reach the global minimum.
Maximum shift on position: enter the value of the maximum shift of the atomic
positions. 0.020 is the suggested value. Increasing this value the explored parameter
space becomes wider so increasing the probability of falling into a local minimum.
Dynamical Occupancy Correction (DOC): automatic detection of atoms in special
position and atoms that share the same position. If this option is not active all refined
atoms are considered in general position (default). DOC will be applied only on the
atoms selected in the column D.O.C., select all atoms if you don't know exactly which
atoms will fall into special positions. DOC slows down the computation time so it
should be avoid if non special position or shared atoms are expected
Pattern: Enter the direction of the preferred orientation and check 'G Factor'. The
March-Dollase correction will be applied and the magnitude of the preferred
orientation will be optimized.

A visual match between observed and calculated powder pattern is plotted when
Simulated Annealing is running, the progress of structure solution is monitored and
the user can examine:
1) the graph of the minimum values of the cost function (CF) vs. the number of moves;
3) the crystal packing by using the button on the JAV viewer.

During the Direct Space runs, three buttons are active on the toolbar of the main window:
opens the JAV viewer for crystal structure visualization.
skips the current run.

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stops the procedure.

Output file
The output file generated from the procedure, contains information on:
1) the starting structure
2) the volume per atom
2) the connectivity
3) the internal and external DOFs
4) the refined parameters by SA
5) each SA or HBB-BC run
6) the summary of all the SA or HBB-BC runs
7) the selected final structure

At the end of each run the structure coordinates are saved in CIF file with name
created by project name with suffix _best1,_best2, ... (e.g. paracetamol_best1.cif is
the best solution, paracetamol_best2.cif is the second best solution, etc.). The order
number in the name represents the position in the list of structures ordered according
to the cost function.
When Direct Space approach fails
When Direct Space approaches fail:
1) The quality of data is not good and the diffraction pattern is not suitable for the
extraction of integrated intensities. In this case can be convenient to perform the
optimization by using the cost function R weighted profile.
2) The starting model is incorrect: bond distances and angles are not entirely
accurate, the number of building blocks is wrong. Improve your model with Cambridge
Structural Database (CSD) or building packages (Avogadro, ChemSketch,
ChemDraw, ...), check for atom in the output file (about 15-20 Ang/atom).
3) The assumption about thermal factors is invalid. Check thermal factors from similar
structures.
4) Space group and cell parameters are not correct. Additionally, in many cases it
may be necessary to carry out a series of independent calculations to test different
potential space groups and/or unit cell choices.
5) The default conditions, for complex structure, cannot be appropriate. Increase the
number of moves and/or runs, try with slower temperature reduction.
The directives in Simulated Annealing

Usually you don't need to read this paragraph unless you are interested to run
Simulated Annealing without interaction with graphic interface. In this case use the
command %sannel to run Simulated Annealing from the input file (*.exp). Use command
%automatic to skip the interaction with the graphical interface and the program will
perform the Simulated Annealing using the default values. An example of input file with
command %automatic and %sannel is the following:

%automatic
%Structure paracetamol
%Job paracetamol
%Data

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Cell 7.100 9.380 11.708 90.0 97.42 90.0

SpaceGroup p 21/n
Pattern paracetamol.xy
Wavelength 1.54056
%fragment paracetamol.mol
%sannel

To modify the default values of SA, some directives can be used after the command %
sannel.
An example of application of directive niter and nrun to increase the percentage of
success in case of structure solution of the largely flexible molecule verapamil
hydrochloride
%Structure verapamil
%Job Verapamil hydrochloride (C27H39N2O4.Cl)
%Data
Cell 7.089 10.593 19.207 100.11 93.75 101.56
SpaceGroup p -1
Pattern verapamil_hydrochloride.xy
Wavelength 1.54056
%fragment verapamil_hydrochloride.mol
%sannel
niter 2000
nrun 20

The following directives must be added after the command %sannel in the input
file to activate some specific features of the Simulated Annealing procedure
Abbreviations for directives name at least 4 character are permissible, i.e. "cost 2" instead
of "cost_function 2".
nrun n
To modify the number of Simulated Annealing runs. The default is 10.
niter n
To modify the number of moves for each temperature step. In a default run the number of
moves is automatically calculated.
resmax val
To define the maximum resolution used by Simulated Annealing. The default value is 2.0 Å.
temper temp
To modify the initial temperature. In a default run the initial temperature is automatically
calculated.
tfactor val
Determines the temperature reduction factor. val ranges between 0 and 1 and its default
value is 0.90.
rotate_around_axis Ax1 Ax2 At1 At2 At3 ...
or
rotate_around_axis Ax1 Ax2 At1 At2 At3 ... theta

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Rotate atoms At1, At2, At3, ... around a rotation axis defined by atoms Ax1 and Ax2.
theta is an optional value (degrees) used to specify the limits of rotation angle from -theta
to +theta.
When rotate directive is used the specified rotation will be included in the panel 'Internal
DOF' of the graphical interface.

E.g.

rotate C1 C4 C5 C6 C7 C8 C9 C10
the phenyl ring C5-C6-C7-C8-C9-C10 will be rigidly rotated around the axis C1-C4
bump
Automatic generation of anti-bumping restraints extended to all C, N, O and S atoms
res atom1 atom2 target_dist tol weight
Apply restraints between 2 atoms. atom1 and atom2 are the labels of atoms. The other
parameters are optional and can be omitted.
target_dist is the ideal distance between the pair of atoms, when omitted the
distance is automatically deduced by using an internal table of distances.
tol is a permitted tolerance, when omitted the default value is 0.2
weight is a user supplied weight. A default weight is specified as 100.

fixrotation atom1 atom2

To fix the internal DOF. atom1 and atom2 are the 2 atoms defining the rotation axis. This
directive is useful when, relying on the prior chemical knowledge of the structure, some
internal DOFs, can be fixed. For example, double bonds in conjugated acyclic systems,
triple bonds, nitrilic triple bonds, etc.
fftranslation atom1 atom2 ....
To fix the translation of fragments containing atom1, atom2, ... It is enough to specify at
least one of atom belonging to the molecular fragment.
E.g.
fftranslation Ag1 Ag2
If Ag1 and Ag2 are in 2 different fragment, the traslation of fragment containing Ag1 will
be fixed and the traslation of other one will be fixed.
ffrotation atom1 atom2 ...
To fix the rotation of fragments containing atom1, atom2, ... It is enough to specify at
least one of atom belonging to the molecular fragment.
refinetf
To refine the thermal parameters.

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shift_atom val
or
shift_atom atom1 atom2 atom3 …. val
To optimize the atomic parameters by applying shifts (up to val) on the atoms with respect
to the centre of gravity of the fragment. The default val is 0.5. Add atom1, atom2,
atom3,… to refine only some specific atoms.
cost_function n
To choose the cost function: 1 for Rw-profile, 2 for RF, 3 for RI. The default choice is 1.

randomize n
To randomize the internal and external DOFs and the atomic parameters (if refined). n is an
optional parameters used as seed of random generator.
rotat n1 n2
To specify the internal DOF using the input file.
doc
or
doc atom1 atom2 atom3 ...
Activate the dynamical occupancy correction (DOC). By default DOC is applied to all the
atoms unless you specify a list of atoms.
E.g.
doc Ni1
DOC will be applied only to the atom Ni1.
po H K L
Activate the March-Dollase preferred orientation correction. H K L are three integer
numbers necessary to specify the direction of the preferred orientation

Usage of command %fragment

The command %fragment can be used to import molecular starting model. This
command can be repeated several times to import more than one molecules. Some
examples are reported.
Input file for the structure solution of the creatine monohydrate

%Structure creatinem
%Job Creatine monohydrate (C4H9N3O2.H2O)
%Data
Cell 12.506 5.046 12.169 90 108.88 90
SpaceGroup P 21/c
Pattern creatinem.xy
Wavelength 1.54056
%fragment creatine.cif
%fragment H2O.sdf

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%sannel
The command %fragment was use to import the cif file of the creatine molecule
(creatine.cif) and the sdf file of the water molecule (H2O.sdf). The cell parameters and
space group reported in the creatine.cif were ignored and the creatine molecule was
imported in the cell and space group indicated by the user in the input file by directive
Cell and SpaceGroup.

Input file for structure solution of S-Ibuprofen containing two molecules of Ibuprofen in the
asymmetric unit (Z'=2)

%Structure S-Ibuprofen (C13 H18 O2)

%Initialize
%Job Structure solution of S-Ibuprofen
%Data
Cell 12.463 8.029 13.538 90 112.93 90
SpaceGroup p 21
Pattern pd_0034.pow
Wavelength 1.54056
%fragment Structure3D_CID_3672.sdf
%fragment Structure3D_CID_3672.sdf
%sannel

Two molecules of ibuprofen were imported using the file Structure3D_CID_3672.sdf

downloaded from the PubChem database (https://pubchem.ncbi.nlm.nih.gov/
compound/962#section=Top).

