Materials Studio Datasheet
Despite the problems associated with peak overlap,a high-quality powder diffraction pattern generally contains enough information for unambiguously deter-mining the corresponding crystal structure.A number of techniques are available to index the pattern,which allows cell parameters to derive from the positions of diffraction peaks.Knowledge of systematic abnces can help determine the most likely space groups.T aking into account the molecular connectivity and the well-known geometry of certain molecular fragments,the atomic arrangement in the unit cell can be described by a small number of parameters.It is possible to deter-mine the structural parameters from the intensity distribution of the 木瓜汤
powder diffraction pattern,although solving crystal structures from powder diffraction data remains a difficult computational problem for more complex crystals.The Powder Solve Approach Reflex Plus helps you to solve various problems:• The Reflex Powder Indexing tools allow you to determine the cell parameters and crystal system by indexing the experimental powder diffraction pattern • The modified Pawley procedure available in the Reflex Powder Refinement module refines the cell parame-ters,peak shape,and background parameters,and is a helpful tool for confirming the indexing result and narrowing down the list of possible space groups • The Powder Solve algorithm performs a arch of ©2006Accelrys,Inc.All rights rerved.Materials Studio and Discover are registered trademarks of Accelrys.Windows is a
registered trademark of Microsoft Corporation.All other brands or product names are trademarks of their respective holders.
This structure of the drug cimetidine was determined from its experimen tal powder diffraction pattern (pictured inside) using the Powder Solve technology.possible arrangements and conformations of the molecular fragments in the unit cell.It finds a struc-ture for which the simulated powder pattern matches the experimental one as cloly as possible and is also chemically viable • A final refinement of the propod solution is performed with the rigid-body Rietveld refinement functi
onality available in Reflex.Powder Indexing Indexing the experimental powder pattern is often the most challenging step in determining crystal structures from powder diffraction data.Four methods are pro-vided for indexing powder patterns:TREOR903,DICVOL914,ITO155,and X-Cell 6.It is important to u a high-quality powder pattern.Such a powder pat-tern typically contains narrow peaks that show little overlap with other peaks,making it easy to identify each peak's 2θposition.Once the cell parameters and lattice class have been determined,systematic abnces can be ud to limit the number of possible space groups.While synchrotron sources usually provide pow-der patterns that are more easily indexed,high-quality laboratory powder diffraction data can also be ud with success.The higher the quality of your powder pattern,the more detailed information it contains,and subquently the greater your chance of success.
Pawley Refinement
Once indexing is complete,a list of possible space groups must be established bad on chirality,density, and consideration of systematic abnces.The Pawley refinement functionality helps confirm the indexing result and explore the effect of systematic abnces,aid-ing in the determination of the possible space groups. In Pawley refinement,various parameters are adjusted t
o minimize the weighted R-factor,R wp,that describes the agreement between the experimental powder dif-fraction pattern and a simulated one.
Peak intensities are treated as independent param-eters.In addition,a wide range of variables can be refined,such as the unit cell,the background,a choice of peak profile and asymmetry functions,crystallite size,lattice strain,and the zero point shift of the dif-fraction pattern.By repeating the Pawley refinement in different space groups,the effect of systematic abnces on the simulated powder diffraction pattern is readily visualized.The refinement is bad on a modified Pawley1,6procedure that consists of two steps.In step one,the integrated intensities and background coeffi-cients are optimized while the peak shape,cell parame-ters,and zero-point shift are fixed.In step two,the opposite takes place,with all parameters being opti-mized except for the intensities and background coeffi-cients.This two-step process is continued until conver-gence is achieved.
Powder So lve
The next step for structure determination involves Powder Solve;an indirect method that employs a Monte Carlo simulated annealing or parallel tempering algo-rithms.Before starting Powder Solve,the ur must define each torsional degree of freedom to be explored during the simulation.One degree
of freedom in the ,translational,rotational,or torsional,is modified by a random amount during each simulated annealing step,after which a powder pattern is calculat-ed.This simulated pattern is then compared to the experimental powder pattern using R wp as a measure of similarity.
Optionally,Powder Solve allows to apply a clo contact penalty function during structure determina-tion.This option is particularly uful when working with low-quality powder data,as it will ensure that Powder Solve finds chemically feasible solutions,with-out 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 and comparing powder patterns continues in order to minimize R wp.Structures with low R wp values are automatically saved to trajectory files.Multiple cycles to determine the structure are performed in order to confirm the final solution.A wide range of compounds have been successfully examined using this methodolo-gy,including solvates,salts,and flexible molecules.
