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Synchrotrons, Mannitol, Prazosin, etc. Synchrotron radiation is accessible, decisive Hydrogen bonding affects molecular conformation. Work performed with V.V. Chernyshev, A.V. Yatsenko, O.B. Ryabova, V.A. Makarov, C.E. Botez, R. Suryanarayanan, C. Nunes.

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  1. Synchrotrons,Mannitol, Prazosin, etc. Synchrotron radiation is accessible, decisive Hydrogen bonding affects molecular conformation Work performed with V.V. Chernyshev, A.V. Yatsenko, O.B. Ryabova, V.A. Makarov, C.E. Botez, R. Suryanarayanan, C. Nunes. See also poster #14 on R-albuterol, S. Cuffini

  2. Physical adsorption of Kr on graphite X-ray diffraction of Kr on exfoliated graphite. Crystallography with one Bragg peak - Kr(1,0)

  3. Experiments at SSRL in 1979. (Moncton, Birgeneau, Horn, Brown, PWS) 20x better angular resolution Substrate coherence length is ~2000Å Completely new picture! There is a disordered phase between the commensurate and incommensurate solids. Interesting new physics. Heroic age of synchrotron radiation. Parasitic on high energy physics. Huge investment of effort to get one or two weeks of access per year.

  4. National Synchrotron Light Source at Brookhaven National Laboratory Produces electromagnetic radiation from IR to -rays. Easy to obtain access. ~75 experimental stations ~2500 users per year Typical of many facilities worldwide: APS, ESRF, SLS, SRS Daresbury, SSRL, …, which are eager for users.

  5. Synchrotron access is for: Academic: Who publish in the open literature* Industrial: Hold data for proprietary reasons** The people who operate these facilities need to have them widely used! * Access by writing competitive proposals or arranging collaboration. ** You have to pay for the prorated cost of operating the facility - ~$250/hour = $2000/pattern at NSLS.

  6. Compare lab vs. synchrotron data sets. This drug has two polymorphs that can’t be quantified except by Rietveld.

  7. THEORY OF POWDER DIFFRACTION (series of elementary recipes) CONTENTS OF UNIT CELL UNIT CELL RECIPROCAL LATTICE, SPACE GROUP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . INTENSITIES POWDER PEAK POSITIONS PHYSICAL SAMPLE AFFECTS LINESHAPES INSTRUMENT AFFECTS PEAK SHAPES OTHER ARTIFACTS: PREFERRED ORIENTATION, ETC. POWDER DIFFRACTION PATTERN

  8. USE OF POWDER DIFFRACITON TO SOLVE A CRYSTAL STRUCTURE Chemical knowledge of contents Data • Start with the best data you can get (but no better). • Get a list of accurate diffraction peak positions. • Figure out a lattice that explains the peaks. • Guess the space group (systematic absences, # molecules). • Search for the best place to put the molecule(s), best conformation of the molecule. • Refine, refine, refine, refine, refine, … • At any stage, you can be forced to jump back to any stage.

  9. Don’t think that people only use powders for organic molecules, or that direct space modelling is the only useful technique Lausenite: Souzalite Fe2(SO4)3·5H2O (Fe,Mg)3(al,Fe)4(PO4)4(OH)6·2H2O J. Majzlan, …, PWS A. Le Bail, …, PWS Direct Methods (EXPO) Real Space (ESPOIR)

  10. #1, 2 This is a data-driven enterprise. Students may think that we spend all our time talking about algorithms, software, etc., but the results are no better than the data! Powder diffraction station at X3B1 beamline, National Synchrotron Light Source, Brookhaven National Laboratory, U. S. A. GE (111) analyzer crystal From storage ring Scintillation detector Monochromatic X-ray beam sample Ionchamber Si(111) double monochromator • Analyzer crystal geometry measures angles – eliminates significant aberrations of familiar Bragg-Brentano diffractometer. • Capillary sample geometry is very helpful. Eliminates preferred orientation, peak shifts that bother flat plate

  11. #3. Indexing Given some values of d spacings, find a lattice that fits them, i.e., find {A,B,C,D,E,F } such that every d can be expressed as 1/d 2 = Ah 2 + Bk 2 + Cl 2 + Dkl + Ehl + Fhk for some integers h, k, l. Familiar programs, in the public domain: TREOR, ITO, DICVOL, have their quirks, but basically they always work, given sufficiently good data. (Often possible with good lab diffractometers, nearly always with synchrotron data.) TOPAS (Alan Coehlo, Bruker AXS) has indexing tools that are qualitatively more powerful.

