Applications of the CSD to Structure Determination from Powder Data
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1 Applications of the CSD to Structure Determination from Powder Data Prof. Alastair J. Florence Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, UK ACS, Salt Lake City, March 2009
2 Overview 1. XRPD in Physical Form Discovery 2. SDPD Overview 3. Selecting Accurate Models Ring conformations: Corina 4. Maximising chances of locating the global minimum Mogul
3 Physical Form Discovery (CPOSS) Polymorphs, solvates, salts and co-crystals I. Crystallise Samples Maximise crystallisation space coverage II. XRPD Fingerprint 5 35 o 2θ, 45 min. per pattern LIMS Interrogate III. Measure Properties CSP IV. Determine Structure Q. Crystal structures are a key outcome, but what if samples are polycrystalline?
4 Structure Determination from Powder Data (SDPD) SX (direct methods) 1000s of I obs to ~1 Å resolution SDPD (global optimisation) 100s of I obs to ~2 Å resolution Loss of information and reduced accuracy of intensity estimates cf. SX Use global optimisation combined with prior chemical information
5 SDPD Global optimisation methods vary: (i) position (x, y, z) = 3 DoF (ii) orientation (θ 1, θ 2, θ 3 ) = 3 DoF and (iii) conformation (τ 1, τ 2...τ n ) = n DoF Of molecule within unit cell to find values that yield best fit between I obs and I calc : N Cl 1. Convert to 3D-model 2D - molecular connectivity N S O O NH 2 S O O 2. Standard bond lengths/ angles used 3. Flexible torsion angles varied freely. Test fit of I calc with I obs (χ 2 ) Vary the structure Random position, orientation and conformation of fragment(s) e.g. 7 degrees of freedom (DoF) = 3 position + 3 orientation + 1 conformation. Global minimum located: structure solved! z-matrix introduces prior chemical information (bond lengths/angles) into the process
6 SDPD Examples Chlorothiazide (DMF) 2 solvate V = 3816 Å 3 P2 1 /c, Z =2, DoF = 38 N frag = 6, N atoms = 94 Sample from solution crystallisation Cyheptamide form II V = 2412 Å 3 P1, Z =4, DoF = 28 N frag = 4, N atoms = 128 Sample from in situ thermal transition Fernandes, P. et al, J. Pharm. Sci. 96(5) (2007) Florence, A. J., et al., CrystEngComm (2008)
7 SDPD Overview Assess Sample: Collect Initial Data Low-angle, fixed-count Data Collection Indexes yes High resolution VCT Data Collection Sp. Gr. / Pawley fit no impurities or partial desolvation? recrystallise Identify suitable model SA Runs (GridMP) Solved yes Rietveld Refinement Analyse / Deposit / Publish no check model: disordered? solvent present? Focus on the role of additional information sources in: (i) Selection of suitable model w.r.t. fixed ring conformations CORINA hydrochlorothiazide; diltiazem hydrochloride (ii) Structure determination MOGUL Chloramphenicol palmitate
8 Ring Conformations Ring conformations are typically fixed in global optimization (GO) methods i.e. if wrong conformation used, GO will fail to solve the structure CORINA: What is it? A rule- & data-based program to automatically generate 3D atomic coordinates. Key strength - generation of multiple ring conformations Systematic conformational analysis for ring systems (n 9 atoms) Generates low-e ring conformations from 2D molecular sketch
9 Examples: HCT & Diltiazem HCl Compounds 1 & 29 in J. Appl. Cryst. (2005). 38, (data can be downloaded from O O NH 2 S Cl H N O O O N + N H O HCT O S O N H Diltiazem HCl [focusing the output on known S, S chiral centres] S Energy window [kj mol -1 ] HCT Diltiazem conformers conformers
10 Ring Conformations: HCT Corina & CSD CORINA CORINA CORINA form HCT form form IIIIII HCT form III HCT form HCT form CASCAB CASCAB CASCAB ODATIX ODATIX YESKIR YESKIR CASMAL CASMAL KASMOH KASMOH ADEFOF ADEFOF ODEFEJ ODATIX
11 Ring Conformations: Diltiazem Corina & CEYHUJ01
12 Mogul: Torsion Angle Constraints Define query
13 Select Ranges to Exclude Visualise selected geometry in related fragments
14 Example: CP, Z = 1, DoF = 29 CSD Refcode: CLAMPL01, Z = 1, orthorhombic, P a, b, c (Å) = 7.805(3), (15), 7.414(2) DoF = 23 internal, 6 external Lab capillary XRPD data Fitted to 2.17 Å; 221 reflections χ χ 2 2 Pr ofile / Pawley Model Lowest χ 2 ratio reached 0 internal DoF (rigid body) internal DoF [0 360 o ] internal DoF [Mogul search space] 2.0
15 CP Comparison of Best solutions SX (CLAMPL01) = red DASH (fixed) = blue DASH (Mogul) = orange DASH (0 360) = green
16 CP Best Free Solution 5 torsions from the best unconstrained SA structure are outwith CSD ranges Torsions SX FREE 1 C(5) C(3) C(4) O(2) C(13) C(12) O(2) C(4) C(13) C(14) C(15) C(16) C(18) C(19) C(20) C(21) C(19) C(20) C(21) C(22) Application of CSD-derived torsion angle constraints: (i) prevents these values occuring during the SA runs (ii) ensures the search utilises only chemically sensible models w.r.t. individual torsions
17 CP Top 10 Solutions (Mogul) Rank (Run) χ 2 ratio 1 (285) (550) (447) (422) (566) (58) (145) (263) (50) (567) 5.9 3/800 reach GM 10 Structure solved reproducibly from batch of SA runs Across lowest χ 2 values returned, significant variation in conformations observed
![CP Solutions 1 & 8 [2 and 5.1] [8] χ 2 = 5.](/docs-images/80/81636732/images/18-1.jpg "1 [1] χ 2 = 2.")
18 CP Solutions 1 & 8 [2 and 5.1] [8] χ 2 = 5.1 [1] χ 2 = 2.0 Different conformations similar packing
19 Summary 3D Model (z-matrix) Construction for Rings: Corina 1. An effective tool for identifying chemically sensible, low-e ring conformations for use in SDPD 2. Trivial calculation times (e.g. <1s for HCT) 3. Not guaranteed that lowest-e conformer = global minimum, but generates most likely candidates for use in SDPD attempts Structure Determination: CSD/MOGUL 1. Torsion angle constraints derived from CSD easy to implement with no computational overhead during SA search 2. Advantageous in the successful solution of complex problems (e.g. internal DOF > ~18, Z > 1) 3. Note: Possible that correct value lies outwith CSD ranges from similar fragments SDPD is a powerful tool for structural analysis of novel crystalline forms Chances of success for structures with significant chemical and/or crystallographic complexity are enhanced with reliable models plus high quality data
20 Acknowledgements University of Strathclyde Ryan Taylor, Alan Kennedy, Xuelian Xu, Philippe Fernandes, Norman Shankland University of Reading Kenneth Shankland CCDC Elna Pidcock Molecular Networks GmbH Christof Schwab Funding CPOSS ( RCUK / EPSRC, Scottish Funding Council, Glasgow Centre for Physical Organic Chemistry
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