Contact

For suggestions and bugs contact corrado.cuocci@ic.cnr.it.

References
Altomare, A., Corriero, N., Cuocci, C., Moliterni, A., Rizzi, R. (2013). J. Appl. Cryst., 46,
779-787.
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Direct Methods combined with Simulated Annealing

Direct Methods combined with Simulated Annealing

in the EXPO2014 program
The information contained in the electron density maps provided by Direct Methods
has been combined with the Simulated Annealing technique in order to solve organic
crystal structures from powder diffraction data. In this procedure each peak of the Fourier
map is in turn associated to all the atoms of the imported model (Altomare et al., 2008).
For each association (the atom of the structural model is moved on the peak) the position

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of the model is fixed, while its orientation and internal conformation have to be found by SA
runs.

Run of Direct Methods combined with Simulated Annealing

Graphic Interface of Direct Methods combined with Simulated Annealing
Output of Direct Methods combined with Simulated Annealing
The Directives in Direct Methods combined with Simulated Annealing
About the construction of the models
Contact and References

Run of Direct Methods combined with Simulated Annealing

After a run of EXPO2014, the procedure can be graphically activated by 'Simulated

Annealing+Direct Methods' option of 'Solve' button in the upper menu of the EXPO2014
window.

Graphic Interface of Direct Methods combined with Simulated Annealing

The dialog window of Direct Methods combined with Simulated Annealing

procedure in EXPO2014 is composed by 3 pages containing the general settings of the
procedure.

The first page 'SA conditions' contains the general settings of the algorithm:

External model filename: the name of the imported starting structural model must be

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 EXPO2014

specified. Some file types can be imported: C.I.F. file (*.cif), Expo fragment or Free
Fractional Format (*.fra), XYZ format (*.xyz), MOPAC file (*.mop), MDL MolFile (*.mol),
Protein Data Bank file (*.pdb), Tripos SYBYL (*.mol2, *.ml2), Fenske-Hall Z-Matrix (*.zmt)
and Shelx File (*.ins).

Refer to openbabel wiki or http://www.ch.ic.ac.uk/chemime for informations about common

molecular file formats.

Refer to http://en.wikipedia.org/wiki/Molecule_editor and http://www.ccp14.ac.uk/

solution/2d_3d_model_builders/index.html for an exhaustive list of programs for building
3D starting models. Suggested free available programs for building 3D models are ACD/
ChemSketch (Windows), Avogadro (all platforms), Marvin (all platforms), Ghemical
(Linux). NIST Chemistry WebBook and Drugbank are useful links to look up fragments.

Resolution: defines the maximum resolution used by Simulated Annealing + Direct

Methods procedure.

The second page 'Fourier map condition' contains the information about the Fourier map
at which the imported starting model will be associated:

Use Direct Methods map: if selected, the program will use the atomic positions of the
Fourier map obtained at the end of the current run of EXPO2014.
Map filename: it is activated only if 'Use Direct Methods map' is de-selected. The filename
of the external Fourier map (in term of atomic positions) must be supply. Some file types
can be imported: C.I.F. file (*.cif), Expo fragment or Free Fractional Format (*.fra), etc.

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Number of peaks of Fourier Map: the number of atomic positions selected from the
map. If 'automatic' is selected, the program will use the 40% of the electron density peaks
(those with the largest intensity) to associate in turn to each model atom. This number can
be reduced by the user if 'automatic' is de-selected.

The third page 'Internal DOF' contains the information about the internal degrees of
freedom (DOFs):

Torsion: List of torsions associated to each refinable internal DOF. The order number of
each atom involved in the torsion angle to vary are also shown. The internal DOFs can be
or not refined (check Refine).
Lower-Upper: range of variation of the torsion angle. 180 means that the allowed range is
(x-180, x+180), where x is the value of the torsion angle in the initial model.

A visual match between the observed and calculated powder diffraction pattern is plotted
when the procedure is running. When Direct Methods combined with Simulated Annealing
procedure are running the progress of structure solution is monitored and the user can
examine:
1) the graph of the minimum value of the cost function (CF) vs. the number of moves;
2) the match between the observed and calculated pattern.

Use the buttons to zoom on graph.

During the Direct Methods combined with Simulated Annealing procedure runs two buttons
on the toolbar are activated:
opens the JAV viewer for crystal structure visualization.

stops the procedure.

Press the button to run the Simulated Annealing+Direct Methods

procedure.

Output of Direct Methods combined with Simulated Annealing

The output file contains information on:

1) the selected peaks of the Fourier Map imported or obtained at the end of a run of
EXPO2014;
2) the imported starting structural model;
3) the table of connectivity;

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4) the list of internal degree of freedoms (DOFs) to be varied;

6) the information about each association: peak of the map-atom of the model;
7) the summary of the ten best associations which are refined in sequence;
8) the selected best final structure.

About the construction of the models

Refer to openbabel wiki or http://www.ch.ic.ac.uk/chemime for information about common

molecular file formats.
Refer to http://en.wikipedia.org/wiki/Molecule_editor and http://www.ccp14.ac.uk/
solution/2d_3d_model_builders/index.html for an exhaustive list of programs for building 3d
molecules. Suggested free available programs for building 3D molecules are ACD/
ChemSketch (windows), Avogadro (linux), Marvin (all platforms), Ghemical (linux) NIST
Chemisty webbook and Drugbank.

Contact

For suggestions and bugs please contact rosanna.rizzi@ic.cnr.it.

References
A. Altomare, R. Caliandro, C. Cuocci, C. Giacovazzo, A. G. G. Moliterni, R. Rizzi and C.
Platteau. 'Direct methods and simulated annealing: a hybrid approach for powder
diffraction data'. J. Appl. Cryst. (2008). 41, 56-61.

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Rietveld Refinement

Rietveld Refinement in EXPO2014

Structure refinement by Rietveld method (Rietveld, 1969) is available in EXPO2014.

Graphical and computing tools are available in the program in order to attain a successful
automatic or user-defined Rietveld refinement.

The refined variables include peak shape parameters, unit cell dimensions, coordinates of
atoms in the structure model, background coefficients, scale factor, isotropic displacement
parameters. Atomic displacement parameters can be refined individually or in a group of
atoms with the same atomic type or the same environment. Correction for the preferred
orientation can be achieved by the March-Dollase approach. The background is described
using empirical functions: classical polynomial function, Chebyshev polynomial function,
cosine Fourier series. The background can also modeled by mouse-click selection of

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 EXPO2014

pattern points. The available peak shape functions are: Pseudo-Voigt, Pearson VII,
Thompson-Cox-Hastings pseudo-Voigt.

The non-linear least squares are carried out by employing the damped Gauss-Newton
method. The refinement convergence condition is reached when the increments on
parameters become smaller with respect to their standard deviations or when the relative
gradient of χ2 minimized function is less then a tolerance value. Tolerance value and the
maximum number of cycles could be suitably modified by the user.

The Le Bail technique can be adopted to perform a full pattern decomposition prior to
Rietveld refinement in order to determine starting values of parameters (background, peak
shape, zero shift and unit cell dimensions) to refine. This strategy is suggested especially if
the available structure model is not completed (McCusker et al., 1999) or when the starting
model is too different from the target model.

The refinement can be carried out by following two alternative approaches: 1) the user can
decide the refinement strategy via graphic interface; 2) an automatic refinement schedule
can be applied. In the automatic mode, groups of parameters are refined according to a
fixed sequence as established in the Rietveld guidelines (Young, 1995). In the last step of
refinement all parameters are refined simultaneously.
The knowledge of molecular geometry can be exploited in the refinement in form of
restraints on bond distances, angles and planes. To simplify the setting of restraints, the
program is able to extract from the connectivity of the initial model the possible restraints
providing a list of current and target values. The user can select the restraints to be
included in the refinement procedure and eventually modify the target value.

Some figures of merit are available in order to follow the progress and evaluate the quality
of refinement: the weighted profile R-factor and the unweighted profile R-factor calculated
for the full pattern (Rwp, Rp); the corresponding figures background-subtracted (Rwp', Rp');
the statistically expected R value (Rexp); the goodness-of-fit (Rwp/Rexp); the Durbin-Watson
d-statistic. R values similar to those used in case of single crystal data are also available:
RF and the Bragg-intensity R (Rb)which use the structure factor moduli extracted from the
experimental profile. In addition, graphical tools are available for visualizing: 1) the
observed, calculated and difference pattern and the cumulative χ2 value; 2) the evolution of
the structure model during the refinement in real time.

