These crystals will make your crystallographer happ

C.L. Carpenter-Warren (7162505)

Mark Elsegood (1249893)

English

Loughborough University Institutional Repository

These Crystals Will Make Your Crystallographer Happy Dr. Mark R. J. ELSEGOOD and Cameron L. CARPENTER-WARREN  LOUGHBOROUGH UNIVERSITY Overview  Roles   Crystals – Desirable features   Methods of Crystallisation   Case Studies. BCA 2016 What’s Your Role ?  Synthetic Chemist  Synthetic Chemist/Crystallographer  Crystallographer advising synthetic Chemists BCA 2016 Crystal growth Work with nature – but stack the odds in your favour. Crystallisation occurs in two steps: • Nucleation  • Growth  Nucleation can occur at: • A seed crystal • Particle of dust • Imperfection in the vessel  BCA 2016 Considerations when growing a crystal • Solubility of compound  • Amount of compound needed to grow a crystal  • Location and conditions of crystal growth  • Size of crystal required for diffraction analysis  • It is not an exact science – may need to try many methods/conditions   BCA 2016 Desirable Crystal Features  Flat faces  Straight edges  Sharp vertices  Optical clarity  No re-entrant angles  Extinguish plane polarised light. BCA 2016       √   OK          X Twinned Some Decent crystals BCA 2016 http://www.nature.com/nchem/journal/v5/n10/images/nchem.1730-f2.jpg Some Decent crystals BCA 2016 http://www.nature.com/nmat/journal/v7/n7/images/nmat2211-f1.jpg Some Decent crystals BCA 2016 http://college.wfu.edu/chemistry/research/xray/wp-content/uploads/DSCN2917.jpg Optical Inspection – Take a proper look  Every lab should have a jewellers lupe for initial inspection. 20-30X magnification.   Then check under a polarising microscope. BCA 2016 BCA 2016 Polarising Microscope Desirable Crystals • The large flat crystal shows well defined, faces with minimal imperfections.  • When rotated 90° under polarised light, the crystal extinguishes the light.  • This is a preliminary indication that a crystal is of good quality. BCA 2016 Crystal rotated under polarised light BCA 2016 Undesirable Crystals • Crystals grown via the evaporation method:  • The crystals are of decent quality, however they’re covered in a fine crust, a result of the evaporation process.  • Also dust and a fibre have contaminated the sample due to the open lid setup. BCA 2016 Glassware   Crystals have flat faces, so use glassware with flat surfaces.  A round-bottomed flask /Schlenk tube is not the best choice unless sample is unstable.  Sample vials have flat bottoms – a better choice if air stable.  Rinse samples vials before use – the cardboard boxes they come in can shed paper fibres which act as nucleation sites.  Use new or annealed glassware, not vessels that have been washed up many times and have micro-scratches which also act as nucleation sites.  Silicone coatings can be applied to reduce nucleation sites. BCA 2016 Want a small number of large crystals not many small ones. Solvent choice   • Use pure solvents, not mixtures like ‘40-60 petrol’.  • Evaporation and slow cooling may be the only choices for compounds soluble only in non-polar solvents.  • Solvents with H-bonding ability may promote crystallisation of compounds with H-bond donors/acceptors by solvate formation.  • Avoid solvents with very long alkyl chains .  BCA 2016 Amount of compound required • Typically 5-20mg  • An NMR sample is a great place to start: • It is the best solution you’re likely to prepare • NEVER throw away your NMR sample if you may need the crystal structure  • NMR solution preparation: 1. Use high purity solvent (right) 2. Filter solution to remove impurities 3. Use new/clean glassware e.g. 99.5% purity Acetone BCA 2016 Crystal growth conditions Factors affecting size and quality of crystals obtained: • Solvents/solutions   • Method   • Nucleation sites available  • Vibrational disturbances  • Temperature and light conditions/variations  • Rate of change of conditions Create an environment which changes very slowly over time BCA 2016 Common crystallisation techniques  • Slow evaporation  • Vapour diffusion  • Liquid diffusion  • Liquid diffusion (H-tube)  • Very slow cooling  • Sublimation BCA 2016 See also Peter Müllers article: Crystallography Reviews, (2009), 15, 57-83. Slow evaporation BCA 2016 Slow evaporation BCA 2016 Slow evaporation Pros and Cons Pros:  • Easy to set up • Often works  Cons: • Volume of solution decreases, so crystals can dry out, form crusts or desolvate   BCA 2016 Vapour diffusion BCA 2016 Vapour diffusion BCA 2016 Vapour diffusion Pros and Cons Pros:  • Volume increases so crystals don’t dry out, form crusts, or desolvate  Cons: • None BCA 2016 Liquid diffusion BCA 2016 Liquid diffusion BCA 2016 Put a lid on! Case Study 1 – An Arene-Ru salt. BCA 2016 [(η6-p-cy)Ru(η6:η6-C16H16)Ru(η6-C6Me6)][BF4]4  - No decent crystals.   All-in-One Liquid diffusion/Ion Exchange/Crystallisation with NaBPh4 gave:  [(η6-p-cy)Ru(η6:η6 - C16H16)Ru(η6-C6Me6)][BF4]3[BPh4] Case Study 1 – An Arene-Ru salt. BCA 2016 [(η6-p-cy)Ru(η6:η6 - C16H16)Ru(η6-C6Me6)][BF4]3[BPh4] Liquid diffusion (H-Tube) BCA 2016 Liquid diffusion (H-Tube) Pros and Cons Pros:  • Ideal for growing crystals that are very insoluble i.e. can’t be recrystallized. • Diffusion dictates that reaction/crystallisation will be slow (a good thing)  Cons: • None BCA 2016 Liquid diffusion (H-Tube) BCA 2016 Put Parafilm over the tops Very slow cooling BCA 2016 Sublimation BCA 2016 BCA 2016 Schlenk tube with cold finger for sublimation crystallisation. Case Study 2. A pyrene. A good example to illustrate problems and routes to improvement.  BCA 2016 Optically imperfect.  Some hairline cracks.  Striations under polarised light.  Turns out to be twinned. Case Study 2. A pyrene. The structure was determined. BCA 2016 X 2 By-product Hexane of crystallisation – at least a pure solvent was used. Case Study 2. A pyrene. What advice can we give to avoid the twinning & improve the result?  Need to change something/anything. 1.  Run a column to remove the by-product impurity. 2. Switch from hexane (C6) to pentane (C5) or heptane (C7), etc. BCA 2016 Asymmetric unit. Other crystallisation techniques • Thermal gradient  • Counterions or ionisation  • Co-crystals and clathrate  • Reactant diffusion  • Melting and recrystallization   • Similar crystal seeding  • Gel crystallisation  • Parr bomb for MOFs etc.  BCA 2016 Summary  Be aware of the factors that govern crystallisation.  Use knowledge of the compound to guide choice of crystallisation method and conditions.  Try as many methods as possible.  L earn from imperfect results to achieve better outcomes.     BCA 2016 Summary  Be aware of the factors that govern crystallisation.  Use knowledge of the compound to guide choice of crystallisation method and conditions.  Try as many methods as possible.  L earn from imperfect results to achieve better outcomes.  If all else fails – grow a beard! BCA 2016 From: A Book of BEARDS By Justin James Muir 

These crystals will make your crystallographer happy

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These crystals will make your crystallographer happy

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