BIOVIA MATERIALS STUDIOREFLEX PLUSDATASHEETBIOVIA Materials Studio Reflex Plus is an advanced versionof BIOVIA Materials Studio Reflex, adding the extensively
validated Powder Solve1,2 technology to the standard BIOVIAMaterials Studio Reflex functionality. BIOVIA Materials Studio
Reflex Plus offers a complete package for determining crystal
structures from medium-to-high quality powder diffraction
data.
The ideal method for solving crystal structures is singlecrystal X-ray diffraction. Growing single crystals of appropriate
size, however, is often difficult or even impossible, whereas
powder samples are readily available for analysis by powder
diffractometry.
Despite the problems associated with peak overlap, a highquality powder diffraction pattern generally contains enoughinformation for unambiguously determining the corresponding
crystal structure. A number of techniques are available toindex the pattern, which allows cell parameters to derive fromthe positions of diffraction peaks. Knowledge of systematicabsences can help determine the most likely space groups.
Taking into account the molecular connectivity and thewellknown geometry of certain molecular fragments, theatomic arrangement in the unit cell can be described by asmall number of parameters. It is possible to determine thesestructural parameters from the intensity distribution of thepowder diffraction pattern, although solving crystal structuresfrom powder diffraction data remains a difficult computational
problem for more complex crystals.

THE POWDER SOLVE APPROACH
BIOVIA Materials Studio Reflex Plus helps you to solve various
problems:• The BIOVIA Materials Studio Reflex Powder Indexing tools
allow you to determine the cell parameters and crystalsystem by indexing the experimental powder diffraction
pattern• The modified Pawley procedure available in the BIOVIA
Materials Studio Reflex Powder Refinement module refines
the cell parameters, peak shape, and background arameters,
and is a helpful tool for confirming the indexing result andnarrowing down the list of possible space groups• The Powder Solve algorithm performs a search of possible
arrangements and conformations of the molecular fragmentsin the unit cell. It finds a structure for which the simulated
powder pattern matches the experimental one as closely as
possible and is also chemically viable• A final refinement of the proposed solution is performed withthe rigid-body Rietveld refinement functionality available in
BIOVIA Materials Studio Reflex.

POWDER INDEXING
Indexing the experimental powder pattern is often the mostchallenging step in determining crystal structures from powder
diffraction data. Four methods are provided for indexing
powder patterns: TREOR903, DICVOL914, ITO155, and X-Cell6.
It is important to use a high-quality powder pattern. Such apowder pattern typically contains narrow peaks that show littleoverlap with other peaks, making it easy to identify each peak’s
20 position. Once the cell parameters and lattice class havebeen determined, systematic absences can be used to limit thenumber of possible space groups.
While synchrotron sources usually provide powder patterns
that are more easily indexed, high-quality laboratory powder
diffraction data can also be used with success. The higher thequality of your powder pattern, the more detailed information it
contains, and subsequently the greater your chance of success.

Figure 1: This structure of the drug cimetidine
was determined from its experimental powder
diffraction pattern (pictured inside) using thePowder Solve technology.

PAWLEY REFINEMENT
Once indexing is complete, a list of possible space groups mustbe established based on chirality, density, and considerationof systematic absences. The Pawley refinement functionality
helps confirm the indexing result and explore the effectof systematic absences, aiding in the determination of
the possible space groups. In Pawley refinement, various
parameters are adjusted to minimize the weighted R-factor,Rwp, that describes the agreement between the experimental
powder diffraction pattern and a simulated one.
Peak intensities are treated as independent parameters. Inaddition, a wide range of variables can be refined, such as
the unit cell, the background, a choice of peak profile andasymmetry functions, crystallite size, lattice strain, and thezero point shift of the diffraction pattern. By repeating thePawley refinement in different space groups, the effect ofsystematic absences on the simulated powder diffraction
pattern is readily visualized. The refinement is based on amodified Pawley1,6 procedure that consists of two steps. In
step one, the integrated intensities and background coefficientsare optimized while the peak shape, cell parameters, and zeropoint shift are fixed. In step two, the opposite takes place, withall parameters being optimized except for the intensities andbackground coefficients. This two-step process is continued
until convergence is achieved.

POWDER SOLVE

energy in conjunctionwith Rwp during a Rietveld refinement
process optimizing a combined figure of merit so that not
only the simulated pattern of the resulting structure matches
the experimental diffraction data, but also the potential
energy of the structure is close to a global minimum. Pareto
optimization10 can be used to calculate a set of possible
optimal refinement solutions automatically as a sequence ofRietveld refinement with energies calculations with changing
energy weights. Pareto optimization for a structure solution
represents a trade-off to provide best possible Rwp(min) andenergy(min) compromises.

THE BIOVIA MATERIALS STUDIO ADVANTAGEBIOVIA Materials Studio Reflex Plus is a operated within theBIOVIA Materials Studio® environment, allowing for a high degreeof interactivity with other BIOVIA Materials Studio products andWindows® applications. The molecules or molecular fragments
used in the structure search can be easily constructed using
BIOVIA Materials Studio sketching and molecular mechanics
tools, or by being imported from other sources.
Results obtained by indexing, Pawley refinement, structure
solution, and Rietveld refinement are readily passed on between
the different modules involved in the structure determination
procedure. A powerful rigid body Rietveld refinement program
is available to carry out the final structure refinement. Crystal
structures are readily visualized using BIOVIA Materials StudioVisualizer.