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where:
N is the total number of counts in the pattern and P is the number of refined parameters.

Preparing Input file for Rietveld Refinement

To run EXPO2014 for Rietveld refinement, first you need to create the input file. This is an
example of the typical input file:
%Structure paracetamol
%Initialize
%Job paracetamol
%Data
Cell 7.100 9.380 11.708 90.0 97.42 90.0
SpaceGroup p 21/n
Pattern paracetamol.xy
Wavelength 1.54056
%fragment paracetamol.cif
%rietveld

It is supposed that the cell parameters and the space group have been determined
before and a structure model is available and imported by using the command %
fragment followed by the file name containing the structure. %rietveld is a
command to access to the Rietveld Refinement graphical interface.

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 EXPO2014

Alternatively, when a structure model is available, you can access directly to the
graphic interface from menu "Refine" > "Rietveld"

Constraints
Constraints are defined as exact mathematical relationships between least squares
parameters and can be used to reduce the number of parameters.

Symmetry constraints, required to conserve the space-group symmetry requirements,

are mandatory and automatically deduced and imposed by the program. For example, an
atom on the special position ( 0.5 , 0.5 , 0.5 ) in P -1 should not be refined at all and its
parameters are constrained to these special values. Alternatively, an atom on the special
position (x, x, x) in space-group P23 can be refined but must be constrained to have equal
shifts applied in the x, y and z directions. Lattice symmetry establishes specific
relationships between the unit cell dimensions (e.g, in cubic a=b=c and
alpha=beta=gamma). EXPO2014 automatically deduce and impose these constraints.

Constraints are often employed to control site occupancies when disorder is present in
one or more sites. It is not uncommon in minerals to find an atomic site that can be
occupied by either of two element types. For example, if three atoms A, B, and C occupy
the same site then, assuming the full total occupancy of the site, the following relationship
(or constraint) results: occA + occB + occC = 1. Thus, only two of the fractional occupancies
should be refined, for example, occA and occB are free least squares variables but occC =
1 - occA - occB. Atomic displacement parameters (ADP) are made to shift synchronously.
EXPO2014 automatically identifies atoms that occupy the same site and impose the
constrains on site occupancies and on ADPs.

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Other constraints may be imposed by the user. Clicking on the button 'Constraints' in the
'Crystal Structure' section is possible to access to a dialogue window to define group of
ADPs that can have the same shift.

Contraints are applied to H atoms by using the riding model. This technique is used to
move H atoms synchronously with the C atoms to which they are bonded, thereby
preserving the bond length and direction. The isotropic displacement parameters Uiso of
the hydrogens are constrained to be 1.2 times of that of the heavy atom to which they are
attached. The factor 1.2 can be changed by graphic interface.

Contact
For suggestions and bugs contact:
angela.altomare@ic.cnr.it
annagrazia.moliterni@ic.cnr.it
rosanna.rizzi@ic.cnr.it

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 EXPO2014

corrado.cuocci@ic.cnr.it

References

Rietveld, H.M.: A profile refinement method for nuclear and magnetic structures. J. Appl.
Cryst. 2 (1969) 65–71.
McCusker, L.B.; Von Dreele, R.B.; Cox, D.E.; Louër, D.; Scardi, P.: Rietveld refinement
guidelines. J. Appl. Cryst. (1999). 32, 36-50
The Rietveld Method. Edited by R. A. Young, Oxford University Press, Oxford (1995)

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Commands of EXPO2014 and their use

Commands of EXPO2014 and their use

The input file name for EXPO2014 is constituted by the name of the structure to
analyze followed by the suffix .exp, i.e.
name.exp
The input consists of a sequence of commands, directives and comments. The commands
are headed by '%' character and directives must follow the related command.

For the default run see Example 1.

EXPO recognizes the following commands:

%WINDOW Graphic window is required

%NOWINDOW Graphic window is suppressed
This command is used to specify the name of the structure to
investigate. The program creates the name of the files adding the
appropriate extension to the structure name. The file names are:
%STRUCTURE
string.bin -> binary file
string
string.out -> output file
If this command is not used the default string "STRUCT" (instead
of the name of the structure) is used to create file names
%JOB caption A caption is printed in the output
Initialize the direct access file (to override previous results and
%INITIALIZE
data)
%DATA Data input routine
%NTREOR Indexing routine
%EXTRACTION Integrated intensities extraction routine
%NORMAL Normalization routine

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%INVARIANTS Invariants routine

%PHASE Converge-tangent routine
%FOURIER Fourier/Least-Squares routine
%MENU
%END End of the input file
The program runs in default conditions from the last given
%CONTINUE
command up to the end
%PATTERSON Patterson map calculation routine
%REFINE Fourier/Least-Squares restart routine
%RECYCLE Extraction recycle routine
%SANNEL direct space routines
%SDIRECT Direct Methods combined with direct space routine
%EXPORT Export files (xxx=hkl,cif,xyz,frac)
filename.xxx
Directives are described below, in the sections dedicated to the various routines.
All commands and directives are in free format (between columns 1-80) and are cases
independent. Only the first four characters are significant. The keywords can start in any
position. If the first non-blank character is ">", then the record is interpreted as a comment.
EXPO2014 preserves intermediate results in the file named name.bin (binary file or
project file). For example, if invariant estimates have been already obtained during a
previous run of EXPO2014, in a new run the command %INVARIANTS can be omitted.

Commands can be given in any order, under the following conditions:

· first routine used must be DATA, if it has not been used in a previous run;

· EXTRACTION routine must be used to extract integrated intensities from the

diffraction pattern, if a reflections file is not supplied by the user;

· NORMAL must be used if reflections file has been supplied or EXTRACTION step
has been performed;

· INVARIANT routine has no meaning if diffraction moduli are not normalized;

· PHASE routine has no meaning if no triplets have been calculated;

· FOURIER routine cannot run before PHASE routine (unless a fragment information is
supplied by the user; in this case only DATA, EXTRACTION and FOURIER
commands are needed).

The minimal information needed by EXPO2014 for a full run (from indexing to structure
solution) is constituted by (see Example 1):

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· cell parameters (not necessary if N-TREOR program is used)

· space group symbol (not necessary if the Space Group Determination procedure is
applied by using "findspace" directive)

· cell content

· diffraction pattern (or reflections if an external reflection file is provided by any profile
fitting program)

· wavelength

· type of radiation (if neutron or synchrotron data have been used; home diffractometer
data is the default).

EXPO2014 prints results in a file named name.out.

Add '%EXPORT filename.xxx' in the input file to export files. Filename is the name of file to
export and xxx define the type of file. Use xxx=cif, xyz, frac to export structure model
respectively in cif file, xyz cartesian coordinates, fractional coordinates; use xxx=hkl to
export file with hkl, extracted structure factors, calculated structure factors, phases from the
obtained model.
In the following example, the command export before '%data' is used to export hkl and cif
file and it will be processed only at the end of structure solution process with Direct
Methods.
%structure cime
%job structure cime
%init
%export cime.hkl
%export cime.cif
%data
pattern cime.pow
cont s 4 c 40 n 24 h 64
wave 1.52904
cell 10.6986 18.8181 6.8246 90.000 111.284 90.000
space p 21/n
sync
%continue

An other example in case of structure solution with Simulated Annealing

%Structure paracetamol
%Job paracetamol
%Initialize%Initialize
%export paracetamol.hkl
%export paracetamol.cif
%Data
Cell 7.100 9.380 11.708 90.0 97.42 90.0

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 EXPO2014

SpaceGroup p 21/n
Content c 32 o 8 n 4 h 36
Pattern paracetamol.pow
Wavelength 1.54056
%fragment paracetamol.mol
%sannel
%continue

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Description of EXPO2014 commands

Description of EXPO2014 commands

The main modules of the program are:

EXPO, LIST, DATA, NTREOR, EXTRACTION, NORMAL, INVARIANTS, PHASE,

FOURIER/LEAST-SQUARES, DIRECT, PATTERSON.

EXPO module

It interprets commands and calls desired routines.

LIST module

It is the software interface between EXPO2013 and the direct access file on which data
and results are stored.

DATA module

This routine reads the basic crystallographic informations like cell parameters, space
group symbol (it may be also found by the program, using "findspace" directive),
wavelength, unit cell content and the counts (or reflections). It includes a modified version of
the subroutine SYMM Burzlaff & Hountas (1982). Symmetry operators are directly derived
from the space group symbol.
An external file (containing counts or reflections) is supplied by the user. If an external
reflection file is supplied (avoiding the extraction step), diffraction data are checked in
order to find out equivalent reflections or systematically absent reflections (which are then
excluded from the data set).