  12. Prazosin Designer drug – selective antagonist for α1-adrenoceptors (blood pressure). Four other polymorphs claimed in US Patents 4092315, 4739055, 4816455, and JP Patent 03206088. Department of Medicinal Chemistry, State Scientific Center of Antibiotics, Moscow, could not reproduce any of them. Patent literature : Literature Military intelligence : Intelligence

  13. Four of the lines in the Powder Diffraction File for that compound are impurities, not seen in our pattern. Throw them away and use TOPAS to index the lab data. Triclinic TOPAS FOM = 15.99 a = 8.717Å b = 7.572Å c = 16.381Å α = 90.01° β = 72.43° γ = 108.95° Vol = 969Å3 x x x x Errors 0.021° ± 0.024° (There is a lot of not-quite-good data in the data bases. Is not-quite-good distinguishable from bad?)

  14. Given sufficiently good data -> pattern can be indexed easily Data quality = sample  instrument If a pattern from a good instrument* cannot be indexed, there is something wrong with the sample *Test your instrument by trying to index known phases of comparable complexity. Acetaminophen and Ibuprofen are good organic test cases to get started.

  15. #5. Make a model of the molecule, put it into the lattice. Move the model around seeking best agreement between calculated and observed diffraction patterns. Lots of options: software DASH, PSSP, FOX, TOPAS, PowderSolve, … In this case, assumed P1, coauthor searched nine parameters with software developed with H. Schenk. _ Cl

  16. #6. Refine, refine, … If your presumed rough solution is close enough, you can roll down hill to the correct solution, using refinement programs such as GSAS, TOPAS, FULLPROF, … 2 ~100 refined variables

  17. THE GLOBAL TOPOLOGY MAY LOOK MORE LIKE THIS

  18. Any fit looks good on this scale d = 1.47Å χ2 = 2.31, Rwp=5.92%. No restraints except for tethering all H atoms.

  19. Same steps for prazosin free base – only 6 search coordinates Monoclinic, Cc, χ2 = 2.78, Rwp=5.92%

  20. Planarity of the aromatic rings gives a measure of the degree of accuracy of the finished atomic geometry.

  21. Prazosin refinements. Geometry of piperazine ring Hydrochloride N17 C18 Free base

  22. Free base 1 N-H…N 3.02Å 1 N-H…O 3.02Å Hydrochloride 3 N-H…Cl

  23. Prazosin conclusions: • That wasn’t so hard • Of relevance to quantitative modeling of structure-activity relationships Hydrochloride Free base Hydrochloride methanol solvate (single xtl) Prazosin2 tetrachloro-copper(II) (s x)

  24. The rest of the talk • Enalapril Maleate. Y.H. Kiang, Merck • Proxy for a real business problem. • Delta D-Mannitol • Mannitol hemihydrate

  25. Enalapril Maleate is a potent angiotensin converting enzyme (ACE) inhibitor with two known polymorphs, Form I and Form II. The single crystal structure of Form I has been known for almost twenty years. On the other hand, the crystal structure of Form II has never been reported before because of the difficulty to obtain single crystals of this polymorph, which is made by water slurry of Form I. The crystal structure of Form II is of interest for several reasons: 1. Form II is the more stable of the two polymorphs. 2. The two forms are structurally similar based on X-ray, IR, and solid-state NMR. 3. The conformation of ACE inhibitors is important to their biological activity.