The next step for structure determination involves Powder
Solve; an indirect method that employs a Monte Carlo simulated
annealing or parallel tempering algorithms. Before starting
Powder Solve, the user must define each torsional degree offreedom to be explored during the simulation. One degree offreedom in the system, i.e., translational, rotational, or torsional,
is modified by a random amount during each simulated
annealing step, after which a powder pattern is calculated.
This simulated pattern is then compared to the experimental
powder pattern using Rwp as a measure of similarity.
Optionally, Powder Solve allows to apply a close contact
penalty function during structure determination. This option
is particularly useful when working with low-quality powder
data, as it will ensure that Powder Solve finds chemicallyfeasible solutions, without bad contacts between structural
fragments. When a promising structure is found Powder
Solve performs a rigid-body Rietveld refinement with respect
to the parameter space to locate the local minimum. The
iterative process of modifying one degree of freedom andcomparing powder patterns continues in order to minimize
Rwp. Structures with low Rwp values are automatically saved
to trajectory files. Multiple cycles to determine the structure are
performed in order to confirm the final solution. A wide rangeof compounds have been successfully examined using thismethodology, including solvates, salts, and flexible molecules.

RIETVELD REFINEMENT
The final step for structure determination is Rietveld refinement8,9
where users can refine candidate crystal structures obtained
from Powder Solve against experimental powder diffraction
data by minimizing the weighted R-factor, Rwp. Flexibility isprovided through the wide range of refinement parameters
available -unit cell, atomic, peak profile and asymmetry,
crystallite size and strain broadening, preferred orientation,
background, zero-point shift, intensities. Rietveld refinementwith energies incorporates an accurate description of potential

Figure 2: Comparison of the experimental powder
diffraction pattern of cimetidine with thepattern simulated for the crystal structure asdetermined by BIOVIA Materials Studio Reflex Plus.

Finally, results can easily be shared with colleagues and copiedand pasted to standard word processors, spreadsheets, andpresentation packages.

FEATURESGeneral• BIOVIA Materials Studio Reflex Plus is a complete packagefor structure determination from powder diffraction data,
covering indexing, Pawley refinement, structure solution,
and Rietveld refinement• Reads in a variety of diffractometer file formats including
Bruker, Stoe, Scintag, Jade, Philips, JCAMP, Galactic SPC,GSAS raw, ILL, PAnalytical XRDML• Allows for different X-ray sources with multiple wavelengths
and user-defined polarization• Suitable for X-ray, neutron, and electron diffraction.

REFERENCES:
1. G.E. Engel, S.Wilke,O. König, K.D.M.Harris and F.J.J. Leusen, J. Appl. Cryst., 1999, 32, 1169-1179.
2. G. A. Stephenson, J. Pharm. Sci., 2000, 89, 958.
3. P.E.Werner, L. Eriksson and M.Westdahl, J. Appl.Cryst., 1968, 1, 108-113.
4. A. Boultif and D. Louer, J. Appl. Cryst., 1991, 24, 987.
5. J.W.Visser, J. Appl. Cryst., 1969, 2, 89.
6. M.A.Neuman, J. Appl. Cryst., 2003, 36, 356-365.
7. G.S. Pawley., J. Appl. Cryst., 1981, 14, 357.
8. H. M. Rietveld, J. Appl. Cryst., 2, 65-71 (1969).

POWDER SOLVE• Final parameters from Pawley refinement are automaticallytransferred to Powder Solve• Choice of two global search algorithms, MC simulated
annealing and MC parallel tempering• Close contact penalty function ensures chemically viablesolutions• Automated tool to estimate the appropriate number of steps
for each structure solution problem• Determination of preferred orientation correction during
structure solution search• Automatic setting of all simulation parameters.
• Multiple structure solution cycles can be performed toconfirm results• As structures produce lower Rwp values, they are saved to atrajectory file• Automatic rigid body Rietveld refinement of promising
structures during structure solution search• Extensive analysis tools to examine results from single ormultiple structure solution cycles• Proposed solution can be further refined with the rigid body
Rietveld Refinement tool
• Works with good quality lab data as well as synchroton data
• Based on full profile comparison - moderate peak overlap nota problem• Well validated for complex compounds, including solvates,salts, and flexible molecules• Works for organics and inorganics• Client-server architecture allows calculations to run on
powerful servers, while analysis is performed

9. R. A.Young, “The Rietveld Method”, Oxford University Press (1993).
10. D.A.Van Veldhuinzen, G.B. Lamont, Evolutionary Computation, 8, 125 (2000).
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• Can handle any possible space group, both standard andnonstandard settings, accounting for systematic absences• Benefits from straightforward interaction with other BIOVIA
Materials Studio products as well as other PC applications• Pawley refinement and Rietveld refinement jobs canbe submitted to remote server machines in addition tosynchronous execution on local client• Powerful but easy to use; intuitive definition of degrees offreedom

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