N-TREOR module

This routine performs the indexing step (a peak search procedure is automatically carried
out by the program before the indexing step). If available, an external peak positions file
can be supplied to the program and the automatic peak search procedure will be skipped

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 EXPO2014

by EXPO2014. The indexing procedure retains the basic search algorithm of TREOR90,
(Werner et al., 1985) and has been strengthened in the last version of N-TREOR09
(Altomare et al., 2009).

EXTRACTION module

In this module diffraction integrated intensities are extracted from the powder diffraction
pattern.
To calculate the integrated intensities, the program uses the Le Bail algorithm (Le Bail,
Duroy & Fourquet, 1988) and combines it with a least squares procedure minimizing the
quantity:

åwi (yoi - yci) 2 (1)

NORMAL module

In this module diffraction intensities are normalized using the Wilson method
(Wilson, 1942). Statistical analysis of the intensities is made in order to suggest the
presence or absence of the inversion centre, to identify the possible presence and type of
pseudotranslational symmetry (Cascarano et al., 1988 a,b; Fan, Yao & Qian, 1988) and to
detect preferred orientation effects (Altomare et al., 1994; Altomare et al., 1996). Possible
deviations (of displacive type) from ideal pseudotranslational symmetry are also detected.
All the above information is used as prior information in the integrated intensities extraction
process, unless the directive NOPSEUDO is given to the program.
When some additional prior information, besides positivity and atomicity of electron
density, is available, then a suitable renormalization of structure factors is made.

INVARIANTS module

Up to 10000 triplets relating reflections with normalized E values greater than a

given threshold (strong triplets) are stored for active use in the phasing process. Also
triplets (PSI-ZERO triplets) relating two reflections with large E and one with E close to zero
are generated: they are used to define a special figure of merit (PSCOMB). Special types
of triplets (PSI-E triplets) based on two strong and one intermediate reflections (just below
the threshold of strong reflections) are calculated and used in the FOURIER/LEAST-
SQUARES module in order to extend phase information (Altomare et al., 1991).
Negative quartets are generated by combining the psi-zero triplets in pairs, and those with
cross-magnitudes smaller than a given threshold are estimated by means of their first

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 EXPO2014

representation, as described by Giacovazzo (1976). These quartets are used to provide an

important contribution to the CPHASE FOM.

PHASE module

In the EXPO2014 program the most reliable one-phase s.s. are treated as known
phases. Besides triplets, also the most reliable negative quartets and two-phase s.s. may
be actively used.
Each relationship is used with its proper weight: the concentration parameter of the first
representation for quartets and two-phase s.s., and C or G for triplets.

- CONVERGENCE/DIVERGENCE PROCEDURE -

The convergence procedure (Germain et al., 1970) is a convenient way of defining an

optimum starting set of phases to be expanded by the tangent formula or by any other
algorithm.
When the P10 formula is used, as a default, a special convergence process is devised
which chooses the starting set.

Once the starting set has been defined, a good pathway for phase expansion is
determined by a divergence procedure. In the divergence map, starting from the reflections
in the starting set, each new reflection is linked to the preceding ones with the highest value
of < a >.

- PHASE EXTENSION AND REFINEMENT -

The starting set defined by the preceding step is usually formed by the origin (and
enantiomorph) fixing reflections, a few one phase s.s. and a number of other phases which
may be obtained:
a) by magic integer permutation (White & Woolfson, 1975; Main, 1978),
b) by a random approach (Baggio et al., 1978; Burla et al., 1992).
The option a) is the default, b) runs if the directive RANDOM is used. In this last case a
large number (depending on the available computer time) of trials can be requested.

FOURIER/LEAST-SQUARES module

The sets of phases generated by the tangent routine are first expanded through psi-E
relationships and then passed to the fast fourier transform routine written by L.F.Ten Eick
(1977) and subsequently modified by the MULTAN team (Main et al., 1980).

DIRECT module

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 EXPO2014

In this module some "direct-space" approaches for solving crystal structures from powder
diffraction data, can be used. The basic idea is to actively use structural and geometrical
information, available a priori, during the structure solution process.

LABELLING procedure

The atomic species assigned to the peaks of an electron density map obtained at the end
of a direct method procedure, can be modified using chemical information about the
structure. The procedure (Altomare et al., 2002) requires: 1) the prior information on the
number and coordination of the heavy atoms (the procedure can only handle tetrahedral
and octohedral coordinations); 2) the range of the typical distances between heavy atoms;
3) the range of the typical distances between heavy and light atoms.

POLPO procedure

Using the "%polyhedra" command, two procedures can be activated. Both of them use a
Monte Carlo approach and exploit the experimental information about the heavy - atom
connectivity. The first one (POLPO1) (Altomare et al., 2000) is suggested when all the
heavy atoms are rightly positioned and labelled. It is able to correctly locate the light atoms.
The second one (POLPO2) (Giacovazzo et al., 2002) is able to position one or more
missing cations and surrounding anions.

PATTERSON module

In the EXPO2014 program it is possible to compute a PATTERSON map using various

coefficients.
By using a special directive (INVERSION) it is possible to exploit the positivity of the
electron density (in the direct space) in the extraction routine. The so-modified Patterson
map is inverted providing a set of structure factor values to use in a new extraction
process.

References
Altomare A., Burla M.C., Cascarano G., Giacovazzo C., Guagliardi A., Moliterni, A.G.G. &
Polidori, G. (1996). J. Appl. Cryst. 29, 341-345.
Altomare A., Cascarano G., Giacovazzo C., Guagliardi A., Burla M.C., Polidori G. &
Camalli M. (1994). J. Appl. Cryst. 27, 435 - 436.
Altomare A., Cascarano G., Giacovazzo C. & Viterbo D. (1991). Acta Cryst. A47, 744-748.
Altomare, A., Campi, G., Cuocci, C., Eriksson, L., Giacovazzo, C., Moliterni, A., Rizzi, R. &
Werner, P.-E. (2009). J. Appl. Cryst. 42, 768-775.35,182-184.
Altomare A., Giacovazzo C., Guagliardi A. Moliterni A.G.G., Rizzi R. (2000). J. Appl. Cryst.
33, 1305-1310.
Altomare A., Giacovazzo C., Ianigro M., Moliterni A.G.G., Rizzi R. (2002). J. Appl. Cryst.
35, 21-27.

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 EXPO2014

Baggio R., Woolfson M.M., Declerq J.P. & Germain G. (1978). Acta Cryst. A34, 883-892.
Burla M.C., Cascarano G. & Giacovazzo C. (1992). Acta Cryst. A48, 906-912
Burzlaff H. & Hountas A. (1982). J. Appl. Cryst. 15, 464-467.
Cascarano G., Giacovazzo C. & Luic' M. (1988a). Acta Cryst. A44, 176-183.
Cascarano G., Giacovazzo C. & Luic' M. (1988b). Acta Cryst. A44, 183-188
Fan H., Yao J. & Qian J. (1988). Acta Cryst. A44, 688-691.
Germain G., Main P. & Woolfson M.M. (1970). Acta Cryst. B26, 274-285.
Giacovazzo C. (1976). Acta Cryst. A32, 958-966.
Giacovazzo C., Altomare A., Cuocci C., Moliterni A.G.G., Rizzi R. (2002). J. Appl. Cryst.
35, 422-429
Le Bail A., Duroy H. & Fourquet J.L. (1988). Math. Res. Bull. 23, 447-452.
Main P. (1978). Acta Cryst. A34, 31-38.
Main P., Fiske S.J., Hull S.E., Lessinger L., Germain G., Declercq J.P. & Woolfson M.M.
(1980) - MULTAN80, a system of computer programs for the automatic solution of crystal
structures from x-ray diffraction data - Univ. of York, England.
Ten Eick L.F. (1977). Acta Cryst. A33, 977-979.
Werner P.-E., Eriksson L. & Westdahl M. (1985). J.Appl.Cryst. 18, 367-370.
White P.S. & Woolfson M.M. (1975). Acta Cryst. A31, 53-56.
Wilson, A. J. C. (1942). Determination of Absolute from Relative X-Ray Intensity Data.
Nature, Load.
150, 152.
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Preparation of data

Preparation of data for the DATA routine

This routine reads the basic crystallographic information like cell parameters, space
group symbol (it may be also found by the program, using "findspace" directive),
wavelength, unit cell content and the counts (or reflections). It includes a modified version of
the subroutine SYMM Burzlaff & Hountas (1982). Symmetry operators are directly derived
from the space group symbol.
An external file (containing counts or reflections) is supplied by the user. If an external
reflection file is supplied (avoiding the extraction step),diffraction data are checked in order
to find out equivalent reflections or systematically absent reflections (which are then
excluded from the data set).

ALPHA

It is used to start the alpha2 stripping.

CELL a b c a b g

cell dimensions a, b, and c are in angstroms, a, b and g in degrees.