Rietveld Refinment
The final step for structure determination is Rietveld refinement8,9where urs can refine candidate crystal structures obtained from Powder Solve against experi-mental powder diffraction data by minimizing the weighted R-factor,R wp.Flexibility is provided through the wide range of refinement parameters available -unit cell,atomic,peak profile and asymmetry,crystal-lite size and strain broadening,preferred orientation, background,zero-point shift,intensities.Rietveld refinement with energies incorporates an accurate description of potential energy in conjunction with R wp during a Rietveld refinement process optimizing a combined figure of merit so that not only the simulated pattern of the resulting structure matches the experi-mental diffraction data,but also the potential energy of the structure is clo to a global minimum.Pareto opti-mization10can be ud to calculate a t of possible optimal refinement solutions automatically as a quence of Rietveld refinement with energies calcula-tions with changing energy weights.Pareto optimiza-tion for a structure solution reprents a trade-off to provide best possible R wp(min) and energy(min) com-promis.
The Materials Studio Advantage Reflex Plus is a operated within the Materials Studio®environment,allowing for a high degree of interactivity with other M aterials Studio products and Windows®applications.The molecules or molecular fragments ud in the structure arch can be easily constructed using M aterials Studio sketching and molecular
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Reflex Plus
be submitted to remote rver machines in addition
to synchronous execution on local client
• Powerful but easy to u;intuitive definition of
degrees of freedom
Powder Solve
• Final parameters from Pawley refinement are
automatically transferred to Powder Solve
• Choice of two global arch algorithms,MC simulated
annealing and MC parallel tempering
• Clo contact penalty function ensures chemically
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• Automated tool to estimate the appropriate number
of steps for each structure solution problem
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• Determination of preferred orientation correction
during structure solution arch
• Automatic tting of all simulation parameters.
• Multiple structure solution cycles can be performed
to confirm results
• As structures produce lower R wp values,they are
saved to a trajectory file
• Automatic rigid body Rietveld refinement of promis-
ing structures during structure solution arch
缘起性空• Extensive analysis tools to examine results from sin-
gle or multiple structure solution cycles
• Propod solution can be further refined with the
rigid body Rietveld Refinement tool
• W orks with good quality lab data as well as
synchroton data
• Bad on full profile comparison - moderate peak
overlap not a problem
• W ell validated for complex compounds,including
solvates,salts,and flexible molecules
• W orks for organics and inorganics
• Client-rver architecture allows calculations to run
on powerful rvers,while analysis is performed System Details
Operated through the M aterials Studio ur interface
on Windows® 2000 and XP.CPU intensive powder
indexing and Powder Solve calculations can be execut-
ed on Windows ® 2000,2003,XP,SGI IRIX,Red Hat
Linux (Intel IA32,Intel IA64,EM64T,and compatibles),
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SuSe Linux (Intel IA 32,EM64T,and compatibles),and
Accel rys European Headqua rter s 334Cambridge Science Park Cambridge,CB 4 OWN,UK Tel:+44 1223 228500Accel rys Corporate Headqua rter s
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San Diego,CA 92121
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bethuneTel:+1 858 799 5000Accel rys Asia Headqua rter s Nishi-shimbashi TS Bldg 11F Nishi-shimbashi 3-3-1,Minato-ku,Tokyo,105-0003,Japan Tel:+81 3 3578 3860ms_ds_009_0305HP Tru64 operating systems.
CPU intensive powder refinement calculations can be
executed on Windows 2000,2003,XP ,SGI IRX,Red Hat
Linux (Intel IA32,EM64T,and compatibles),and SuSe
Linux (IntelIA32,EM64T,and compatibles) operating
systems.
References
1.G.E.Engel,S.Wilke,O.König,K.D.M.Harris and
F.J.J.Leun,J.Appl.Cryst.,1999,32,1169-1179.
2.G.A.Stephenson,J.Pharm.Sci .,2000,89,958.
3.P .E.W erner,L.Eriksson and M.W estdahl,J.Appl.
Cryst .,1968,1,108-113.
4.A.Boultif and D.Louer,J.Appl.Cryst.,1991,24,987.
5.J.W .Visr,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).
9.R.A.Y oung,"The Rietveld Method ",Oxford
University Press (1993).
10.D.A.V an V eldhuinzen,G.B.Lamont,Evolutionary
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Computation ,8,125 (2000).
