Direct space methods for crystal structure determination from powder diffraction data have become widely available and popular in recent years and have successfully 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
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'.
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 |
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 model for Simulated Annealing in MDL Molfile format (*.mol). This command can be repeated several times to import more than one 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).
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.
Instead of command "%fragment name_starting_model.ext", with ext=mol, frac, cif etc, you can import the starting structural model directly from the graphic interface from 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.
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:
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 moves: the number of moves for each step of temperature is Np*N*20 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.
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):
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.
Dynamical Occupancy Correction: 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).
Press the button 'Atomic parameters' to access to the following dialog window:
X Y Z: check the buttons on column 'X Y Z' to refine the atom positions, in this case the fragment is not rigid but the atom positions are shifted respect to the barycentre. Click on label 'X Y Z' 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.
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.
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.
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.
stops the procedure.
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 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.
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 |
To modify the default values of SA, some directives can be used after the command %sannel.
An example of application of directive NRUN
%automatic |
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 Ax1 Ax2 At1 At2 At3 ...
or
rotate Ax1 Ax2 At1 At2 At3 ... theta
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.
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
Activate the dynamical occupancy correction
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
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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