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CONTENTS El1 n1 El2 n2 El3 n3 .........

Unit cell contents. Eli is the chemical symbol of atomic species i, ni is the corresponding
number of atoms in the unit cell (to a maximum of 8 atomic species). For each chemical
element up to Cf (Z=98) X-ray scattering factor constants are stored, together with
information on the atomic number and weight, covalent and Van-der-Waals radii, etc. in a
file (see notes on implementation). Neutron scattering factors are coded in the program for
elements up to Pu (Z=94).

EQUIPORTION

If this directive is given the overall intensity of a group of overlapping reflections is

equiportioned among the reflections in the group (equal E-values are obtained).

EXTEFILE string

This directive is used to supply an external file containing 'd' or '2q' values of peak
positions. In the latter case the additional '2-THETA' directive has to be used.
If this directive is used the program will skip the automatic "peaksearch " procedure.

FILETYPE string

This directive is used to specify the format of input file containing the diffraction data. string
defines the type of file and can be 'counts', 'xy', 'double', 'gsas'.

If the directive FILETYPE string is absent or string is 'counts' the first three number at the
beginning of the counts file must be the 2theta minimum, 2theta step and 2theta maximum.
The following lines must be counts. The number of counts for row or the format of counts
can vary.

#Example 1: use, in the input file, the directive 'FILETYPE counts' or nothing
7.00 0.020 100.00
3017 2925 3056 2983 3008 2953 2875 2976 2886 2928
2973 2831 2960 2821 2854 2900 2857 2798 2876 2798
2819 2865 2830 2735 2771 2813 2806 2704 2823 2878
2793 2795 2756 2722 2705 2736 2802 2657 2811 2736
2753 2722 2780 2734 2795 2741 2812 2808 2713 2746
2696 2747 2799 2876 2741 2921 2776 2966 3017 3082
3058 3193 3147 3309 3319 3404 3490 3554 3684 3845
4015 4069 4293 4450 4657 4905 5201 5587 5796 6172

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 EXPO2014

6646 7225 7834 8918 9767 10641 11891 13411 15091 17902
....................................................................................................................
#Example 2: use, in the input file, directive 'FILETYPE counts' or nothing
6 0.01 55.98
412.98
404.51
412.40
405.57
403.30
405.94
404.89
389.39
396.55
408.00
403.24
385.44
396.46
393.20
390.52
401.58

.............................................................................................................

If string is 'xy' the counts file contains 2theta in the first column and the intensities in the
second one. The format of counts can vary.

#The use of directive 'FILETYPE xy'

4.700 4769.000 69.05795
4.714 4860.000 69.71370
4.729 4794.000 69.23872
4.743 4857.000 69.69218
4.758 4837.000 69.54855
4.772 4891.000 69.93568
4.787 4788.000 69.19537
4.801 4886.000 69.89993
4.816 4720.000 68.70226
4.830 4688.000 68.46897
4.845 4690.000 68.48357
4.859 4867.000 69.76389
4.874 4800.000 69.28204

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4.888 4863.000 69.73521

...........................................................................................................................

If string is 'double' the first line in the counts file contains 2theta minimum, 2theta step,
2theta maximum. The rest of file contains intensities and standard deviations on separated
lines.

#The use of directive 'FILETYPE double'

3.000 0.005 41.600
3567.2 3405.3 3370.1 3432.4 3476.2 3526.9 3354.7 3596.6 3476.8 3676.7
67.27 65.44 65.16 65.78 66.12 66.55 64.64 67.14 66.08 67.88
3623.0 3703.6 3555.1 3500.3 3558.6 3584.8 3606.2 3556.8 3710.3 3704.8
67.46 68.33 66.89 66.12 66.77 67.00 67.75 66.77 68.73 68.03
3721.0 3670.7 3775.1 3796.4 3820.9 3880.8 3809.1 3922.7 3963.5 3919.6
68.76 67.82 68.60 69.04 69.28 70.05 69.39 69.91 70.44 70.11
4062.6 4104.5 4148.8 4219.5 4221.6 4376.3 4294.3 4439.1 4349.1 4500.5
71.69 71.85 71.87 72.61 72.61 73.94 73.66 74.44 74.18 75.39
4449.2 4704.1 4833.7 4851.3 4892.2 5105.9 5143.3 5161.8 5272.0 5418.5
74.34 77.34 78.13 78.37 78.02 79.82 80.53 80.55 81.09 81.93
5543.3 5635.8 5918.0 6007.9 6406.6 6395.2 6515.0 6753.3 7255.9 7464.6
83.36 84.18 86.37 86.95 89.58 89.58 90.60 91.99 95.62 96.94
7811.5 8415.6 8597.6 9251.3 9995.7 10714.5 11097.2 11067.4 10678.3 9864.0
98.89 102.81 103.75 107.71 111.43 115.71 117.76 117.40 115.54 110.72
.............................................................................................................................

In the previous cases comment records can appear at the beginning of data file if the first
character is '#' or '!' or '>'. Examples in directory examples.

'FILETYPE gsas' can be used to read counts files in GSAS standard format with keyword
TYPE='STD' and TYPE='ESD'.

FINDSPACE

This directive is used in order to find a possible space group when the cell parameters are
known.

FWHM x

This directive supplies the value of x for the overlapping calculation. Two reflections are
assumed to be in overlapping if 2q1 -2q2 < x * FWHM. Default is x = 0.1.

HISTOGRAM n

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n is the number of bars in the histogram for the alpha2 stripping procedure (only if ALPHA
directive is used).

ISOTOPE El sf

To modify the value of the neutron scattering factor for element El using the value sf. (It must
be used if NEUTRON directive is given).

MOREPEAKS

This directive is used together with the peaksearch directive in order to add more low
intensity peaks to the set of peaks already detected via the peaksearch directive.

NEUTRON

This directive is used to specify that neutron radiation has been used.

NOREFINE

This directive is used to skip the cluster refinement step in the peak search procedure.

PATTERN filename

Filename is the name of the profile counts file (up to 40 characters). It is used to change the
default. [Default is name.pow where name is defined using the command %STRUCTURE].

RANGE thmin thmax

Only intensities included in the range thmin-thmax will be considered; thmin and thmax are
the minimum and maximum 2q value of the powder pattern respectively.

REF2 string

This directive is used to supply an external reflection file. EXPO reads directly the output
provided by any profile fitting program. HKL, FWHM and F**2 must be supplied [default
format is (3i4,2f15.4)]. If a comment line is at the beginning of the reflection file, the first
character must be '>'. If this directive is used, the directives 'pattern' and 'range' must not
be introduced.

SHIFT sx sy sz

Origin shift components if desired by the user. They must be integral multiples of 1/24.

SPACEGROUP string

String is the symbol of the space group, according to International Tables (1974). Blanks

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 EXPO2014

are necessary among the terms constituting the space group symbol (see examples at the
end of this manual).

SYNCHROTRON

This directive is used to specify that synchrotron radiation has been used.

STEP step_value

You can use this directive to specify that your data were collected at fixed step. This
directive is activated when the data file contains two columns (2theta values and
intensities) and you are using the directive 'FILETYPE xy'. If you use the directive STEP,
the first column is ignored and the program automatically recreates the 2theta values by
using step_value for the step and the first 2theta value in the data file.

THCORR x

x is the Dq0 value that is used to correct by zeropoint shift the set of 2q peak positions.
The shift value will be egual to 2(n-1)Dq0, where n is the sequential number of the N-TREOR
trial.
If this directive is not introduced the Dq0 default value is the experimental 2q step.

2-THETA

This directive is used combined with the EXTEFILE directive to supply to the indexing
program N-TREOR09 an external file containing 2q values of peak positions.

WAVELENGTH w

w is the wavelength (in Angstrom) used to collect the powder pattern.

References
Burzlaff H. & Hountas A. (1982). J. Appl. Cryst. 15, 464-467.
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Examples

Examples of input for EXPO2014

Example 1

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 EXPO2014

The following example shows the default use of EXPO2014 in case of indexed pattern.
Most of the structures can be solved in this way. Diffraction data are in the file crox.pow.
The content of the file crox.exp is

%structure crox
%job CROX- data from home diffractometer
%initialize
%data
pattern crox.pow
cell 5.447 6.5576 12.1147 106.382 95.715 77.970
content Cr 8 O 21
wavelength 1.3922
spacegroup p -1
%continue

Default "profile counts file" name: crox.pow

crox.pow content:

6.0000 0.02 100.0

1166. 1179. 1224. 1172. 1221. 1159. 1204. 1347.
1295. 1146.
1353. 1188. 1214. 1250. 1253. 1240. 1285. 1344.
1314. 1324.
1438. 1444. 1463. 1522. 1664. 1548. 1836. 1865.
1913. 2160.
2367. 2412. 2856. 3186. 3681. 4280. 4941. 5883.
7298. 8978.
11248. 14375. 20187. 25377. 23771. 15690. 8496. 6385.
5553. 5022.
4643. 4371. 4202. 3840. 3684. 3296. 3199. 3047.
2833. 2710.
2567. 2334. 2412. 2156. 2163. 2134. 1981. 1981.
2033. 1901.
1849. 1768. 1761. 1709. 1654. 1616. 1580. 1629.
1561. 1609.
1658. 1609. 1493. 1334. 1298. 1331. 1305. 1289.
1292. 1214.
1149. 1182. 1081. 1146. 1094. 1065. 1030. 1055.
981. 1020.
1046. 981. 971. 1049. 975. 965. 900. 929.
861. 858.

