Winpssp - A computer program for the crystal structure solution of organic solids from X-ray powder diffraction

1. WinPSSP: a computer program applying
direct-space methods for the crystal
structure solution of molecular solids from
X-ray powder diffraction
Silvina Pagola,1Alekos Polymeros,2 and Nikolaos Kourkoumelis3
1 Department of Chemistry and Biochemistry, Hampton University, Hampton, VA, 23668 and
Department of Applied Science, College of William & Mary, Williamsburg, VA, USA.
2 Department of Physics, University of Ioannina, 45110, Ioannina, Greece,
3Department of Medical Physics, Medical School, University of Ioannina, 45110, Ioannina, Greece.
ACA Meeting, New Orleans, May 30, 2017

2. Outline
► Other free-distribution software used with WinPSSP
► WinPSSP workflow
► Definition of input data for WinPSSP
► 3-amino-5-mercapto-1,2,4-triazole (rigid molecule)
► Phenylpyridine hydroxybenzoic acid co-crystal (two flexible
fragments to locate)
► Drofenine hydrochloride (relocation of flexible
fragments based on model-biased Le Bail fits)
1) Computer programs PSSP (2010) and WinPSSP (2017)
2) Examples of molecular location with WinPSSP:
3) Acknowledgements

3. ►Pssp is published in J. Appl. Cryst. (2010) 43, 370-376
►Pssp was written in 1998 (P. W. Stephens, X3B1 powder diffraction
beamline, NSLS-I, BNL, USA) in the C/C++ language with contributions of
a few other people.
Pssp description and use (in MS_DOS)
►Ascii text input and
output files
► Pssp is a direct-space methods program used to find the atomic
coordinates of molecular solids from X-ray powder diffraction.

4. ►http://users.uoi.gr/nkourkou/winpssp/ (free-distribution website)
Free-distribution program WinPSSP
►A GUI for PSSP was written by N. Kourkoumelis and A. Polymeros
(University of Ioannina, Greece) in Pascal Delphi.
►Published in J. Appl. Cryst. (2017) 50, 293-303.

5. Free-distribution software used with WinPSSP
Space group symmetry (P21/c, P1, P212121, P21, C2/c)
STRUCTURE SOLUTION
(molecular location)

RIETVELD REFINEMENT (setup rigid bodies, or refine with bond
angle and distance restraints).
Add H with WinGX/SHELX, CRYSTALS
(WinPLOTR, CMPR)
ITO
DICVOL06
McMAILLE
TREOR, N-TREOR
CRYSFIRE
WinPSSP
I”obs”,hkl (*.rfl, *.hkl files) and FWHM
Peak positions
Unit-cell parameters
INDEXING
Systematic absences & International Tables for Crystallography
Volume A
LeBail method (GSAS, FULLPROF)PATTERN DECOMPOSITION
Output data
(approximate atomic coordinates)
Input data
GSAS
*.cif files
*.rfl files, FWHM

6. WinPSSP
workflow
Input data
0.01
0.10
1.00
10.00
S
80
100
odels(%)
<S>
Smin
0.0010.0100.1001.00010.000
Temperature
0.01
0.10
1.00
10.00
S
0
20
40
60
80
100
Acceptedtrialmodels(%)
<S>
Smin
Output data
Costfunction(S)
(T)
2
''',
''''''''', )()(










hkl
hkl
lkhhkl
lkhlkhlkhhklhklhkl
A
BAFBA
S
?
xmol ymol, zmol, f, c, w, t1 ...tn

7. Example 1: 3-amino-5-mercapto-1,2,4-triazole
From an equally weighted Le Bail fit (GSAS)
a= 3.9986 Å, b=12.3796 Å, c=9.8468 Å, b=102.13°; V=476.6 Å3 ; 17 Å3 per non-H atom
P21/c; Z=4 ; 1 molecule in the general position

8. WinPSSP performance in “routine”
problems
(Submitted to the Journal
of Applied Crystallography)
► H atoms are not used to solve structures
► Most common space groups

9. WinPSSP: estimation of the number of models required to
solve structures
Number of structural parameters

10. Example 2: 4-hydroxybenzoic phenylpyridine
co-crystal (flexible molecules)
HBA
PP

11. Large molecular solids solved with pssp
Part of this figure was extracted from: David, W. I. F., Shankland, K., McCusker, L. B. and Baerlocher, Ch.
“Structure determinaton from powder diffraction data”, Oxford Univ. Press, 2002
Jaborosalactol 24
(77 atoms)
2000
2010
NumberofCSDentries
Number of atoms (including H when reported)
2008
2012
N-acetyl-L-phenylalanyl-NH2
(116 atoms, Z’=4)
Amcinonide
(142 atoms, Z’=2)
WinPSSP
(molecular
location)
GSAS
(model-
biased *.rfl)
WinPSSP
(molecular
re-location)
Rietveld fit
(GSAS)
Input data
(equally
weighted *.rfl)
end
Altomare et al., J. Res. Natl. Inst.
Stand. Technol. 109, 125-132
(2004)
Malaria pigment
(43 atoms)

12. Example 3: WinPSSP facilitates the relocation of
flexible fragments using a model-biased Le Bail fit

13. ► Use of the National Synchrotron Light Source, Brookhaven National
Laboratory, supported by the U.S. Department of Energy, Office of Science,
Office of Basic Energy Sciences, under Contract No. DE-AC02-98CH10886.
► Use of the Advanced Photon Source at Argonne National Laboratory supported
by the U. S. Department of Energy, Office of Science, Office of Basic Energy
Sciences, under Contract No. DE-AC02-06CH11357.
► I am grateful to ODU for the use of the Rigaku Miniflex II powder diffractometer.
► I am grateful for partial funding from ICDD GIA 08-04.
► Distribution website: http://users.uoi.gr/nkourkou/winpssp/
Acknowledgements
Thanks !