  26. Lab(Sealed Tube) and Synchrotron XRD patterns of Enalapril Maleate Form I Cu Ka1 Form II 2 q Form I l=1.15Å, Form II 2q

  27. Enalapril Maleate form II Orthorhombic P212121 a=17.838 b=6.640 c=11.649 b=106.29 a=33.987 b=6.642 c=11.210 form I Monoclinic P21 23 parameters: 11 enalapril torsions (+2 maleate) + 6 orientation + 6 position At the time of the original work, we couldn’t solve from simulated annealing. We could have benefited from the systematic geometric insights presented by Claire Gervais

  28. green:carbon yellow:nitrogen red:oxygen Form II Form I Y.-H. Kiang of Merck found the solution by hand, using Cerius. Y.-H. Kiang, Ashfia Huq, Peter W. Stephens, Wei Xu, Journal of Pharmaceutical Sciences 92, 1844-53 (2003)

  29. Real business problem: _____ has a patented polymorph of _____ , and suspects that _____ is selling material that infringes. It is desired to examine the commercial tablets and determine the polymorph of the API for potential litigation. Proxy: Examine commercial tablet of Endocet 500/7.5 Gross tablet 607 mg Acetaminophen 500 mg – known lattice & structure Oxycodone (as HCl) 7.5 mg – pattern in PDF but lattice unknown,* * In general, I’d like to get better info into the PDF database. Please get in touch if you can help.

  30. of acetaminophen

  31. Powder patterns of oxycodone hydrochloride from ICDD Powder Diffraction File. Strucutures and lattices are not known.

  32. H H OH OH H H | | | | | | H - C - C - C - C - C - C - H | | | | | | OH OH H H OH OH Back to structures: Mannitol D-Mannitol (naturally produced in various plants) Long-standing confusion about how many forms of D-mannitol exist – finally laid to rest by Burger, Henck, & co. (2000). (Their II, I, and III are more commonly known as α, β, δ) α and β were solved from single crystals in 1968. δ (lowest melting) identified in 1968, but no single crystals grown (until ~2002, Henck & Benet-Buchholz, unpublished). We solved the structure of δ from a powder sample (with 20% β) Mannitol is widely used as an excipient in freeze-drying; metastable hydrate discovered by Lian Yu. TGA shows it is hemihydrate. Structure solved from powder sample with 26% δ, 2% β, ~10% ice.

  33. P 21 21 21 8.942 x 18.798 x 4.893Å 205.6 Å3 / molecule Middle melting P 21 21 21 8.672 x 16.875 x 5.560Å 203.4 Å3 / molecule Highest melting P 21 5.089 x 18.250 x 4.917Å β = 118.304° 201.0 Å3 / molecule Lowest melting Present work

  34. All the same steps. At extraction, we did a Le Bail refinement of the δ lattice along with Rietveld refinement of (known) β structure. λ = 0.70224Å

  35. Alpha D-mannitol, H bonds (beta is very similar) 4-cycle Zig-zag chain

  36. Delta D-mannitol, H bonds One zig-zag chain

  37. alpha beta The molecules in alpha, beta, delta D-mannitol are essentially identical delta

  38. Mannitol hemihydrate Start with the best data possible? Play the hand you’re dealt!

  39. Intensity (counts) TGA (a) DSC (b) (c) (d) 2 (degrees) (e) Lab x-ray (Minnesota) Lab x-rays identify the sample TGA -> hemihydrate

  40. Index the peaks that are not any other identified phase to a triclinic lattice: 9.896 x 10.542 x 4.786 Å, 102.59°, 86.09°, 116.08°, 2 mannitol in P1.

  41. Search two independent mannitol molecules, one O atom. Several different starts. B A

  42. Hydrogen bonding pattern in hemihydrate Conformation with one leg lifted water Normal conformation

  43. Only mannitol hemihydrate has an OH twisted up into the plane of the C-C-C-C-C-C backbone. What is the energy cost relative to the conformation of all other observed mannitol crystal structures? Is there no way to pack “table” mannitols and a water of solvation without straining the molecule?

  44. Structure determination from powders requires: • Good data • Fundamental understanding of the available tools • Motivation Choose good problems. If you are stuck with a crystallographic problem, try a synchrotron.* You pay taxes – claim your share. Find one where there is already a strong program of structure determination. * Also single crystal.

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