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874. 929. 835. 793. 839. 787. 907. 858.

822. 826.

Example 2

The Ka2 stripping with a 3 bars histogram is requested.

%structure dada
%job DADA- data from home diffractometer
%initialize
%data
spacegroup p 21 21 21
cell 7.13115 9.9077 12.9256 90.0 90.0 90.0
content Si 12 Ti 4 K 8 O 40
wavelength 1.540562
pattern dada.pow
alpha2
histogram 3
%continue

dada.pow content is:

10.00 0.02 95.00

457.0
437.0
421.0
475.0
469.0
425.0
465.0
405.0
447.0
461.0
433.0
433.0
433.0
415.0
453.0
451.0
429.0
453.0
427.0

Example 3
Data are from neutron source.
%structure cfcl
%job CFCL - data from neutron source
%initialize

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 EXPO2014

%data
pattern cfcl.pow
cell 10.168 14.964 5.100 90.000 90.000 90.000
content C 8 F 16 Cl 16
spacegroup f d d 2
wavelength 1.595
neutron
%continue

Example 4

A Pseudo-Voigt function will be used and the background in each interval will be described
by a constant. The counts file format is not the default one and the graphic window is
suppressed.
%structure mes
%job MES - data from home diffractometer
%initialize
%data
pattern mes.pow
cell 8.588 9.931 11.105 90.0 93.754 90.0
content C 24 N 4 O 20 S 4 H 52
spacegroup p 21/c
wavelength 1.5406
%extraction
pvoigt
polynomial 0
%end

Example 5

The starting values of the integrated intensities in the extraction step are supplied by the
user in the file "yono.ext" and the number of least-square cycles is set to 40.
%structure yono
%job YONO - Synchrotron data
%initialize
%data
pattern yono.pow
cell 9.385 16.394 3.627 90.000 101.067 90.000
content Y 8 O 26 N 2 H 18

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 EXPO2014

spacegroup p 21
wavelength 1.2323
synchrotron
%extraction
frecycle yono.ext
ncycle 40
%end

Example 6

The preliminary fitting of the standard peak is skipped and the starting 2q shift value is
supplied by the user (the program refines it).
%structure agpz
%job AGPZ - data from home diffractometer
%init
%data
pattern agpz.pow
cell 6.526 20.059 6.464 90.000 90.000 90.000
spacegroup p b c a
content Ag 8 N 16 C 24 H 24
wavelength 1.54056
%extraction
nosing
zeroprof 0.02
%continue

Example 7

Neutron data and a deuterium atom in the cell content are used. Fast graphic interaction for
the integrated intensities extraction process is activated.
%structure baco
%job BACO - Neutron data
%initialize
%data
neutron
isotope H 0.67
pattern baco.pow
cell 10.0632 7.9330 6.8487 90.0 122.3423 90.0

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spacegroup C 2/m
content Ba 4 C 8 O 20 H 8
wavelength 1.909
%extraction
fast
%continue

Example 8

The program restarts from the PHASE procedure.

A random approach is used and the best 100 sets of phases, over 250 trials, are retained
in the direct access file. No Fourier is required.
%structure nizr
%phase
random
maxtrials 250
minfom 1.0 100
%end

Example 9

The program restarts from the FOURIER procedure.

Only the E-map corresponding to the set number 7 and the complete FOURIER/LEAST-
SQUARES procedure for set number 10 are requested by the user.
%structure nbpo
%fourier
set 7
recyc 0
%fourier
set 10
%continue

Example 10

To view only the structure previously produced by FOURIER routine.

%window
%structure crox
%menu
%end

Example 11
Use of the pseudotranslational symmetry (if it is present) as prior information for a new
extraction process is inhibited. Use of nopse directive after command %normal.

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%structure agpz
%job AGPZ - data from home diffractometer
%initialize
%data
pattern agpz.pow
cell 6.526 20.059 6.464 90.000 90.000 90.000
spacegroup p b c a
content Ag 8 N 16 C 24 H 24
wavelength 1.54056
%extraction
%normal
nopseudo
%continue

Example 12

Use of the triplets estimation as prior information for a new extraction process.
%structure mes
%job MES - data from home diffractometer
%initialize
%data
pattern mes.pow
cell 8.588 9.931 11.105 90.0 93.754 90.0
content C 24 N 4 O 20 S 4 H 52
spacegroup p 21/c
wavelength 1.5406
%extraction
%normal
nopseudo
%invariants
estimation
%continue

Example 13

Use of the Patterson map inversion as prior information for a new extraction process.
%structure lasi
%job lasi - Neutron data
%initialize
%data
pattern lasi.pow
cell 5.4059 8.7934 14.2754 90.000 112.731 90.00
content La 8 Si 8 O 8
spacegroup p 21/c
wavelength 2.3400
neutron
%extraction

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%normal
nopse
%patterson
inverse
%continue

Example 14

A known fragment is used to complete the structure by applying the FOURIER/LEAST-

SQUARES procedure. The binary file "sapo.bin" must exist.
%structure sapo
%fourier
fragment SAPO.FRA
%continue

Coordinates are in the file "SAPO.FRA" which contains

Si .00000 .00000 .00000

Example 15

The indexing process is performed.

%structure gapo
%job GAPO - Synchrotron data
%initialize
%data
wave 1.24012
pattern gapo.pow
synchrotron
%ntreor
%end

Example 16

If a set of d (or 2 q) values is already available, the automatic peak search procedure is
skipped:
%structure mes
%job MES - data from home diffractometer
%initialize
%data
pattern mes.pow
wavelength 1.5406
2-theta
extefile mes.pea
%ntreor

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 EXPO2014

VOL = 6000, CEM = 40,

%end

'mes.pea' is an ASCII file containing the 2q peak positions.

The N-TREOR09 directives 'VOL = 6000' and 'CEM = 40' activate a search for a cell
having a maximum volume of 6000 Å3 and maximum axis value of 40 Å.

Example 17

Use of the change label procedure to relabel the peaks of an electron density map
obtained by applying the FOURIER procedure. The binary file "vfi.bin" must exist.
%structure vfi
%job VFI - Synchrotron data
%changelab
label 3 al 3 p
coord 4 4
dwei 3.1 0.5
dlig 1.9 0.5
%continue

Example 18

The POLPO1 procedure is applied to locate the light atoms around each specified heavy
atoms. The crox.fra file contains the cations coordinates.
The binary file 'crox.bin' must exist.
%structure crox
%job CROX - home diffractometer data
%polyhedra
fragment crox.fra
octahedron 1 1.92 0.2 0.2
tetrahedron 2 1.75 0.2 0.2
tetrahedron 3 1.75 0.2 0.2
tetrahedron 4 1.75 0.2 0.2
%continue

Example 19

The POLPO2 procedure is applied to locate one or more missing cations and surronding
anions. The sapo.fra file contains the located cations coordinates.
The binary file 'sapo.bin' must exist.

%structure sapo
%job SAPO - data from home diffractometer
%polyhedra
fragment sapo.fra
tetrahedron Si 1 1.6 0.2 0.2
tetrahedron Si 2 1.6 0.2 0.2
missing 1 2 Si tetrahedron 1.6 0.2 0.2

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missing 1 2 Si tetrahedron 1.6 0.2 0.2

%continue

Example 20

To find the space group.

%structure cf3br
%job CF3BR - Neutron data
%init
%data
pattern cf3br.pow
cell 8.146 5.85 7.962 90. 111.722 90.
cont c 4 br 4 f 12
wave 1.911
neutro
findspace
%continue

Table 1

Classes of reflections corresponding to the low index pseudo-translational symmetry.

1) h+k+l= 1n 2) h= 2n 3) k= 2n
4) l= 2n 5) h+k+l= 2n 6) h+k= 2n
7) h+l= 2n 8) k+l= 2n 9) h= 3n
10) k= 3n 11) l= 3n 12) h+k= 3n
13) h+l= 3n 14) k+l= 3n 15) h+k+l= 3n
16) h+k+2l= 3n 17) h+2k+l= 3n 18) 2h+k+l= 3n
19) h+2k= 3n 20) h+2l= 3n 21) k+2l= 3n
22) l= 4n 23) k= 4n 24) h= 4n
25) h+k= 4n 26) h+l= 4n 27) k+l= 4n
28) h+k+l= 4n 29) 2h+2k+l= 4n 30) 2h+k+2l= 4n
31) h+2k+2l= 4n 32) 2h+k+l= 4n 33) h+2k+l= 4n
34) h+k+2l= 4n 35) h+2k= 4n 36) h+2l= 4n
37) k+2l= 4n 38) 2h +k= 4n 39) 2h+l= 4n
40) 2k+l= 4n 41) 3h+3k+l= 4n 42) 3h+k+3l= 4n
43) h+3k+3l= 4n 44) h+2k+3l= 4n 45) h+3k+2l= 4n
46) 3h+k+2l= 4n 47) h+3k= 4n 48) h+3l= 4n
49) k+3l= 4n 50) 3k+2l= 6n 51) 2k+3l= 6n
52) 2h+3k= 6n 53) 3h+2k= 6n 54) 3h+2l= 6n
55) 2h+3l= 6n 56) 2h+2k+3l= 6n 57) 3h+2k+3l= 6n
58) 3h+3k+2l= 6n 59) 4k+3l=12n 60) 4h+3l=12n
61) 4h+3k=12n 62) 3k+4l=12n 63) 3h+4k=12n
64) 3h+4l=12n 65) h = 2n & k = 2n 66) h = 2n & l = 2n
67) k = 2n & l = 2n 68) h = 2n & k+l = 2n 69) k = 2n & h+l = 2n

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 EXPO2014

h = 2n & k= 2n &
70) l = 2n & h+k = 2n 71) h+k = 2n & h+l = 2n 72)
l= 2n
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Crystal Structure Visualization

Crystal Structure Visualization

EXPO2014 includes a viewer for 3D crystal structure visualization. This viewer is a
modified version of Jav (Just Another Viewer), program to visualize structural models and
electron density maps.
The program uses GTK Cairo and OpenGL libraries which are distributed under the GPL
(GNU General Public License).

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 EXPO2014

Created with the Personal Edition of HelpNDoc: Single source CHM, PDF, DOC and HTML Help creation

How to
Many possibilities are available to interact with the program: through the toolbar, the menu
and using keyboard/mouse.

The menu items follow:

· File
· Modify
· Select
· View
· Tools
· Info

Created with the Personal Edition of HelpNDoc: Single source CHM, PDF, DOC and HTML Help creation

File
The sub-menu File is shown on the left. It allows:

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 EXPO2014

Import Opens a coordinate file

Export Saves a coordinate file
Screens Produces an image file of Jav screen
hot
Exit Closes the viewer

Import

It is possible to read crystal structure from the following types of file:

· Crystallographic Information File (*.cif) http://www.iucr.org/resources/cif
· MDL Molfile (*.mol) http://accelrys.com/products/informatics/cheminformatics/ctfile-
formats/no-fee.php
· MOPAC File Formats. It can handle data structure in Cartesian coordinates or in
internal coordinates. http://openmopac.net/manual/index.html
· Tripos SYBYL Mol2 File (*.mol2, *.ml2) http://tripos.com/data/support/mol2.pdf
· Protein Data Bata Bank (*.pdb) http://www.wwpdb.org/
· Fenske-Hall Z-matrix (*.zmt), Z-matrix file created by Open Babel
· Free Form Fractional (*.fra, *.frac) http://openbabel.org/wiki/Free_Form_Fractional
· XYZ Cartesian Format (*.xyz) http://en.wikipedia.org/wiki/XYZ_file_format
· Input/Output files of SHELXL (*.ins,*.res) http://shelx.uni-ac.gwdg.de/SHELX/

EXPO2014 can also read the coordinates of the final molecular geometry in the output files
generated by well known quantum chemistry programs:

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 EXPO2014

· GAMESS output file (*.out,*.log) http://www.msg.ameslab.gov/gamess/

· NWCHEM output file (*.out,*.log) http://www.nwchem-sw.org/index.php/Main_Page
· MOPAC output file (*.out) http://openmopac.net/MOPAC2016.html
· ABINIT output file (*.out) http://www.abinit.org/

Isolated atoms and some common chemical geometries (tetrahedron, octahedron, square
plane) can also imported. They are useful building blocks in structure solution by global
optimization.

Export

Information about the currently displayed crystal structure can be in following text files:
· Crystallographic Information File (*.cif) http://www.iucr.org/resources/cif
· Input/Output files of SHELXL (*.ins,*.res) http://shelx.uni-ac.gwdg.de/SHELX/
· Free Form Fractional (*.fra, *.frac) http://openbabel.org/wiki/Free_Form_Fractional
· Protein Data Bata Bank (*.pdb) http://www.wwpdb.org/
· POV-Ray input file (*.pov) input file for the freeware program POV-Ray. http://
www.povray.org/download/
· MDL Molfile (*.mol) http://accelrys.com/products/informatics/cheminformatics/ctfile-
formats/no-fee.php
· Fenske-Hall Z-matrix (*.zmt), Z-matrix file created by Open Babel
· MDL Molfile (*.mol) http://accelrys.com/products/informatics/cheminformatics/ctfile-
formats/no-fee.php
· XYZ Cartesian Format (*.xyz) http://en.wikipedia.org/wiki/XYZ_file_format
· MOPAC File Formats with cartesian coordinates. http://openmopac.net/manual/
index.html

EXPO2014 create input files for well known quantum chemistry programs. Input files for
GAMESS and NWCHEM contain keywords for geometry optimization by density functional

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theory (DFT) calculations to perform using the B3LYP functional and a standard 6-31G*
basis set. This approach is useful to generate molecular model with accurate angles and
bond lengths, suitable as a starting model for structure solution by real space methods

· GAMESS input file (*.inp,*.gamin) http://www.msg.ameslab.gov/gamess/

· NWCHEM input file (*.out,*.log) http://www.nwchem-sw.org/index.php/Main_Page
· GAUSSIAN Cartesian Input (*.com, *.gau) http://www.gaussian.com/
· GAUSSIAN Z-matrix Input (*.gzmat) http://www.gaussian.com/
· ABINIT input file (*.in) http://www.abinit.org/

Screenshot
Images of crystal structure displayed in the graphic area can be saved in files of different
following formats:
· Bitmap File (*.bmp)
· ICO file (*.ico)
· jpeg file (*.jpg)
· Portable Network Graphics file (*.png)
· Tagged Image File (*.tif)

Exit
This is used to exit the program.

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Modify
The sub-menu Modify is shown on the left. It allows:

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Undo/Redo
Delete
Selection
Delete
Bonds
Delete All
Type
Change
Species
Rename

Renumber
Sort by
Species
Edit
structure
Add
fragments

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Select
The sub-menu Select is shown on the left. It allows:

Selection Mode
Zoom Mode
Manipulation Mode
Invert selection
Select none
Select Type

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View
The sub-menu View is shown on the left. It allows:

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Preferences
Symmetry
Zoom
Rotate
Label All Atoms
Label except
Hydrogens
Label Type
Show/Hide
View Plane
Polyhedra
Polyhedra
Properties
Contacts

Preferences

Some details about models are reported.

The following window shows what modifications con be applied to the model.

In order to get a better view of a model it is possible to tune the radius of the spheres

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representing the atoms and the radius of the cylinders representing the bonds. The atom
colors can be modified.

Polyhedra Properties
This window provides some tools to set the properties of the polyhedra; it is possible to
visualize or to hide some of them, it is possible to change the colors and the transparency,
to show or to hide the edges etc.

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View plane

Set the preferred view plane.

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Tools
The sub-menu Tools is shown on the left. It allows:

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Geometry Optimization

Quantum-chemical calculations have been successfully used to complement the

experimental X-ray powder diffraction (XRPD) data at several stages of the structure
solution process:

· To optimize the molecular geometry in the gas phase to obtain accurate starting
molecular structure suitable for structure solution by real space methods. In this stage
different levels of theory are applied: molecular mechanics, semi-empirical methods,
Hartree-Fock methods, density functional theory (DFT).

· To minimize the energy of crystal structure and provide reasonable bond lengths and
angles to input into the Rietveld refinement as chemical restraints. Calculations are
performed using plane wave DFT with dispersion correction (DFT-D).

· Because it is difficult to accurately locate the positions of H atoms from the XRPD data,
energy optimization provides the most reasonable approach to compute optimal
positions for the H atoms as the final step, with unit cell and non-H atomic positions
fixed to those established by Rietveld refinement.

· To clarify an ambiguity concerning the orientation of functional group that could not be
distinguished on the basis of the XRPD data alone.

· Geometry optimization with DFT-D approach in the solid state has been applied to
refine the crystal structure when Rietveld refinement yielded inaccurate molecular
geometry, providing results whose accuracy is comparable to that of single-crystal
refinement.

· To assess the correctness of experimental organic crystal structures

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EXPO2014 provides crystallographers with tools to perform theoretical calculations for the
geometry optimization. The first geometry optimization should be done with a faster level of
theory, such as molecular mechanics or a semiempirical method. Once a geometry close
to the correct geometry has been obtained with this lower level of theory, it is used as the
starting geometry for a second optimization at the final, more accurate level of theory (e.g.,
DFT).

Geometry optimization by molecular-mechanics force fields

In molecular mechanics, the energy of a compound consists of the sum of simple classical
equations and the molecule is described as a collection of balls (corresponding to the
atoms) held together by springs (corresponding to the bonds). The molecular mechanics
model clearly does not use wave function and electrons are not explicitly included.
The total potential energy is typically taken to be the sum of the bond stretching energy Estr ,
the bending energy Ebend , the twisting (or torsion) energy Etor , and the energy of interaction
between non-bonded atoms Enon-bond. The last contribution includes van der Waals, steric,
and electrostatic interactions between atoms not chemically bound.
Etot = Estr + Ebend + Etor + Enon-bond

The equations for the potential energy terms contain parameters and the specified set of
equations and parameters is called the force field. The constants in this equation are
obtained either from spectroscopic data or ab initio calculations. A set of equations with
their associated constants is called a force field. Many good force fields have already been
developed and they differ in the number of terms in the energy expression, the complexity
of those terms, and the way in which the constants were obtained.
To optimize the geometry and find the more stable conformation, each of the forces fi

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acting on a nucleus by electrons and other nuclei must vanish:

fi = - ¶Etot/¶qi

where qi are the nuclear coordinates of i-th atom.

In EXPO2014 two molecular mechanics force fields are used:

· The Merck molecular force field (MMFF) can be used for organic molecules and
biomolecules [1]

· The Universal force field (UFF) is a full periodic table force field. This is widely used for
system containing inorganic elements [2]
In EXPO2014 the support for molecular mechanics is provided using the class
OBForceField from the library Open Babel [3]
Clicking on Tools > Optimize Geometry > Optimize MMFF94 force field will be applied
and in case of failure (e.g. inorganic elements) UFF will be executed. Use Modify> Undo
Optimize Geometry to restore the initial molecular geometry.

The geometry optimization can also be applied only on selected atoms:

· click on to activate the selection mode,

· select by mouse atoms to apply the geometry optimization,

· click on Tools > Optimize Geometry > Optimize Selected Atoms.

Geometry optimization by MOPAC

There are two general approaches to solving the Schrödinger equation of a molecular
system: semi-empirical and ab initio methods. The semi-empirical methods assume an
approximate Hamiltonian operator and the calculations are further simplified by
approximating integrals with various experimental data such as ionization energies,
electronic spectral transition energies, and bond energies. On the other hand, ab initio
methods use a “correct” Hamiltonian operator, which includes kinetic energy of the
electrons, attractions between electrons and nuclei, and repulsions between electrons and
those between nuclei, to calculate all integrals without making use of any experimental data
other than the values of the fundamental constants. An example of these methods is the
self-consistent field (SCF) method first introduced by D. R. Hartree and V. Fock in the
1920s.
MOPAC (Molecular Orbital PACkage) is one of the most widely used semi-empirical
software packages and is designed for a wide range of functionality. We tested version
2012 and 2016. MOPAC is not distributed with EXPO, so a copy of the software needs to
be separately downloaded. For more information or to obtain a copy, please visit http://
www.openmopac.net/MOPAC2016.html, the software is currently free for academic use.
An interface of MOPAC is provided in EXPO and allows users to perform a gas-phase
geometry optimization. This approach is useful to generate molecular model with accurate
angles and bond lengths, suitable as a starting model for structure solution by real space
methods. The advantage of semi-empirical calculations is that they are much faster than

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SCF or DFT methods and can be applied routinely to large system.

A MOPAC optimization is performed selecting Tools > Optimize Geometry > MOPAC
from the principal menu.
The calculation is performed by choosing the following options in the MOPAC dialogue
window:

Title: define the title of the calculations, e.g., the name of molecule. It is reported in the
second line of the MOPAC input file
Method: Different semi-empirical Hamiltonians are available and are used in the
electronic part of the calculation to obtain molecular orbitals and its derivative with respect
to molecular geometry. Not all chemical elements are supported by the selected
Hamiltonian. For more information about the elements available for the specified method
see the geometry section in MOPAC manual: http://openmopac.net/manual/
Charge: Write the charge of studied system

Multiplicity: Allow the user to specify the number of singly occupied orbitals. Singlet is the
default, and specify a closed shell that includes the most of organic molecules; doublet
specify one singly occupied orbital (e.g. organic radicals); triplet specifies two singly
occupied orbitals; and so forth. If the multiplicity is unknown, you have to try all.
Format : Geometries can be specified within MOPAC using the Cartesian coordinate
definition or the Gaussian Z-matrix format. The position of molecule in the cell unit will be
lost if the geometry is defined in Z-matrix format.
Mopac Program: EXPO2014 automatically locates the position where MOPAC exists, if
MOPAC is installed in a standard directory (C:/Program Files/MOPAC/ on Windows, /opt/
mopac/ on Linux) or the environmental variable PATH includes the installation directory,
otherwise the MOPAC executable must be specified directly by the user.
If you click on Submit, MOPAC will be launched and at the end of the geometry
optimization, the new geometry will be displayed and an output file, called
structure_name_mopac.out, will be produced in the working directory. The output file can
be viewed from Tools> Optimize Geometry> View Mopac Output. You can read
previously generated MOPAC output files and display the molecular geometry from File >

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Import Structure and selecting 'MOPAC Output File (*.out)' in the file extension menu.

Before performing the calculation, add the missing hydrogen. You can use the option
Tools>Add Hydrogens. Wrong starting geometry, missing hydrogens or wrong
multiplicity are possible causes of an incorrect result. In this situation use Modify> Undo
Optimize Geometry to restore the initial geometry, then read the output file to find a
possible cause of error.
Additional calculations can be performed by clicking the preview button and changing the
input file. For example, it may be particularly important to calculate the bond order: add the
keyword BONDS in the first line and bond order between all pairs of atoms will be printed
in the output file.

Geometry optimization by density functional theory (DFT)

Another approach closely related to the ab initio methods that has gained increasing
prominence in recent years is the DFT. This method bypasses the determination of the
wavefunction ψ. Instead, it determines the molecular electronic probability density ρ directly
and then calculates the energy of the system from ρ.
EXPO2014 creates input files for well known quantum chemistry programs, clicking on File
> Import Structure. Input files for GAMESS [4] and NWCHEM [5] contain keywords for
geometry optimization by density functional theory (DFT) calculations to perform using the
B3LYP functional and a standard 6-31G* basis set.
In addition Tools > Optimize Crystal Structure by DFT-D can create an NWCHEM input
file for the optimization of crystal structure by plane wave density function theory with
Grimme dispersion correction. In order to obtain a good accuracy on the interatomic
distances, you should do a convergence test with respect the cutoff energy and a
convergence study associated with the sampling of the Brillouin zone.

References
[1] Thomas A. Halgren, J. Comput. Chem., 17, 490-519 (1996)

[2] J. Am. Chem. Soc. 1992, Vol. 114, No. 25, 10024-10035

[3] N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison. "Open

Babel: An open chemical toolbox." J. Cheminf. (2011), 3, 33.

[4] http://www.msg.ameslab.gov/gamess/

[5] http://www.nwchem-sw.org/index.php/Main_Page

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Info
The sub-menu Info is shown on the left. It allows:

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Structure Info on the structure.

List of Atoms List of Atoms.
List of Bonds List of Bond Distances.
List of Bond Angles List of Bond Angles.
List of Torsion Angles List of Torsion Angles.
Bar Chart Histogram of the peak
intensities.
List of Contacts
Geometry Some geometric calculations
can be performed.
Sphere list of atoms around a selected
atom

Structure

In the following tabs detailed information of the model are reported.

List of Atoms

The second tab contains the information related to the atoms.

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List of Bonds

The third tab contains the list of the bond distances.

List of Bond Angles

The fourth tab contains the list of the bond angles.

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List of Torsion Angles

The fifth tab contains the list of the torsion angles.

Bar Chart

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The tab Bar Chart contains the histograms of the fourier intensities of the atoms.

List of Contacts

The tab Contacts contains a list of non bonded contacts.

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Geometry
The value of the distances, angles and torsion angles among the atoms can be calculated.

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